Citrus Sinensis ID: 014486

---

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-------420---
Protein Sequence
MGETRDNEYEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSFQCLVLGSF
Secondary Structure (PSIPRED)
ccccccccccccccccHHHccccccccccccccccccccccEEcccccccccccHHHHHHHHHcccccccHHHHHHHHHHHcccEEEEEccccccccHHHHHHHHHccccccccEEEEEEcccHHHHHHHHHHHHHHHccccccEEEEEEccccHHHHHHHHHccccEEEEcccHHHHHHHHccccccccccEEEEEcccccccccccHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHccccEEEEEcccccccccccEEEEEEcccccHHHHHHHHHHcccccEEEEEEccHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHccccccEEEEccccccccccccccEEEEccccccccccccccccccccccccEEEEEcccHHHHHHHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccHHHHHHcccccccccccccccccccccccccHHHccccHHHHHHHHHcccccccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHHHHccccEEEEEEccccHHHHHHHHHccccEEEEEcccHHHHHHHcccccHHHEEEEEEcHHHHHHHHcccHHHHHHHHHHccHHHcEEEEEccccHHHHHHHHHHHcccEEEEEEcccEEEcccEEEEEEEEccHHHHHHHHHHHHcccccEEEEEEccHHHHHHHHHHHHHccccHHHHcccHHHHHHHHHHHHHHccccEEEEEEEHHHccccccccEEEEEEcccccccHHEEEEccccccccccEEEEEEccHHHHHHHHHHHHHHHccccccccccHHHc
Coil and Loop (DISEMBL)
mgetrdneyedelldyeeedaqapdsvatkangeaakkgyvgihssgfrdfllkPELLRAIVDSgfehpsevqhecipqaILGMDVICQaksgmgktAVFVLSTlqqtepnpgqVTALVLCHTRELAYQICHEFerfstylpdiKVAVFYGGVNIKIHKDLlknecpqivvgtpgRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCkkfmqdpmeiyvddeAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEcnfpsicihsgmsqEERLTRykgfkegnKRILVATDLvgrgidierVNIVInydmpdsadtylhrvgragrfgtkgLAITFVssasdsdiLNQVSKFMFLLIGSFqclvlgsf
Flexible Loop (DISEMBL)
mgetrdneyEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALArdkdlslknVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPsicihsgmsqeERLTRykgfkegnkrilvatdlvgrgidIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSFQCLVLGSF
Low Complexity Region (SEG)
MGETRDNeyedelldyeeedAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSFQCLVLGSF
Disordered region (IsUnstruct)
*************************************KGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSFQCLVL***
Disordered Region (DISOPRED)
******************************************IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSFQCL*****
Disordered Region (DISEMBL)
**********DELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSFQCLVLGSF
Disordered Region (DISPRO)
*********************************************SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSFQCLV****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGETRDNEYEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSFQCLVLGSF
Positional Conservation
no confident homologs detected

---

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	423	2.2.26 [Sep-21-2011]
Q9LFN6	427	DEAD-box ATP-dependent RN	yes	no	0.957	0.948	0.926	0.0
Q56XG6	427	DEAD-box ATP-dependent RN	yes	no	0.957	0.948	0.926	0.0
Q0JM17	432	DEAD-box ATP-dependent RN	yes	no	0.957	0.937	0.877	0.0
Q5JK84	432	DEAD-box ATP-dependent RN	no	no	0.957	0.937	0.872	0.0
Q5WR10	428	Spliceosome RNA helicase	yes	no	0.929	0.918	0.727	1e-174
Q5RE47	428	Spliceosome RNA helicase	yes	no	0.929	0.918	0.727	1e-174
Q29024	428	Spliceosome RNA helicase	yes	no	0.929	0.918	0.727	1e-174
P60024	428	Spliceosome RNA helicase	yes	no	0.929	0.918	0.727	1e-174
Q5TM17	428	Spliceosome RNA helicase	yes	no	0.929	0.918	0.727	1e-174
Q13838	428	Spliceosome RNA helicase	yes	no	0.929	0.918	0.727	1e-174

>sp|Q9LFN6|RH56_ARATH DEAD-box ATP-dependent RNA helicase 56 OS=Arabidopsis thaliana GN=RH56 PE=2 SV=2

 Score =  751 bits (1940), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/407 (92%), Positives = 392/407 (96%), Gaps = 2/407 (0%)

Query: 1   MGETRDNE-YEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
           MG+ RDNE YE+ELLDYEEED + PDS   K NGEA KKGYVGIHSSGFRDFLLKPELLR
Sbjct: 1   MGDARDNEAYEEELLDYEEEDEKVPDS-GNKVNGEAVKKGYVGIHSSGFRDFLLKPELLR 59

Query: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
           AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP+PGQV+ALV
Sbjct: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPSPGQVSALV 119

Query: 120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
           LCHTRELAYQIC+EF RFSTYLPD KV+VFYGGVNIKIHKDLLKNECP IVVGTPGR+LA
Sbjct: 120 LCHTRELAYQICNEFVRFSTYLPDTKVSVFYGGVNIKIHKDLLKNECPHIVVGTPGRVLA 179

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
           LAR+KDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV
Sbjct: 180 LAREKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239

Query: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 299
           CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE+EKNRKLNDLLDALDFNQVVIFVKSVS
Sbjct: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEMEKNRKLNDLLDALDFNQVVIFVKSVS 299

Query: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
           RAAELNKLLVECNFPSICIHSGMSQEERLTRYK FKEG+KRILVATDLVGRGIDIERVNI
Sbjct: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKSFKEGHKRILVATDLVGRGIDIERVNI 359

Query: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           VINYDMPDSADTYLHRVGRAGRFGTKGLAITFV+SASDS++LNQV +
Sbjct: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVASASDSEVLNQVQE 406

ATP-binding RNA helicase involved in pre-mRNA splicing. Required for the export of mRNA out of the nucleus.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q56XG6|RH15_ARATH DEAD-box ATP-dependent RNA helicase 15 OS=Arabidopsis thaliana GN=RH15 PE=2 SV=3

 Score =  751 bits (1940), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/407 (92%), Positives = 392/407 (96%), Gaps = 2/407 (0%)

Query: 1   MGETRDNE-YEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
           MG+ RDNE YE+ELLDYEEED + PDS   K NGEA KKGYVGIHSSGFRDFLLKPELLR
Sbjct: 1   MGDARDNEAYEEELLDYEEEDEKVPDS-GNKVNGEAVKKGYVGIHSSGFRDFLLKPELLR 59

Query: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
           AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP+PGQV+ALV
Sbjct: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPSPGQVSALV 119

Query: 120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
           LCHTRELAYQIC+EF RFSTYLPD KV+VFYGGVNIKIHKDLLKNECP IVVGTPGR+LA
Sbjct: 120 LCHTRELAYQICNEFVRFSTYLPDTKVSVFYGGVNIKIHKDLLKNECPHIVVGTPGRVLA 179

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
           LAR+KDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV
Sbjct: 180 LAREKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239

Query: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 299
           CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE+EKNRKLNDLLDALDFNQVVIFVKSVS
Sbjct: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEMEKNRKLNDLLDALDFNQVVIFVKSVS 299

Query: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
           RAAELNKLLVECNFPSICIHSGMSQEERLTRYK FKEG+KRILVATDLVGRGIDIERVNI
Sbjct: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKSFKEGHKRILVATDLVGRGIDIERVNI 359

Query: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           VINYDMPDSADTYLHRVGRAGRFGTKGLAITFV+SASDS++LNQV +
Sbjct: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVASASDSEVLNQVQE 406

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q0JM17|RH56_ORYSJ DEAD-box ATP-dependent RNA helicase 56 OS=Oryza sativa subsp. japonica GN=Os01g0549700 PE=2 SV=2

 Score =  726 bits (1875), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/408 (87%), Positives = 377/408 (92%), Gaps = 3/408 (0%)

Query: 2   GETRDNE-YEDELLDYEEEDAQAPDSVATKANG--EAAKKGYVGIHSSGFRDFLLKPELL 58
            E +DNE YE++L+DYEEE     D  A  AN   +  KKGYVGIHSSGFRDFLLKPELL
Sbjct: 4   AEVKDNEVYEEDLVDYEEEVENGTDGGANAANASADVVKKGYVGIHSSGFRDFLLKPELL 63

Query: 59  RAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTAL 118
           RAI D GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLS+LQQ +P  GQV AL
Sbjct: 64  RAIQDCGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSSLQQIDPVAGQVGAL 123

Query: 119 VLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL 178
           VLCHTRELAYQICHEFERFS YLP++KVAVFYGGV+IK HKDLLKN+CP IVVGTPGRIL
Sbjct: 124 VLCHTRELAYQICHEFERFSKYLPEVKVAVFYGGVHIKKHKDLLKNDCPHIVVGTPGRIL 183

Query: 179 ALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRP 238
           ALAR+KDLSLKNVRHFILDECDKML+SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRP
Sbjct: 184 ALAREKDLSLKNVRHFILDECDKMLDSLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRP 243

Query: 239 VCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSV 298
           VCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE EKNRKLNDLLDALDFNQVVIFVKSV
Sbjct: 244 VCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEAEKNRKLNDLLDALDFNQVVIFVKSV 303

Query: 299 SRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVN 358
           SRAAELNKLL ECNFP+I IHSGM+QEERLTRYK FKEG+KRILVATDLVGRGIDIERVN
Sbjct: 304 SRAAELNKLLCECNFPAISIHSGMTQEERLTRYKNFKEGHKRILVATDLVGRGIDIERVN 363

Query: 359 IVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           IVINYDMPDSAD+YLHRVGRAGRFGTKGLAITFVSSASDSD+LNQV +
Sbjct: 364 IVINYDMPDSADSYLHRVGRAGRFGTKGLAITFVSSASDSDVLNQVQE 411

ATP-binding RNA helicase involved in pre-mRNA splicing. Required for the export of mRNA out of the nucleus.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5JK84|RH15_ORYSJ DEAD-box ATP-dependent RNA helicase 15 OS=Oryza sativa subsp. japonica GN=Os01g0550000 PE=2 SV=1

 Score =  723 bits (1865), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/408 (87%), Positives = 378/408 (92%), Gaps = 3/408 (0%)

Query: 2   GETRDNE-YEDELLDYEEE--DAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELL 58
            E +DNE YE++L+DYEEE  +     + A  A+ +  KKGYVGIHSSGFRDFLLKPELL
Sbjct: 4   AEVKDNEVYEEDLVDYEEEVENGADGGAAAANASADVVKKGYVGIHSSGFRDFLLKPELL 63

Query: 59  RAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTAL 118
           RAI D GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLS+LQQ +P  GQV AL
Sbjct: 64  RAIQDCGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSSLQQIDPVAGQVGAL 123

Query: 119 VLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL 178
           VLCHTRELAYQICHEFERFS YLP++KVAVFYGGV+IK HKDLLKN+CP IVVGTPGRIL
Sbjct: 124 VLCHTRELAYQICHEFERFSKYLPEVKVAVFYGGVHIKKHKDLLKNDCPHIVVGTPGRIL 183

Query: 179 ALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRP 238
           ALAR+KDLSLKNVRHFILDECDKML+SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRP
Sbjct: 184 ALAREKDLSLKNVRHFILDECDKMLDSLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRP 243

Query: 239 VCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSV 298
           VCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE EKNRKLNDLLDALDFNQVVIFVKSV
Sbjct: 244 VCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEAEKNRKLNDLLDALDFNQVVIFVKSV 303

Query: 299 SRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVN 358
           SRAAELNKLL ECNFP+I IHSGM+QEERLTRYK FKEG+KRILVATDLVGRGIDIERVN
Sbjct: 304 SRAAELNKLLCECNFPAISIHSGMTQEERLTRYKNFKEGHKRILVATDLVGRGIDIERVN 363

Query: 359 IVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           IVINYDMPDSAD+YLHRVGRAGRFGTKGLAITFVSSASDSD+LNQV +
Sbjct: 364 IVINYDMPDSADSYLHRVGRAGRFGTKGLAITFVSSASDSDVLNQVQE 411

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5WR10|DX39B_CANFA Spliceosome RNA helicase DDX39B OS=Canis familiaris GN=DDX39B PE=3 SV=1

 Score =  612 bits (1579), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 296/407 (72%), Positives = 342/407 (84%), Gaps = 14/407 (3%)

Query: 6   DNEYEDELLDYEEEDAQAPDSVATKANGEAA--------KKGYVGIHSSGFRDFLLKPEL 57
           +N+ ++ELLDYEE      D V T A G+ +        K  YV IHSSGFRDFLLKPEL
Sbjct: 3   ENDVDNELLDYEE------DEVETAAGGDGSEAPAKKDVKGSYVSIHSSGFRDFLLKPEL 56

Query: 58  LRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTA 117
           LRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKSGMGKTAVFVL+TLQQ EP  GQV+ 
Sbjct: 57  LRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSV 116

Query: 118 LVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI 177
           LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG++IK  +++LK  CP IVVGTPGRI
Sbjct: 117 LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 176

Query: 178 LALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIR 237
           LALAR+K L+LK+++HFILDECDKMLE LDMRRDVQEIF+MTPH+KQVMMFSATLSKEIR
Sbjct: 177 LALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIR 236

Query: 238 PVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKS 297
           PVC+KFMQDPMEI+VDDE KLTLHGL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKS
Sbjct: 237 PVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKS 296

Query: 298 VSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV 357
           V R   L +LLVE NFP+I IH GM QEERL+RY+ FK+  +RILVAT+L GRG+DIERV
Sbjct: 297 VQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERV 356

Query: 358 NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQV 404
           NI  NYDMP+ +DTYLHRV RAGRFGTKGLAITFVS  +D+ ILN V
Sbjct: 357 NIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDV 403

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Canis familiaris (taxid: 9615)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5RE47|DX39B_PONAB Spliceosome RNA helicase DDX39B OS=Pongo abelii GN=DDX39B PE=2 SV=1

 Score =  612 bits (1578), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 296/407 (72%), Positives = 342/407 (84%), Gaps = 14/407 (3%)

Query: 6   DNEYEDELLDYEEEDAQAPDSVATKANGEAA--------KKGYVGIHSSGFRDFLLKPEL 57
           +N+ ++ELLDYE+      D V T A G+ A        K  YV IHSSGFRDFLLKPEL
Sbjct: 3   ENDVDNELLDYED------DEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPEL 56

Query: 58  LRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTA 117
           LRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKSGMGKTAVFVL+TLQQ EP  GQV+ 
Sbjct: 57  LRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSV 116

Query: 118 LVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI 177
           LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG++IK  +++LK  CP IVVGTPGRI
Sbjct: 117 LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 176

Query: 178 LALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIR 237
           LALAR+K L+LK+++HFILDECDKMLE LDMRRDVQEIF+MTPH+KQVMMFSATLSKEIR
Sbjct: 177 LALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIR 236

Query: 238 PVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKS 297
           PVC+KFMQDPMEI+VDDE KLTLHGL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKS
Sbjct: 237 PVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKS 296

Query: 298 VSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV 357
           V R   L +LLVE NFP+I IH GM QEERL+RY+ FK+  +RILVAT+L GRG+DIERV
Sbjct: 297 VQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERV 356

Query: 358 NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQV 404
           NI  NYDMP+ +DTYLHRV RAGRFGTKGLAITFVS  +D+ ILN V
Sbjct: 357 NIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDV 403

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q29024|DX39B_PIG Spliceosome RNA helicase DDX39B OS=Sus scrofa GN=DDX39B PE=2 SV=2

 Score =  612 bits (1578), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 296/407 (72%), Positives = 342/407 (84%), Gaps = 14/407 (3%)

Query: 6   DNEYEDELLDYEEEDAQAPDSVATKANGEAA--------KKGYVGIHSSGFRDFLLKPEL 57
           +N+ ++ELLDYE+      D V T A G+ A        K  YV IHSSGFRDFLLKPEL
Sbjct: 3   ENDVDNELLDYED------DEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPEL 56

Query: 58  LRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTA 117
           LRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKSGMGKTAVFVL+TLQQ EP  GQV+ 
Sbjct: 57  LRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSV 116

Query: 118 LVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI 177
           LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG++IK  +++LK  CP IVVGTPGRI
Sbjct: 117 LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 176

Query: 178 LALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIR 237
           LALAR+K L+LK+++HFILDECDKMLE LDMRRDVQEIF+MTPH+KQVMMFSATLSKEIR
Sbjct: 177 LALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIR 236

Query: 238 PVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKS 297
           PVC+KFMQDPMEI+VDDE KLTLHGL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKS
Sbjct: 237 PVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKS 296

Query: 298 VSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV 357
           V R   L +LLVE NFP+I IH GM QEERL+RY+ FK+  +RILVAT+L GRG+DIERV
Sbjct: 297 VQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERV 356

Query: 358 NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQV 404
           NI  NYDMP+ +DTYLHRV RAGRFGTKGLAITFVS  +D+ ILN V
Sbjct: 357 NIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDV 403

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Sus scrofa (taxid: 9823)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P60024|DX39B_PANTR Spliceosome RNA helicase DDX39B OS=Pan troglodytes GN=DDX39B PE=3 SV=1

 Score =  612 bits (1578), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 296/407 (72%), Positives = 342/407 (84%), Gaps = 14/407 (3%)

Query: 6   DNEYEDELLDYEEEDAQAPDSVATKANGEAA--------KKGYVGIHSSGFRDFLLKPEL 57
           +N+ ++ELLDYE+      D V T A G+ A        K  YV IHSSGFRDFLLKPEL
Sbjct: 3   ENDVDNELLDYED------DEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPEL 56

Query: 58  LRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTA 117
           LRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKSGMGKTAVFVL+TLQQ EP  GQV+ 
Sbjct: 57  LRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSV 116

Query: 118 LVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI 177
           LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG++IK  +++LK  CP IVVGTPGRI
Sbjct: 117 LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 176

Query: 178 LALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIR 237
           LALAR+K L+LK+++HFILDECDKMLE LDMRRDVQEIF+MTPH+KQVMMFSATLSKEIR
Sbjct: 177 LALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIR 236

Query: 238 PVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKS 297
           PVC+KFMQDPMEI+VDDE KLTLHGL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKS
Sbjct: 237 PVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKS 296

Query: 298 VSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV 357
           V R   L +LLVE NFP+I IH GM QEERL+RY+ FK+  +RILVAT+L GRG+DIERV
Sbjct: 297 VQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERV 356

Query: 358 NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQV 404
           NI  NYDMP+ +DTYLHRV RAGRFGTKGLAITFVS  +D+ ILN V
Sbjct: 357 NIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDV 403

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Pan troglodytes (taxid: 9598)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5TM17|DX39B_MACMU Spliceosome RNA helicase DDX39B OS=Macaca mulatta GN=DDX39B PE=3 SV=1

 Score =  612 bits (1578), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 296/407 (72%), Positives = 342/407 (84%), Gaps = 14/407 (3%)

Query: 6   DNEYEDELLDYEEEDAQAPDSVATKANGEAA--------KKGYVGIHSSGFRDFLLKPEL 57
           +N+ ++ELLDYE+      D V T A G+ A        K  YV IHSSGFRDFLLKPEL
Sbjct: 3   ENDVDNELLDYED------DEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPEL 56

Query: 58  LRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTA 117
           LRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKSGMGKTAVFVL+TLQQ EP  GQV+ 
Sbjct: 57  LRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSV 116

Query: 118 LVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI 177
           LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG++IK  +++LK  CP IVVGTPGRI
Sbjct: 117 LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 176

Query: 178 LALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIR 237
           LALAR+K L+LK+++HFILDECDKMLE LDMRRDVQEIF+MTPH+KQVMMFSATLSKEIR
Sbjct: 177 LALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIR 236

Query: 238 PVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKS 297
           PVC+KFMQDPMEI+VDDE KLTLHGL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKS
Sbjct: 237 PVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKS 296

Query: 298 VSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV 357
           V R   L +LLVE NFP+I IH GM QEERL+RY+ FK+  +RILVAT+L GRG+DIERV
Sbjct: 297 VQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERV 356

Query: 358 NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQV 404
           NI  NYDMP+ +DTYLHRV RAGRFGTKGLAITFVS  +D+ ILN V
Sbjct: 357 NIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDV 403

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Macaca mulatta (taxid: 9544)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q13838|DX39B_HUMAN Spliceosome RNA helicase DDX39B OS=Homo sapiens GN=DDX39B PE=1 SV=1

 Score =  612 bits (1578), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 296/407 (72%), Positives = 342/407 (84%), Gaps = 14/407 (3%)

Query: 6   DNEYEDELLDYEEEDAQAPDSVATKANGEAA--------KKGYVGIHSSGFRDFLLKPEL 57
           +N+ ++ELLDYE+      D V T A G+ A        K  YV IHSSGFRDFLLKPEL
Sbjct: 3   ENDVDNELLDYED------DEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPEL 56

Query: 58  LRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTA 117
           LRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKSGMGKTAVFVL+TLQQ EP  GQV+ 
Sbjct: 57  LRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSV 116

Query: 118 LVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI 177
           LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG++IK  +++LK  CP IVVGTPGRI
Sbjct: 117 LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 176

Query: 178 LALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIR 237
           LALAR+K L+LK+++HFILDECDKMLE LDMRRDVQEIF+MTPH+KQVMMFSATLSKEIR
Sbjct: 177 LALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIR 236

Query: 238 PVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKS 297
           PVC+KFMQDPMEI+VDDE KLTLHGL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKS
Sbjct: 237 PVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKS 296

Query: 298 VSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV 357
           V R   L +LLVE NFP+I IH GM QEERL+RY+ FK+  +RILVAT+L GRG+DIERV
Sbjct: 297 VQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERV 356

Query: 358 NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQV 404
           NI  NYDMP+ +DTYLHRV RAGRFGTKGLAITFVS  +D+ ILN V
Sbjct: 357 NIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDV 403

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Homo sapiens (taxid: 9606)

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	423
225430261	428	PREDICTED: DEAD-box ATP-dependent RNA he	0.959	0.948	0.950	0.0
224092470	428	predicted protein [Populus trichocarpa]	0.959	0.948	0.943	0.0
449528365	427	PREDICTED: DEAD-box ATP-dependent RNA he	0.959	0.950	0.938	0.0
224143128	428	predicted protein [Populus trichocarpa]	0.959	0.948	0.936	0.0
317106728	455	JHL06P13.3 [Jatropha curcas]	0.955	0.887	0.935	0.0
118482305	428	unknown [Populus trichocarpa]	0.959	0.948	0.938	0.0
225442993	428	PREDICTED: DEAD-box ATP-dependent RNA he	0.959	0.948	0.936	0.0
297807157	427	hypothetical protein ARALYDRAFT_487950 [	0.957	0.948	0.928	0.0
297811229	427	hypothetical protein ARALYDRAFT_909079 [	0.957	0.948	0.926	0.0
18416493	427	DEAD-box ATP-dependent RNA helicase 56 [	0.957	0.948	0.926	0.0

>gi|225430261|ref|XP_002285072.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 56-like [Vitis vinifera]

 Score =  770 bits (1988), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/407 (95%), Positives = 395/407 (97%), Gaps = 1/407 (0%)

Query: 1   MGETRDNE-YEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
           MGETRDN+ YE+ELLDYEEE+ +APDSV  K NGEAAKKGYVGIHSSGFRDFLLKPELLR
Sbjct: 1   MGETRDNDAYEEELLDYEEEEDKAPDSVTGKVNGEAAKKGYVGIHSSGFRDFLLKPELLR 60

Query: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
           AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP  GQV ALV
Sbjct: 61  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPVTGQVAALV 120

Query: 120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
           LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP IVVGTPGRILA
Sbjct: 121 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPHIVVGTPGRILA 180

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
           LARDKDL+LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV
Sbjct: 181 LARDKDLALKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 240

Query: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 299
           CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS
Sbjct: 241 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 300

Query: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
           RAAELNKLLVECNFPSICIHSGM QEERLTRYKGFKEG+KRILVATDLVGRGIDIERVNI
Sbjct: 301 RAAELNKLLVECNFPSICIHSGMPQEERLTRYKGFKEGHKRILVATDLVGRGIDIERVNI 360

Query: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSD+LNQV +
Sbjct: 361 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDVLNQVQE 407

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224092470|ref|XP_002309623.1| predicted protein [Populus trichocarpa] gi|222855599|gb|EEE93146.1| predicted protein [Populus trichocarpa]

 Score =  766 bits (1977), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 384/407 (94%), Positives = 392/407 (96%), Gaps = 1/407 (0%)

Query: 1   MGETRDNE-YEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
           MGETRDN+ YE+ELLDYEEED +APDSV  K NGEA KKGYVGIHSSGFRDFLLKPELLR
Sbjct: 1   MGETRDNDTYEEELLDYEEEDEKAPDSVGAKVNGEAVKKGYVGIHSSGFRDFLLKPELLR 60

Query: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
           +IVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP  GQV ALV
Sbjct: 61  SIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPTSGQVIALV 120

Query: 120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
           LCHTRELAYQICHEFERFSTYLPD KVAVFYGGVNIK HKDLLKNECP IVVGTPGRILA
Sbjct: 121 LCHTRELAYQICHEFERFSTYLPDTKVAVFYGGVNIKTHKDLLKNECPHIVVGTPGRILA 180

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
           LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV
Sbjct: 181 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 240

Query: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 299
           CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL+ELEKNRKLNDLLDALDFNQVVIFVKSVS
Sbjct: 241 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLTELEKNRKLNDLLDALDFNQVVIFVKSVS 300

Query: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
           RAAELNKLLVECNFPSICIHSGMSQEERL RYKGFKEG+KRILVATDLVGRGIDIERVNI
Sbjct: 301 RAAELNKLLVECNFPSICIHSGMSQEERLMRYKGFKEGHKRILVATDLVGRGIDIERVNI 360

Query: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSD+LNQV +
Sbjct: 361 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDVLNQVQE 407

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449528365|ref|XP_004171175.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 56-like [Cucumis sativus]

 Score =  766 bits (1977), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 381/406 (93%), Positives = 395/406 (97%)

Query: 1   MGETRDNEYEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRA 60
           MGETRDNEYE+ELLDYEEE+ +APDSV  K NGEA KKGYVGIHSSGFRDFLLKPELLRA
Sbjct: 1   MGETRDNEYEEELLDYEEEEEKAPDSVGAKVNGEAGKKGYVGIHSSGFRDFLLKPELLRA 60

Query: 61  IVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVL 120
           IVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ +P  GQV+ALVL
Sbjct: 61  IVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIDPVAGQVSALVL 120

Query: 121 CHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILAL 180
           CHTRELAYQICHEFERFSTYLPD+KVAVFYGGVNIKIHKDLLKNECP IVVGTPGRILAL
Sbjct: 121 CHTRELAYQICHEFERFSTYLPDLKVAVFYGGVNIKIHKDLLKNECPHIVVGTPGRILAL 180

Query: 181 ARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVC 240
           +RDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVC
Sbjct: 181 SRDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVC 240

Query: 241 KKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSR 300
           KKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE+EKNRKLNDLLDALDFNQVVIFVKSV+R
Sbjct: 241 KKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEMEKNRKLNDLLDALDFNQVVIFVKSVNR 300

Query: 301 AAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIV 360
           AAEL+KLLVECNFPSICIHSGMSQEERLTRYKGFKEG+KRILVATDLVGRGIDIERVNIV
Sbjct: 301 AAELDKLLVECNFPSICIHSGMSQEERLTRYKGFKEGHKRILVATDLVGRGIDIERVNIV 360

Query: 361 INYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           INYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSA+DSD+LN V +
Sbjct: 361 INYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSAADSDVLNNVQE 406

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224143128|ref|XP_002324856.1| predicted protein [Populus trichocarpa] gi|222866290|gb|EEF03421.1| predicted protein [Populus trichocarpa]

 Score =  763 bits (1969), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 381/407 (93%), Positives = 392/407 (96%), Gaps = 1/407 (0%)

Query: 1   MGETRDNE-YEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
           MGETRDN+ YE+ELLDYEEED +APDSV  K NGEA KKGYVGIHSSGFRDFLLKPELLR
Sbjct: 1   MGETRDNDAYEEELLDYEEEDDKAPDSVGAKVNGEAVKKGYVGIHSSGFRDFLLKPELLR 60

Query: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
           +IVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP  GQV ALV
Sbjct: 61  SIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPTSGQVIALV 120

Query: 120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
           LCHTRELAYQICHEFERFSTYLPD KVAVFYGGVN+K HKDLLKNECP +VVGTPGRILA
Sbjct: 121 LCHTRELAYQICHEFERFSTYLPDTKVAVFYGGVNVKTHKDLLKNECPHVVVGTPGRILA 180

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
           LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFK+TPHDKQVMMFSATLSKEIRPV
Sbjct: 181 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKLTPHDKQVMMFSATLSKEIRPV 240

Query: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 299
           CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL+ELEKNRKLNDLLDALDFNQVVIFVKSVS
Sbjct: 241 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLTELEKNRKLNDLLDALDFNQVVIFVKSVS 300

Query: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
           RAAELNKLLVECNFPSICIHSGMSQEERL RYKGFKEG+KRILVATDLVGRGIDIERVNI
Sbjct: 301 RAAELNKLLVECNFPSICIHSGMSQEERLMRYKGFKEGHKRILVATDLVGRGIDIERVNI 360

Query: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSD+LNQV +
Sbjct: 361 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDVLNQVQE 407

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|317106728|dbj|BAJ53224.1| JHL06P13.3 [Jatropha curcas]

 Score =  761 bits (1965), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 379/405 (93%), Positives = 393/405 (97%), Gaps = 1/405 (0%)

Query: 1   MGETRDNE-YEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
           MGE +DN+ YE+ELLDYEEED +APDSV+ KA  E+AKKGYVGIHSSGFRDFLLKPELLR
Sbjct: 1   MGEVKDNDAYEEELLDYEEEDEKAPDSVSAKAGAESAKKGYVGIHSSGFRDFLLKPELLR 60

Query: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
           AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP  GQV ALV
Sbjct: 61  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPVAGQVAALV 120

Query: 120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
           LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIK+HKD+LKNECP IVVGTPGRILA
Sbjct: 121 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKVHKDILKNECPHIVVGTPGRILA 180

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
           LARDKDL LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV
Sbjct: 181 LARDKDLGLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 240

Query: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 299
           CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL+E+EKNRKLNDLLDALDFNQVVIFVKSV+
Sbjct: 241 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLTEMEKNRKLNDLLDALDFNQVVIFVKSVN 300

Query: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
           RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEG+KRILVATDLVGRGIDIERVNI
Sbjct: 301 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGHKRILVATDLVGRGIDIERVNI 360

Query: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQV 404
           V+NYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSD+LNQV
Sbjct: 361 VVNYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDVLNQV 405

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118482305|gb|ABK93079.1| unknown [Populus trichocarpa]

 Score =  761 bits (1965), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 382/407 (93%), Positives = 391/407 (96%), Gaps = 1/407 (0%)

Query: 1   MGETRDNE-YEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
           MGETRDN+ YE+ELLDYEEED +APDSV  K NGEA KKGYVGIHSSGFRDFLLKPELLR
Sbjct: 1   MGETRDNDTYEEELLDYEEEDEKAPDSVGAKVNGEAVKKGYVGIHSSGFRDFLLKPELLR 60

Query: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
           +IVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP  GQV ALV
Sbjct: 61  SIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPTSGQVIALV 120

Query: 120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
           LCHTRELAYQICHEFERFSTYLPD KVAVFYGGVNIK HKDLLKNECP IVVGTPGRILA
Sbjct: 121 LCHTRELAYQICHEFERFSTYLPDTKVAVFYGGVNIKTHKDLLKNECPHIVVGTPGRILA 180

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
           LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV
Sbjct: 181 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 240

Query: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 299
           CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL+ELEKNRKLNDLL ALDFNQVVIFVKSVS
Sbjct: 241 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLTELEKNRKLNDLLGALDFNQVVIFVKSVS 300

Query: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
           RAAELNKLLVECNFPSICIHSGMSQEERL RYKGFKEG+KRILVATDLVGRGIDIERV+I
Sbjct: 301 RAAELNKLLVECNFPSICIHSGMSQEERLMRYKGFKEGHKRILVATDLVGRGIDIERVDI 360

Query: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSD+LNQV +
Sbjct: 361 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDVLNQVQE 407

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225442993|ref|XP_002268833.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 56 [Vitis vinifera] gi|297743441|emb|CBI36308.3| unnamed protein product [Vitis vinifera]

 Score =  759 bits (1959), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 381/407 (93%), Positives = 393/407 (96%), Gaps = 1/407 (0%)

Query: 1   MGETRDNE-YEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
           MGE RDN+ YE+ELLDYEEED +APDSVA+KA GE+AKKGYVGIHSSGFRDFLLKPELLR
Sbjct: 1   MGEARDNDAYEEELLDYEEEDEKAPDSVASKAAGESAKKGYVGIHSSGFRDFLLKPELLR 60

Query: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
           +IVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP  GQV ALV
Sbjct: 61  SIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPVAGQVAALV 120

Query: 120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
           LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGV+IK HKDLLKNECP IVVGTPGRILA
Sbjct: 121 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVSIKTHKDLLKNECPHIVVGTPGRILA 180

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
           LARDKDL LK+VRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV
Sbjct: 181 LARDKDLGLKHVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 240

Query: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 299
           CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS
Sbjct: 241 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 300

Query: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
           RAAELNKLL+ECNFPSICIHSGM QEERLTRYK FKEG+KRILVATDLVGRGIDIERVNI
Sbjct: 301 RAAELNKLLMECNFPSICIHSGMPQEERLTRYKNFKEGHKRILVATDLVGRGIDIERVNI 360

Query: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSD+LNQV +
Sbjct: 361 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDVLNQVQE 407

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297807157|ref|XP_002871462.1| hypothetical protein ARALYDRAFT_487950 [Arabidopsis lyrata subsp. lyrata] gi|297317299|gb|EFH47721.1| hypothetical protein ARALYDRAFT_487950 [Arabidopsis lyrata subsp. lyrata]

 Score =  753 bits (1945), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/407 (92%), Positives = 392/407 (96%), Gaps = 2/407 (0%)

Query: 1   MGETRDNE-YEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
           MG+ RDNE YE+ELLDYEEED + PDS   K NGEA KKGYVGIHSSGFRDFLLKPELLR
Sbjct: 1   MGDARDNEAYEEELLDYEEEDEKVPDS-GNKVNGEAVKKGYVGIHSSGFRDFLLKPELLR 59

Query: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
           AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP+PGQV+ALV
Sbjct: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPSPGQVSALV 119

Query: 120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
           LCHTRELAYQIC+EF RFSTYLPD KV+VFYGGVNIKIHKDLLKNECP IVVGTPGR+LA
Sbjct: 120 LCHTRELAYQICNEFVRFSTYLPDTKVSVFYGGVNIKIHKDLLKNECPHIVVGTPGRVLA 179

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
           LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV
Sbjct: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239

Query: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 299
           CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE+EKNRKLNDLLDALDFNQVVIFVKSVS
Sbjct: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEMEKNRKLNDLLDALDFNQVVIFVKSVS 299

Query: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
           RAAELNKLLVECNFPSICIHSGMSQEERLTRYK FKEG+KRILVATDLVGRGIDIERVNI
Sbjct: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKSFKEGHKRILVATDLVGRGIDIERVNI 359

Query: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           VINYDMPDSADTYLHRVGRAGRFGTKGLAITFV+SASDS++LNQV +
Sbjct: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVASASDSEVLNQVQE 406

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297811229|ref|XP_002873498.1| hypothetical protein ARALYDRAFT_909079 [Arabidopsis lyrata subsp. lyrata] gi|297319335|gb|EFH49757.1| hypothetical protein ARALYDRAFT_909079 [Arabidopsis lyrata subsp. lyrata]

 Score =  752 bits (1941), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/407 (92%), Positives = 392/407 (96%), Gaps = 2/407 (0%)

Query: 1   MGETRDNE-YEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
           MG+ RDNE YE+ELLDYEEED + PDS  +K NGEA KKGYVGIHSSGFRDFLLKPELLR
Sbjct: 1   MGDARDNEAYEEELLDYEEEDEKVPDS-GSKVNGEAVKKGYVGIHSSGFRDFLLKPELLR 59

Query: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
           AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP+PGQV+ALV
Sbjct: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPSPGQVSALV 119

Query: 120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
           LCHTRELAYQIC+EF RFSTYLPD KV+VFYGGVNIKIHKDLLKNECP IVVGTPGR+LA
Sbjct: 120 LCHTRELAYQICNEFVRFSTYLPDTKVSVFYGGVNIKIHKDLLKNECPHIVVGTPGRVLA 179

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
           LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV
Sbjct: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239

Query: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 299
           CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL+E+EKNRKLNDLLDALDFNQVVIFVKSVS
Sbjct: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLNEMEKNRKLNDLLDALDFNQVVIFVKSVS 299

Query: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
           RAAELNKLLVECNFPSICIHSGMSQEERLTRYK FKEG+KRILVATDLVGRGIDIERVNI
Sbjct: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKSFKEGHKRILVATDLVGRGIDIERVNI 359

Query: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           VINYDMPDSADTYLHRVGRAGRFGTKGLAITFV+SASDS +LNQV +
Sbjct: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVASASDSTVLNQVQE 406

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18416493|ref|NP_568245.1| DEAD-box ATP-dependent RNA helicase 56 [Arabidopsis thaliana] gi|186522075|ref|NP_568244.2| DEAD-box ATP-dependent RNA helicase 56 [Arabidopsis thaliana] gi|108861899|sp|Q9LFN6.2|RH56_ARATH RecName: Full=DEAD-box ATP-dependent RNA helicase 56 gi|322510107|sp|Q56XG6.3|RH15_ARATH RecName: Full=DEAD-box ATP-dependent RNA helicase 15 gi|14190381|gb|AAK55671.1|AF378868_1 AT5g11200/F2I11_90 [Arabidopsis thaliana] gi|15450405|gb|AAK96496.1| AT5g11170/F2I11_60 [Arabidopsis thaliana] gi|16323360|gb|AAL15393.1| AT5g11200/F2I11_90 [Arabidopsis thaliana] gi|24111365|gb|AAN46806.1| At5g11170/F2I11_60 [Arabidopsis thaliana] gi|110740954|dbj|BAE98572.1| DEAD BOX RNA helicase RH15 - like protein [Arabidopsis thaliana] gi|332004259|gb|AED91642.1| DEAD-box ATP-dependent RNA helicase 56 [Arabidopsis thaliana] gi|332004262|gb|AED91645.1| DEAD-box ATP-dependent RNA helicase 56 [Arabidopsis thaliana]

 Score =  751 bits (1940), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/407 (92%), Positives = 392/407 (96%), Gaps = 2/407 (0%)

Query: 1   MGETRDNE-YEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
           MG+ RDNE YE+ELLDYEEED + PDS   K NGEA KKGYVGIHSSGFRDFLLKPELLR
Sbjct: 1   MGDARDNEAYEEELLDYEEEDEKVPDS-GNKVNGEAVKKGYVGIHSSGFRDFLLKPELLR 59

Query: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
           AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP+PGQV+ALV
Sbjct: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPSPGQVSALV 119

Query: 120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
           LCHTRELAYQIC+EF RFSTYLPD KV+VFYGGVNIKIHKDLLKNECP IVVGTPGR+LA
Sbjct: 120 LCHTRELAYQICNEFVRFSTYLPDTKVSVFYGGVNIKIHKDLLKNECPHIVVGTPGRVLA 179

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
           LAR+KDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV
Sbjct: 180 LAREKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239

Query: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 299
           CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE+EKNRKLNDLLDALDFNQVVIFVKSVS
Sbjct: 240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEMEKNRKLNDLLDALDFNQVVIFVKSVS 299

Query: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
           RAAELNKLLVECNFPSICIHSGMSQEERLTRYK FKEG+KRILVATDLVGRGIDIERVNI
Sbjct: 300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKSFKEGHKRILVATDLVGRGIDIERVNI 359

Query: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           VINYDMPDSADTYLHRVGRAGRFGTKGLAITFV+SASDS++LNQV +
Sbjct: 360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVASASDSEVLNQVQE 406

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	423
TAIR|locus:2147987	427	UAP56a "homolog of human UAP56	0.957	0.948	0.896	3.1e-193
TAIR|locus:2148027	486	UAP56b "homolog of human UAP56	0.586	0.510	0.856	3.5e-191
UNIPROTKB|Q13838	428	DDX39B "Spliceosome RNA helica	0.898	0.887	0.747	7.4e-153
UNIPROTKB|Q29024	428	DDX39B "Spliceosome RNA helica	0.898	0.887	0.747	7.4e-153
UNIPROTKB|Q3T147	428	DDX39B "Spliceosome RNA helica	0.898	0.887	0.747	9.5e-153
ZFIN|ZDB-GENE-040426-2902	427	ddx39ab "DEAD (Asp-Glu-Ala-Asp	0.900	0.892	0.746	9.5e-153
UNIPROTKB|Q5WR10	428	DDX39B "Spliceosome RNA helica	0.898	0.887	0.747	1.2e-152
MGI|MGI:99240	428	Ddx39b "DEAD (Asp-Glu-Ala-Asp)	0.888	0.878	0.758	2.5e-152
RGD|70923	428	Ddx39b "DEAD (Asp-Glu-Ala-Asp)	0.888	0.878	0.758	2.5e-152
UNIPROTKB|F1SCH3	475	DDX39A "Uncharacterized protei	0.905	0.806	0.738	3.2e-152

TAIR|locus:2147987 UAP56a "homolog of human UAP56 a" [Arabidopsis thaliana (taxid:3702)]

 Score = 1872 (664.0 bits), Expect = 3.1e-193, P = 3.1e-193
 Identities = 365/407 (89%), Positives = 379/407 (93%)

Query:     1 MGETRDNXXXXXXXXXXXXXAQ-APDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
             MG+ RDN              +  PDS   K NGEA KKGYVGIHSSGFRDFLLKPELLR
Sbjct:     1 MGDARDNEAYEEELLDYEEEDEKVPDS-GNKVNGEAVKKGYVGIHSSGFRDFLLKPELLR 59

Query:    60 AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
             AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP+PGQV+ALV
Sbjct:    60 AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPSPGQVSALV 119

Query:   120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
             LCHTRELAYQIC+EF RFSTYLPD KV+VFYGGVNIKIHKDLLKNECP IVVGTPGR+LA
Sbjct:   120 LCHTRELAYQICNEFVRFSTYLPDTKVSVFYGGVNIKIHKDLLKNECPHIVVGTPGRVLA 179

Query:   180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
             LAR+KDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV
Sbjct:   180 LAREKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239

Query:   240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVS 299
             CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE+EKNRKLNDLLDALDFNQVVIFVKSVS
Sbjct:   240 CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEMEKNRKLNDLLDALDFNQVVIFVKSVS 299

Query:   300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
             RAAELNKLLVECNFPSICIHSGMSQEERLTRYK FKEG+KRILVATDLVGRGIDIERVNI
Sbjct:   300 RAAELNKLLVECNFPSICIHSGMSQEERLTRYKSFKEGHKRILVATDLVGRGIDIERVNI 359

Query:   360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
             VINYDMPDSADTYLHRVGRAGRFGTKGLAITFV+SASDS++LNQV +
Sbjct:   360 VINYDMPDSADTYLHRVGRAGRFGTKGLAITFVASASDSEVLNQVQE 406

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005730 "nucleolus" evidence=IDA

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

GO:0005829 "cytosol" evidence=RCA

GO:0009506 "plasmodesma" evidence=IDA

TAIR|locus:2148027 UAP56b "homolog of human UAP56 b" [Arabidopsis thaliana (taxid:3702)]

 Score = 1096 (390.9 bits), Expect = 3.5e-191, Sum P(2) = 3.5e-191
 Identities = 214/250 (85%), Positives = 223/250 (89%)

Query:     1 MGETRDNXXXXXXXXXXXXXAQ-APDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLR 59
             MG+ RDN              +  PDS   K NGEA KKGYVGIHSSGFRDFLLKPELLR
Sbjct:     1 MGDARDNEAYEEELLDYEEEDEKVPDS-GNKVNGEAVKKGYVGIHSSGFRDFLLKPELLR 59

Query:    60 AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
             AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ EP+PGQV+ALV
Sbjct:    60 AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQIEPSPGQVSALV 119

Query:   120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
             LCHTRELAYQIC+EF RFSTYLPD KV+VFYGGVNIKIHKDLLKNECP IVVGTPGR+LA
Sbjct:   120 LCHTRELAYQICNEFVRFSTYLPDTKVSVFYGGVNIKIHKDLLKNECPHIVVGTPGRVLA 179

Query:   180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
             LAR+KDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV
Sbjct:   180 LAREKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239

Query:   240 CKKFMQDPME 249
             CKKFMQD +E
Sbjct:   240 CKKFMQDFLE 249

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0005618 "cell wall" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

GO:0009506 "plasmodesma" evidence=IDA

UNIPROTKB|Q13838 DDX39B "Spliceosome RNA helicase DDX39B" [Homo sapiens (taxid:9606)]

 Score = 1491 (529.9 bits), Expect = 7.4e-153, P = 7.4e-153
 Identities = 290/388 (74%), Positives = 332/388 (85%)

Query:    25 DSVATKANGEAAK-------KG-YVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHEC 76
             D V T A G+ A+       KG YV IHSSGFRDFLLKPELLRAIVD GFEHPSEVQHEC
Sbjct:    16 DEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHEC 75

Query:    77 IPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER 136
             IPQAILGMDV+CQAKSGMGKTAVFVL+TLQQ EP  GQV+ LV+CHTRELA+QI  E+ER
Sbjct:    76 IPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYER 135

Query:   137 FSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFIL 196
             FS Y+P++KVAVF+GG++IK  +++LK  CP IVVGTPGRILALAR+K L+LK+++HFIL
Sbjct:   136 FSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFIL 195

Query:   197 DECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEA 256
             DECDKMLE LDMRRDVQEIF+MTPH+KQVMMFSATLSKEIRPVC+KFMQDPMEI+VDDE 
Sbjct:   196 DECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDET 255

Query:   257 KLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSI 316
             KLTLHGL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I
Sbjct:   256 KLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAI 315

Query:   317 CIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRV 376
              IH GM QEERL+RY+ FK+  +RILVAT+L GRG+DIERVNI  NYDMP+ +DTYLHRV
Sbjct:   316 AIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 375

Query:   377 GRAGRFGTKGLAITFVSSASDSDILNQV 404
              RAGRFGTKGLAITFVS  +D+ ILN V
Sbjct:   376 ARAGRFGTKGLAITFVSDENDAKILNDV 403

GO:0005524 "ATP binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0006406 "mRNA export from nucleus" evidence=IGI;IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IGI

GO:0000346 "transcription export complex" evidence=IDA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IDA

GO:0008186 "RNA-dependent ATPase activity" evidence=IDA

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

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0008380 "RNA splicing" evidence=IDA

GO:0000245 "spliceosomal complex assembly" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0043008 "ATP-dependent protein binding" evidence=IDA

GO:0005687 "U4 snRNP" evidence=IDA

GO:0005688 "U6 snRNP" evidence=IDA

GO:0030621 "U4 snRNA binding" evidence=IDA

GO:0017070 "U6 snRNA binding" evidence=IDA

GO:0010501 "RNA secondary structure unwinding" evidence=IDA

UNIPROTKB|Q29024 DDX39B "Spliceosome RNA helicase DDX39B" [Sus scrofa (taxid:9823)]

 Score = 1491 (529.9 bits), Expect = 7.4e-153, P = 7.4e-153
 Identities = 290/388 (74%), Positives = 332/388 (85%)

Query:    25 DSVATKANGEAAK-------KG-YVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHEC 76
             D V T A G+ A+       KG YV IHSSGFRDFLLKPELLRAIVD GFEHPSEVQHEC
Sbjct:    16 DEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHEC 75

Query:    77 IPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER 136
             IPQAILGMDV+CQAKSGMGKTAVFVL+TLQQ EP  GQV+ LV+CHTRELA+QI  E+ER
Sbjct:    76 IPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYER 135

Query:   137 FSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFIL 196
             FS Y+P++KVAVF+GG++IK  +++LK  CP IVVGTPGRILALAR+K L+LK+++HFIL
Sbjct:   136 FSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFIL 195

Query:   197 DECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEA 256
             DECDKMLE LDMRRDVQEIF+MTPH+KQVMMFSATLSKEIRPVC+KFMQDPMEI+VDDE 
Sbjct:   196 DECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDET 255

Query:   257 KLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSI 316
             KLTLHGL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I
Sbjct:   256 KLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAI 315

Query:   317 CIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRV 376
              IH GM QEERL+RY+ FK+  +RILVAT+L GRG+DIERVNI  NYDMP+ +DTYLHRV
Sbjct:   316 AIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 375

Query:   377 GRAGRFGTKGLAITFVSSASDSDILNQV 404
              RAGRFGTKGLAITFVS  +D+ ILN V
Sbjct:   376 ARAGRFGTKGLAITFVSDENDAKILNDV 403

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0043008 "ATP-dependent protein binding" evidence=IEA

GO:0030621 "U4 snRNA binding" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0005688 "U6 snRNP" evidence=IEA

GO:0005687 "U4 snRNP" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

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

GO:0000346 "transcription export complex" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q3T147 DDX39B "Spliceosome RNA helicase DDX39B" [Bos taurus (taxid:9913)]

 Score = 1490 (529.6 bits), Expect = 9.5e-153, P = 9.5e-153
 Identities = 290/388 (74%), Positives = 331/388 (85%)

Query:    25 DSVATKANGEAAK-------KG-YVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHEC 76
             D V T A G+ A+       KG YV IHSSGFRDFLLKPELLRAIVD GFEHPSEVQHEC
Sbjct:    16 DEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHEC 75

Query:    77 IPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER 136
             IPQAILGMDV+CQAKSGMGKTAVFVL+TLQQ EP  GQV+ LV+CHTRELA+QI  E+ER
Sbjct:    76 IPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYER 135

Query:   137 FSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFIL 196
             FS Y+P +KVAVF+GG++IK  +++LK  CP IVVGTPGRILALAR+K L+LK+++HFIL
Sbjct:   136 FSKYMPSVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFIL 195

Query:   197 DECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEA 256
             DECDKMLE LDMRRDVQEIF+MTPH+KQVMMFSATLSKEIRPVC+KFMQDPMEI+VDDE 
Sbjct:   196 DECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDET 255

Query:   257 KLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSI 316
             KLTLHGL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I
Sbjct:   256 KLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAI 315

Query:   317 CIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRV 376
              IH GM QEERL+RY+ FK+  +RILVAT+L GRG+DIERVNI  NYDMP+ +DTYLHRV
Sbjct:   316 AIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 375

Query:   377 GRAGRFGTKGLAITFVSSASDSDILNQV 404
              RAGRFGTKGLAITFVS  +D+ ILN V
Sbjct:   376 ARAGRFGTKGLAITFVSDENDAKILNDV 403

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

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0043008 "ATP-dependent protein binding" evidence=IEA

GO:0030621 "U4 snRNA binding" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0005688 "U6 snRNP" evidence=IEA

GO:0005687 "U4 snRNP" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

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

GO:0000346 "transcription export complex" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

ZFIN|ZDB-GENE-040426-2902 ddx39ab "DEAD (Asp-Glu-Ala-Asp) box polypeptide 39Ab" [Danio rerio (taxid:7955)]

 Score = 1490 (529.6 bits), Expect = 9.5e-153, P = 9.5e-153
 Identities = 285/382 (74%), Positives = 328/382 (85%)

Query:    23 APDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL 82
             AP+S A     E  K  YV IHSSGFRDFLLKPELLRAIVD GFEHPSEVQHECIPQAIL
Sbjct:    22 APESAAPVGKKEV-KGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAIL 80

Query:    83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP 142
             GMD++CQAKSGMGKTAVFVL+TLQQ EP  GQV+ LV+CHTRELA+QI  E+ERFS Y+P
Sbjct:    81 GMDILCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELAFQISKEYERFSKYMP 140

Query:   143 DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM 202
              +KVAVF+GG++IK  +D+LK  CP IVVGTPGRILAL R+K L+LKNV+HF+LDECDKM
Sbjct:   141 TVKVAVFFGGMSIKKDEDVLKKSCPHIVVGTPGRILALVRNKTLNLKNVKHFVLDECDKM 200

Query:   203 LESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHG 262
             LE LDMRRDVQ+IF++TPH+KQ MMFSATLSKEIRPVC+KFMQDPME++VDDE KLTLHG
Sbjct:   201 LEQLDMRRDVQDIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKLTLHG 260

Query:   263 LVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGM 322
             L Q+Y KL + EKNRKL DLLD L+FNQVVIFVKSV R   L++LLVE NFP+I IH GM
Sbjct:   261 LQQYYCKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCVALSQLLVEQNFPAIAIHRGM 320

Query:   323 SQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRF 382
             +QEERL+RY+ FK+  +RILVAT+L GRG+DIERVNIV NYDMP+ +DTYLHRV RAGRF
Sbjct:   321 AQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF 380

Query:   383 GTKGLAITFVSSASDSDILNQV 404
             GTKGLAITFVS  +D+ ILN V
Sbjct:   381 GTKGLAITFVSDETDAKILNDV 402

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|Q5WR10 DDX39B "Spliceosome RNA helicase DDX39B" [Canis lupus familiaris (taxid:9615)]

 Score = 1489 (529.2 bits), Expect = 1.2e-152, P = 1.2e-152
 Identities = 290/388 (74%), Positives = 331/388 (85%)

Query:    25 DSVATKANGEA----AKK----GYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHEC 76
             D V T A G+     AKK     YV IHSSGFRDFLLKPELLRAIVD GFEHPSEVQHEC
Sbjct:    16 DEVETAAGGDGSEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHEC 75

Query:    77 IPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER 136
             IPQAILGMDV+CQAKSGMGKTAVFVL+TLQQ EP  GQV+ LV+CHTRELA+QI  E+ER
Sbjct:    76 IPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYER 135

Query:   137 FSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFIL 196
             FS Y+P++KVAVF+GG++IK  +++LK  CP IVVGTPGRILALAR+K L+LK+++HFIL
Sbjct:   136 FSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFIL 195

Query:   197 DECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEA 256
             DECDKMLE LDMRRDVQEIF+MTPH+KQVMMFSATLSKEIRPVC+KFMQDPMEI+VDDE 
Sbjct:   196 DECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDET 255

Query:   257 KLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSI 316
             KLTLHGL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I
Sbjct:   256 KLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAI 315

Query:   317 CIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRV 376
              IH GM QEERL+RY+ FK+  +RILVAT+L GRG+DIERVNI  NYDMP+ +DTYLHRV
Sbjct:   316 AIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 375

Query:   377 GRAGRFGTKGLAITFVSSASDSDILNQV 404
              RAGRFGTKGLAITFVS  +D+ ILN V
Sbjct:   376 ARAGRFGTKGLAITFVSDENDAKILNDV 403

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0043008 "ATP-dependent protein binding" evidence=IEA

GO:0030621 "U4 snRNA binding" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0005688 "U6 snRNP" evidence=IEA

GO:0005687 "U4 snRNP" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

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

GO:0000346 "transcription export complex" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

MGI|MGI:99240 Ddx39b "DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B" [Mus musculus (taxid:10090)]

 Score = 1486 (528.2 bits), Expect = 2.5e-152, P = 2.5e-152
 Identities = 286/377 (75%), Positives = 328/377 (87%)

Query:    29 TKANGEAAKKG-YVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVI 87
             T+A  +   KG YV IHSSGFRDFLLKPELLRAIVD GFEHPSEVQHECIPQAILGMDV+
Sbjct:    27 TEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVL 86

Query:    88 CQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA 147
             CQAKSGMGKTAVFVL+TLQQ EP  GQV+ LV+CHTRELA+QI  E+ERFS Y+P++KVA
Sbjct:    87 CQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVA 146

Query:   148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLD 207
             VF+GG++IK  +++LK  CP IVVGTPGRILALAR+K L+LK+++HFILDECDKMLE LD
Sbjct:   147 VFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 206

Query:   208 MRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHY 267
             MRRDVQEIF+MTPH+KQVMMFSATLSKEIRPVC+KFMQDPMEI+VDDE KLTLHGL Q+Y
Sbjct:   207 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYY 266

Query:   268 IKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEER 327
             +KL + EKNRKL DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I IH GM QEER
Sbjct:   267 VKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER 326

Query:   328 LTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGL 387
             L+RY+ FK+  +RILVAT+L GRG+DIERVNI  NYDMP+ +DTYLHRV RAGRFGTKGL
Sbjct:   327 LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL 386

Query:   388 AITFVSSASDSDILNQV 404
             AITFVS  +D+ ILN V
Sbjct:   387 AITFVSDENDAKILNDV 403

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=ISO

GO:0000346 "transcription export complex" evidence=ISO

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0006810 "transport" evidence=IEA

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

GO:0008186 "RNA-dependent ATPase activity" evidence=ISO

GO:0008380 "RNA splicing" evidence=ISO

GO:0010501 "RNA secondary structure unwinding" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=ISO

GO:0030621 "U4 snRNA binding" evidence=ISO

GO:0043008 "ATP-dependent protein binding" evidence=ISO

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=ISO

GO:0051028 "mRNA transport" evidence=IEA

RGD|70923 Ddx39b "DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B" [Rattus norvegicus (taxid:10116)]

 Score = 1486 (528.2 bits), Expect = 2.5e-152, P = 2.5e-152
 Identities = 286/377 (75%), Positives = 328/377 (87%)

Query:    29 TKANGEAAKKG-YVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVI 87
             T+A  +   KG YV IHSSGFRDFLLKPELLRAIVD GFEHPSEVQHECIPQAILGMDV+
Sbjct:    27 TEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVL 86

Query:    88 CQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA 147
             CQAKSGMGKTAVFVL+TLQQ EP  GQV+ LV+CHTRELA+QI  E+ERFS Y+P++KVA
Sbjct:    87 CQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVA 146

Query:   148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLD 207
             VF+GG++IK  +++LK  CP IVVGTPGRILALAR+K L+LK+++HFILDECDKMLE LD
Sbjct:   147 VFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 206

Query:   208 MRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHY 267
             MRRDVQEIF+MTPH+KQVMMFSATLSKEIRPVC+KFMQDPMEI+VDDE KLTLHGL Q+Y
Sbjct:   207 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYY 266

Query:   268 IKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEER 327
             +KL + EKNRKL DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I IH GM QEER
Sbjct:   267 VKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER 326

Query:   328 LTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGL 387
             L+RY+ FK+  +RILVAT+L GRG+DIERVNI  NYDMP+ +DTYLHRV RAGRFGTKGL
Sbjct:   327 LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL 386

Query:   388 AITFVSSASDSDILNQV 404
             AITFVS  +D+ ILN V
Sbjct:   387 AITFVSDENDAKILNDV 403

GO:0000245 "spliceosomal complex assembly" evidence=IEA;ISO

GO:0000346 "transcription export complex" evidence=IEA;ISO

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004004 "ATP-dependent RNA helicase activity" evidence=IEA;ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=IEA;ISO

GO:0005687 "U4 snRNP" evidence=IEA;ISO

GO:0005688 "U6 snRNP" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

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

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

GO:0008186 "RNA-dependent ATPase activity" evidence=ISO

GO:0008380 "RNA splicing" evidence=ISO

GO:0010501 "RNA secondary structure unwinding" evidence=IEA;ISO

GO:0016607 "nuclear speck" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=IEA;ISO

GO:0030621 "U4 snRNA binding" evidence=IEA;ISO

GO:0043008 "ATP-dependent protein binding" evidence=IEA;ISO

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA;ISO

UNIPROTKB|F1SCH3 DDX39A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 1485 (527.8 bits), Expect = 3.2e-152, P = 3.2e-152
 Identities = 283/383 (73%), Positives = 327/383 (85%)

Query:    22 QAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAI 81
             QAP   A     +  K  YV IHSSGFRDFLLKPELLRAIVD GFEHPSEVQHECIPQAI
Sbjct:    68 QAPPENAPAPPKKDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAI 127

Query:    82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYL 141
             LGMDV+CQAKSGMGKTAVFVL+TLQQ EP  GQVT LV+CHTRELA+QI  E+ERFS Y+
Sbjct:   128 LGMDVLCQAKSGMGKTAVFVLATLQQIEPVNGQVTVLVMCHTRELAFQISKEYERFSKYM 187

Query:   142 PDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDK 201
             P +KV+VF+GG++IK  +++LK  CP +VVGTPGRILAL R++ L+LKNV+HF+LDECDK
Sbjct:   188 PSVKVSVFFGGLSIKKDEEVLKKNCPHVVVGTPGRILALVRNRSLNLKNVKHFVLDECDK 247

Query:   202 MLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLH 261
             MLE LDMRRDVQEIF++TPH+KQ MMFSATLSKEIRPVC+KFMQDPME++VDDE KLTLH
Sbjct:   248 MLEQLDMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKLTLH 307

Query:   262 GLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSG 321
             GL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I IH G
Sbjct:   308 GLQQYYVKLKDSEKNRKLFDLLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRG 367

Query:   322 MSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR 381
             M+QEERL+RY+ FK+  +RILVAT+L GRG+DIERVNIV NYDMP+ +DTYLHRV RAGR
Sbjct:   368 MAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR 427

Query:   382 FGTKGLAITFVSSASDSDILNQV 404
             FGTKGLAITFVS  +D+ ILN V
Sbjct:   428 FGTKGLAITFVSDENDAKILNDV 450

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5RE47	DX39B_PONAB	3, ., 6, ., 4, ., 1, 3	0.7272	0.9290	0.9182	yes	no
A7TLA0	SUB21_VANPO	3, ., 6, ., 4, ., 1, 3	0.6244	0.9669	0.9274	N/A	no
A7EIX7	SUB2_SCLS1	3, ., 6, ., 4, ., 1, 3	0.6718	0.9007	0.8581	N/A	no
Q5WR10	DX39B_CANFA	3, ., 6, ., 4, ., 1, 3	0.7272	0.9290	0.9182	yes	no
A4RBS3	SUB2_MAGO7	3, ., 6, ., 4, ., 1, 3	0.6626	0.9645	0.9357	N/A	no
Q5ZHZ0	DX39B_CHICK	3, ., 6, ., 4, ., 1, 3	0.7223	0.9290	0.9182	yes	no
O13792	SUB2_SCHPO	3, ., 6, ., 4, ., 1, 3	0.7066	0.9385	0.9147	yes	no
A6ZXP4	SUB2_YEAS7	3, ., 6, ., 4, ., 1, 3	0.6580	0.9078	0.8609	N/A	no
Q18212	DX39B_CAEEL	3, ., 6, ., 4, ., 1, 3	0.7035	0.9361	0.9317	yes	no
Q0TXZ2	SUB2_PHANO	3, ., 6, ., 4, ., 1, 3	0.6352	0.9574	0.9246	N/A	no
Q6CH90	SUB2_YARLI	3, ., 6, ., 4, ., 1, 3	0.6306	0.9456	0.9070	yes	no
Q2U6P7	SUB2_ASPOR	3, ., 6, ., 4, ., 1, 3	0.6674	0.9408	0.9024	yes	no
O00148	DX39A_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7175	0.9432	0.9344	no	no
A7TJT7	SUB22_VANPO	3, ., 6, ., 4, ., 1, 3	0.6252	0.9763	0.9343	N/A	no
Q9Z1N5	DX39B_MOUSE	3, ., 6, ., 4, ., 1, 3	0.7331	0.9432	0.9322	yes	no
Q4WCW2	SUB2_ASPFU	3, ., 6, ., 4, ., 1, 3	0.6494	0.9408	0.8883	yes	no
Q759L6	SUB2_ASHGO	3, ., 6, ., 4, ., 1, 3	0.6288	0.9669	0.9337	yes	no
Q5ASK8	SUB2_EMENI	3, ., 6, ., 4, ., 1, 3	0.6443	0.9219	0.8986	yes	no
P0CQ97	SUB2_CRYNB	3, ., 6, ., 4, ., 1, 3	0.6881	0.9385	0.8981	N/A	no
P0CQ96	SUB2_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.6881	0.9385	0.8981	yes	no
Q0CGJ9	SUB2_ASPTN	3, ., 6, ., 4, ., 1, 3	0.6650	0.9338	0.9018	N/A	no
Q63413	DX39B_RAT	3, ., 6, ., 4, ., 1, 3	0.7331	0.9432	0.9322	yes	no
Q9LFN6	RH56_ARATH	3, ., 6, ., 4, ., 1, 3	0.9262	0.9574	0.9484	yes	no
Q2H4D0	SUB2_CHAGB	3, ., 6, ., 4, ., 1, 3	0.6491	0.9574	0.9331	N/A	no
Q6FL17	SUB2_CANGA	3, ., 6, ., 4, ., 1, 3	0.6370	0.9763	0.9407	yes	no
A3LST5	SUB2_PICST	3, ., 6, ., 4, ., 1, 3	0.6626	0.9669	0.9445	yes	no
A5DDN0	SUB2_PICGU	3, ., 6, ., 4, ., 1, 3	0.6706	0.9645	0.9444	N/A	no
Q5TM17	DX39B_MACMU	3, ., 6, ., 4, ., 1, 3	0.7272	0.9290	0.9182	yes	no
Q5U216	DX39A_RAT	3, ., 6, ., 4, ., 1, 3	0.7175	0.9432	0.9344	no	no
Q27268	DX39B_DROME	3, ., 6, ., 4, ., 1, 3	0.7142	0.9243	0.9221	yes	no
Q6BME5	SUB2_DEBHA	3, ., 6, ., 4, ., 1, 3	0.6523	0.9669	0.9402	yes	no
Q0JM17	RH56_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8774	0.9574	0.9375	yes	no
Q5JK84	RH15_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8725	0.9574	0.9375	no	no
Q3T147	DX39B_BOVIN	3, ., 6, ., 4, ., 1, 3	0.7272	0.9290	0.9182	yes	no
Q29024	DX39B_PIG	3, ., 6, ., 4, ., 1, 3	0.7272	0.9290	0.9182	yes	no
A2R0B5	SUB2_ASPNC	3, ., 6, ., 4, ., 1, 3	0.6786	0.9408	0.9045	yes	no
Q56XG6	RH15_ARATH	3, ., 6, ., 4, ., 1, 3	0.9262	0.9574	0.9484	yes	no
P60024	DX39B_PANTR	3, ., 6, ., 4, ., 1, 3	0.7272	0.9290	0.9182	yes	no
A1CMQ7	SUB2_ASPCL	3, ., 6, ., 4, ., 1, 3	0.6626	0.9408	0.9024	N/A	no
Q1DI07	SUB2_COCIM	3, ., 6, ., 4, ., 1, 3	0.6595	0.9408	0.8984	N/A	no
A6R603	SUB2_AJECN	3, ., 6, ., 4, ., 1, 3	0.6587	0.9408	0.9004	N/A	no
Q8VDW0	DX39A_MOUSE	3, ., 6, ., 4, ., 1, 3	0.72	0.9432	0.9344	no	no
Q13838	DX39B_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7272	0.9290	0.9182	yes	no
A1DL85	SUB2_NEOFI	3, ., 6, ., 4, ., 1, 3	0.6626	0.9408	0.9024	N/A	no
Q6CM95	SUB2_KLULA	3, ., 6, ., 4, ., 1, 3	0.6232	0.9669	0.9359	yes	no
Q07478	SUB2_YEAST	3, ., 6, ., 4, ., 1, 3	0.6580	0.9078	0.8609	yes	no
A5E3W5	SUB2_LODEL	3, ., 6, ., 4, ., 1, 3	0.6618	0.9645	0.9422	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_pg.C_LG_VI1784	SubName- Full=Putative uncharacterized protein; (428 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.IV.3602.1	hypothetical protein (264 aa)						•			0.800
	gw1.261.1.1	annotation not avaliable (75 aa)						•			0.800
	gw1.226.19.1	hypothetical protein (164 aa)						•			0.800
	fgenesh4_pg.C_LG_II002243	hypothetical protein (274 aa)						•			0.800
	estExt_fgenesh4_pg.C_LG_I1776	hypothetical protein (212 aa)						•			0.800
	estExt_fgenesh4_kg.C_LG_X0079	hypothetical protein (251 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	423
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-132
cd00268	203	cd00268, DEADc, DEAD-box helicases	3e-85
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	4e-84
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	7e-75
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	5e-74
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	2e-73
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	6e-63
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	9e-62
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	4e-59
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	4e-48
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-46
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	5e-46
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	5e-46
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	4e-45
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	4e-37
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	2e-32
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	6e-29
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	4e-28
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	5e-14
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	4e-13
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	4e-13
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	1e-11
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	2e-11
COG1205	851	COG1205, COG1205, Distinct helicase family with a	8e-11
cd09639	353	cd09639, Cas3_I, CRISPR/Cas system-associated prot	3e-09
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	2e-08
TIGR01587	358	TIGR01587, cas3_core, CRISPR-associated helicase C	5e-08
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	3e-07
COG1203	733	COG1203, COG1203, CRISPR-associated helicase Cas3	8e-07
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	4e-06
PRK09751	1490	PRK09751, PRK09751, putative ATP-dependent helicas	9e-06
TIGR00580	926	TIGR00580, mfd, transcription-repair coupling fact	2e-05
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	4e-05
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	7e-05
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	3e-04
COG1197	1139	COG1197, Mfd, Transcription-repair coupling factor	0.001
PRK13767	876	PRK13767, PRK13767, ATP-dependent helicase; Provis	0.002
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	0.003
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	0.003

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

 Score =  390 bits (1003), Expect = e-132
 Identities = 148/372 (39%), Positives = 218/372 (58%), Gaps = 6/372 (1%)

Query: 45  SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLST 104
              F    L PELL+A+ D GFE P+ +Q   IP  + G DV+ QA++G GKTA F+L  
Sbjct: 28  PPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPL 87

Query: 105 LQQ--TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL 162
           LQ+         V+AL+L  TRELA QI  E  +    L  ++VAV YGGV+I+   + L
Sbjct: 88  LQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEAL 147

Query: 163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHD 222
           K     IVV TPGR+L L +   L L  V   +LDE D+ML+ +    D+++I K  P D
Sbjct: 148 K-RGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLD-MGFIDDIEKILKALPPD 205

Query: 223 KQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEA-KLTLHGLVQHYIKL-SELEKNRKLN 280
           +Q ++FSAT+  +IR + ++++ DP+EI V  E  + TL  + Q Y+++ SE EK   L 
Sbjct: 206 RQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLL 265

Query: 281 DLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKR 340
            LL   D  +V++FV++     EL + L +  F    +H  + QEER    + FK+G  R
Sbjct: 266 KLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELR 325

Query: 341 ILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDI 400
           +LVATD+  RG+DI  V+ VINYD+P   + Y+HR+GR GR G KG+AI+FV+   +   
Sbjct: 326 VLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKK 385

Query: 401 LNQVSKFMFLLI 412
           L ++ K +   +
Sbjct: 386 LKRIEKRLERKL 397

Length = 513

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

 Score =  258 bits (662), Expect = 3e-85
 Identities = 84/205 (40%), Positives = 121/205 (59%), Gaps = 5/205 (2%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F +  L PELLR I   GFE P+ +Q   IP  + G DVI QA++G GKTA F++  L++
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 108 --TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNE 165
               P      AL+L  TRELA QI     +   +  ++KV V YGG +I      LK  
Sbjct: 61  LDPSPKKDGPQALILAPTRELALQIAEVARKLGKH-TNLKVVVIYGGTSIDKQIRKLKR- 118

Query: 166 CPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQV 225
            P IVV TPGR+L L     L L  V++ +LDE D+ML+ +     ++EI K+ P D+Q 
Sbjct: 119 GPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLD-MGFEDQIREILKLLPKDRQT 177

Query: 226 MMFSATLSKEIRPVCKKFMQDPMEI 250
           ++FSAT+ KE+R + +KF+++P+ I
Sbjct: 178 LLFSATMPKEVRDLARKFLRNPVRI 202

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. Length = 203

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

 Score =  262 bits (672), Expect = 4e-84
 Identities = 139/361 (38%), Positives = 208/361 (57%), Gaps = 6/361 (1%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F    L  +LLR I   GFE PS +Q   I   + G D I QA+SG GKTA FV++ LQ 
Sbjct: 30  FDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQL 89

Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            + +     AL+L  TRELA QI         YL  ++     GG  ++   + LK    
Sbjct: 90  IDYDLNACQALILAPTRELAQQIQKVVLALGDYL-KVRCHACVGGTVVRDDINKLKAGV- 147

Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
            +VVGTPGR+  +   + L + +++ FILDE D+ML S   +  + ++FK  P D QV +
Sbjct: 148 HMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEML-SRGFKGQIYDVFKKLPPDVQVAL 206

Query: 228 FSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLLDAL 286
           FSAT+  EI  +  KFM+DP  I V  + +LTL G+ Q Y+ + + E K   L DL + L
Sbjct: 207 FSATMPNEILELTTKFMRDPKRILVKKD-ELTLEGIRQFYVAVEKEEWKFDTLCDLYETL 265

Query: 287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD 346
              Q +I+  +  +   L K + E +F   C+H  M Q++R    + F+ G+ R+L+ TD
Sbjct: 266 TITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTD 325

Query: 347 LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           L+ RGID+++V++VINYD+P S + Y+HR+GR+GRFG KG+AI FV+   D + L ++ +
Sbjct: 326 LLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTP-DDIEQLKEIER 384

Query: 407 F 407
            
Sbjct: 385 H 385

Length = 401

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

 Score =  240 bits (615), Expect = 7e-75
 Identities = 123/348 (35%), Positives = 190/348 (54%), Gaps = 18/348 (5%)

Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP 112
           L P LL  + + G+   + +Q + +P  + G DVI QAK+G GKTA F L  LQ+ +   
Sbjct: 11  LPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKR 70

Query: 113 GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVG 172
            +V ALVLC TRELA Q+  E  R + ++P+IKV    GGV +    D L++    I+VG
Sbjct: 71  FRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHG-AHIIVG 129

Query: 173 TPGRILALARDKDLSLKNVRHFILDECDKMLESLDM--RRDVQEIFKMTPHDKQVMMFSA 230
           TPGRIL   R   L L  +   +LDE D+M   LDM  +  +  I +  P  +Q ++FSA
Sbjct: 130 TPGRILDHLRKGTLDLDALNTLVLDEADRM---LDMGFQDAIDAIIRQAPARRQTLLFSA 186

Query: 231 TLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQ 290
           T  + I  + ++F +DP+E+ V+    L    + Q + ++S  E+   L  LL  L    
Sbjct: 187 TYPEGIAAISQRFQRDPVEVKVESTHDLP--AIEQRFYEVSPDERLPALQRLL--LHHQP 242

Query: 291 V--VIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEER---LTRYKGFKEGNKRILVAT 345
              V+F  +     E+   L    F ++ +H  + Q +R   L R   F   +  +LVAT
Sbjct: 243 ESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVR---FANRSCSVLVAT 299

Query: 346 DLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVS 393
           D+  RG+DI+ +  VINY++    + ++HR+GR GR G+KGLA++ V+
Sbjct: 300 DVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVA 347

Length = 460

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

 Score =  237 bits (607), Expect = 5e-74
 Identities = 129/373 (34%), Positives = 195/373 (52%), Gaps = 23/373 (6%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F +  L   LL A+ D G+  P+ +Q E IP A+ G DV+  A +G GKTA F+L  LQ 
Sbjct: 3   FSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQH 62

Query: 108 ----TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLK 163
                    G    L+L  TRELA Q+  +    + +   + +A   GGV    H ++  
Sbjct: 63  LLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHT-HLDIATITGGVAYMNHAEVF- 120

Query: 164 NECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDM--RRDVQEIFKMTPH 221
           +E   IVV TPGR+L   ++++   + V   ILDE D+ML   DM   +D++ I   T  
Sbjct: 121 SENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRML---DMGFAQDIETIAAETRW 177

Query: 222 DKQVMMFSATL-SKEIRPVCKKFMQDPMEIYVD----DEAKLTLHGLVQHYIKLSELEKN 276
            KQ ++FSATL    ++   ++ + DP+E+  +    +  K+      Q Y +  +LE  
Sbjct: 178 RKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIH-----QWYYRADDLEHK 232

Query: 277 RK-LNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFK 335
              L  LL   +  + ++FV++  R  EL   L +       +   M Q +R    K   
Sbjct: 233 TALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLT 292

Query: 336 EGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSA 395
           +G   +LVATD+  RGIDI+ V+ VIN+DMP SADTYLHR+GR GR G KG AI+ V  A
Sbjct: 293 DGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLV-EA 351

Query: 396 SDSDILNQVSKFM 408
            D  +L ++ +++
Sbjct: 352 HDHLLLGKIERYI 364

Length = 434

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

 Score =  241 bits (616), Expect = 2e-73
 Identities = 131/365 (35%), Positives = 201/365 (55%), Gaps = 4/365 (1%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  LK  +L A+ D G+E PS +Q ECIP  + G DV+  A++G GKTA F L  L  
Sbjct: 8   FADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHN 67

Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            +P       LVL  TRELA Q+      FS ++  + V   YGG    +    L+ + P
Sbjct: 68  LDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALR-QGP 126

Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
           QIVVGTPGR+L   +   L L  +   +LDE D+ML  +    DV+ I    P   Q  +
Sbjct: 127 QIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLR-MGFIEDVETIMAQIPEGHQTAL 185

Query: 228 FSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALD 287
           FSAT+ + IR + ++FM++P E+ +      T   + Q Y  +  + KN  L   L+A D
Sbjct: 186 FSATMPEAIRRITRRFMKEPQEVRIQSSVT-TRPDISQSYWTVWGMRKNEALVRFLEAED 244

Query: 288 FNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL 347
           F+  +IFV++ +   E+ + L    + S  ++  M+Q  R    +  K+G   IL+ATD+
Sbjct: 245 FDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDV 304

Query: 348 VGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF 407
             RG+D+ER+++V+NYD+P  +++Y+HR+GR GR G  G A+ FV +  +  +L  + + 
Sbjct: 305 AARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVEN-RERRLLRNIERT 363

Query: 408 MFLLI 412
           M L I
Sbjct: 364 MKLTI 368

Length = 629

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

 Score =  209 bits (533), Expect = 6e-63
 Identities = 121/351 (34%), Positives = 192/351 (54%), Gaps = 20/351 (5%)

Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQ---QTE 109
           L P++LRA+ + G+  P+ +Q + IP  + G D++  A++G GKTA F L  LQ     +
Sbjct: 8   LSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQ 67

Query: 110 PNPGQ---VTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNEC 166
           P+      V AL+L  TRELA QI      +S YL +I+  V +GGV+I      L+   
Sbjct: 68  PHAKGRRPVRALILTPTRELAAQIGENVRDYSKYL-NIRSLVVFGGVSINPQMMKLRGGV 126

Query: 167 PQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMR--RDVQEIFKMTPHDKQ 224
             ++V TPGR+L L     + L  V   +LDE D+ML   DM    D++ +    P  +Q
Sbjct: 127 -DVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRML---DMGFIHDIRRVLAKLPAKRQ 182

Query: 225 VMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRK---LND 281
            ++FSAT S +I+ + +K + +P+EI V    + T    V  ++    ++K RK   L+ 
Sbjct: 183 NLLFSATFSDDIKALAEKLLHNPLEIEV--ARRNTASEQVTQHVHF--VDKKRKRELLSQ 238

Query: 282 LLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRI 341
           ++   ++ QV++F ++   A  L + L +    S  IH   SQ  R      FK G+ R+
Sbjct: 239 MIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRV 298

Query: 342 LVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFV 392
           LVATD+  RG+DIE +  V+NY++P+  + Y+HR+GR GR    G A++ V
Sbjct: 299 LVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLV 349

Length = 456

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

 Score =  206 bits (526), Expect = 9e-62
 Identities = 114/358 (31%), Positives = 195/358 (54%), Gaps = 14/358 (3%)

Query: 46  SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTL 105
           + F DF L PEL+ AI D GF + + +Q + +   + G D I +A++G GKTA F++S +
Sbjct: 87  TRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISII 146

Query: 106 QQTEPNP-------GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNI-KI 157
            Q    P       G+  AL++  TREL  QI  +    + Y   + V  F GG++  K 
Sbjct: 147 NQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKY-TGLNVMTFVGGMDFDKQ 205

Query: 158 HKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFK 217
            K L    C  I+V TPGR+L   +  ++ L  V   +LDE D+ML+ +     V++I +
Sbjct: 206 LKQLEARFC-DILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLD-MGFIPQVRQIIR 263

Query: 218 MTPH--DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEK 275
            TP   ++Q ++FSAT + ++  + K++  DP  + ++ E       + QH   ++  +K
Sbjct: 264 QTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENV-ASDTVEQHVYAVAGSDK 322

Query: 276 NRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFK 335
            + L +L+    + +V++F         + + LV+    +  +   + Q +R+   +GF+
Sbjct: 323 YKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFR 382

Query: 336 EGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVS 393
           EG  R+LVATD+ GRGI I+ ++ VIN+ +P+  D Y+HR+GR GR G  G++I+F  
Sbjct: 383 EGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAG 440

Length = 475

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

 Score =  201 bits (513), Expect = 4e-59
 Identities = 126/376 (33%), Positives = 195/376 (51%), Gaps = 28/376 (7%)

Query: 33  GEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKS 92
           GE   K  V    + F D++LK     ++ ++GF  P+ +Q +  P A+ G D+I  A++
Sbjct: 122 GENVPKPVVSFEYTSFPDYILK-----SLKNAGFTEPTPIQVQGWPIALSGRDMIGIAET 176

Query: 93  GMGKTAVFVLST----LQQTEPNPGQ-VTALVLCHTRELAYQICHEFERFSTYLPDIKVA 147
           G GKT  F+L        Q     G     LVL  TRELA QI  +  +F      I+  
Sbjct: 177 GSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASS-KIRNT 235

Query: 148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE--- 204
           V YGGV  +     L+    +I++  PGR++        +L+ V + +LDE D+ML+   
Sbjct: 236 VAYGGVPKRGQIYALRRGV-EILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGF 294

Query: 205 SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEI----RPVCKKFMQDPMEIYVDDEAKLTL 260
              +R+ V +I    P D+Q +M+SAT  KE+    R +CK   ++P+ + V        
Sbjct: 295 EPQIRKIVSQI---RP-DRQTLMWSATWPKEVQSLARDLCK---EEPVHVNVGSLDLTAC 347

Query: 261 HGLVQHYIKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICI 318
           H + Q    + E EK  KL  LL  +  D ++++IFV++   A  L K L    +P++CI
Sbjct: 348 HNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCI 407

Query: 319 HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGR 378
           H    QEER      FK G   I++ATD+  RG+D++ V  VIN+D P+  + Y+HR+GR
Sbjct: 408 HGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGR 467

Query: 379 AGRFGTKGLAITFVSS 394
            GR G KG + TF++ 
Sbjct: 468 TGRAGAKGASYTFLTP 483

Length = 545

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

 Score =  169 bits (430), Expect = 4e-48
 Identities = 116/356 (32%), Positives = 190/356 (53%), Gaps = 19/356 (5%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLST--- 104
           F DF L P+++ A+   GF + + +Q   +P  + G DV  QA++G GKT  F+ +T   
Sbjct: 10  FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69

Query: 105 -LQQTEPNPGQVT---ALVLCHTRELAYQICHEFERF--STYLPDIKVAVFYGGVNIKIH 158
            L    P   +V    AL++  TRELA QI  + E    +T L   K+ + YGG      
Sbjct: 70  LLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGL---KLGLAYGGDGYDKQ 126

Query: 159 KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKM 218
             +L++    I++GT GR++  A+   ++L  ++  +LDE D+M + L   +D++ +F+ 
Sbjct: 127 LKVLESG-VDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFD-LGFIKDIRWLFRR 184

Query: 219 TPHDKQ--VMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKN 276
            P   Q   M+FSATLS  +R +  + M +P  + V+ E K T H + +     S  EK 
Sbjct: 185 MPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQK-TGHRIKEELFYPSNEEKM 243

Query: 277 RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSG-MSQEERLTRYKGFK 335
           R L  L++    ++ +IF  +  R  E+   L   +   + + +G ++Q++RL   + F 
Sbjct: 244 RLLQTLIEEEWPDRAIIFANTKHRCEEIWGHL-AADGHRVGLLTGDVAQKKRLRILEEFT 302

Query: 336 EGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITF 391
            G+  ILVATD+  RG+ I  V  V NYD+PD  + Y+HR+GR GR G  G +I+ 
Sbjct: 303 RGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358

Length = 423

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

 Score =  159 bits (403), Expect = 1e-46
 Identities = 67/202 (33%), Positives = 100/202 (49%), Gaps = 4/202 (1%)

Query: 61  IVDSGFEHPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV 119
           I   GFE     Q E I   + G  DVI  A +G GKT   +L  L+  +   G    LV
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGG-RVLV 59

Query: 120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA 179
           L  TRELA Q   E ++    L  +KV   YGG + +     L++    I+V TPGR+L 
Sbjct: 60  LVPTRELAEQWAEELKKLGPSLG-LKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLD 118

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV 239
           L  +  LSL NV   ILDE  ++L+       ++++ K+ P + Q+++ SAT  +EI  +
Sbjct: 119 LLENDKLSLSNVDLVILDEAHRLLDG-GFGDQLEKLLKLLPKNVQLLLLSATPPEEIENL 177

Query: 240 CKKFMQDPMEIYVDDEAKLTLH 261
            + F+ DP+ I V       + 
Sbjct: 178 LELFLNDPVFIDVGFTPLEPIE 199

Length = 201

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

 Score =  156 bits (396), Expect = 5e-46
 Identities = 66/169 (39%), Positives = 96/169 (56%), Gaps = 3/169 (1%)

Query: 70  SEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQ 129
           + +Q + IP  + G DV+ QA +G GKT  F+L  LQ   P  G   ALVL  TRELA Q
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60

Query: 130 ICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA-LARDKDLSL 188
           I  E ++    L  ++VA+  GG ++K     LK     I+VGTPGR+L  L R K   L
Sbjct: 61  IYEELKKLFKILG-LRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLL 119

Query: 189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIR 237
           KN++  +LDE  ++L+      D++EI    P D+Q+++ SATL + + 
Sbjct: 120 KNLKLLVLDEAHRLLDM-GFGDDLEEILSRLPPDRQILLLSATLPRNLE 167

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

 Score =  165 bits (420), Expect = 5e-46
 Identities = 120/366 (32%), Positives = 187/366 (51%), Gaps = 29/366 (7%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVL----- 102
           F    L P+LL  +  +G+E P+ +Q + IP A+ G  ++  A +G GKTA F++     
Sbjct: 123 FSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISR 182

Query: 103 -STLQQTEPNPGQ-VTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKD 160
             T++   P+  +   A+VL  TREL  Q+  + +     LP  K A+  GG       D
Sbjct: 183 CCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLP-FKTALVVGG-------D 234

Query: 161 LLKNECPQI------VVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQE 214
            +  +  +I      +VGTPGR++ L    D+ L NV   +LDE D MLE    R  V +
Sbjct: 235 AMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLER-GFRDQVMQ 293

Query: 215 IFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE 274
           IF+      QV++FSAT+S E+        +D + I + +  +     + Q  I +   +
Sbjct: 294 IFQALSQ-PQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPN-KAVKQLAIWVETKQ 351

Query: 275 KNRKLNDLLDALDFNQ--VVIFVKSVSRAAEL--NKLLVECNFPSICIHSGMSQEERLTR 330
           K +KL D+L +    +   V+FV S    A+L  N + V     ++ IH   S +ER   
Sbjct: 352 KKQKLFDILKSKQHFKPPAVVFVSS-RLGADLLANAITVVTGLKALSIHGEKSMKERREV 410

Query: 331 YKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAIT 390
            K F  G   ++VAT ++GRG+D+ RV  VI +DMP++   Y+H++GRA R G KG AI 
Sbjct: 411 MKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIV 470

Query: 391 FVSSAS 396
           FV+   
Sbjct: 471 FVNEED 476

Length = 518

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

 Score =  164 bits (416), Expect = 4e-45
 Identities = 115/361 (31%), Positives = 190/361 (52%), Gaps = 28/361 (7%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F  F L P LL  +  +GF   + +Q   +P A+ G DV  QA++G GKT  F+++ + +
Sbjct: 11  FSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNR 70

Query: 108 --TEP-----NPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKD 160
             + P      P    AL+L  TRELA QI  +  +F   L  ++ A+ YGGV+    ++
Sbjct: 71  LLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADL-GLRFALVYGGVDYDKQRE 129

Query: 161 LLKNECPQIVVGTPGRILA-LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMT 219
           LL+ +   +++ TPGR++  + + K +SL      +LDE D+M + L   +D++ + +  
Sbjct: 130 LLQ-QGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFD-LGFIKDIRFLLRRM 187

Query: 220 PH--DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNR 277
           P    +Q ++FSATLS  +  +  + M +P ++ V+ E  +T   + Q     ++ EK  
Sbjct: 188 PERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETET-ITAARVRQRIYFPADEEKQT 246

Query: 278 KLNDLLD------ALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSG-MSQEERLTR 330
            L  LL        + F     FV+ V+R  E +   V        + SG + Q++R + 
Sbjct: 247 LLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVG-------VLSGDVPQKKRESL 299

Query: 331 YKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAIT 390
              F++G   ILVATD+  RG+ I+ V  V NYD+P  A+ Y+HR+GR  R G +G AI+
Sbjct: 300 LNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAIS 359

Query: 391 F 391
           F
Sbjct: 360 F 360

Length = 572

>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 =  131 bits (332), Expect = 4e-37
 Identities = 55/130 (42%), Positives = 74/130 (56%), Gaps = 2/130 (1%)

Query: 264 VQHYIKLSELEKNRKLNDLLD--ALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSG 321
           ++ Y+   E EK   L +LL        +V+IF  S     EL +LL +       +H  
Sbjct: 2   IKQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGD 61

Query: 322 MSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR 381
            SQEER    K F+EG   +LVATD++ RGID+  V++VINYD+P S  +YL R+GRAGR
Sbjct: 62  GSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGR 121

Query: 382 FGTKGLAITF 391
            G KG AI  
Sbjct: 122 AGQKGTAILL 131

Length = 131

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

 Score =  119 bits (300), Expect = 2e-32
 Identities = 53/149 (35%), Positives = 72/149 (48%), Gaps = 5/149 (3%)

Query: 84  MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD 143
            DV+  A +G GKT   +L  L+  +   G    LVL  TRELA Q+    +        
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKGGQV-LVLAPTRELANQVAERLKELF--GEG 57

Query: 144 IKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML 203
           IKV    GG +IK  ++ L +    IVVGTPGR+L       LSLK +   ILDE  ++L
Sbjct: 58  IKVGYLIGGTSIK-QQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLL 116

Query: 204 ESLDMRRDVQEIFKMTPHDKQVMMFSATL 232
                     +I    P D+QV++ SAT 
Sbjct: 117 NQGFGLL-GLKILLKLPKDRQVLLLSATP 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 =  107 bits (270), Expect = 6e-29
 Identities = 38/78 (48%), Positives = 53/78 (67%)

Query: 306 KLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDM 365
           KLL +       +H G+SQEER    + F+ G  ++LVATD+ GRGID+  VN+VINYD+
Sbjct: 1   KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60

Query: 366 PDSADTYLHRVGRAGRFG 383
           P +  +Y+ R+GRAGR 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 =  105 bits (265), Expect = 4e-28
 Identities = 37/81 (45%), Positives = 51/81 (62%)

Query: 303 ELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN 362
           EL +LL E       +H G+SQEER      F  G  ++LVATD+  RG+D+  V++VI 
Sbjct: 2   ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVII 61

Query: 363 YDMPDSADTYLHRVGRAGRFG 383
           YD+P S  +Y+ R+GRAGR G
Sbjct: 62  YDLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score = 73.8 bits (182), Expect = 5e-14
 Identities = 97/354 (27%), Positives = 151/354 (42%), Gaps = 42/354 (11%)

Query: 55  PELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKT-AVF--VLSTLQQTEPN 111
              +R      F   +  Q   IP+   G +V+  A +G GKT A F  V++ L      
Sbjct: 9   DPRVREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKG 68

Query: 112 P--GQVTALVLCHTRELAYQICHEFERFSTYLP--DIKVAVFYGGVNIKIHKDLLKNECP 167
                + AL +   + L   I     R    L    I+VAV +G       + +LKN  P
Sbjct: 69  KLEDGIYALYISPLKALNNDI---RRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNP-P 124

Query: 168 QIVVGTPGRILALARDKDLS--LKNVRHFILDECDKMLESLDMRRDVQ-----EIFKMTP 220
            I++ TP  +  L         L++VR+ I+DE   + ES   +R VQ     E  +   
Sbjct: 125 HILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAES---KRGVQLALSLERLRELA 181

Query: 221 HDKQVMMFSATLS--KEIRPVCKKFM---QDPMEIY-VDDEAKLTLHGLV-QHYIKLSEL 273
            D Q +  SAT+   +E+     KF+    DP EI  V    KL +  +     +   E 
Sbjct: 182 GDFQRIGLSATVGPPEEVA----KFLVGFGDPCEIVDVSAAKKLEIKVISPVEDLIYDEE 237

Query: 274 EKNRKLNDLLDALDFNQ-VVIFVKSVSRA----AELNKLLVECNFPSICIHSG-MSQEER 327
                   + + +  ++  +IF  + S A      L KL  +     I +H G +S+E R
Sbjct: 238 LWAALYERIAELVKKHRTTLIFTNTRSGAERLAFRLKKLGPD----IIEVHHGSLSRELR 293

Query: 328 LTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR 381
           L   +  KEG  + +VAT  +  GIDI  +++VI    P S + +L R+GRAG 
Sbjct: 294 LEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347

Length = 814

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

 Score = 70.2 bits (172), Expect = 4e-13
 Identities = 68/369 (18%), Positives = 126/369 (34%), Gaps = 76/369 (20%)

Query: 83  GMDVICQAKSGMGKT--AVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTY 140
               +    +G GKT  A   ++ L+++         LVL  T+EL  Q     ++F   
Sbjct: 55  ERRGVIVLPTGAGKTVVAAEAIAELKRS--------TLVLVPTKELLDQWAEALKKF--L 104

Query: 141 LPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHF---ILD 197
           L + ++ ++ GG      K+L   E  ++ V T   +  LAR + L       F   I D
Sbjct: 105 LLNDEIGIYGGG-----EKEL---EPAKVTVAT---VQTLARRQLLDEFLGNEFGLIIFD 153

Query: 198 EC-----DKMLESLDM---------------RRDVQEIFKMTPHDKQVMMFSATLSKEIR 237
           E            L++               R D   I  +      ++ +  +L + I 
Sbjct: 154 EVHHLPAPSYRRILELLSAAYPRLGLTATPEREDGGRIGDLFDLIGPIV-YEVSLKELID 212

Query: 238 PVCKKFMQDPMEIYV------------DDEAKLTLHGLVQHY-------IKLSELEKNRK 278
              + ++     + +              E+      L            +   +   RK
Sbjct: 213 ---EGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRAENEARRIAIASERK 269

Query: 279 LNDLLDALDFN----QVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGF 334
           +  +   L  +    + +IF   V  A E+ KL +        I     +EER    + F
Sbjct: 270 IAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERF 328

Query: 335 KEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRF--GTKGLAITFV 392
           + G  ++LV   ++  G+DI   +++I      S   ++ R+GR  R   G +       
Sbjct: 329 RTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLRPAEGKEDTLALDY 388

Query: 393 SSASDSDIL 401
           S   D    
Sbjct: 389 SLVPDDLGE 397

Length = 442

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

 Score = 70.5 bits (173), Expect = 4e-13
 Identities = 43/131 (32%), Positives = 68/131 (51%), Gaps = 3/131 (2%)

Query: 268 IKLSELEKNRKLNDLLDALDFNQV---VIFVKSVSRAAELNKLLVECNFPSICIHSGMSQ 324
           ++ S ++KN K   LLD L  ++    +I+  S  +  EL + L      ++  H+G+S 
Sbjct: 201 LRFSVVKKNNKQKFLLDYLKKHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSN 260

Query: 325 EERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGT 384
           + R    + F   + +++VAT+  G GID   V  VI+YDMP + ++Y    GRAGR G 
Sbjct: 261 KVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGL 320

Query: 385 KGLAITFVSSA 395
              AI   S A
Sbjct: 321 PAEAILLYSPA 331

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

 Score = 66.2 bits (162), Expect = 1e-11
 Identities = 36/113 (31%), Positives = 55/113 (48%), Gaps = 1/113 (0%)

Query: 292 VIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRG 351
           +I+  +  +  EL + L +    +   H+G+S EER    + F     +++VAT+  G G
Sbjct: 234 IIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMG 293

Query: 352 IDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQV 404
           ID   V  VI+YD+P S ++Y    GRAGR G    AI   S   D      +
Sbjct: 294 IDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPE-DIRWQRYL 345

Length = 590

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

 Score = 65.5 bits (160), Expect = 2e-11
 Identities = 79/398 (19%), Positives = 140/398 (35%), Gaps = 108/398 (27%)

Query: 86  VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIK 145
           +I  A +G GKT +  L  +  T    G    + +   + LA +   EF R       I+
Sbjct: 51  LIS-APTGSGKTLIA-LLAILSTL-LEGGGKVVYIVPLKALAEEKYEEFSRLEELG--IR 105

Query: 146 VAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDEC------ 199
           V +  G  ++   + L +     ++V TP ++ +L R +   ++ V   ++DE       
Sbjct: 106 VGISTGDYDLD-DERLARY---DVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDR 161

Query: 200 --DKMLESL--DMRRDVQEIFKMTPHDKQVMMFSATLS---------------KEIRPVC 240
               +LES+   MRR  + I        +++  SATL                 + RPV 
Sbjct: 162 TRGPVLESIVARMRRLNELI--------RIVGLSATLPNAEEVADWLNAKLVESDWRPV- 212

Query: 241 KKFM---QDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDL-LDALDFN-QVVIFV 295
                           D  K           K   L  +    +L L++L    QV++FV
Sbjct: 213 -PLRRGVPYVGAFLGADGKK-----------KTWPLLIDNLALELVLESLAEGGQVLVFV 260

Query: 296 KS----VSRAAELNKLL--------------------------VECNFPSICI------- 318
            S       A +L   +                           E    +  +       
Sbjct: 261 HSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFH 320

Query: 319 HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGID-IERVNIVINYDMPDSADT------ 371
           H+G+ +E+R      F++G  ++LV+T  +  G++   R  I+ +    D          
Sbjct: 321 HAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPV 380

Query: 372 --YLHRVGRAGR--FGTKGLAITFVSSASDSDILNQVS 405
              L   GRAGR  +   G AI   +S  + + L ++ 
Sbjct: 381 LDVLQMAGRAGRPGYDDYGEAIILATSHDELEYLAELY 418

Length = 766

>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 = 63.6 bits (155), Expect = 8e-11
 Identities = 85/372 (22%), Positives = 145/372 (38%), Gaps = 53/372 (14%)

Query: 49  RDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQT 108
              L    L  A+V +G E     Q + +     G +V+    +G GKT  F+L  L   
Sbjct: 51  FPELRDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHL 110

Query: 109 EPNPGQVTALVLCHTRELAY-QICHEFERFSTYLPD----IKVAVFYGGVNIKIHKDLLK 163
             +P    AL+L  T  LA  Q     ER    + D    +    + G    +  + +++
Sbjct: 111 LRDP-SARALLLYPTNALANDQA----ERLRELISDLPGKVTFGRYTGDTPPEERRAIIR 165

Query: 164 NECPQIVVGTPGRI-LALARDKDLS---LKNVRHFILDECD----------KMLESLDMR 209
           N  P I++  P  +   L R+ D     L+N+++ ++DE             +L    +R
Sbjct: 166 NP-PDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALL----LR 220

Query: 210 RDVQEIFKMTPHDKQVMMFSATLS--KEIRPVCKKFMQDPMEIYVDDEA------KLTLH 261
           R +    +      Q++  SATL+   E     ++      E+ VD++            
Sbjct: 221 R-LLRRLRRYGSPLQIICTSATLANPGEF---AEELFGRDFEVPVDEDGSPRGLRYFVRR 276

Query: 262 GLVQHYIKLSE-LEKNRKLNDLLDALDFN--QVVIFVKSVSRAAELNK-------LLVEC 311
                 +  S       +L  L   L  N  Q ++F +S  +   L              
Sbjct: 277 EPPIRELAESIRRSALAELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGK 336

Query: 312 NFPSICIH-SGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMP-DSA 369
              ++  + +G+ +EER      FKEG    ++AT+ +  GIDI  ++ VI Y  P  S 
Sbjct: 337 LLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSV 396

Query: 370 DTYLHRVGRAGR 381
            ++  R GRAGR
Sbjct: 397 LSFRQRAGRAGR 408

Length = 851

>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3

 Score = 57.8 bits (140), Expect = 3e-09
 Identities = 47/176 (26%), Positives = 79/176 (44%), Gaps = 23/176 (13%)

Query: 222 DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKN---RK 278
           D  +++ SATL K +    K++ +  +    ++E  L L    +      E +K      
Sbjct: 154 DVPILLMSATLPKFL----KEYAEK-IGYVEENEP-LDLKPNERAPFIKIESDKVGEISS 207

Query: 279 LNDLLDAL-DFNQVVIFVKSVSRAAELNKLLVECN--FPSICIHSGMSQ------EERLT 329
           L  LL+ +     V I V +V RA E  + L E       + IHS  ++      E  L 
Sbjct: 208 LERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRAKKEAELL 267

Query: 330 RYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTK 385
               FK+  K ++VAT ++   +DI  V+++I    P   D+ + R+GR  R+G K
Sbjct: 268 LE--FKKSEKFVIVATQVIEASLDIS-VDVMITELAP--IDSLIQRLGRLHRYGEK 318

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I. Length = 353

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

 Score = 55.5 bits (134), Expect = 2e-08
 Identities = 27/91 (29%), Positives = 40/91 (43%), Gaps = 4/91 (4%)

Query: 301 AAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIV 360
            A L  L +         H+G+    R   +  F+    +++VAT   G GI+   V  V
Sbjct: 243 TASLQNLGIAAG----AYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFV 298

Query: 361 INYDMPDSADTYLHRVGRAGRFGTKGLAITF 391
           I+Y +P S ++Y    GRAGR G       F
Sbjct: 299 IHYSLPKSMESYYQESGRAGRDGLPSECHLF 329

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|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3

 Score = 54.0 bits (130), Expect = 5e-08
 Identities = 41/176 (23%), Positives = 78/176 (44%), Gaps = 20/176 (11%)

Query: 222 DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLT--LHGLVQHYIKLSELEKN--- 276
           D  +++ SATL K +    K++ +  +     +E           +H     E +K    
Sbjct: 155 DVPILLMSATLPKFL----KEYAEK-IGYVEFNEPLDLKEERRFERHRFIKIESDKVGEI 209

Query: 277 RKLNDLLDAL-DFNQVVIFVKSVSRAAELNKLLVEC--NFPSICIHSGMSQEERLTRYK- 332
             L  LL+ +    ++ I V +V RA E  + L E       + +HS  ++++R  +   
Sbjct: 210 SSLERLLEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAE 269

Query: 333 ---GFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTK 385
                K+  K ++VAT ++   +DI   +++I    P   D+ + R+GR  R+G K
Sbjct: 270 LLEEMKKNEKFVIVATQVIEASLDIS-ADVMITELAP--IDSLIQRLGRLHRYGRK 322

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 [Mobile and extrachromosomal element functions, Other]. Length = 358

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

 Score = 52.3 bits (126), Expect = 3e-07
 Identities = 32/114 (28%), Positives = 51/114 (44%), Gaps = 12/114 (10%)

Query: 291 VVIFVKSVSRAAELNKLLVECNFPSICI----------HSGMSQEERLTRYKGFKEGNKR 340
           V++F +    A E+   L +       +            GMSQ+E+      F++G   
Sbjct: 369 VIVFTEYRDTAEEIVNFLKK-IGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYN 427

Query: 341 ILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSS 394
           +LVAT +   G+DI  V++VI Y+   S    + R GR GR   KG  +  V+ 
Sbjct: 428 VLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGR-KRKGRVVVLVTE 480

Length = 542

>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]

 Score = 50.9 bits (122), Expect = 8e-07
 Identities = 33/139 (23%), Positives = 62/139 (44%), Gaps = 18/139 (12%)

Query: 229 SATLSKEIRPVCKKFMQDPMEIYV-------DDEAKLTLHGLVQHYIKLSELEKNRKLND 281
           SATL   ++   KK +    E+         +DE  L      +  + + +  +   +  
Sbjct: 377 SATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLK----RKERVDVEDGPQEELIEL 432

Query: 282 LLDALD-FNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQE-----ERLTRYKGFK 335
           + + +    +V++ V +V RA EL + L E     + +HS  + +     ER  + K FK
Sbjct: 433 ISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELK-KLFK 491

Query: 336 EGNKRILVATDLVGRGIDI 354
           +    I+VAT ++  G+DI
Sbjct: 492 QNEGFIVVATQVIEAGVDI 510

Length = 733

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

 Score = 48.6 bits (116), Expect = 4e-06
 Identities = 25/77 (32%), Positives = 42/77 (54%)

Query: 319 HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGR 378
           H+G+  + R    + F+  + +I+VAT   G GI+   V  V+++D+P + ++Y    GR
Sbjct: 267 HAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGR 326

Query: 379 AGRFGTKGLAITFVSSA 395
           AGR G    A+ F   A
Sbjct: 327 AGRDGLPAEAMLFYDPA 343

Length = 607

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

 Score = 48.0 bits (114), Expect = 9e-06
 Identities = 24/62 (38%), Positives = 35/62 (56%)

Query: 319 HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGR 378
           H  +S+E+R    +  K G  R +VAT  +  GID+  V++VI    P S  + L R+GR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367

Query: 379 AG 380
           AG
Sbjct: 368 AG 369

Length = 1490

>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd)

 Score = 46.2 bits (110), Expect = 2e-05
 Identities = 31/99 (31%), Positives = 44/99 (44%), Gaps = 10/99 (10%)

Query: 295 VKSVSRAAELNKLLVECNFP--SICI-HSGMSQEERLTRYKGFKEGNKRILVATDLVGRG 351
           ++S+ + A   + LV    P   I I H  M++ E       F +G  ++LV T ++  G
Sbjct: 670 IESIEKLATQLRELV----PEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETG 725

Query: 352 IDIERVN--IVINYDMPDSADTYLHRVGRAGRFGTKGLA 388
           IDI   N  I+   D    A  Y  R GR GR   K  A
Sbjct: 726 IDIPNANTIIIERADKFGLAQLYQLR-GRVGRSKKKAYA 763

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 transcribed 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 926

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

 Score = 45.4 bits (108), Expect = 4e-05
 Identities = 83/341 (24%), Positives = 136/341 (39%), Gaps = 78/341 (22%)

Query: 84  MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP- 142
           M+ + Q   G GKT V  L+ L        QV   ++  T  LA Q  H +      L  
Sbjct: 257 MNRLLQGDVGSGKTLVAALAML-AAIEAGYQV--ALMAPTEILAEQ--H-YNSLRNLLAP 310

Query: 143 -DIKVAVFYGGVNIKIHKDLL---KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDE 198
             I+VA+  G +  K  K+LL    +    +VVGT     AL ++K +  K +   I+DE
Sbjct: 311 LGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTH----ALIQEK-VEFKRLALVIIDE 365

Query: 199 CDK--MLESLDMRRDVQEIFKMTPHDKQVMMFSAT-------LSK-------EIR--PVC 240
             +  + +   +R   Q     TPH   V++ SAT       L+         I   P  
Sbjct: 366 QHRFGVEQRKKLREKGQG--GFTPH---VLVMSATPIPRTLALTVYGDLDTSIIDELPPG 420

Query: 241 KKFMQDPMEIYV--DDEAKLTLHGLVQHYIKLS-ELEKNRK------LNDLLDALDFNQV 291
           +K    P+   +   DE           Y  +  E+ K R+      L +  + LD    
Sbjct: 421 RK----PITTVLIKHDEKD-------IVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAA 469

Query: 292 VIFVKSVSRA-AELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGR 350
               + + +A  + N  L+         H  M  +E+    + F+EG   ILVAT ++  
Sbjct: 470 EALYERLKKAFPKYNVGLL---------HGRMKSDEKEAVMEEFREGEVDILVATTVIEV 520

Query: 351 GIDIERVNIVINYDMPDSADTY----LHRV-GRAGRFGTKG 386
           G+D+    +++  D    A+ +    LH++ GR GR   + 
Sbjct: 521 GVDVPNATVMVIED----AERFGLSQLHQLRGRVGRGDHQS 557

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

>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional

 Score = 44.9 bits (107), Expect = 7e-05
 Identities = 34/116 (29%), Positives = 55/116 (47%), Gaps = 23/116 (19%)

Query: 93  GMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGG 152
           G+GKTA+ +L   ++     G+V  L+L  T+ L  Q    F +F   +P+ K+ VF G 
Sbjct: 39  GLGKTAIALLVIAERLHKKGGKV--LILAPTKPLVEQHAEFFRKFLN-IPEEKIVVFTGE 95

Query: 153 VNIKIHKDLLKNECPQIVVGTP---------GRILALARDKDLSLKNVRHFILDEC 199
           V+ +   +L +    +++V TP         GRI         SL++V   I DE 
Sbjct: 96  VSPEKRAELWEKA--KVIVATPQVIENDLIAGRI---------SLEDVSLLIFDEA 140

Length = 773

>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional

 Score = 42.9 bits (102), Expect = 3e-04
 Identities = 23/61 (37%), Positives = 35/61 (57%)

Query: 321 GMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAG 380
           GMSQ+E++     F+ G   +LV+T +   G+DI  V++VI Y+   S    + R GR G
Sbjct: 406 GMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTG 465

Query: 381 R 381
           R
Sbjct: 466 R 466

Length = 773

>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

 Score = 41.1 bits (97), Expect = 0.001
 Identities = 27/91 (29%), Positives = 40/91 (43%), Gaps = 18/91 (19%)

Query: 301 AAELNKLLVECNFPSICI-HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVN- 358
           A  L +L+ E     I + H  M + E       F  G   +LV T ++  GIDI   N 
Sbjct: 820 AERLRELVPEA---RIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANT 876

Query: 359 IVINYDMPDSADTY----LH----RVGRAGR 381
           I+I     + AD +    L+    RVGR+ +
Sbjct: 877 III-----ERADKFGLAQLYQLRGRVGRSNK 902

Length = 1139

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

 Score = 40.3 bits (95), Expect = 0.002
 Identities = 22/64 (34%), Positives = 36/64 (56%)

Query: 317 CIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRV 376
             HS +S+E RL   +  K G  +++V++  +  GIDI  +++V+    P S    L R+
Sbjct: 319 AHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRI 378

Query: 377 GRAG 380
           GRAG
Sbjct: 379 GRAG 382

Length = 876

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

 Score = 39.8 bits (93), Expect = 0.003
 Identities = 80/360 (22%), Positives = 141/360 (39%), Gaps = 54/360 (15%)

Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQTEPN 111
           +  +  R +   G E    VQ   +   +L G +++  + +  GKT +  L+ + +    
Sbjct: 201 IPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSG 260

Query: 112 PGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP---Q 168
             ++  L L     LA Q   +F+   + L  +KVA+  G   IK  ++ +  +      
Sbjct: 261 GKKM--LFLVPLVALANQKYEDFKERYSKL-GLKVAIRVGMSRIKTREEPVVVDTSPDAD 317

Query: 169 IVVGT-PGRILALARDKDLSLKNVRHFILDECDKMLESLDM--RRD--VQEIFKMTPHDK 223
           I+VGT  G    L   KDL   ++   ++DE    LE  +   R D  +  +  + P   
Sbjct: 318 IIVGTYEGIDYLLRTGKDL--GDIGTVVIDEI-HTLEDEERGPRLDGLIGRLRYLFP-GA 373

Query: 224 QVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHG-----LVQHY-IKLSELEKNR 277
           Q +  SAT+             +P E+     AKL L+      L +H     +E EK  
Sbjct: 374 QFIYLSATVG------------NPEELAKKLGAKLVLYDERPVPLERHLVFARNESEKWD 421

Query: 278 KLNDLLDALDFN---------QVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERL 328
            +  L+   +F+         Q ++F  S  R  EL   L      +   H+G+  +ER 
Sbjct: 422 IIARLVKR-EFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERK 480

Query: 329 TRYKGFKEGNKRILVATDLVGRGID-------IERVNIVINYDMPDSADTYLHRVGRAGR 381
           +  + F       +V T  +  G+D        E + + I +        +   +GRAGR
Sbjct: 481 SVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAMGIEWLSVRE---FQQMLGRAGR 537

Length = 830

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

 Score = 39.9 bits (93), Expect = 0.003
 Identities = 25/86 (29%), Positives = 38/86 (44%)

Query: 308 LVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPD 367
           L E    +   H  M   +R    K + +    I+ AT   G GI+   V  VI++ +P 
Sbjct: 700 LQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPK 759

Query: 368 SADTYLHRVGRAGRFGTKGLAITFVS 393
           S + Y    GRAGR G +   + + S
Sbjct: 760 SIEGYHQECGRAGRDGQRSSCVLYYS 785

Length = 1195

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	423
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PTZ00110	545	helicase; Provisional	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0347	731	consensus RNA helicase [RNA processing and modific	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	100.0
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
KOG4284	980	consensus DEAD box protein [Transcription]	100.0
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	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
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK13767	876	ATP-dependent helicase; Provisional	100.0
PRK02362	737	ski2-like helicase; Provisional	100.0
PRK00254	720	ski2-like helicase; Provisional	100.0
COG1201	814	Lhr Lhr-like helicases [General function predictio	100.0
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	100.0
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	100.0
PRK01172	674	ski2-like helicase; Provisional	100.0
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	100.0
PRK10689	1147	transcription-repair coupling factor; Provisional	100.0
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	100.0
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	100.0
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	100.0
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	100.0
PRK09401	1176	reverse gyrase; Reviewed	100.0
PHA02653	675	RNA helicase NPH-II; Provisional	100.0
PHA02558	501	uvsW UvsW helicase; Provisional	100.0
COG1202	830	Superfamily II helicase, archaea-specific [General	100.0
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	100.0
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
PRK14701	1638	reverse gyrase; Provisional	100.0
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	100.0
COG1204	766	Superfamily II helicase [General function predicti	100.0
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	100.0
PRK13766	773	Hef nuclease; Provisional	100.0
COG1205	851	Distinct helicase family with a unique C-terminal	100.0
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	100.0
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	100.0
PRK09200	790	preprotein translocase subunit SecA; Reviewed	100.0
KOG0354	746	consensus DEAD-box like helicase [General function	100.0
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	100.0
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	100.0
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	100.0
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	100.0
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	100.0
KOG0353	695	consensus ATP-dependent DNA helicase [General func	100.0
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	100.0
PRK04914	956	ATP-dependent helicase HepA; Validated	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
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	100.0
PRK05580	679	primosome assembly protein PriA; Validated	100.0
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	100.0
PRK09694	878	helicase Cas3; Provisional	100.0
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	100.0
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	100.0
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	100.0
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.98
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.98
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.97
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.97
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.97
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.97
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.97
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.97
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.97
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	99.97
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.97
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.96
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.96
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.96
KOG0387	923	consensus Transcription-coupled repair protein CSB	99.95
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.95
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.94
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.94
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.94
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.94
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.93
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	99.93
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	99.93
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.93
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.93
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	99.93
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.92
COG4096	875	HsdR Type I site-specific restriction-modification	99.92
KOG1123	776	consensus RNA polymerase II transcription initiati	99.92
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.92
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	99.91
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	99.91
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	99.91
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.91
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	99.91
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.91
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.89
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	99.88
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.88
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.87
PRK05298	652	excinuclease ABC subunit B; Provisional	99.87
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.86
COG4889	1518	Predicted helicase [General function prediction on	99.86
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.86
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.86
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	99.85
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	99.85
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.85
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.84
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.83
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	99.83
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.82
KOG1002	791	consensus Nucleotide excision repair protein RAD16	99.82
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.82
KOG4439	901	consensus RNA polymerase II transcription terminat	99.81
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.8
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	99.8
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	99.79
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.78
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.78
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.76
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.74
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.74
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	99.71
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.7
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.69
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.68
PRK14873	665	primosome assembly protein PriA; Provisional	99.67
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.66
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.66
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.65
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	99.65
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	99.56
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	99.52
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.5
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.49
COG0610	962	Type I site-specific restriction-modification syst	99.47
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	99.47
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.43
KOG2340	698	consensus Uncharacterized conserved protein [Funct	99.26
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	99.13
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.1
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.1
KOG1001	674	consensus Helicase-like transcription factor HLTF/	99.07
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.04
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.77
PRK15483	986	type III restriction-modification system StyLTI en	98.76
COG3587	985	Restriction endonuclease [Defense mechanisms]	98.71
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	98.66
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	98.65
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.61
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.51
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.49
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.48
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	98.47
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	98.35
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	98.29
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.23
PRK10536	262	hypothetical protein; Provisional	98.15
PF13245	76	AAA_19: Part of AAA domain	98.14
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	98.09
KOG1803	649	consensus DNA helicase [Replication, recombination	98.07
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	98.03
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.03
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	98.03
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.97
KOG0383	696	consensus Predicted helicase [General function pre	97.94
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.84
PF13871	278	Helicase_C_4: Helicase_C-like	97.83
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	97.76
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.76
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.73
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.7
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.66
KOG0298	1394	consensus DEAD box-containing helicase-like transc	97.6
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.6
PRK04296	190	thymidine kinase; Provisional	97.56
KOG1805	1100	consensus DNA replication helicase [Replication, r	97.51
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.47
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.47
KOG1131	755	consensus RNA polymerase II transcription initiati	97.42
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	97.39
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.37
PRK06526	254	transposase; Provisional	97.3
PRK14974	336	cell division protein FtsY; Provisional	97.3
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.28
TIGR00376	637	DNA helicase, putative. The gene product may repre	97.25
PRK05642	234	DNA replication initiation factor; Validated	97.24
PRK08084	235	DNA replication initiation factor; Provisional	97.21
smart00382	148	AAA ATPases associated with a variety of cellular	97.19
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.18
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.17
PRK11054	684	helD DNA helicase IV; Provisional	97.17
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.15
PRK08181	269	transposase; Validated	97.14
PRK06893	229	DNA replication initiation factor; Validated	97.11
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.06
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	97.04
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.02
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.98
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.96
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	96.96
PRK08727	233	hypothetical protein; Validated	96.93
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	96.91
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	96.89
PHA02533	534	17 large terminase protein; Provisional	96.87
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	96.7
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.67
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	96.66
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	96.65
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.61
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.6
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	96.59
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	96.58
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	96.57
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	96.52
PRK12402	337	replication factor C small subunit 2; Reviewed	96.52
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	96.51
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	96.49
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	96.46
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.46
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.45
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	96.41
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	96.4
PRK08116	268	hypothetical protein; Validated	96.39
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.38
PF13173	128	AAA_14: AAA domain	96.38
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	96.38
PRK12422	445	chromosomal replication initiation protein; Provis	96.37
PRK14088	440	dnaA chromosomal replication initiation protein; P	96.37
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	96.36
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.35
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	96.34
PLN03025	319	replication factor C subunit; Provisional	96.33
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.32
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	96.28
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.26
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.22
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	96.22
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.19
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.18
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	96.17
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.09
PRK07952	244	DNA replication protein DnaC; Validated	96.08
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.08
PRK06835	329	DNA replication protein DnaC; Validated	96.06
PRK06921	266	hypothetical protein; Provisional	96.05
PRK12377	248	putative replication protein; Provisional	96.02
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	96.01
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.99
PRK08903	227	DnaA regulatory inactivator Hda; Validated	95.97
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	95.97
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	95.95
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	95.94
PRK14873	665	primosome assembly protein PriA; Provisional	95.93
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	95.93
PTZ00293	211	thymidine kinase; Provisional	95.92
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	95.92
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	95.92
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	95.92
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	95.9
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	95.89
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	95.87
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	95.86
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	95.83
PHA03372	668	DNA packaging terminase subunit 1; Provisional	95.83
PRK00411	394	cdc6 cell division control protein 6; Reviewed	95.82
PHA03368	738	DNA packaging terminase subunit 1; Provisional	95.81
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	95.81
PRK08769	319	DNA polymerase III subunit delta'; Validated	95.81
PRK14086	617	dnaA chromosomal replication initiation protein; P	95.81
PHA03333	752	putative ATPase subunit of terminase; Provisional	95.79
PHA02544	316	44 clamp loader, small subunit; Provisional	95.78
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	95.76
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.76
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.73
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.73
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.72
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	95.7
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	95.7
COG0593	408	DnaA ATPase involved in DNA replication initiation	95.67
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	95.67
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	95.65
PRK09183	259	transposase/IS protein; Provisional	95.64
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	95.6
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.6
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	95.58
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.58
PF00004	132	AAA: ATPase family associated with various cellula	95.58
CHL00181	287	cbbX CbbX; Provisional	95.51
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	95.49
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	95.47
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.46
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	95.45
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	95.4
COG3973	747	Superfamily I DNA and RNA helicases [General funct	95.4
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	95.39
COG3972	660	Superfamily I DNA and RNA helicases [General funct	95.39
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.39
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	95.36
COG2256	436	MGS1 ATPase related to the helicase subunit of the	95.34
PRK08533	230	flagellar accessory protein FlaH; Reviewed	95.34
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.28
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	95.25
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	95.24
KOG0298	1394	consensus DEAD box-containing helicase-like transc	95.19
PRK09112	351	DNA polymerase III subunit delta'; Validated	95.18
PRK07471	365	DNA polymerase III subunit delta'; Validated	95.18
PRK08699	325	DNA polymerase III subunit delta'; Validated	95.18
PRK06871	325	DNA polymerase III subunit delta'; Validated	95.16
PRK06964	342	DNA polymerase III subunit delta'; Validated	95.15
PRK00440	319	rfc replication factor C small subunit; Reviewed	95.15
PRK10867	433	signal recognition particle protein; Provisional	95.14
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	95.14
PRK07940	394	DNA polymerase III subunit delta'; Validated	95.13
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	95.12
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	95.05
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.05
PRK05580	679	primosome assembly protein PriA; Validated	95.01
PRK13342	413	recombination factor protein RarA; Reviewed	95.0
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	94.94
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	94.91
TIGR00595	505	priA primosomal protein N'. All proteins in this f	94.91
PRK04195	482	replication factor C large subunit; Provisional	94.9
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	94.88
TIGR00959	428	ffh signal recognition particle protein. This mode	94.85
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	94.84
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	94.82
KOG2028	554	consensus ATPase related to the helicase subunit o	94.81
PRK06067	234	flagellar accessory protein FlaH; Validated	94.71
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	94.71
PHA00729	226	NTP-binding motif containing protein	94.7
PRK10416	318	signal recognition particle-docking protein FtsY;	94.7
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	94.64
cd03115	173	SRP The signal recognition particle (SRP) mediates	94.64
PRK06090	319	DNA polymerase III subunit delta'; Validated	94.57
PRK13341	725	recombination factor protein RarA/unknown domain f	94.54
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	94.5
PRK07993	334	DNA polymerase III subunit delta'; Validated	94.5
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.46
COG0378	202	HypB Ni2+-binding GTPase involved in regulation of	94.46
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	94.45
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	94.43
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	94.39
PF05729	166	NACHT: NACHT domain	94.37
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	94.34
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	94.3
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	94.28
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	94.23
PRK13851	344	type IV secretion system protein VirB11; Provision	94.23
PRK05973	237	replicative DNA helicase; Provisional	94.17
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	94.13
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	94.1
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	94.04
COG4626	546	Phage terminase-like protein, large subunit [Gener	93.97
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	93.94
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	93.93
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	93.93
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	93.92
PRK06904	472	replicative DNA helicase; Validated	93.9
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	93.87
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	93.87
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	93.83
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	93.81
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	93.8
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	93.8
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	93.79
PRK07004	460	replicative DNA helicase; Provisional	93.76
PRK05748	448	replicative DNA helicase; Provisional	93.63
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	93.57
PRK10436	462	hypothetical protein; Provisional	93.56
PRK09376	416	rho transcription termination factor Rho; Provisio	93.54
PRK08006	471	replicative DNA helicase; Provisional	93.51
PRK04841	903	transcriptional regulator MalT; Provisional	93.48
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	93.42
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	93.36
PRK08506	472	replicative DNA helicase; Provisional	93.35
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	93.33
COG1484	254	DnaC DNA replication protein [DNA replication, rec	93.33
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	93.32
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	93.32
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	93.31
TIGR00665	434	DnaB replicative DNA helicase. This model describe	93.28
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	93.28
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	93.27
PRK08840	464	replicative DNA helicase; Provisional	93.25
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	93.18
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	93.18
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	93.15
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	93.12
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	93.12
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	93.11
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	92.91
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	92.88
PRK08058	329	DNA polymerase III subunit delta'; Validated	92.78
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	92.75
PRK09087	226	hypothetical protein; Validated	92.63
PRK11823	446	DNA repair protein RadA; Provisional	92.62
PRK10689	1147	transcription-repair coupling factor; Provisional	92.53
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	92.51
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	92.51
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	92.44
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	92.41
PRK04328	249	hypothetical protein; Provisional	92.41
TIGR00767	415	rho transcription termination factor Rho. Members	92.33
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	92.32
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	92.29
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	92.29
TIGR02533	486	type_II_gspE general secretory pathway protein E.	92.27
PRK13764	602	ATPase; Provisional	92.24
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	92.21
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	92.2
PRK08760	476	replicative DNA helicase; Provisional	92.2
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	92.13
PHA00012	361	I assembly protein	92.07
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	92.06
PRK13897	606	type IV secretion system component VirD4; Provisio	92.02
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	91.98
PRK07399	314	DNA polymerase III subunit delta'; Validated	91.97
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	91.95
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	91.91
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	91.86
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	91.81
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	91.78
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	91.75
COG1485	367	Predicted ATPase [General function prediction only	91.73
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	91.7
PRK10865	857	protein disaggregation chaperone; Provisional	91.62
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	91.56
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	91.51
PRK09165	497	replicative DNA helicase; Provisional	91.51
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	91.48
PF12846	304	AAA_10: AAA-like domain	91.43
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	91.34
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	91.21
PRK05636	505	replicative DNA helicase; Provisional	91.18
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	91.17
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	91.13
PF13555	62	AAA_29: P-loop containing region of AAA domain	91.09
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	91.08
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	90.97
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	90.94
PHA02542	473	41 41 helicase; Provisional	90.92
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	90.85
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	90.8
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	90.79
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	90.76
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	90.66
COG1855	604	ATPase (PilT family) [General function prediction	90.61
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	90.52
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	90.45
cd01128	249	rho_factor Transcription termination factor rho is	90.39
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	90.31
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	90.29
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	90.29
PRK13850	670	type IV secretion system protein VirD4; Provisiona	90.06
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	90.0
PRK06321	472	replicative DNA helicase; Provisional	89.99
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	89.87
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	89.79
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	89.76
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	89.72
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	89.58
PRK14701	1638	reverse gyrase; Provisional	89.55
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	89.55
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	89.51
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	89.5
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	89.5
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	89.48
KOG1806	1320	consensus DEAD box containing helicases [Replicati	89.47
TIGR02237	209	recomb_radB DNA repair and recombination protein R	89.46
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	89.18
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	89.06

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

Probab=100.00  E-value=1.5e-69  Score=463.40  Aligned_cols=366  Identities=36%  Similarity=0.619  Sum_probs=346.3

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ..+|.++++.|.+++++...|+..|+++|+++||.++.|+++|..|.||||||.+|++|+++++...+..+.++|++|||
T Consensus        60 ~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtR  139 (476)
T KOG0330|consen   60 FKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTR  139 (476)
T ss_pred             hcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEecCcH
Confidence            34699999999999999999999999999999999999999999999999999999999999999998889999999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHh-cCCCCCCCccEEEEcCcchhh
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALAR-DKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~-~~~~~~~~~~~vVvDE~h~~~  203 (423)
                      +||.|+.+.+..+.... ++++.++.||.+...+...+.+. |+|+|+||++|.+++. ...+.+..++++|+||||+++
T Consensus       140 ELA~QI~e~fe~Lg~~i-glr~~~lvGG~~m~~q~~~L~kk-PhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlL  217 (476)
T KOG0330|consen  140 ELAQQIAEQFEALGSGI-GLRVAVLVGGMDMMLQANQLSKK-PHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLL  217 (476)
T ss_pred             HHHHHHHHHHHHhcccc-CeEEEEEecCchHHHHHHHhhcC-CCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhhh
Confidence            99999999999998776 99999999999999998888877 6999999999999988 667889999999999999999


Q ss_pred             ccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHH
Q 014486          204 ESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLL  283 (423)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll  283 (423)
                      + .+|...+..|++.++..+|.+++|||++..+..+....+..|..+...... ...+.+.++|..++...|...+..++
T Consensus       218 d-~dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky-~tv~~lkQ~ylfv~~k~K~~yLV~ll  295 (476)
T KOG0330|consen  218 D-MDFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKY-QTVDHLKQTYLFVPGKDKDTYLVYLL  295 (476)
T ss_pred             h-hhhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccchh-cchHHhhhheEeccccccchhHHHHH
Confidence            9 899999999999999999999999999999999998888889888776654 45677788899999999999999999


Q ss_pred             HhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEc
Q 014486          284 DALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINY  363 (423)
Q Consensus       284 ~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~  363 (423)
                      +...++.+||||++...++.++-.|+..|+.+..+||.|++..|...++.|++|..+||+||+++++|+|+|.+++||+|
T Consensus       296 ~e~~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVNy  375 (476)
T KOG0330|consen  296 NELAGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVDVVVNY  375 (476)
T ss_pred             HhhcCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCceEEEec
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhhh
Q 014486          364 DMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSF  415 (423)
Q Consensus       364 ~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (423)
                      |.|.+..+|+||+||++|+|.+|.++.+++. ++.+.+..|+..+++.+.+.
T Consensus       376 DiP~~skDYIHRvGRtaRaGrsG~~ItlVtq-yDve~~qrIE~~~gkkl~~~  426 (476)
T KOG0330|consen  376 DIPTHSKDYIHRVGRTARAGRSGKAITLVTQ-YDVELVQRIEHALGKKLPEY  426 (476)
T ss_pred             CCCCcHHHHHHHcccccccCCCcceEEEEeh-hhhHHHHHHHHHHhcCCCcc
Confidence            9999999999999999999999999999986 99999999999999887653

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

Probab=100.00  E-value=1.7e-66  Score=473.60  Aligned_cols=359  Identities=35%  Similarity=0.599  Sum_probs=328.3

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC------CCCCeEEEE
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP------NPGQVTALV  119 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~------~~~~~~~li  119 (423)
                      ..|..+++++.+..+|+..||..|+|+|.+.||.++.|+|++..+.||||||++|++|++.++..      .+.+|.+||
T Consensus        91 ~~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLV  170 (519)
T KOG0331|consen   91 AAFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLV  170 (519)
T ss_pred             hhhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEE
Confidence            36899999999999999999999999999999999999999999999999999999999988775      455789999


Q ss_pred             EecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCc
Q 014486          120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDEC  199 (423)
Q Consensus       120 l~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~  199 (423)
                      ++|||+||.|+.+.+.++.... .++..+++||.....+...+.++ .+|+|+||++|.++++.+...++++.++|+|||
T Consensus       171 L~PTRELA~QV~~~~~~~~~~~-~~~~~cvyGG~~~~~Q~~~l~~g-vdiviaTPGRl~d~le~g~~~l~~v~ylVLDEA  248 (519)
T KOG0331|consen  171 LAPTRELAVQVQAEAREFGKSL-RLRSTCVYGGAPKGPQLRDLERG-VDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEA  248 (519)
T ss_pred             EcCcHHHHHHHHHHHHHHcCCC-CccEEEEeCCCCccHHHHHHhcC-CcEEEeCChHHHHHHHcCCccccceeEEEeccH
Confidence            9999999999999999998886 68899999999999999999998 599999999999999999999999999999999


Q ss_pred             chhhccCCcHHHHHHHHHhC-CCCceEEEEeccCCccHHHHHHHhccCCceeeeccc-cccccccceEEEEEeChHHHHH
Q 014486          200 DKMLESLDMRRDVQEIFKMT-PHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDE-AKLTLHGLVQHYIKLSELEKNR  277 (423)
Q Consensus       200 h~~~~~~~~~~~~~~~~~~~-~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  277 (423)
                      |+|++ .+|...++++...+ ++..|++++|||+|.++..++..++.++..+.+... .......+.+....+....|..
T Consensus       249 DrMld-mGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~  327 (519)
T KOG0331|consen  249 DRMLD-MGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAKLR  327 (519)
T ss_pred             Hhhhc-cccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHHHH
Confidence            99999 89999999999999 556689999999999999999999999988877655 4445566677777788888988


Q ss_pred             HHHHHHHhh---cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCC
Q 014486          278 KLNDLLDAL---DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDI  354 (423)
Q Consensus       278 ~l~~ll~~~---~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~  354 (423)
                      .+..+|...   .++|+||||.++..|+.+...|+..++++..+||+.++.+|..+++.|++|+..|||||+++++|||+
T Consensus       328 ~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi  407 (519)
T KOG0331|consen  328 KLGKLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDV  407 (519)
T ss_pred             HHHHHHHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCC
Confidence            888888776   46799999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHH
Q 014486          355 ERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFM  408 (423)
Q Consensus       355 ~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~  408 (423)
                      |++++||+||+|.++++|+||+||+||+|++|.++.|++.... .....+.+.+
T Consensus       408 ~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~-~~a~~l~~~l  460 (519)
T KOG0331|consen  408 PDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNA-KLARELIKVL  460 (519)
T ss_pred             ccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHH-HHHHHHHHHH
Confidence            9999999999999999999999999999999999999986433 3333333333

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

Probab=100.00  E-value=2.3e-63  Score=473.29  Aligned_cols=366  Identities=40%  Similarity=0.655  Sum_probs=338.6

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC--CCCCeEEEEEecC
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP--NPGQVTALVLCHT  123 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~--~~~~~~~lil~P~  123 (423)
                      ..|.++++++.++++|.+.||..|+|+|..+||.++.|+|+++.++||||||++|++|+++.+..  ......+||++||
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PT  108 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPT  108 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCC
Confidence            56999999999999999999999999999999999999999999999999999999999999763  3222129999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                      |+||.|+++.+..+....+++++..++||.+...+...+..+ ++|+|+||+++++++....+.+..++++|+||||+++
T Consensus       109 RELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~-~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADrmL  187 (513)
T COG0513         109 RELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRG-VDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRML  187 (513)
T ss_pred             HHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcC-CCEEEECccHHHHHHHcCCcchhhcCEEEeccHhhhh
Confidence            999999999999998876578999999999999999888887 7999999999999999999999999999999999999


Q ss_pred             ccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeecccc-ccccccceEEEEEeChHH-HHHHHHH
Q 014486          204 ESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEA-KLTLHGLVQHYIKLSELE-KNRKLND  281 (423)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~-~~~~l~~  281 (423)
                      + .+|...+..+...++.+.|++++|||+|..+..+...++.+|..+.+.... ......+.+.++.+...+ |...+..
T Consensus       188 d-~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~  266 (513)
T COG0513         188 D-MGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLK  266 (513)
T ss_pred             c-CCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHH
Confidence            9 799999999999999999999999999999999999999999877776332 236677888888888766 9999999


Q ss_pred             HHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEE
Q 014486          282 LLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVI  361 (423)
Q Consensus       282 ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi  361 (423)
                      +++.....++||||++...++.++..|...|+++..+||++++.+|.+++..|++|+.+|||||+++++|||+|++++||
T Consensus       267 ll~~~~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~~Vi  346 (513)
T COG0513         267 LLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVI  346 (513)
T ss_pred             HHhcCCCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccceeE
Confidence            99988888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchh
Q 014486          362 NYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIG  413 (423)
Q Consensus       362 ~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  413 (423)
                      +||+|.++..|+||+||+||+|..|.++.|+.+..+...+..+++.++..+.
T Consensus       347 nyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~~~l~~ie~~~~~~~~  398 (513)
T COG0513         347 NYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLP  398 (513)
T ss_pred             EccCCCCHHHheeccCccccCCCCCeEEEEeCcHHHHHHHHHHHHHHhcccc
Confidence            9999999999999999999999999999999986688999999999876533

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=8.1e-62  Score=463.42  Aligned_cols=362  Identities=33%  Similarity=0.585  Sum_probs=331.3

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      .+|.++++++.+.++|.+.||..|+|+|+++++.++.|+++++++|||+|||++|++|+++.+......+++||++||++
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            46999999999999999999999999999999999999999999999999999999999998876665668999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~  205 (423)
                      |+.|+.+.++.+....+++++..++||.+...+...+..+ ++|+|+||+++..++......+.++++||+||||.+.+ 
T Consensus        84 La~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~-~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~-  161 (460)
T PRK11776         84 LADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHG-AHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLD-  161 (460)
T ss_pred             HHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCC-CCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhC-
Confidence            9999999999988776688999999999988887777765 69999999999999998888899999999999999998 


Q ss_pred             CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHh
Q 014486          206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDA  285 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~  285 (423)
                      .+|...+..+...++...|++++|||+++.+..+...++..+..+.+....  ....+.+.+..+....+...+..++..
T Consensus       162 ~g~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~--~~~~i~~~~~~~~~~~k~~~l~~ll~~  239 (460)
T PRK11776        162 MGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTH--DLPAIEQRFYEVSPDERLPALQRLLLH  239 (460)
T ss_pred             cCcHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCC--CCCCeeEEEEEeCcHHHHHHHHHHHHh
Confidence            789999999999999999999999999999999888888888777665443  234466777788888888999999988


Q ss_pred             hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccC
Q 014486          286 LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDM  365 (423)
Q Consensus       286 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~  365 (423)
                      ..+.++||||++++.++.+++.|...++.+..+||++++.+|..+++.|++|+.+|||||+++++|+|+|++++||++++
T Consensus       240 ~~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI~~d~  319 (460)
T PRK11776        240 HQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYEL  319 (460)
T ss_pred             cCCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEEEecC
Confidence            88889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcch
Q 014486          366 PDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLI  412 (423)
Q Consensus       366 ~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (423)
                      |.++..|+||+||+||+|+.|.+++|+.+ .+...+..+++.++..+
T Consensus       320 p~~~~~yiqR~GRtGR~g~~G~ai~l~~~-~e~~~~~~i~~~~~~~~  365 (460)
T PRK11776        320 ARDPEVHVHRIGRTGRAGSKGLALSLVAP-EEMQRANAIEDYLGRKL  365 (460)
T ss_pred             CCCHhHhhhhcccccCCCCcceEEEEEch-hHHHHHHHHHHHhCCCC
Confidence            99999999999999999999999999986 45667788888887644

>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=2.6e-62  Score=401.72  Aligned_cols=366  Identities=38%  Similarity=0.646  Sum_probs=340.8

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ..+|++.++++.+++.+++.||+.|..+|+.|+++++.|++++.++..|+|||.+|.+.++....-+....++||++|||
T Consensus        26 ~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTR  105 (400)
T KOG0328|consen   26 IPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTR  105 (400)
T ss_pred             ccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeEEEecChH
Confidence            45799999999999999999999999999999999999999999999999999999999998888777777999999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      +||.|+.+.+..+.... ++++....||.+..++.+.+..|+ +++.+||++++++++...+....++++|+|||+.+++
T Consensus       106 ELa~Qi~~vi~alg~~m-nvq~hacigg~n~gedikkld~G~-hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL~  183 (400)
T KOG0328|consen  106 ELAVQIQKVILALGDYM-NVQCHACIGGKNLGEDIKKLDYGQ-HVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEMLN  183 (400)
T ss_pred             HHHHHHHHHHHHhcccc-cceEEEEecCCccchhhhhhcccc-eEeeCCCchHHHHHHhccccccceeEEEeccHHHHHH
Confidence            99999999999998876 899999999999999999998775 9999999999999999999999999999999999999


Q ss_pred             cCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChH-HHHHHHHHHH
Q 014486          205 SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEL-EKNRKLNDLL  283 (423)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~ll  283 (423)
                       .+|...+-.+++.+|+..|++++|||+|.++......|+.+|..+.+.... ...+.+.++++.+... +|...+.++.
T Consensus       184 -kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrde-ltlEgIKqf~v~ve~EewKfdtLcdLY  261 (400)
T KOG0328|consen  184 -KGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDE-LTLEGIKQFFVAVEKEEWKFDTLCDLY  261 (400)
T ss_pred             -hhHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCC-CchhhhhhheeeechhhhhHhHHHHHh
Confidence             699999999999999999999999999999999999999999998776554 4567777787777554 4999999998


Q ss_pred             HhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEc
Q 014486          284 DALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINY  363 (423)
Q Consensus       284 ~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~  363 (423)
                      ..+.-...+|||+++..++++.+.+++.++.+...||+|++++|..++..|+.|+.+|||+|++.++|+|+|.+++||+|
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            88877899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhhh
Q 014486          364 DMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSF  415 (423)
Q Consensus       364 ~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (423)
                      |+|.+.+.|+||+||.||.|.+|.++.|+. .++...+..+++++...+..+
T Consensus       342 DLP~nre~YIHRIGRSGRFGRkGvainFVk-~~d~~~lrdieq~yst~i~em  392 (400)
T KOG0328|consen  342 DLPNNRELYIHRIGRSGRFGRKGVAINFVK-SDDLRILRDIEQYYSTQIDEM  392 (400)
T ss_pred             CCCccHHHHhhhhccccccCCcceEEEEec-HHHHHHHHHHHHHHhhhcccc
Confidence            999999999999999999999999999997 578889999999998766543

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=4.2e-61  Score=453.65  Aligned_cols=363  Identities=31%  Similarity=0.506  Sum_probs=319.5

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC-------CCCeEE
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN-------PGQVTA  117 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~-------~~~~~~  117 (423)
                      ..+|+++++++.++++|.+.||..|+|+|+++||.++.|+|+++.||||||||++|++|+++.+...       ..++++
T Consensus         7 ~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~   86 (423)
T PRK04837          7 EQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRA   86 (423)
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceE
Confidence            4579999999999999999999999999999999999999999999999999999999999766422       234689


Q ss_pred             EEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEc
Q 014486          118 LVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILD  197 (423)
Q Consensus       118 lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvD  197 (423)
                      ||++|+++||.|+++.+..+.... ++++..++||.+...+...+.++ ++|+|+||+++..++....+.+.+++++|+|
T Consensus        87 lil~PtreLa~Qi~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l~~~-~~IlV~TP~~l~~~l~~~~~~l~~v~~lViD  164 (423)
T PRK04837         87 LIMAPTRELAVQIHADAEPLAQAT-GLKLGLAYGGDGYDKQLKVLESG-VDILIGTTGRLIDYAKQNHINLGAIQVVVLD  164 (423)
T ss_pred             EEECCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhcCC-CCEEEECHHHHHHHHHcCCcccccccEEEEe
Confidence            999999999999999999988776 78999999998887777777665 6999999999999998888899999999999


Q ss_pred             CcchhhccCCcHHHHHHHHHhCCC--CceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHH
Q 014486          198 ECDKMLESLDMRRDVQEIFKMTPH--DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEK  275 (423)
Q Consensus       198 E~h~~~~~~~~~~~~~~~~~~~~~--~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  275 (423)
                      |||++.+ .+|...+..++..++.  ..+.+++|||++..+.......+..+..+.+..... ....+.+.+.......+
T Consensus       165 Ead~l~~-~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~-~~~~i~~~~~~~~~~~k  242 (423)
T PRK04837        165 EADRMFD-LGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQK-TGHRIKEELFYPSNEEK  242 (423)
T ss_pred             cHHHHhh-cccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCc-CCCceeEEEEeCCHHHH
Confidence            9999988 7899999999988874  456899999999998888877887777665543322 22334445555666778


Q ss_pred             HHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCC
Q 014486          276 NRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIE  355 (423)
Q Consensus       276 ~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~  355 (423)
                      ...+..++......++||||++.+.++.+.+.|...|+++..+||++++.+|..+++.|++|+++|||||+++++|+|+|
T Consensus       243 ~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip  322 (423)
T PRK04837        243 MRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIP  322 (423)
T ss_pred             HHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCcc
Confidence            88888888877778999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcch
Q 014486          356 RVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLI  412 (423)
Q Consensus       356 ~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (423)
                      ++++||+|++|.++..|+||+||+||.|+.|.+++|+.+ .+...+..+++.++..+
T Consensus       323 ~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~-~~~~~~~~i~~~~~~~~  378 (423)
T PRK04837        323 AVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACE-EYALNLPAIETYIGHSI  378 (423)
T ss_pred             ccCEEEEeCCCCchhheEeccccccCCCCCeeEEEEeCH-HHHHHHHHHHHHhCCCC
Confidence            999999999999999999999999999999999999986 45666788888887654

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=5.9e-61  Score=461.31  Aligned_cols=367  Identities=31%  Similarity=0.522  Sum_probs=319.9

Q ss_pred             ccccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC-----CCCCe
Q 014486           41 VGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP-----NPGQV  115 (423)
Q Consensus        41 ~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-----~~~~~  115 (423)
                      .+....+|+++++++.++++|.++||..|+|+|.++||.++.|+++++.+|||||||++|++|++..+..     ...++
T Consensus       125 ~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp  204 (545)
T PTZ00110        125 VPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGP  204 (545)
T ss_pred             CCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCc
Confidence            3444568999999999999999999999999999999999999999999999999999999999876432     23356


Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEE
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFI  195 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vV  195 (423)
                      .+|||+||++||.|+.+.++.+.... ++++..++||.....+...+.++ ++|+|+||++|.+++......+.++++||
T Consensus       205 ~~LIL~PTreLa~Qi~~~~~~~~~~~-~i~~~~~~gg~~~~~q~~~l~~~-~~IlVaTPgrL~d~l~~~~~~l~~v~~lV  282 (545)
T PTZ00110        205 IVLVLAPTRELAEQIREQCNKFGASS-KIRNTVAYGGVPKRGQIYALRRG-VEILIACPGRLIDFLESNVTNLRRVTYLV  282 (545)
T ss_pred             EEEEECChHHHHHHHHHHHHHHhccc-CccEEEEeCCCCHHHHHHHHHcC-CCEEEECHHHHHHHHHcCCCChhhCcEEE
Confidence            89999999999999999999998765 78899999999888777777776 69999999999999998888899999999


Q ss_pred             EcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhcc-CCceeeeccccccccccceEEEEEeChHH
Q 014486          196 LDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQ-DPMEIYVDDEAKLTLHGLVQHYIKLSELE  274 (423)
Q Consensus       196 vDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  274 (423)
                      +||||++++ .+|...+..++..+++..|++++|||+|..+..+.+.++. .+..+.+..........+.+.+..+....
T Consensus       283 iDEAd~mld-~gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~~~  361 (545)
T PTZ00110        283 LDEADRMLD-MGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHE  361 (545)
T ss_pred             eehHHhhhh-cchHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEechh
Confidence            999999998 7899999999999999999999999999998888887775 45555444333223344555666666777


Q ss_pred             HHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCC
Q 014486          275 KNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGI  352 (423)
Q Consensus       275 ~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gl  352 (423)
                      |...+..++...  ...++||||++++.++.+++.|+..++++..+||++++.+|..+++.|++|+.+|||||+++++|+
T Consensus       362 k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGI  441 (545)
T PTZ00110        362 KRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGL  441 (545)
T ss_pred             HHHHHHHHHHHhcccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCC
Confidence            778888888765  467999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcc
Q 014486          353 DIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLL  411 (423)
Q Consensus       353 d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  411 (423)
                      |+|++++||+|++|.++..|+||+||+||.|+.|.+++|+++ .+......+.+.|...
T Consensus       442 Di~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~-~~~~~~~~l~~~l~~~  499 (545)
T PTZ00110        442 DVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTP-DKYRLARDLVKVLREA  499 (545)
T ss_pred             CcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECc-chHHHHHHHHHHHHHc
Confidence            999999999999999999999999999999999999999986 4555666666665543

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

Probab=100.00  E-value=9.4e-63  Score=434.90  Aligned_cols=357  Identities=34%  Similarity=0.604  Sum_probs=324.8

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCC---eEEEEEec
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQ---VTALVLCH  122 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~---~~~lil~P  122 (423)
                      .+|.+++|+..+++++..+||..|+|+|..+||-.+.|++++.+|.||||||.+|++|+++++.-.+.+   .++||+||
T Consensus       181 ~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~P  260 (691)
T KOG0338|consen  181 ESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVP  260 (691)
T ss_pred             hhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEec
Confidence            379999999999999999999999999999999999999999999999999999999999987755533   48999999


Q ss_pred             ChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhc-CCCCCCCccEEEEcCcch
Q 014486          123 TRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARD-KDLSLKNVRHFILDECDK  201 (423)
Q Consensus       123 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~-~~~~~~~~~~vVvDE~h~  201 (423)
                      ||+|+.|+++..++++... ++.++...||.+...+...+.+. |+|+|+||++|.+++.+ ..+++.++.++|+||||+
T Consensus       261 TRELaiQv~sV~~qlaqFt-~I~~~L~vGGL~lk~QE~~LRs~-PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADR  338 (691)
T KOG0338|consen  261 TRELAIQVHSVTKQLAQFT-DITVGLAVGGLDLKAQEAVLRSR-PDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADR  338 (691)
T ss_pred             cHHHHHHHHHHHHHHHhhc-cceeeeeecCccHHHHHHHHhhC-CCEEEecchhHHHHhccCCCccccceeEEEechHHH
Confidence            9999999999999998876 79999999999999999999888 69999999999998875 468899999999999999


Q ss_pred             hhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEe---ChHHHHHH
Q 014486          202 MLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL---SELEKNRK  278 (423)
Q Consensus       202 ~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~  278 (423)
                      +++ .+|...+..+...+++++|.+++||||+..+..++...+..|..+++++..... ..+.+-++.+   .+..+...
T Consensus       339 MLe-egFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a-~~LtQEFiRIR~~re~dRea~  416 (691)
T KOG0338|consen  339 MLE-EGFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTA-PKLTQEFIRIRPKREGDREAM  416 (691)
T ss_pred             HHH-HHHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccc-hhhhHHHheeccccccccHHH
Confidence            999 899999999999999999999999999999999999999999999998876544 3334444433   34557778


Q ss_pred             HHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCC
Q 014486          279 LNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVN  358 (423)
Q Consensus       279 l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~  358 (423)
                      +..++.......+|||+.+.+.|+.+.-.|.-.|+.+.-+||.+++.+|.+.++.|++.+++|||||+++++|+|++++.
T Consensus       417 l~~l~~rtf~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~  496 (691)
T KOG0338|consen  417 LASLITRTFQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQ  496 (691)
T ss_pred             HHHHHHHhcccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCcccee
Confidence            88888888889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHH
Q 014486          359 IVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF  407 (423)
Q Consensus       359 ~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~  407 (423)
                      .||+|.+|.+...|+||+||+.|+|..|..+.|+... +..+++.|-+.
T Consensus       497 tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~-dRkllK~iik~  544 (691)
T KOG0338|consen  497 TVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGES-DRKLLKEIIKS  544 (691)
T ss_pred             EEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccc-cHHHHHHHHhh
Confidence            9999999999999999999999999999999999854 66666665544

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=6.9e-61  Score=464.39  Aligned_cols=363  Identities=36%  Similarity=0.638  Sum_probs=330.2

Q ss_pred             CCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           47 GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        47 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      +|.++++++.++++|.++||..|+|+|.++|+.++.++++++.+|||+|||++|++|+++.+......+++||++||++|
T Consensus         7 ~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreL   86 (629)
T PRK11634          7 TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTREL   86 (629)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHH
Confidence            59999999999999999999999999999999999999999999999999999999999887766566799999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccC
Q 014486          127 AYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESL  206 (423)
Q Consensus       127 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~  206 (423)
                      +.|+++.+..+....+++++..++||.+...+...+..+ ++|+|+||+++++++....+.++++++||+||||.++. .
T Consensus        87 a~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~-~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~-~  164 (629)
T PRK11634         87 AVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQG-PQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLR-M  164 (629)
T ss_pred             HHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCC-CCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhh-c
Confidence            999999999998877789999999999888877777666 69999999999999998888899999999999999988 7


Q ss_pred             CcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhh
Q 014486          207 DMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDAL  286 (423)
Q Consensus       207 ~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~  286 (423)
                      +|...+..++..++...|++++|||+|..+..+.+.++..+..+.+.... .....+.+.+..+....+...+..++...
T Consensus       165 gf~~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~-~~~~~i~q~~~~v~~~~k~~~L~~~L~~~  243 (629)
T PRK11634        165 GFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSV-TTRPDISQSYWTVWGMRKNEALVRFLEAE  243 (629)
T ss_pred             ccHHHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCcc-ccCCceEEEEEEechhhHHHHHHHHHHhc
Confidence            89999999999999999999999999999999888898888776655433 23345566677777778888899999888


Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCC
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMP  366 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~  366 (423)
                      ...++||||+++..+..+++.|...++.+..+|+++++.+|..+++.|++|+++|||||+++++|+|+|++++||+|++|
T Consensus       244 ~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~P  323 (629)
T PRK11634        244 DFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIP  323 (629)
T ss_pred             CCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCCC
Confidence            77899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchh
Q 014486          367 DSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIG  413 (423)
Q Consensus       367 ~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  413 (423)
                      .++..|+||+||+||.|+.|.+++|+.+ .+...+..+++.++..+.
T Consensus       324 ~~~e~yvqRiGRtGRaGr~G~ai~~v~~-~e~~~l~~ie~~~~~~i~  369 (629)
T PRK11634        324 MDSESYVHRIGRTGRAGRAGRALLFVEN-RERRLLRNIERTMKLTIP  369 (629)
T ss_pred             CCHHHHHHHhccccCCCCcceEEEEech-HHHHHHHHHHHHhCCCcc
Confidence            9999999999999999999999999985 456778888888776654

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

Probab=100.00  E-value=1.4e-61  Score=426.67  Aligned_cols=358  Identities=30%  Similarity=0.517  Sum_probs=323.9

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC----CCCeEEEEE
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN----PGQVTALVL  120 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~----~~~~~~lil  120 (423)
                      ...|+.+.+++..++++..+||..+|++|+..++.++.|+++++.|-||+|||++|++|+++.+...    ..+..++|+
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            3468899999999999999999999999999999999999999999999999999999999875543    244589999


Q ss_pred             ecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC-CCCCCccEEEEcCc
Q 014486          121 CHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD-LSLKNVRHFILDEC  199 (423)
Q Consensus       121 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~-~~~~~~~~vVvDE~  199 (423)
                      ||||+||.|.+.+++++....+++.+..+.||.+...+...+.++ ++|+|+||++|.+++++.. +.+.+++++|+|||
T Consensus       161 ~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~-~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEA  239 (543)
T KOG0342|consen  161 CPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKG-CNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEA  239 (543)
T ss_pred             cccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhcc-ccEEEeCCchHHhHhhcCCcchhhccceeEeecc
Confidence            999999999999999999998899999999999999999999996 6999999999999888654 45677889999999


Q ss_pred             chhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccC-Cceeeeccc-cccccccceEEEEEeChHHHHH
Q 014486          200 DKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQD-PMEIYVDDE-AKLTLHGLVQHYIKLSELEKNR  277 (423)
Q Consensus       200 h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  277 (423)
                      |++++ .+|+..+..+.+.++..+|.+++|||.++.+..+....+.. +..+.+... .......+.+.++..+...+..
T Consensus       240 DrlLd-~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~~f~  318 (543)
T KOG0342|consen  240 DRLLD-IGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDSRFS  318 (543)
T ss_pred             hhhhh-cccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccchHH
Confidence            99999 99999999999999999999999999999999998887765 555555443 3345566777788888888888


Q ss_pred             HHHHHHHhhcC-CcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCC
Q 014486          278 KLNDLLDALDF-NQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIER  356 (423)
Q Consensus       278 ~l~~ll~~~~~-~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~  356 (423)
                      .+..+++.+.. .++||||++......+++.|....+++..+||+.++..|..+..+|++.+..||+||++++||+|+|+
T Consensus       319 ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~  398 (543)
T KOG0342|consen  319 LLYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDIPD  398 (543)
T ss_pred             HHHHHHHHhcCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCCCC
Confidence            88888888766 89999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHH
Q 014486          357 VNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVS  405 (423)
Q Consensus       357 ~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~  405 (423)
                      ++.||+|++|.++.+|+||+||+||.|..|.++++..+ ++...+..+.
T Consensus       399 V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p-~El~Flr~LK  446 (543)
T KOG0342|consen  399 VDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAP-WELGFLRYLK  446 (543)
T ss_pred             ceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeCh-hHHHHHHHHh
Confidence            99999999999999999999999999999999999986 5666666665

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=2e-60  Score=451.63  Aligned_cols=361  Identities=33%  Similarity=0.599  Sum_probs=321.1

Q ss_pred             CCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC------CCeEEEEE
Q 014486           47 GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP------GQVTALVL  120 (423)
Q Consensus        47 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~------~~~~~lil  120 (423)
                      +|+++++++.+.++|.++||..|+++|.++++.++.++|+++.+|||+|||++|++|+++.+....      ..+++||+
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            588999999999999999999999999999999999999999999999999999999998764321      23479999


Q ss_pred             ecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcc
Q 014486          121 CHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECD  200 (423)
Q Consensus       121 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h  200 (423)
                      +||++||.|+.+.++.+.... ++++..++|+.+...+...+... ++|+|+||++|+.++......++++++||+||||
T Consensus        82 ~PtreLa~Qi~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~-~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah  159 (456)
T PRK10590         82 TPTRELAAQIGENVRDYSKYL-NIRSLVVFGGVSINPQMMKLRGG-VDVLVATPGRLLDLEHQNAVKLDQVEILVLDEAD  159 (456)
T ss_pred             eCcHHHHHHHHHHHHHHhccC-CCEEEEEECCcCHHHHHHHHcCC-CcEEEEChHHHHHHHHcCCcccccceEEEeecHH
Confidence            999999999999999988765 78899999999888777766655 6999999999999988888889999999999999


Q ss_pred             hhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHH
Q 014486          201 KMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLN  280 (423)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  280 (423)
                      ++.+ .++...+..++..++...|++++|||++..+..+...++..+..+.+.... .....+.+.+..+....+...+.
T Consensus       160 ~ll~-~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~-~~~~~i~~~~~~~~~~~k~~~l~  237 (456)
T PRK10590        160 RMLD-MGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRN-TASEQVTQHVHFVDKKRKRELLS  237 (456)
T ss_pred             HHhc-cccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEeccc-ccccceeEEEEEcCHHHHHHHHH
Confidence            9998 788899999999999999999999999998888888888887766554332 22344555666666677777788


Q ss_pred             HHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEE
Q 014486          281 DLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIV  360 (423)
Q Consensus       281 ~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~v  360 (423)
                      .++......++||||++++.++.+++.|...++.+..+||++++.+|..+++.|++|+++|||||+++++|+|+|++++|
T Consensus       238 ~l~~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~V  317 (456)
T PRK10590        238 QMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHV  317 (456)
T ss_pred             HHHHcCCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEE
Confidence            88777777899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcch
Q 014486          361 INYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLI  412 (423)
Q Consensus       361 i~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (423)
                      |+|++|.++.+|+||+||+||.|..|.+++|+.. .+...+..+++.++..+
T Consensus       318 I~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~-~d~~~~~~ie~~l~~~~  368 (456)
T PRK10590        318 VNYELPNVPEDYVHRIGRTGRAAATGEALSLVCV-DEHKLLRDIEKLLKKEI  368 (456)
T ss_pred             EEeCCCCCHHHhhhhccccccCCCCeeEEEEecH-HHHHHHHHHHHHhcCCC
Confidence            9999999999999999999999999999999985 57778889999888665

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

Probab=100.00  E-value=2.5e-60  Score=416.01  Aligned_cols=357  Identities=30%  Similarity=0.531  Sum_probs=322.2

Q ss_pred             CCcCCC--CCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC--C---CCCeEEEE
Q 014486           47 GFRDFL--LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP--N---PGQVTALV  119 (423)
Q Consensus        47 ~~~~~~--l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~--~---~~~~~~li  119 (423)
                      .|++++  |++++++++...||..+||.|..+||.++.++|+++.++||||||++|++|+++.+..  .   +....+||
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            466554  5699999999999999999999999999999999999999999999999999987722  2   22347899


Q ss_pred             EecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCC--CCCccEEEEc
Q 014486          120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLS--LKNVRHFILD  197 (423)
Q Consensus       120 l~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~--~~~~~~vVvD  197 (423)
                      |+|||+|+.|+.+.+..|...++++++..+.||.+...+.+.+....++|+|+||++|.+++++....  +..+.++|+|
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            99999999999999999998888999999999999999999998888899999999999999875544  5599999999


Q ss_pred             CcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccc-cccccceEEEEEeChHHHH
Q 014486          198 ECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAK-LTLHGLVQHYIKLSELEKN  276 (423)
Q Consensus       198 E~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  276 (423)
                      |||++++ .+|...+..|+..+|++++.=++|||...++.++....+.+|..+.+..... ..+..+...|..+....|.
T Consensus       165 EADrLld-mgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~  243 (567)
T KOG0345|consen  165 EADRLLD-MGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADEKL  243 (567)
T ss_pred             chHhHhc-ccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecHHHHH
Confidence            9999999 9999999999999999999999999999999999999999999988766553 2445566778889999999


Q ss_pred             HHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC--CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCC
Q 014486          277 RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC--NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDI  354 (423)
Q Consensus       277 ~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~  354 (423)
                      ..+..++.+...+++|||+++...++.....|...  +.++..+||.|.+.+|..++..|.+....+|+||+++++|+|+
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            99999999988899999999999999999888765  6788899999999999999999999888999999999999999


Q ss_pred             CCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHH
Q 014486          355 ERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVS  405 (423)
Q Consensus       355 ~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~  405 (423)
                      |+++.||+||+|.++..|.||+||++|.|..|.+++|+.+ .+..+..-+.
T Consensus       324 p~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p-~E~aYveFl~  373 (567)
T KOG0345|consen  324 PGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNP-REEAYVEFLR  373 (567)
T ss_pred             CCceEEEecCCCCChhHHHhhcchhhhccCccceEEEecc-cHHHHHHHHH
Confidence            9999999999999999999999999999999999999998 5555544433

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.4e-59  Score=451.42  Aligned_cols=363  Identities=30%  Similarity=0.520  Sum_probs=318.8

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC-------CCCeEEE
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN-------PGQVTAL  118 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~-------~~~~~~l  118 (423)
                      .+|.+|++++.++++|.+.||..|+|+|.++||.++.|+|+++.+|||||||++|++|+++.+...       ...+++|
T Consensus         9 ~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raL   88 (572)
T PRK04537          9 LTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRAL   88 (572)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            469999999999999999999999999999999999999999999999999999999999876421       1246899


Q ss_pred             EEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC-CCCCCCccEEEEc
Q 014486          119 VLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK-DLSLKNVRHFILD  197 (423)
Q Consensus       119 il~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~-~~~~~~~~~vVvD  197 (423)
                      ||+|+++|+.|+++.+..+.... ++++..++|+.....+...+..+ ++|+|+||++|++++... .+.+..+++||||
T Consensus        89 Il~PTreLa~Qi~~~~~~l~~~~-~i~v~~l~Gg~~~~~q~~~l~~~-~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViD  166 (572)
T PRK04537         89 ILAPTRELAIQIHKDAVKFGADL-GLRFALVYGGVDYDKQRELLQQG-VDVIIATPGRLIDYVKQHKVVSLHACEICVLD  166 (572)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHHhCC-CCEEEECHHHHHHHHHhccccchhheeeeEec
Confidence            99999999999999999998775 78999999999888777766655 699999999999988764 4678889999999


Q ss_pred             CcchhhccCCcHHHHHHHHHhCCC--CceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHH
Q 014486          198 ECDKMLESLDMRRDVQEIFKMTPH--DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEK  275 (423)
Q Consensus       198 E~h~~~~~~~~~~~~~~~~~~~~~--~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  275 (423)
                      |||.+.+ .+|...+..++..++.  ..|++++|||++..+..+...++..+..+...... .....+.+.+.......+
T Consensus       167 EAh~lld-~gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~-~~~~~i~q~~~~~~~~~k  244 (572)
T PRK04537        167 EADRMFD-LGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETET-ITAARVRQRIYFPADEEK  244 (572)
T ss_pred             CHHHHhh-cchHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEecccc-ccccceeEEEEecCHHHH
Confidence            9999988 7899999999988876  68999999999999888888888777665544332 233444555666667778


Q ss_pred             HHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCC
Q 014486          276 NRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIE  355 (423)
Q Consensus       276 ~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~  355 (423)
                      ...+..++......++||||+++..++.+++.|...++.+..+||++++.+|..+++.|++|+++|||||+++++|||+|
T Consensus       245 ~~~L~~ll~~~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip  324 (572)
T PRK04537        245 QTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHID  324 (572)
T ss_pred             HHHHHHHHhcccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCcc
Confidence            88888888877788999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchh
Q 014486          356 RVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIG  413 (423)
Q Consensus       356 ~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  413 (423)
                      ++++||+|+.|.++..|+||+||+||.|..|.+++|+++. +...+..++++++..+.
T Consensus       325 ~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~-~~~~l~~i~~~~~~~~~  381 (572)
T PRK04537        325 GVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACER-YAMSLPDIEAYIEQKIP  381 (572)
T ss_pred             CCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHH-HHHHHHHHHHHHcCCCC
Confidence            9999999999999999999999999999999999999864 55668888888876653

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

Probab=100.00  E-value=3.3e-61  Score=401.83  Aligned_cols=365  Identities=38%  Similarity=0.635  Sum_probs=344.6

Q ss_pred             ccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           43 IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        43 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      .+...|++|.+.++++..+.++||+.|.|+|.++||..+.|++++..+..|+|||.+|++|+++.........+++|++|
T Consensus        82 TkG~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVP  161 (459)
T KOG0326|consen   82 TKGNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVP  161 (459)
T ss_pred             ccCccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEee
Confidence            34567999999999999999999999999999999999999999999999999999999999999999988889999999


Q ss_pred             ChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchh
Q 014486          123 TRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM  202 (423)
Q Consensus       123 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~  202 (423)
                      +++||.|....++++.+.. ++++.+.+||++...+.-.+... .+++|+||++++++..++--.+++...+|+||||.+
T Consensus       162 trelALQtSqvc~~lskh~-~i~vmvttGGT~lrDDI~Rl~~~-VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKl  239 (459)
T KOG0326|consen  162 TRELALQTSQVCKELSKHL-GIKVMVTTGGTSLRDDIMRLNQT-VHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKL  239 (459)
T ss_pred             cchhhHHHHHHHHHHhccc-CeEEEEecCCcccccceeeecCc-eEEEEcCChhHHHHHhcccccchhceEEEechhhhh
Confidence            9999999999999999887 79999999999988887777666 699999999999999999889999999999999999


Q ss_pred             hccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHH
Q 014486          203 LESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDL  282 (423)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l  282 (423)
                      ++ ..|...+..+...+|+.+|++++|||+|-.+..+...++.+|.++.+-.+  .....+.++|..+.+..|..-+..+
T Consensus       240 Ls-~~F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~e--Ltl~GvtQyYafV~e~qKvhCLntL  316 (459)
T KOG0326|consen  240 LS-VDFQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLMEE--LTLKGVTQYYAFVEERQKVHCLNTL  316 (459)
T ss_pred             hc-hhhhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehhhh--hhhcchhhheeeechhhhhhhHHHH
Confidence            98 89999999999999999999999999999999999999999998887655  5667888999999999999999999


Q ss_pred             HHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE
Q 014486          283 LDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN  362 (423)
Q Consensus       283 l~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~  362 (423)
                      ...+.-+..||||++.+.++.+++.+.+.|+.+..+|+.|.+..|.+++..|++|.++.||||+.+.+|+|++.+++||+
T Consensus       317 fskLqINQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVIN  396 (459)
T KOG0326|consen  317 FSKLQINQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVIN  396 (459)
T ss_pred             HHHhcccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEe
Confidence            88888889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchh
Q 014486          363 YDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIG  413 (423)
Q Consensus       363 ~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  413 (423)
                      ||.|++.++|.||+||.||.|..|.++.+++ .++...+..|++.+|..+.
T Consensus       397 FDfpk~aEtYLHRIGRsGRFGhlGlAInLit-yedrf~L~~IE~eLGtEI~  446 (459)
T KOG0326|consen  397 FDFPKNAETYLHRIGRSGRFGHLGLAINLIT-YEDRFNLYRIEQELGTEIK  446 (459)
T ss_pred             cCCCCCHHHHHHHccCCccCCCcceEEEEEe-hhhhhhHHHHHHHhccccc
Confidence            9999999999999999999999999999998 4677889999999997764

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=9e-59  Score=440.01  Aligned_cols=361  Identities=34%  Similarity=0.581  Sum_probs=316.2

Q ss_pred             CCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC----CCCCeEEEEEec
Q 014486           47 GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP----NPGQVTALVLCH  122 (423)
Q Consensus        47 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~----~~~~~~~lil~P  122 (423)
                      +|+++++++.+++.|.++||..|+++|.++++.++.++++++.+|||+|||++|++|++..+..    ..+.+++||++|
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            5899999999999999999999999999999999999999999999999999999999987542    223458999999


Q ss_pred             ChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchh
Q 014486          123 TRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM  202 (423)
Q Consensus       123 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~  202 (423)
                      +++|+.|+.+.+..+.... ++++..++|+.....+...+..+ ++|+|+||++|+.++....+.+.++++||+||||++
T Consensus        82 t~eLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l~~~-~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~  159 (434)
T PRK11192         82 TRELAMQVADQARELAKHT-HLDIATITGGVAYMNHAEVFSEN-QDIVVATPGRLLQYIKEENFDCRAVETLILDEADRM  159 (434)
T ss_pred             cHHHHHHHHHHHHHHHccC-CcEEEEEECCCCHHHHHHHhcCC-CCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHH
Confidence            9999999999999998776 78999999999888777666655 699999999999999988888999999999999999


Q ss_pred             hccCCcHHHHHHHHHhCCCCceEEEEeccCCc-cHHHHHHHhccCCceeeeccccccccccceEEEEEeC-hHHHHHHHH
Q 014486          203 LESLDMRRDVQEIFKMTPHDKQVMMFSATLSK-EIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS-ELEKNRKLN  280 (423)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~  280 (423)
                      .+ .+|...+..+...++...|++++|||++. .+..+...++..+..+....... ....+.+.+.... ...+...+.
T Consensus       160 l~-~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~-~~~~i~~~~~~~~~~~~k~~~l~  237 (434)
T PRK11192        160 LD-MGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRR-ERKKIHQWYYRADDLEHKTALLC  237 (434)
T ss_pred             hC-CCcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcc-cccCceEEEEEeCCHHHHHHHHH
Confidence            98 78999999999999989999999999985 46667777777777665544322 2333444444444 356777788


Q ss_pred             HHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEE
Q 014486          281 DLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIV  360 (423)
Q Consensus       281 ~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~v  360 (423)
                      .++......++||||++++.++.++..|...++.+..+||++++.+|..+++.|++|+++|||||+++++|+|+|++++|
T Consensus       238 ~l~~~~~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~V  317 (434)
T PRK11192        238 HLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHV  317 (434)
T ss_pred             HHHhcCCCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCEE
Confidence            88877677899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcch
Q 014486          361 INYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLI  412 (423)
Q Consensus       361 i~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (423)
                      |+|++|.+...|+||+||+||+|..|.+++++.. .+...+..+++++...+
T Consensus       318 I~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~-~d~~~~~~i~~~~~~~~  368 (434)
T PRK11192        318 INFDMPRSADTYLHRIGRTGRAGRKGTAISLVEA-HDHLLLGKIERYIEEPL  368 (434)
T ss_pred             EEECCCCCHHHHhhcccccccCCCCceEEEEecH-HHHHHHHHHHHHHhccc
Confidence            9999999999999999999999999999999974 56677888888777554

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

Probab=100.00  E-value=8.1e-59  Score=445.54  Aligned_cols=364  Identities=32%  Similarity=0.500  Sum_probs=313.1

Q ss_pred             ccccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC-------CCC
Q 014486           41 VGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP-------NPG  113 (423)
Q Consensus        41 ~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-------~~~  113 (423)
                      .+....+|+++++++.++++|.+.||..|+|+|.++|+.++.|+++++.+|||||||++|++|++..+..       ...
T Consensus       116 ~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~  195 (518)
T PLN00206        116 VPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQR  195 (518)
T ss_pred             CCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccC
Confidence            3345567999999999999999999999999999999999999999999999999999999999976431       224


Q ss_pred             CeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccE
Q 014486          114 QVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRH  193 (423)
Q Consensus       114 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~  193 (423)
                      ++++||++||++||.|+.+.++.+.... ++++..+.||.....+...+..+ ++|+|+||++|..++......+.++++
T Consensus       196 ~~~aLIL~PTreLa~Qi~~~~~~l~~~~-~~~~~~~~gG~~~~~q~~~l~~~-~~IiV~TPgrL~~~l~~~~~~l~~v~~  273 (518)
T PLN00206        196 NPLAMVLTPTRELCVQVEDQAKVLGKGL-PFKTALVVGGDAMPQQLYRIQQG-VELIVGTPGRLIDLLSKHDIELDNVSV  273 (518)
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHHHhcCC-CCEEEECHHHHHHHHHcCCccchheeE
Confidence            5699999999999999999999887665 67888888988877777777666 699999999999999888888999999


Q ss_pred             EEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChH
Q 014486          194 FILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEL  273 (423)
Q Consensus       194 vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  273 (423)
                      ||+||||++.+ .+|...+..+...++ ..|++++|||+++.+..+...+...+..+....... ....+.+....+...
T Consensus       274 lViDEad~ml~-~gf~~~i~~i~~~l~-~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~-~~~~v~q~~~~~~~~  350 (518)
T PLN00206        274 LVLDEVDCMLE-RGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNR-PNKAVKQLAIWVETK  350 (518)
T ss_pred             EEeecHHHHhh-cchHHHHHHHHHhCC-CCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCC-CCcceeEEEEeccch
Confidence            99999999998 789999988888875 679999999999999888888887777666544332 223344555556666


Q ss_pred             HHHHHHHHHHHhhc--CCcEEEEEcChhhHHHHHHHHHh-CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCcccc
Q 014486          274 EKNRKLNDLLDALD--FNQVVIFVKSVSRAAELNKLLVE-CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGR  350 (423)
Q Consensus       274 ~~~~~l~~ll~~~~--~~~~ivf~~~~~~~~~l~~~L~~-~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~  350 (423)
                      .+...+.+++....  ..++||||+++..++.+++.|.. .++.+..+||++++.+|..+++.|++|+.+|||||+++++
T Consensus       351 ~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~r  430 (518)
T PLN00206        351 QKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGR  430 (518)
T ss_pred             hHHHHHHHHHHhhcccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhc
Confidence            67777777776543  35899999999999999999975 5899999999999999999999999999999999999999


Q ss_pred             CCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhc
Q 014486          351 GIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFL  410 (423)
Q Consensus       351 Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (423)
                      |+|+|++++||+|++|.++.+|+||+||+||.|..|.+++|+++ ++...+..+.+.|..
T Consensus       431 GiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~-~~~~~~~~l~~~l~~  489 (518)
T PLN00206        431 GVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNE-EDRNLFPELVALLKS  489 (518)
T ss_pred             cCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEch-hHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999985 455566666666653

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.3e-58  Score=442.28  Aligned_cols=363  Identities=31%  Similarity=0.584  Sum_probs=320.6

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC-------CCeEEE
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP-------GQVTAL  118 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~-------~~~~~l  118 (423)
                      ..|.++++++.+.++|.+.||..|+++|.++++.++.|+|+++.+|||||||++|++|++..+...+       +.+++|
T Consensus        87 ~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aL  166 (475)
T PRK01297         87 TRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRAL  166 (475)
T ss_pred             CCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEE
Confidence            4688999999999999999999999999999999999999999999999999999999998765432       245899


Q ss_pred             EEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcC
Q 014486          119 VLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDE  198 (423)
Q Consensus       119 il~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE  198 (423)
                      ||+||++|+.|+.+.++.+.... ++++..++||.+...+...+....++|+|+||++|+.+.......+.++++|||||
T Consensus       167 il~PtreLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDE  245 (475)
T PRK01297        167 IIAPTRELVVQIAKDAAALTKYT-GLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDE  245 (475)
T ss_pred             EEeCcHHHHHHHHHHHHHhhccC-CCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEech
Confidence            99999999999999999987765 78999999998887777777666679999999999998888888899999999999


Q ss_pred             cchhhccCCcHHHHHHHHHhCCC--CceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHH
Q 014486          199 CDKMLESLDMRRDVQEIFKMTPH--DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKN  276 (423)
Q Consensus       199 ~h~~~~~~~~~~~~~~~~~~~~~--~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  276 (423)
                      +|.+.+ .++...+..+...++.  ..|++++|||++.......+.+...+..+.+..... ......+.+......++.
T Consensus       246 ah~l~~-~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~-~~~~~~~~~~~~~~~~k~  323 (475)
T PRK01297        246 ADRMLD-MGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENV-ASDTVEQHVYAVAGSDKY  323 (475)
T ss_pred             HHHHHh-cccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcC-CCCcccEEEEEecchhHH
Confidence            999988 7888888888888764  579999999999998888888888776665543322 223344555666667777


Q ss_pred             HHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCC
Q 014486          277 RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIER  356 (423)
Q Consensus       277 ~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~  356 (423)
                      ..+..++......++||||++++.++.+++.|...++.+..+||++++.+|.++++.|++|++++||||+++++|+|+++
T Consensus       324 ~~l~~ll~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~  403 (475)
T PRK01297        324 KLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDG  403 (475)
T ss_pred             HHHHHHHHhcCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccC
Confidence            88888888777789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcch
Q 014486          357 VNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLI  412 (423)
Q Consensus       357 ~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (423)
                      +++||++++|.++..|+||+||+||.|+.|.+++|+++. +...+..+++.++..+
T Consensus       404 v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~-d~~~~~~~~~~~~~~~  458 (475)
T PRK01297        404 ISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGED-DAFQLPEIEELLGRKI  458 (475)
T ss_pred             CCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHH-HHHHHHHHHHHhCCCC
Confidence            999999999999999999999999999999999999854 6667888998888665

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

Probab=100.00  E-value=4.3e-59  Score=413.15  Aligned_cols=358  Identities=34%  Similarity=0.555  Sum_probs=328.1

Q ss_pred             cCCcccccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC------
Q 014486           37 KKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP------  110 (423)
Q Consensus        37 ~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~------  110 (423)
                      +.+..+-+..+|++.+++..+++.+...||..|+|+|+.++|..++++|+|..+.||||||.+|++|++..+..      
T Consensus       236 kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~  315 (673)
T KOG0333|consen  236 KGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMAR  315 (673)
T ss_pred             cCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcch
Confidence            44455556678999999999999999999999999999999999999999999999999999999999865432      


Q ss_pred             ---CCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCC
Q 014486          111 ---NPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLS  187 (423)
Q Consensus       111 ---~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~  187 (423)
                         .-.+|.++++.||++|++|+.++-.+|...+ ++++..+.||.+.+++--.+..++ +|+|+||+.|.+.+.+..+-
T Consensus       316 ~en~~~gpyaiilaptReLaqqIeeEt~kf~~~l-g~r~vsvigg~s~EEq~fqls~gc-eiviatPgrLid~Lenr~lv  393 (673)
T KOG0333|consen  316 LENNIEGPYAIILAPTRELAQQIEEETNKFGKPL-GIRTVSVIGGLSFEEQGFQLSMGC-EIVIATPGRLIDSLENRYLV  393 (673)
T ss_pred             hhhcccCceeeeechHHHHHHHHHHHHHHhcccc-cceEEEEecccchhhhhhhhhccc-eeeecCchHHHHHHHHHHHH
Confidence               2245689999999999999999999999887 799999999999998877888885 99999999999999999999


Q ss_pred             CCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCC-------------------------ceEEEEeccCCccHHHHHHH
Q 014486          188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHD-------------------------KQVMMFSATLSKEIRPVCKK  242 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~-------------------------~~~v~~SAT~~~~~~~~~~~  242 (423)
                      ++++.+||+|||+++.+ .+|...+..++..++..                         .|.+++|||+|+.+..+++.
T Consensus       394 l~qctyvvldeadrmiD-mgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~  472 (673)
T KOG0333|consen  394 LNQCTYVVLDEADRMID-MGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARS  472 (673)
T ss_pred             hccCceEeccchhhhhc-ccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHH
Confidence            99999999999999998 89999999998877641                         48999999999999999999


Q ss_pred             hccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCC
Q 014486          243 FMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGM  322 (423)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~  322 (423)
                      ++..|..+++..... ..+.+.+.....+...+...|.+++++....++|||+|+.+.++.+++.|.+.|+.+..|||+-
T Consensus       473 ylr~pv~vtig~~gk-~~~rveQ~v~m~~ed~k~kkL~eil~~~~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k  551 (673)
T KOG0333|consen  473 YLRRPVVVTIGSAGK-PTPRVEQKVEMVSEDEKRKKLIEILESNFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGK  551 (673)
T ss_pred             HhhCCeEEEeccCCC-CccchheEEEEecchHHHHHHHHHHHhCCCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCc
Confidence            999999888776654 4466778888888999999999999999889999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccH
Q 014486          323 SQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDS  398 (423)
Q Consensus       323 ~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  398 (423)
                      ++++|+.++..|++|..+|||||+++++|||+|++.+||+|++++++.+|.||+||+||+|+.|.++.|+++.+..
T Consensus       552 ~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~  627 (673)
T KOG0333|consen  552 SQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTA  627 (673)
T ss_pred             cHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchhH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999986655

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

Probab=100.00  E-value=4.4e-59  Score=394.46  Aligned_cols=367  Identities=32%  Similarity=0.524  Sum_probs=328.5

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ...|..+++++++.+.|.++|+..|+|+|..+||.++.|+|+|-+|.||||||.+|.+|+++++...+.+.-++|++||+
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            45699999999999999999999999999999999999999999999999999999999999999999988999999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC----CCCCCccEEEEcCcc
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD----LSLKNVRHFILDECD  200 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~----~~~~~~~~vVvDE~h  200 (423)
                      +||.|+.+.|....... ++++.+++||.+.-.+...+... |+++|+||+++..++....    +.+.+++++|+|||+
T Consensus        86 ELA~QiaEQF~alGk~l-~lK~~vivGG~d~i~qa~~L~~r-PHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEAD  163 (442)
T KOG0340|consen   86 ELALQIAEQFIALGKLL-NLKVSVIVGGTDMIMQAAILSDR-PHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEAD  163 (442)
T ss_pred             HHHHHHHHHHHHhcccc-cceEEEEEccHHHhhhhhhcccC-CCeEecCccccccccccCCccchhhhhceeeEEecchh
Confidence            99999999998887665 89999999999888777777666 6999999999999887652    447889999999999


Q ss_pred             hhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeec-cccccccccceEEEEEeChHHHHHHH
Q 014486          201 KMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVD-DEAKLTLHGLVQHYIKLSELEKNRKL  279 (423)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l  279 (423)
                      ++++ ..|...+..+...+|..+|.+++|||+...+......-...+..+... ..+......+.+.|+.++...+...+
T Consensus       164 rvL~-~~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~vkdaYL  242 (442)
T KOG0340|consen  164 RVLA-GCFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDVKDAYL  242 (442)
T ss_pred             hhhc-cchhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhhhHHHH
Confidence            9998 799999999999999999999999999988766544333332222222 23445566777888999999998888


Q ss_pred             HHHHHhh---cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCC
Q 014486          280 NDLLDAL---DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIER  356 (423)
Q Consensus       280 ~~ll~~~---~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~  356 (423)
                      ..++...   +.+.++||+++..+++.++..|+..++.+..+||.|++.+|...+.+|+.+..+|||||+++++|+|+|.
T Consensus       243 v~~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~  322 (442)
T KOG0340|consen  243 VHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPT  322 (442)
T ss_pred             HHHHhhhhhccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCc
Confidence            8888654   3578999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhhh
Q 014486          357 VNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSF  415 (423)
Q Consensus       357 ~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (423)
                      +..||+++.|.+|.+|+||+||+.|+|..|.++.|+. ..+.+.+..|++..|..++..
T Consensus       323 V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt-~rDv~l~~aiE~~igkKl~e~  380 (442)
T KOG0340|consen  323 VELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVT-QRDVELLQAIEEEIGKKLTEY  380 (442)
T ss_pred             eeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEec-hhhHHHHHHHHHHHhcccccc
Confidence            9999999999999999999999999999999999999 678889999999999888754

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=7.9e-59  Score=413.74  Aligned_cols=358  Identities=28%  Similarity=0.512  Sum_probs=331.3

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC----CCCeEEEEEe
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN----PGQVTALVLC  121 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~----~~~~~~lil~  121 (423)
                      ..|.+|+++....+.|.+.+|..|+.+|+++||..++|++++-++.||||||++|++|+++.+...    ..+..||||+
T Consensus        69 ~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIIS  148 (758)
T KOG0343|consen   69 KKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIIS  148 (758)
T ss_pred             hhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEec
Confidence            469999999999999999999999999999999999999999999999999999999999876432    2455799999


Q ss_pred             cChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC-CCCCCCccEEEEcCcc
Q 014486          122 HTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK-DLSLKNVRHFILDECD  200 (423)
Q Consensus       122 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~-~~~~~~~~~vVvDE~h  200 (423)
                      |||+||.|+++.+.+.+... ++..+.+.||.+...+...+..  .+|+||||++|+.++... .+.-.++.++|+|||+
T Consensus       149 PTRELA~QtFevL~kvgk~h-~fSaGLiiGG~~~k~E~eRi~~--mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEAD  225 (758)
T KOG0343|consen  149 PTRELALQTFEVLNKVGKHH-DFSAGLIIGGKDVKFELERISQ--MNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEAD  225 (758)
T ss_pred             chHHHHHHHHHHHHHHhhcc-ccccceeecCchhHHHHHhhhc--CCeEEechHHHHHHhhhcCCCCCCcceEEEeccHH
Confidence            99999999999999998886 8999999999998877776655  499999999999988654 5677899999999999


Q ss_pred             hhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeecccc-ccccccceEEEEEeChHHHHHHH
Q 014486          201 KMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEA-KLTLHGLVQHYIKLSELEKNRKL  279 (423)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l  279 (423)
                      ++++ ++|...+..|...+|+.+|.+++|||.+..+.++++..+.+|..+.+.... ...+..+.+.|+.++..+|+..|
T Consensus       226 R~LD-MGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki~~L  304 (758)
T KOG0343|consen  226 RMLD-MGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLEDKIDML  304 (758)
T ss_pred             HHHH-HhHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEehhhHHHHH
Confidence            9999 999999999999999999999999999999999999999999998877444 56667788899999999999999


Q ss_pred             HHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC--CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCC
Q 014486          280 NDLLDALDFNQVVIFVKSVSRAAELNKLLVEC--NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV  357 (423)
Q Consensus       280 ~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~  357 (423)
                      ..+++.+...++|||+.+.+++..++..+.+.  |++...+||.|++..|..++..|...+.-||+||+++++|+|+|.+
T Consensus       305 ~sFI~shlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaV  384 (758)
T KOG0343|consen  305 WSFIKSHLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAV  384 (758)
T ss_pred             HHHHHhccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCccc
Confidence            99999999999999999999999999999876  8899999999999999999999999999999999999999999999


Q ss_pred             CEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHH
Q 014486          358 NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF  407 (423)
Q Consensus       358 ~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~  407 (423)
                      +.||++|+|.++.+|+||+||+.|.+..|.++++..+.++..++..|++.
T Consensus       385 dwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~~l~~Lq~k  434 (758)
T KOG0343|consen  385 DWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEEEAMLKKLQKK  434 (758)
T ss_pred             ceEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhHHHHHHHHHHc
Confidence            99999999999999999999999999999999999998888888888876

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=5.5e-57  Score=425.21  Aligned_cols=366  Identities=38%  Similarity=0.649  Sum_probs=317.2

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ..+|+++++++.+.++|.+.||..|+|+|.++++.++.++++++.+|||+|||++|+++++..+.....+.++||++|++
T Consensus        27 ~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~  106 (401)
T PTZ00424         27 VDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTR  106 (401)
T ss_pred             cCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCH
Confidence            46799999999999999999999999999999999999999999999999999999999998876555556899999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      +|+.|+.+.+..+.... .+.+....|+.....+...+..+ ++|+|+||+++...+......+.++++||+||+|.+.+
T Consensus       107 ~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~  184 (401)
T PTZ00424        107 ELAQQIQKVVLALGDYL-KVRCHACVGGTVVRDDINKLKAG-VHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLS  184 (401)
T ss_pred             HHHHHHHHHHHHHhhhc-CceEEEEECCcCHHHHHHHHcCC-CCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHHh
Confidence            99999999998887654 67788888888877777666666 59999999999998888888899999999999999987


Q ss_pred             cCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeCh-HHHHHHHHHHH
Q 014486          205 SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE-LEKNRKLNDLL  283 (423)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~ll  283 (423)
                       .++...+..++..+++..|++++|||+|+........++..+..+...... .....+...+..... ..+...+..++
T Consensus       185 -~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~  262 (401)
T PTZ00424        185 -RGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDE-LTLEGIRQFYVAVEKEEWKFDTLCDLY  262 (401)
T ss_pred             -cchHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCC-cccCCceEEEEecChHHHHHHHHHHHH
Confidence             678888888999999999999999999998888877777777655443322 223334444444433 33556667777


Q ss_pred             HhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEc
Q 014486          284 DALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINY  363 (423)
Q Consensus       284 ~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~  363 (423)
                      ......++||||+++++++.+++.|...++.+..+||++++.+|..+++.|++|+++|||||+++++|+|+|++++||++
T Consensus       263 ~~~~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~  342 (401)
T PTZ00424        263 ETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINY  342 (401)
T ss_pred             HhcCCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEE
Confidence            76677899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhhh
Q 014486          364 DMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSF  415 (423)
Q Consensus       364 ~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (423)
                      ++|.+...|.||+||+||.|+.|.++.++++ .+...+..+++.+...++..
T Consensus       343 ~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~-~~~~~~~~~e~~~~~~~~~~  393 (401)
T PTZ00424        343 DLPASPENYIHRIGRSGRFGRKGVAINFVTP-DDIEQLKEIERHYNTQIEEM  393 (401)
T ss_pred             CCCCCHHHEeecccccccCCCCceEEEEEcH-HHHHHHHHHHHHHCCccccc
Confidence            9999999999999999999999999999975 56778888898888776653

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

Probab=100.00  E-value=9.6e-60  Score=381.30  Aligned_cols=371  Identities=75%  Similarity=1.180  Sum_probs=345.0

Q ss_pred             hhhhccccccccccCCCc-cccccccccccCCcccccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceE
Q 014486            9 YEDELLDYEEEDAQAPDS-VATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVI   87 (423)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~i   87 (423)
                      .++|+.|+++++++..+. ++.+...+..+..+.+++++.|++|.+.|++++++.+.||++|...|.++||...-|-+++
T Consensus         4 ~e~dlldyeeeee~~~~~~~~~~~~~~d~kgsyv~ihssgfrdfllkpellraivdcgfehpsevqhecipqailgmdvl   83 (387)
T KOG0329|consen    4 VEEDLLDYEEEEEEQADQESAPAGPKKDKKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVL   83 (387)
T ss_pred             hhhhhhcccccccccCCccCCCCCccccccCcEEEEeccchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhh
Confidence            567788887777665553 4444555567778999999999999999999999999999999999999999999999999


Q ss_pred             EEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCC
Q 014486           88 CQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP  167 (423)
Q Consensus        88 i~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (423)
                      +.|..|.|||.+|+++.++++.+..+...+|++|.||+||-|+..++.+|.++.|++++.+++||.++......+.+ +|
T Consensus        84 cqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~-~P  162 (387)
T KOG0329|consen   84 CQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKN-CP  162 (387)
T ss_pred             eecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhC-CC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988 68


Q ss_pred             cEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCC
Q 014486          168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDP  247 (423)
Q Consensus       168 ~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~  247 (423)
                      +|+|+||++++.+.++..+++++++..|+|||+.++++.+.++.++.+++..|...|++.+|||++++++..++.++.+|
T Consensus       163 hivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~lDMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdP  242 (387)
T KOG0329|consen  163 HIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDP  242 (387)
T ss_pred             eEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHHHHHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCc
Confidence            99999999999999999999999999999999999998999999999999999999999999999999999999999999


Q ss_pred             ceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHH
Q 014486          248 MEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEER  327 (423)
Q Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r  327 (423)
                      .+++++.+.+.....+.++|+...+.+|+..+.+++..+..+.++||+.+...       |              +    
T Consensus       243 mEi~vDdE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~LeFNQVvIFvKsv~R-------l--------------~----  297 (387)
T KOG0329|consen  243 MEIFVDDEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVLEFNQVVIFVKSVQR-------L--------------S----  297 (387)
T ss_pred             hhhhccchhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhhhhcceeEeeehhhh-------h--------------h----
Confidence            99999999999999999999999999999999999999999999999988765       0              0    


Q ss_pred             HHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHH
Q 014486          328 LTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF  407 (423)
Q Consensus       328 ~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~  407 (423)
                            |   ..+ +|+|+..++|+|+.+++.+++||.|.+..+|.||+|||||.|.+|.++.|++...+..+++.++..
T Consensus       298 ------f---~kr-~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdR  367 (387)
T KOG0329|consen  298 ------F---QKR-LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNPVQDR  367 (387)
T ss_pred             ------h---hhh-hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHHHhchhhHh
Confidence                  2   123 899999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             Hhcchhhh
Q 014486          408 MFLLIGSF  415 (423)
Q Consensus       408 ~~~~~~~~  415 (423)
                      +...+..+
T Consensus       368 f~v~i~eL  375 (387)
T KOG0329|consen  368 FEVNIKEL  375 (387)
T ss_pred             hhccHhhc
Confidence            88877654

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

Probab=100.00  E-value=1.4e-57  Score=392.16  Aligned_cols=368  Identities=30%  Similarity=0.507  Sum_probs=329.6

Q ss_pred             ccccCCCCc-CCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC------CCC
Q 014486           41 VGIHSSGFR-DFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP------NPG  113 (423)
Q Consensus        41 ~~~~~~~~~-~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~------~~~  113 (423)
                      .+.+.++|+ .|...+++.+++.+.||..|+|+|.++||.+++|++++..+.||+|||++|++|.+.++..      ...
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            455566775 4667799999999999999999999999999999999999999999999999998866543      335


Q ss_pred             CeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccE
Q 014486          114 QVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRH  193 (423)
Q Consensus       114 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~  193 (423)
                      ++.+|+++||++|+.|+.-++.++..  .+.+..+++||.+..++...+..+ .+|+++||++|.++.-.+..++..+.+
T Consensus       294 ~p~~lvl~ptreLalqie~e~~kysy--ng~ksvc~ygggnR~eqie~lkrg-veiiiatPgrlndL~~~n~i~l~siTY  370 (629)
T KOG0336|consen  294 GPGVLVLTPTRELALQIEGEVKKYSY--NGLKSVCVYGGGNRNEQIEDLKRG-VEIIIATPGRLNDLQMDNVINLASITY  370 (629)
T ss_pred             CCceEEEeccHHHHHHHHhHHhHhhh--cCcceEEEecCCCchhHHHHHhcC-ceEEeeCCchHhhhhhcCeeeeeeeEE
Confidence            56899999999999999988887753  388999999999999999999888 699999999999999999999999999


Q ss_pred             EEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChH
Q 014486          194 FILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEL  273 (423)
Q Consensus       194 vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  273 (423)
                      +|+|||+++++ ++|.+.+++++-..++++|+++.|||+|..+..++..++..|..+++..........+.+.++...+.
T Consensus       371 lVlDEADrMLD-MgFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i~v~~d~  449 (629)
T KOG0336|consen  371 LVLDEADRMLD-MGFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNIIVTTDS  449 (629)
T ss_pred             EEecchhhhhc-ccccHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeEEecccH
Confidence            99999999999 99999999999999999999999999999999999999999999988877766666677777777778


Q ss_pred             HHHHHHHHHHHhh-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCC
Q 014486          274 EKNRKLNDLLDAL-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGI  352 (423)
Q Consensus       274 ~~~~~l~~ll~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gl  352 (423)
                      ++...+..++++. ...|+||||..+..|+.+...|.-.|+....+||+-.+.+|+..+..|+.|+++|||+|+.+++|+
T Consensus       450 ~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGl  529 (629)
T KOG0336|consen  450 EKLEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGL  529 (629)
T ss_pred             HHHHHHHHHHHhcCCCceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCC
Confidence            8888888888776 457999999999999999999998899999999999999999999999999999999999999999


Q ss_pred             CCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchh
Q 014486          353 DIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIG  413 (423)
Q Consensus       353 d~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  413 (423)
                      |+++++||++||.|.+++.|+||+||+||+|.+|..+.|+. ..+-.+...|-+.|..+-+
T Consensus       530 Dv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt-~~D~~~a~eLI~ILe~aeQ  589 (629)
T KOG0336|consen  530 DVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLT-RNDWSMAEELIQILERAEQ  589 (629)
T ss_pred             CchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEEe-hhhHHHHHHHHHHHHHhhh
Confidence            99999999999999999999999999999999999999987 4555666666666654433

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

Probab=100.00  E-value=2.2e-57  Score=406.78  Aligned_cols=365  Identities=34%  Similarity=0.556  Sum_probs=324.5

Q ss_pred             ccccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC--------
Q 014486           41 VGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP--------  112 (423)
Q Consensus        41 ~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~--------  112 (423)
                      .+.+...|.+-.+.+.+..+++..++..|+|+|+.+||.+..|++++++|+||||||.+|++|++..+...+        
T Consensus        69 ~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~  148 (482)
T KOG0335|consen   69 VPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESG  148 (482)
T ss_pred             cCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccC
Confidence            334444788778888999999999999999999999999999999999999999999999999998765432        


Q ss_pred             --CCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCC
Q 014486          113 --GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKN  190 (423)
Q Consensus       113 --~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~  190 (423)
                        ..|.++|++||++|+.|++++.+++.... .+++..++||.+...+...+..++ +|+|+||++|.++++...+.+.+
T Consensus       149 ~~~~P~~lIlapTReL~~Qi~nea~k~~~~s-~~~~~~~ygg~~~~~q~~~~~~gc-dIlvaTpGrL~d~~e~g~i~l~~  226 (482)
T KOG0335|consen  149 GGVYPRALILAPTRELVDQIYNEARKFSYLS-GMKSVVVYGGTDLGAQLRFIKRGC-DILVATPGRLKDLIERGKISLDN  226 (482)
T ss_pred             CCCCCceEEEeCcHHHhhHHHHHHHhhcccc-cceeeeeeCCcchhhhhhhhccCc-cEEEecCchhhhhhhcceeehhh
Confidence              35799999999999999999999997665 889999999999999999898885 99999999999999999999999


Q ss_pred             ccEEEEcCcchhhccCCcHHHHHHHHHhCCC----CceEEEEeccCCccHHHHHHHhccC-CceeeeccccccccccceE
Q 014486          191 VRHFILDECDKMLESLDMRRDVQEIFKMTPH----DKQVMMFSATLSKEIRPVCKKFMQD-PMEIYVDDEAKLTLHGLVQ  265 (423)
Q Consensus       191 ~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~----~~~~v~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  265 (423)
                      ++++|+|||+++++..+|.+.++.+......    ..|.+++|||.|..+...+..++.+ ...+.+.. .......+.+
T Consensus       227 ~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~r-vg~~~~ni~q  305 (482)
T KOG0335|consen  227 CKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGR-VGSTSENITQ  305 (482)
T ss_pred             CcEEEecchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEee-ecccccccee
Confidence            9999999999999988999999999987754    6899999999999999887777776 33333333 3345577788


Q ss_pred             EEEEeChHHHHHHHHHHHHhhc----CC-----cEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhc
Q 014486          266 HYIKLSELEKNRKLNDLLDALD----FN-----QVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKE  336 (423)
Q Consensus       266 ~~~~~~~~~~~~~l~~ll~~~~----~~-----~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~  336 (423)
                      ....+.+..|...+.+++....    .+     +++|||.+++.+..+...|...++++..+||.-++.+|.+.++.|+.
T Consensus       306 ~i~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~  385 (482)
T KOG0335|consen  306 KILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRN  385 (482)
T ss_pred             EeeeecchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhc
Confidence            8888999999999999987554    23     79999999999999999999999999999999999999999999999


Q ss_pred             CCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHh
Q 014486          337 GNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       337 ~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                      |+..+||||+++++|+|+|+|+|||+||+|.+..+|+||+||+||.|+.|.++.|++ .......+.|.+.|.
T Consensus       386 g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n-~~~~~i~~~L~~~l~  457 (482)
T KOG0335|consen  386 GKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFN-EKNQNIAKALVEILT  457 (482)
T ss_pred             CCcceEEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEec-cccchhHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999998 556666666666665

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

Probab=100.00  E-value=1.2e-56  Score=398.39  Aligned_cols=366  Identities=29%  Similarity=0.489  Sum_probs=312.4

Q ss_pred             cccCCCCcCCCCCHHHHHHHHhC-CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC------CCCC
Q 014486           42 GIHSSGFRDFLLKPELLRAIVDS-GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP------NPGQ  114 (423)
Q Consensus        42 ~~~~~~~~~~~l~~~~~~~l~~~-~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~------~~~~  114 (423)
                      ++.+..|..+++++.+.+.|+.. ++..||.+|+++||.++.|+|++|.++||||||++|++|+++.+..      ...+
T Consensus       132 ~fts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G  211 (708)
T KOG0348|consen  132 PFTSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDG  211 (708)
T ss_pred             ccccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCC
Confidence            34567899999999999999974 9999999999999999999999999999999999999999986532      3355


Q ss_pred             eEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC-CCCCCCccE
Q 014486          115 VTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK-DLSLKNVRH  193 (423)
Q Consensus       115 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~-~~~~~~~~~  193 (423)
                      +-+||++|||+||.|+++.++++.+.+.-+-.+++.||.....+...+.+|+ +|+|+||++|++++.+. .+.++.+++
T Consensus       212 ~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGi-NILIgTPGRLvDHLknT~~i~~s~LRw  290 (708)
T KOG0348|consen  212 PYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGI-NILIGTPGRLVDHLKNTKSIKFSRLRW  290 (708)
T ss_pred             ceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCc-eEEEcCchHHHHHHhccchheeeeeeE
Confidence            6899999999999999999999987776677788999999998999999995 99999999999988764 577899999


Q ss_pred             EEEcCcchhhccCCcHHHHHHHHHhCC-------------CCceEEEEeccCCccHHHHHHHhccCCceeeecccc----
Q 014486          194 FILDECDKMLESLDMRRDVQEIFKMTP-------------HDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEA----  256 (423)
Q Consensus       194 vVvDE~h~~~~~~~~~~~~~~~~~~~~-------------~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~----  256 (423)
                      ||+||+|++++ .+|...+..|++.+.             +..|.+++|||+...+..+....+.+|..+..+...    
T Consensus       291 lVlDEaDrlle-LGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~  369 (708)
T KOG0348|consen  291 LVLDEADRLLE-LGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLN  369 (708)
T ss_pred             EEecchhHHHh-ccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcC
Confidence            99999999999 899999988887662             235789999999999999998888888877622110    


Q ss_pred             --------------------ccccccceEEEEEeChHHHHHHHHHHHHhh----cCCcEEEEEcChhhHHHHHHHHHhC-
Q 014486          257 --------------------KLTLHGLVQHYIKLSELEKNRKLNDLLDAL----DFNQVVIFVKSVSRAAELNKLLVEC-  311 (423)
Q Consensus       257 --------------------~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~----~~~~~ivf~~~~~~~~~l~~~L~~~-  311 (423)
                                          ...++.+.+++..++..-+...+..+|.+.    ...++|||+.+.+.++.-+..|... 
T Consensus       370 p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l  449 (708)
T KOG0348|consen  370 PKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEAL  449 (708)
T ss_pred             cchhhhhhcCCcccccccccccCcHHhhhceEecCCchhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhh
Confidence                                122334556677777776666666665443    5578999999999998888877551 


Q ss_pred             ---------------------CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcc
Q 014486          312 ---------------------NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSAD  370 (423)
Q Consensus       312 ---------------------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~  370 (423)
                                           +.+...+||+|++.+|..++..|...+..||+||+++++|+|+|++++||.|++|.++.
T Consensus       450 ~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~a  529 (708)
T KOG0348|consen  450 LSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTA  529 (708)
T ss_pred             hcccccccCCcccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHH
Confidence                                 34677899999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhc
Q 014486          371 TYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFL  410 (423)
Q Consensus       371 ~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (423)
                      +|+||+||+.|+|.+|.+++|..|.+.. +++.++++-.+
T Consensus       530 dylHRvGRTARaG~kG~alLfL~P~Eae-y~~~l~~~~~~  568 (708)
T KOG0348|consen  530 DYLHRVGRTARAGEKGEALLFLLPSEAE-YVNYLKKHHIM  568 (708)
T ss_pred             HHHHHhhhhhhccCCCceEEEecccHHH-HHHHHHhhcch
Confidence            9999999999999999999999986555 88888877654

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=3.1e-56  Score=387.03  Aligned_cols=361  Identities=30%  Similarity=0.473  Sum_probs=319.9

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC------CCCCeEEEE
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP------NPGQVTALV  119 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~------~~~~~~~li  119 (423)
                      .+|++|++++++++++.+.|+..|+-+|..+||.++.|+|++..|.||||||.+|++|+++.+..      ...++.++|
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            47999999999999999999999999999999999999999999999999999999999986543      345578999


Q ss_pred             EecChHHHHHHHHHHHHHhccCC-CceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC-CCCCCccEEEEc
Q 014486          120 LCHTRELAYQICHEFERFSTYLP-DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD-LSLKNVRHFILD  197 (423)
Q Consensus       120 l~P~~~L~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~-~~~~~~~~vVvD  197 (423)
                      ++||++||+|++..+.++..+++ .+++..+....+.......+ .+.|+|+|+||.+++.++..+. ..+..+.++|+|
T Consensus        99 LvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L-~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvD  177 (569)
T KOG0346|consen   99 LVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVAL-MDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVD  177 (569)
T ss_pred             EechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHH-ccCCCeEEeChHHHHHHHhhccchhhhheeeEEec
Confidence            99999999999999998877664 56666666555555444334 3447999999999999988776 667889999999


Q ss_pred             CcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHH
Q 014486          198 ECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNR  277 (423)
Q Consensus       198 E~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  277 (423)
                      |||.++. .++...+.++...+|+..|.++||||+..++..+-+.++.+|..+.+..........+.++.+.+.+.+|..
T Consensus       178 EADLlls-fGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cse~DKfl  256 (569)
T KOG0346|consen  178 EADLLLS-FGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCSEEDKFL  256 (569)
T ss_pred             hhhhhhh-cccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEeccchhHH
Confidence            9999998 999999999999999999999999999999999999999999998888777777788889999999999988


Q ss_pred             HHHHHHHh-hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcC----------
Q 014486          278 KLNDLLDA-LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD----------  346 (423)
Q Consensus       278 ~l~~ll~~-~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~----------  346 (423)
                      .+..+++- +-.++.|||+|+++.+..+.-.|...|++.++++|.++...|.-++.+|+.|-.+++|||+          
T Consensus       257 llyallKL~LI~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~ee  336 (569)
T KOG0346|consen  257 LLYALLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEE  336 (569)
T ss_pred             HHHHHHHHHHhcCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhc
Confidence            88888764 3568999999999999999999999999999999999999999999999999999999998          


Q ss_pred             -------------------------ccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHH
Q 014486          347 -------------------------LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDIL  401 (423)
Q Consensus       347 -------------------------~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~  401 (423)
                                               -.++|||+.++.+|++||+|.++..|+||+||++|++++|.++.|+.+.++.. .
T Consensus       337 e~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~g-~  415 (569)
T KOG0346|consen  337 EVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEFG-K  415 (569)
T ss_pred             cccccccccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHhh-h
Confidence                                     24689999999999999999999999999999999999999999999866553 2


Q ss_pred             HHHHHHHh
Q 014486          402 NQVSKFMF  409 (423)
Q Consensus       402 ~~~~~~~~  409 (423)
                      ..+++.+.
T Consensus       416 ~~le~~~~  423 (569)
T KOG0346|consen  416 ESLESILK  423 (569)
T ss_pred             hHHHHHHh
Confidence            45554443

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

Probab=100.00  E-value=2e-55  Score=374.56  Aligned_cols=361  Identities=32%  Similarity=0.563  Sum_probs=322.3

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccC--CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG--MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~--~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      .+|+++.|+|++++.|+.++|..|+.+|..++|.++..  ++.|.++..|+|||.+|.+.++.+....-..|.++.|+|+
T Consensus        90 ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaPt  169 (477)
T KOG0332|consen   90 KSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPT  169 (477)
T ss_pred             ccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceeeCch
Confidence            47999999999999999999999999999999999985  7799999999999999999999999988888899999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhc-CCCCCCCccEEEEcCcchh
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARD-KDLSLKNVRHFILDECDKM  202 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~-~~~~~~~~~~vVvDE~h~~  202 (423)
                      ++||.|+.+.+.+++++. +++..+..-+.....-. .+   ..+|+++||+.+.++... ....+..++++|+|||+.+
T Consensus       170 rELA~Q~~eVv~eMGKf~-~ita~yair~sk~~rG~-~i---~eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~M  244 (477)
T KOG0332|consen  170 RELAPQTGEVVEEMGKFT-ELTASYAIRGSKAKRGN-KL---TEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVM  244 (477)
T ss_pred             HHHHHHHHHHHHHhcCce-eeeEEEEecCcccccCC-cc---hhheeeCCCccHHHHHHHHHhhChhhceEEEecchhhh
Confidence            999999999999998887 77777666554211111 11   138999999999998776 6678899999999999999


Q ss_pred             hccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeC-hHHHHHHHHH
Q 014486          203 LESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS-ELEKNRKLND  281 (423)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~  281 (423)
                      .+..+|...-.++...+++..|++++|||....+..++.....++..+.+..+. .....+.+.++.+. ..+|...+.+
T Consensus       245 i~tqG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~ee-l~L~~IkQlyv~C~~~~~K~~~l~~  323 (477)
T KOG0332|consen  245 IDTQGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNANVIILKREE-LALDNIKQLYVLCACRDDKYQALVN  323 (477)
T ss_pred             hhcccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCceeeeehhh-ccccchhhheeeccchhhHHHHHHH
Confidence            998889999999999999999999999999999999999999988877776654 34556666666665 4567788888


Q ss_pred             HHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEE
Q 014486          282 LLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVI  361 (423)
Q Consensus       282 ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi  361 (423)
                      +.....-+..||||.++..|.+++..+...|..+..+||++...+|..+++.|+.|..+|||+|++++||+|++.++.||
T Consensus       324 lyg~~tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~Vv  403 (477)
T KOG0332|consen  324 LYGLLTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVV  403 (477)
T ss_pred             HHhhhhhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcccccceEEEEE
Confidence            77766778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EccCCC------CcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcch
Q 014486          362 NYDMPD------SADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLI  412 (423)
Q Consensus       362 ~~~~~~------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (423)
                      +||+|-      +++.|+||+||+||.|++|.++.+++..+...+++.|+++++..+
T Consensus       404 NydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~~~i  460 (477)
T KOG0332|consen  404 NYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIMNKIQKHFNMKI  460 (477)
T ss_pred             ecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHHHHHHHHHHHhhcc
Confidence            999996      788999999999999999999999999999999999999998654

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.7e-55  Score=392.37  Aligned_cols=362  Identities=31%  Similarity=0.535  Sum_probs=296.1

Q ss_pred             ccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccC-CceEEEccCCCcchhHHHHHHhhccCCCC---------
Q 014486           43 IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFVLSTLQQTEPNP---------  112 (423)
Q Consensus        43 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~-~~~ii~~~tGsGKT~~~~~~~~~~~~~~~---------  112 (423)
                      .+.+-|..|+++..++.+|..+||..|+++|...+|....| .|++-.|.||||||++|-+|+++.+...+         
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            34456999999999999999999999999999999999998 78999999999999999999999554322         


Q ss_pred             --CCeE--EEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCC--
Q 014486          113 --GQVT--ALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDL--  186 (423)
Q Consensus       113 --~~~~--~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~--  186 (423)
                        .+++  +||++|||+||.|+.+-+...... +++++..++||.....+.+.+.. +|+|+|+||++|+.++.....  
T Consensus       258 ~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~-t~i~v~si~GGLavqKQqRlL~~-~p~IVVATPGRlweli~e~n~~l  335 (731)
T KOG0347|consen  258 SAKYVKPIALVVTPTRELAHQVKQHLKAIAEK-TQIRVASITGGLAVQKQQRLLNQ-RPDIVVATPGRLWELIEEDNTHL  335 (731)
T ss_pred             HhccCcceeEEecChHHHHHHHHHHHHHhccc-cCeEEEEeechhHHHHHHHHHhc-CCCEEEecchHHHHHHHhhhhhh
Confidence              2234  999999999999999999888776 59999999999999998888877 589999999999999987654  


Q ss_pred             -CCCCccEEEEcCcchhhccCCcHHHHHHHHHhCC-----CCceEEEEeccCCccH---------------------HHH
Q 014486          187 -SLKNVRHFILDECDKMLESLDMRRDVQEIFKMTP-----HDKQVMMFSATLSKEI---------------------RPV  239 (423)
Q Consensus       187 -~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~-----~~~~~v~~SAT~~~~~---------------------~~~  239 (423)
                       .+.+++++|+||+|++.+ .+.-..+..+++.+.     ...|.+.+|||+.-..                     ..+
T Consensus       336 ~~~k~vkcLVlDEaDRmve-kghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~L  414 (731)
T KOG0347|consen  336 GNFKKVKCLVLDEADRMVE-KGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHL  414 (731)
T ss_pred             hhhhhceEEEEccHHHHhh-hccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHH
Confidence             578899999999999998 566677777776665     3679999999984221                     112


Q ss_pred             HHH--hccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEE
Q 014486          240 CKK--FMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSIC  317 (423)
Q Consensus       240 ~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~  317 (423)
                      ++.  +...|..+...... .....+....+.++..+|...+..++..++ +++|||||+++.+.++.-.|...+++...
T Consensus       415 mk~ig~~~kpkiiD~t~q~-~ta~~l~Es~I~C~~~eKD~ylyYfl~ryP-GrTlVF~NsId~vKRLt~~L~~L~i~p~~  492 (731)
T KOG0347|consen  415 MKKIGFRGKPKIIDLTPQS-ATASTLTESLIECPPLEKDLYLYYFLTRYP-GRTLVFCNSIDCVKRLTVLLNNLDIPPLP  492 (731)
T ss_pred             HHHhCccCCCeeEecCcch-hHHHHHHHHhhcCCccccceeEEEEEeecC-CceEEEechHHHHHHHHHHHhhcCCCCch
Confidence            221  22233333322221 122223333444555555555555665555 78999999999999999999999999999


Q ss_pred             EcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          318 IHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       318 ~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      +|+.|.+.+|...+++|++....|||||++++||+|+|++.|||||-.|++..-|+||.||+.|++..|..++++.|.+ 
T Consensus       493 LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e-  571 (731)
T KOG0347|consen  493 LHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQE-  571 (731)
T ss_pred             hhHHHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeChHH-
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999865 


Q ss_pred             HHHHHHHHHHHhc
Q 014486          398 SDILNQVSKFMFL  410 (423)
Q Consensus       398 ~~~~~~~~~~~~~  410 (423)
                      ..-+..|.+-|+.
T Consensus       572 ~~~~~KL~ktL~k  584 (731)
T KOG0347|consen  572 VGPLKKLCKTLKK  584 (731)
T ss_pred             hHHHHHHHHHHhh
Confidence            5555555555553

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

Probab=100.00  E-value=1.2e-55  Score=377.82  Aligned_cols=361  Identities=30%  Similarity=0.550  Sum_probs=319.2

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccC--------CCCCCeE
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTE--------PNPGQVT  116 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~--------~~~~~~~  116 (423)
                      ..+|.+.-++..+++.|++.|+.+|+|+|.+.+|-+++|++.|-.+-||||||++|.+|++....        ..+.+|-
T Consensus       169 IksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~  248 (610)
T KOG0341|consen  169 IKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPY  248 (610)
T ss_pred             hhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCe
Confidence            35788899999999999999999999999999999999999999999999999999998875321        2345668


Q ss_pred             EEEEecChHHHHHHHHHHHHHhcc-----CCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCc
Q 014486          117 ALVLCHTRELAYQICHEFERFSTY-----LPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNV  191 (423)
Q Consensus       117 ~lil~P~~~L~~q~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~  191 (423)
                      .||+||+|+||.|.++.+..+...     +|.++.....||....++.+....+ .+|+|+||++|.+++......+.-+
T Consensus       249 gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~G-vHivVATPGRL~DmL~KK~~sLd~C  327 (610)
T KOG0341|consen  249 GLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRG-VHIVVATPGRLMDMLAKKIMSLDAC  327 (610)
T ss_pred             eEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcC-eeEEEcCcchHHHHHHHhhccHHHH
Confidence            999999999999999999887543     3678888999999999999999998 5999999999999999999999999


Q ss_pred             cEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeC
Q 014486          192 RHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS  271 (423)
Q Consensus       192 ~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  271 (423)
                      +++.+|||+++.+ .+|...++.++..+...+|.+++|||+|..+..+++..+-.|..+.+..-...... +.+....+.
T Consensus       328 RyL~lDEADRmiD-mGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsld-ViQevEyVk  405 (610)
T KOG0341|consen  328 RYLTLDEADRMID-MGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLD-VIQEVEYVK  405 (610)
T ss_pred             HHhhhhhHHHHhh-ccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEEecccccccchh-HHHHHHHHH
Confidence            9999999999999 99999999999999999999999999999999999999999998887665554432 222223344


Q ss_pred             hHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccC
Q 014486          272 ELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRG  351 (423)
Q Consensus       272 ~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~G  351 (423)
                      ...|...+.+.|.... .+++|||.....++.++++|--.|..++.+||+-.+.+|...+..|+.|+-+|||+|++++.|
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            4555555665555443 589999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHh
Q 014486          352 IDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       352 ld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                      +|+|++.|||+||.|..+..|+||+||+||.|++|.+..|++...+...+..+...+.
T Consensus       485 LDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~~~esvLlDLK~LL~  542 (610)
T KOG0341|consen  485 LDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKNQEESVLLDLKHLLQ  542 (610)
T ss_pred             CCCccchhhccCCChHHHHHHHHHhcccCCCCCcceeeeeecccchHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999888877777766554

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

Probab=100.00  E-value=5.5e-52  Score=366.49  Aligned_cols=350  Identities=33%  Similarity=0.506  Sum_probs=315.3

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC-----CCCCeEEEE
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP-----NPGQVTALV  119 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-----~~~~~~~li  119 (423)
                      .++|+.++++..+..++.+..|.+|+|+|.+++|..+.|++++-.|.||||||.+|+.|++.+...     .+.+|..||
T Consensus       222 vtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vi  301 (731)
T KOG0339|consen  222 VTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVI  301 (731)
T ss_pred             cchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEE
Confidence            357999999999999999999999999999999999999999999999999999999999876543     245679999


Q ss_pred             EecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCc
Q 014486          120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDEC  199 (423)
Q Consensus       120 l~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~  199 (423)
                      ++||++||.|+..++++|++.+ ++++..++||.+.-++.+.+..+ +.|+||||++|.+++.-...++.++.++|+||+
T Consensus       302 lvPTrela~Qi~~eaKkf~K~y-gl~~v~~ygGgsk~eQ~k~Lk~g-~EivVaTPgRlid~VkmKatn~~rvS~LV~DEa  379 (731)
T KOG0339|consen  302 LVPTRELASQIFSEAKKFGKAY-GLRVVAVYGGGSKWEQSKELKEG-AEIVVATPGRLIDMVKMKATNLSRVSYLVLDEA  379 (731)
T ss_pred             EeccHHHHHHHHHHHHHhhhhc-cceEEEeecCCcHHHHHHhhhcC-CeEEEechHHHHHHHHhhcccceeeeEEEEech
Confidence            9999999999999999998888 99999999999999999999966 699999999999999999999999999999999


Q ss_pred             chhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEe-ChHHHHHH
Q 014486          200 DKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL-SELEKNRK  278 (423)
Q Consensus       200 h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~  278 (423)
                      +++.+ .+|...++.|....++.+|.+++|||++..+..+++.++..|+.++........ ..+.+....+ .+..|...
T Consensus       380 drmfd-mGfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean-~dITQ~V~V~~s~~~Kl~w  457 (731)
T KOG0339|consen  380 DRMFD-MGFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEAN-EDITQTVSVCPSEEKKLNW  457 (731)
T ss_pred             hhhhc-cccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccc-cchhheeeeccCcHHHHHH
Confidence            99999 899999999999999999999999999999999999999999998876554433 3444444433 34444433


Q ss_pred             -HHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCC
Q 014486          279 -LNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV  357 (423)
Q Consensus       279 -l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~  357 (423)
                       +..|......+++|+|+.....++.++..|+-.++.+..+||++.+.+|.+++..|+.+...||++|+++++|+|++.+
T Consensus       458 l~~~L~~f~S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~i  537 (731)
T KOG0339|consen  458 LLRHLVEFSSEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSI  537 (731)
T ss_pred             HHHHhhhhccCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCcccc
Confidence             3444455566899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccH
Q 014486          358 NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDS  398 (423)
Q Consensus       358 ~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  398 (423)
                      +.||+||...++..+.||+||+||+|.+|.++.+++..+..
T Consensus       538 kTVvnyD~ardIdththrigrtgRag~kGvayTlvTeKDa~  578 (731)
T KOG0339|consen  538 KTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAE  578 (731)
T ss_pred             ceeecccccchhHHHHHHhhhcccccccceeeEEechhhHH
Confidence            99999999999999999999999999999999999976554

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

Probab=100.00  E-value=1e-52  Score=360.93  Aligned_cols=363  Identities=41%  Similarity=0.675  Sum_probs=335.9

Q ss_pred             CCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           47 GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        47 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      +|++++|++++++.++..||+.|+.+|+.||..+..|.++++.+++|+|||.++.+++++.....-....++++.|+++|
T Consensus        27 sfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaPtreL  106 (397)
T KOG0327|consen   27 SFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTREL  106 (397)
T ss_pred             hhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcchHHH
Confidence            79999999999999999999999999999999999999999999999999999999999998777666789999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccC
Q 014486          127 AYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESL  206 (423)
Q Consensus       127 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~  206 (423)
                      +.|.......++... +.++....||.+...+...+....+.|+++||+++...++...+....+++.|+||++.++. .
T Consensus       107 a~qi~~v~~~lg~~~-~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEmLs-~  184 (397)
T KOG0327|consen  107 AQQIQKVVRALGDHM-DVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEMLS-R  184 (397)
T ss_pred             HHHHHHHHHhhhccc-ceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeecchHhhhc-c
Confidence            999998888887765 88898889999888777666665579999999999999998888888899999999999998 8


Q ss_pred             CcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhh
Q 014486          207 DMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDAL  286 (423)
Q Consensus       207 ~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~  286 (423)
                      +|...+..++..+++..|++++|||+|.++....+.++..|..+.+.... ...+.+.+.+..+...+|...+.++.+  
T Consensus       185 gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~-ltl~gikq~~i~v~k~~k~~~l~dl~~--  261 (397)
T KOG0327|consen  185 GFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDE-LTLEGIKQFYINVEKEEKLDTLCDLYR--  261 (397)
T ss_pred             chHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecchh-hhhhheeeeeeeccccccccHHHHHHH--
Confidence            99999999999999999999999999999999999999999998887665 457888888888888889999999988  


Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCC
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMP  366 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~  366 (423)
                      .-...+|||+++..+..+...|...++.+..+|+.+.+.+|..+++.|+.|..+|||+|+.+++|+|+..+..||+|+.|
T Consensus       262 ~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slvinydlP  341 (397)
T KOG0327|consen  262 RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYDLP  341 (397)
T ss_pred             hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhcceeeeeccc
Confidence            55788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhhh
Q 014486          367 DSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSF  415 (423)
Q Consensus       367 ~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (423)
                      .....|+||+||+||.|.+|.++.++. ..+...++.++++++..+...
T Consensus       342 ~~~~~yihR~gr~gr~grkg~~in~v~-~~d~~~lk~ie~~y~~~i~e~  389 (397)
T KOG0327|consen  342 ARKENYIHRIGRAGRFGRKGVAINFVT-EEDVRDLKDIEKFYNTPIEEL  389 (397)
T ss_pred             cchhhhhhhcccccccCCCceeeeeeh-HhhHHHHHhHHHhcCCcceec
Confidence            999999999999999999999999997 467778899999998776543

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

Probab=100.00  E-value=3.8e-51  Score=404.17  Aligned_cols=349  Identities=17%  Similarity=0.261  Sum_probs=270.5

Q ss_pred             CCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHH
Q 014486           53 LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICH  132 (423)
Q Consensus        53 l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~  132 (423)
                      +++.+.++|.+.||..|+++|.++++.++.|+|+++.+|||||||++|++|+++.+...+ ++++||++|+++|+.|+..
T Consensus        21 l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~~-~~~aL~l~PtraLa~q~~~   99 (742)
T TIGR03817        21 AHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDP-RATALYLAPTKALAADQLR   99 (742)
T ss_pred             CCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhCC-CcEEEEEcChHHHHHHHHH
Confidence            789999999999999999999999999999999999999999999999999999886543 4599999999999999999


Q ss_pred             HHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHH-hcC---CCCCCCccEEEEcCcchhhccCCc
Q 014486          133 EFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALA-RDK---DLSLKNVRHFILDECDKMLESLDM  208 (423)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~-~~~---~~~~~~~~~vVvDE~h~~~~~~~~  208 (423)
                      .++++.  ..++++..+.|+...... ..+... ++|+|+||+++...+ ...   ...+.++++||+||+|.+.+  .|
T Consensus       100 ~l~~l~--~~~i~v~~~~Gdt~~~~r-~~i~~~-~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g--~f  173 (742)
T TIGR03817       100 AVRELT--LRGVRPATYDGDTPTEER-RWAREH-ARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRG--VF  173 (742)
T ss_pred             HHHHhc--cCCeEEEEEeCCCCHHHH-HHHhcC-CCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccC--cc
Confidence            999986  237888888888775433 344444 699999999987522 211   12368899999999999865  34


Q ss_pred             HHH-------HHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEe-----------
Q 014486          209 RRD-------VQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL-----------  270 (423)
Q Consensus       209 ~~~-------~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------  270 (423)
                      ...       +.++....+..+|++++|||+++... ....++..+..+. ....... ......+...           
T Consensus       174 g~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~i-~~~~~~~-~~~~~~~~~p~~~~~~~~~~~  250 (742)
T TIGR03817       174 GSHVALVLRRLRRLCARYGASPVFVLASATTADPAA-AASRLIGAPVVAV-TEDGSPR-GARTVALWEPPLTELTGENGA  250 (742)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHH-HHHHHcCCCeEEE-CCCCCCc-CceEEEEecCCcccccccccc
Confidence            433       33333445667899999999998754 5566666554432 2211111 1011111100           


Q ss_pred             -----ChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC--------CCCeEEEcCCCCHHHHHHHHHhhhcC
Q 014486          271 -----SELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC--------NFPSICIHSGMSQEERLTRYKGFKEG  337 (423)
Q Consensus       271 -----~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~--------~~~~~~~~~~~~~~~r~~~~~~f~~~  337 (423)
                           ....+...+..+++.  +.++||||++++.++.++..|++.        +.++..+||++++.+|.++++.|++|
T Consensus       251 ~~r~~~~~~~~~~l~~l~~~--~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G  328 (742)
T TIGR03817       251 PVRRSASAEAADLLADLVAE--GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDG  328 (742)
T ss_pred             ccccchHHHHHHHHHHHHHC--CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcC
Confidence                 112344555556553  579999999999999999988763        56778899999999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCc-ccHHHHHHHHHHHhcchh
Q 014486          338 NKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSA-SDSDILNQVSKFMFLLIG  413 (423)
Q Consensus       338 ~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~  413 (423)
                      ++++||||+++++|||++++++||+++.|.++..|.||+||+||.|+.|.++++.... .+...+..+++.++..++
T Consensus       329 ~i~vLVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~~~~~~~~~e  405 (742)
T TIGR03817       329 ELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHPEALFDRPVE  405 (742)
T ss_pred             CceEEEECchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCHHHHhcCCCc
Confidence            9999999999999999999999999999999999999999999999999999888643 344455556666665443

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.

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

Probab=100.00  E-value=5.4e-52  Score=366.15  Aligned_cols=359  Identities=26%  Similarity=0.389  Sum_probs=290.6

Q ss_pred             CCcCCCCCHHH----------HHHHHhCCCCCCChhhhhccccccc---------CCceEEEccCCCcchhHHHHHHhhc
Q 014486           47 GFRDFLLKPEL----------LRAIVDSGFEHPSEVQHECIPQAIL---------GMDVICQAKSGMGKTAVFVLSTLQQ  107 (423)
Q Consensus        47 ~~~~~~l~~~~----------~~~l~~~~~~~~~~~Q~~~i~~~~~---------~~~~ii~~~tGsGKT~~~~~~~~~~  107 (423)
                      .|..++.+...          .+++.++++.+..|+|..++|+++.         .+|++|.||||||||++|.+||++.
T Consensus       128 ~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~  207 (620)
T KOG0350|consen  128 IFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQL  207 (620)
T ss_pred             eeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHH
Confidence            35566665543          3458899999999999999999864         4789999999999999999999998


Q ss_pred             cCCCC-CCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCC----cEEEechHHHHHHHh
Q 014486          108 TEPNP-GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP----QIVVGTPGRILALAR  182 (423)
Q Consensus       108 ~~~~~-~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~ilv~T~~~l~~~~~  182 (423)
                      +...+ ...+|+||+|+++|+.|+++.|.++.... ++.|..+.|..+.+.+...+.+..+    +|+|+||++|.+++.
T Consensus       208 L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~t-gL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~  286 (620)
T KOG0350|consen  208 LSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGT-GLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLN  286 (620)
T ss_pred             HccCCccceEEEEEeeHHHHHHHHHHHHHHhccCC-ceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhcc
Confidence            87663 45699999999999999999999998775 8899999999999999999988767    999999999999998


Q ss_pred             -cCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHH----------------------------------hCCCCceEEE
Q 014486          183 -DKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFK----------------------------------MTPHDKQVMM  227 (423)
Q Consensus       183 -~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~----------------------------------~~~~~~~~v~  227 (423)
                       ...+.+.+++++||||||++++ ..|...+-.+..                                  .+.+..+.++
T Consensus       287 ~~k~f~Lk~LrfLVIDEADRll~-qsfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~  365 (620)
T KOG0350|consen  287 NTKSFDLKHLRFLVIDEADRLLD-QSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLV  365 (620)
T ss_pred             CCCCcchhhceEEEechHHHHHH-HHHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhh
Confidence             5678899999999999999986 344333322221                                  1122335778


Q ss_pred             EeccCCccHHHHHHHhccCCceeeeccc--cc-cccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHH
Q 014486          228 FSATLSKEIRPVCKKFMQDPMEIYVDDE--AK-LTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAEL  304 (423)
Q Consensus       228 ~SAT~~~~~~~~~~~~~~~~~~~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l  304 (423)
                      +|||+..+-..+....++.|....+...  .. .....+....+......+...+..++......++|+|+++.+.+.++
T Consensus       366 ~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~~~~kpl~~~~lI~~~k~~r~lcf~~S~~sa~Rl  445 (620)
T KOG0350|consen  366 FSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEPKFKPLAVYALITSNKLNRTLCFVNSVSSANRL  445 (620)
T ss_pred             cchhhhcChHHHhhhhcCCCceEEeecccceeeecChhhhhceeecccccchHhHHHHHHHhhcceEEEEecchHHHHHH
Confidence            8888877766666656666643333211  11 11223334444445556778888899888889999999999999999


Q ss_pred             HHHHH----hCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccC
Q 014486          305 NKLLV----ECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAG  380 (423)
Q Consensus       305 ~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~  380 (423)
                      ...|+    ..++++..+.|.++...|...++.|..|.+++|||+++++||+|+.++++||+|++|.+..+|+||+||++
T Consensus       446 ~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTA  525 (620)
T KOG0350|consen  446 AHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTA  525 (620)
T ss_pred             HHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEeecCCCchhhHHHHhhcccc
Confidence            98887    34677778999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCceEEEEEecCcccHHHHHHHHHH
Q 014486          381 RFGTKGLAITFVSSASDSDILNQVSKF  407 (423)
Q Consensus       381 R~g~~~~~~~~~~~~~~~~~~~~~~~~  407 (423)
                      |+|+.|.++.+.+..+.....+.+++.
T Consensus       526 RAgq~G~a~tll~~~~~r~F~klL~~~  552 (620)
T KOG0350|consen  526 RAGQDGYAITLLDKHEKRLFSKLLKKT  552 (620)
T ss_pred             cccCCceEEEeeccccchHHHHHHHHh
Confidence            999999999999987776666655543

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

Probab=100.00  E-value=4.5e-50  Score=394.14  Aligned_cols=334  Identities=20%  Similarity=0.234  Sum_probs=259.9

Q ss_pred             CCCCCHHHHHHHHh-CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHH
Q 014486           50 DFLLKPELLRAIVD-SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAY  128 (423)
Q Consensus        50 ~~~l~~~~~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~  128 (423)
                      .|+++..+...++. +|+..+||+|.++|+.++.|+++++.+|||+|||++|++|++...      ..+|||+|+++|+.
T Consensus       441 ~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~~------GiTLVISPLiSLmq  514 (1195)
T PLN03137        441 NFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALICP------GITLVISPLVSLIQ  514 (1195)
T ss_pred             CCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHcC------CcEEEEeCHHHHHH
Confidence            57777777777766 499999999999999999999999999999999999999998752      27999999999998


Q ss_pred             HHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhc-----CCCcEEEechHHHHH---HHhc--CCCCCCCccEEEEcC
Q 014486          129 QICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN-----ECPQIVVGTPGRILA---LARD--KDLSLKNVRHFILDE  198 (423)
Q Consensus       129 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~ilv~T~~~l~~---~~~~--~~~~~~~~~~vVvDE  198 (423)
                      ++...+...     ++....+.++.....+...+..     +.++|+++||+++..   ++..  .......+.+|||||
T Consensus       515 DQV~~L~~~-----GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDE  589 (1195)
T PLN03137        515 DQIMNLLQA-----NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDE  589 (1195)
T ss_pred             HHHHHHHhC-----CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCc
Confidence            666555442     7888899998877666554432     568999999999852   1211  111234578899999


Q ss_pred             cchhhcc-CCcHHHHHHH--HHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHH-
Q 014486          199 CDKMLES-LDMRRDVQEI--FKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-  274 (423)
Q Consensus       199 ~h~~~~~-~~~~~~~~~~--~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  274 (423)
                      ||++..| .+|+..+..+  +....+..+++++|||++..+...+...+...........  ....++  .+...+... 
T Consensus       590 AHcVSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vfr~S--f~RpNL--~y~Vv~k~kk  665 (1195)
T PLN03137        590 AHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQS--FNRPNL--WYSVVPKTKK  665 (1195)
T ss_pred             chhhhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEeecc--cCccce--EEEEeccchh
Confidence            9999986 4688877664  3333346789999999998887755554433222222111  111222  122222222 


Q ss_pred             HHHHHHHHHHhh-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCC
Q 014486          275 KNRKLNDLLDAL-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGID  353 (423)
Q Consensus       275 ~~~~l~~ll~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld  353 (423)
                      ....+..++... ...+.||||.+++.++.++..|...|+.+..|||+|++.+|..+++.|..|+++|||||.++++|||
T Consensus       666 ~le~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGID  745 (1195)
T PLN03137        666 CLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGIN  745 (1195)
T ss_pred             HHHHHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCC
Confidence            234455555433 3568999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccH
Q 014486          354 IERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDS  398 (423)
Q Consensus       354 ~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  398 (423)
                      +|++++||+|++|.++..|+|++|||||.|.++.|++|++..+..
T Consensus       746 kPDVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~~  790 (1195)
T PLN03137        746 KPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYI  790 (1195)
T ss_pred             ccCCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHHHH
Confidence            999999999999999999999999999999999999999864443

>KOG4284 consensus DEAD box protein [Transcription]

Probab=100.00  E-value=6.3e-51  Score=369.31  Aligned_cols=357  Identities=32%  Similarity=0.550  Sum_probs=325.5

Q ss_pred             cCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           44 HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      ....|+++.+...++..|...+|..|+++|..|||.++.+-|+||.+..|+|||++|.+.+++.+......+..+|++||
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            44578999999999999999999999999999999999999999999999999999999999999888888899999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                      |++|.|+.+.+..++..+.++++.++.||+........+...  +|+|+||+++..+++...++.+.++++|+||||.+.
T Consensus       103 REiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~~--rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~  180 (980)
T KOG4284|consen  103 REIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQT--RIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLM  180 (980)
T ss_pred             hhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhhc--eEEecCchHHHHHHHhcCCCccceeEEEeccHHhhh
Confidence            999999999999999988899999999999988887777664  899999999999999999999999999999999999


Q ss_pred             ccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChH--------HH
Q 014486          204 ESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEL--------EK  275 (423)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~  275 (423)
                      +...|...+..+...+|+.+|++.+|||.|..+...+..++.+|..+....... ..-++.+++......        .|
T Consensus       181 ~t~sfq~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~-~L~GikQyv~~~~s~nnsveemrlk  259 (980)
T KOG4284|consen  181 DTESFQDDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDV-QLFGIKQYVVAKCSPNNSVEEMRLK  259 (980)
T ss_pred             chhhHHHHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccCCc-eeechhheeeeccCCcchHHHHHHH
Confidence            877899999999999999999999999999999999999999998777655443 344555555444322        36


Q ss_pred             HHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCC
Q 014486          276 NRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIE  355 (423)
Q Consensus       276 ~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~  355 (423)
                      ...|..+.+.++....||||+....|+.++..|+..|+++.++.|.|++.+|..+++.++.-..+|||+|+..++|||-+
T Consensus       260 lq~L~~vf~~ipy~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~  339 (980)
T KOG4284|consen  260 LQKLTHVFKSIPYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDAD  339 (980)
T ss_pred             HHHHHHHHhhCchHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCcc
Confidence            77888888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHH
Q 014486          356 RVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQ  403 (423)
Q Consensus       356 ~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~  403 (423)
                      +++.||+.|+|-+..+|.||+|||||.|..|.++.|+....+..-+..
T Consensus       340 ~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e~~~f~~  387 (980)
T KOG4284|consen  340 NVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDERELKGFTA  387 (980)
T ss_pred             ccceEEecCCCcchHHHHHHhhhcccccccceeEEEeccchhhhhhHH
Confidence            999999999999999999999999999999999999987666444333

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=1.1e-49  Score=379.23  Aligned_cols=318  Identities=21%  Similarity=0.255  Sum_probs=247.8

Q ss_pred             CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           64 SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        64 ~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      +||..|+|+|.++++.++.++++++.+|||+|||++|++|++...      ..+||++|+++|+.|+.+.+..+     +
T Consensus         7 ~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~~------~~~lVi~P~~~L~~dq~~~l~~~-----g   75 (470)
T TIGR00614         7 FGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCSD------GITLVISPLISLMEDQVLQLKAS-----G   75 (470)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHcC------CcEEEEecHHHHHHHHHHHHHHc-----C
Confidence            499999999999999999999999999999999999999988642      27899999999999998888754     6


Q ss_pred             ceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHH-hcCCC-CCCCccEEEEcCcchhhcc-CCcHHHHHHH--
Q 014486          144 IKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALA-RDKDL-SLKNVRHFILDECDKMLES-LDMRRDVQEI--  215 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~-~~~~~-~~~~~~~vVvDE~h~~~~~-~~~~~~~~~~--  215 (423)
                      +....+.++.......   ..+..+.++|+++||+.+.... ....+ ...++++||+||||++.+| .+|+..+..+  
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            7777777776654332   2334566899999999875321 00111 4578899999999999875 4577766554  


Q ss_pred             -HHhCCCCceEEEEeccCCccHHHHHHHhcc--CCceeeeccccccccccceEEEEEeChHHHHHHHHHHHH-hhcCCcE
Q 014486          216 -FKMTPHDKQVMMFSATLSKEIRPVCKKFMQ--DPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLD-ALDFNQV  291 (423)
Q Consensus       216 -~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~-~~~~~~~  291 (423)
                       ...+ +..+++++|||+++.....+...+.  .+..+ .....   .+.+. .............+..++. ..++.++
T Consensus       156 l~~~~-~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~-~~s~~---r~nl~-~~v~~~~~~~~~~l~~~l~~~~~~~~~  229 (470)
T TIGR00614       156 LKQKF-PNVPIMALTATASPSVREDILRQLNLKNPQIF-CTSFD---RPNLY-YEVRRKTPKILEDLLRFIRKEFKGKSG  229 (470)
T ss_pred             HHHHc-CCCceEEEecCCCHHHHHHHHHHcCCCCCcEE-eCCCC---CCCcE-EEEEeCCccHHHHHHHHHHHhcCCCce
Confidence             3333 4678999999999877655544432  23222 11111   11121 1111122233445555555 4455567


Q ss_pred             EEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcch
Q 014486          292 VIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADT  371 (423)
Q Consensus       292 ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~  371 (423)
                      ||||++++.++.+++.|+..|+.+..+|+++++.+|..+++.|++|+++|||||+++++|+|+|++++||++++|.|+..
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             hhhcccccCCCCCceEEEEEecCcccH
Q 014486          372 YLHRVGRAGRFGTKGLAITFVSSASDS  398 (423)
Q Consensus       372 ~~Q~~GR~~R~g~~~~~~~~~~~~~~~  398 (423)
                      |+||+||+||.|+++.+++++++.+..
T Consensus       310 y~Qr~GRaGR~G~~~~~~~~~~~~d~~  336 (470)
T TIGR00614       310 YYQESGRAGRDGLPSECHLFYAPADIN  336 (470)
T ss_pred             HHhhhcCcCCCCCCceEEEEechhHHH
Confidence            999999999999999999999875443

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

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2.7e-50  Score=386.12  Aligned_cols=363  Identities=32%  Similarity=0.545  Sum_probs=323.5

Q ss_pred             ccccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC-----CCCCe
Q 014486           41 VGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP-----NPGQV  115 (423)
Q Consensus        41 ~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-----~~~~~  115 (423)
                      .+....+|.+.+++.-++..++++||..|+|+|.+|||+++.|+++|..|.||||||++|++|++.+...     .+.+|
T Consensus       360 ~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGP  439 (997)
T KOG0334|consen  360 CPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGP  439 (997)
T ss_pred             CCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCc
Confidence            3344567999999999999999999999999999999999999999999999999999999999965432     24578


Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCC---CCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLS---LKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~---~~~~~  192 (423)
                      .++|++||++|+.|+.++++.|+... ++.+..++||.....+...+..+ ..|+||||+++.+++-.+...   +.++.
T Consensus       440 i~li~aPtrela~QI~r~~~kf~k~l-~ir~v~vygg~~~~~qiaelkRg-~eIvV~tpGRmiD~l~~n~grvtnlrR~t  517 (997)
T KOG0334|consen  440 IALILAPTRELAMQIHREVRKFLKLL-GIRVVCVYGGSGISQQIAELKRG-AEIVVCTPGRMIDILCANSGRVTNLRRVT  517 (997)
T ss_pred             eEEEEcCCHHHHHHHHHHHHHHHhhc-CceEEEecCCccHHHHHHHHhcC-CceEEeccchhhhhHhhcCCccccccccc
Confidence            99999999999999999999999885 99999999999999999999999 699999999999977655444   45555


Q ss_pred             EEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeC-
Q 014486          193 HFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS-  271 (423)
Q Consensus       193 ~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  271 (423)
                      ++|+||||++.+ .+|.+....|+..+++.+|.+++|||+|..+..+....++.|..+.+.... .....+.+.+..+. 
T Consensus       518 ~lv~deaDrmfd-mgfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~s-vV~k~V~q~v~V~~~  595 (997)
T KOG0334|consen  518 YLVLDEADRMFD-MGFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRS-VVCKEVTQVVRVCAI  595 (997)
T ss_pred             eeeechhhhhhe-eccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccce-eEeccceEEEEEecC
Confidence            999999999995 899999888999999999999999999999999999999888886665433 34456666777777 


Q ss_pred             hHHHHHHHHHHHHhh-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCcccc
Q 014486          272 ELEKNRKLNDLLDAL-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGR  350 (423)
Q Consensus       272 ~~~~~~~l~~ll~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~  350 (423)
                      +.+|...+.++|... ..+++||||.+.+.|+.+.+.|.+.|+++..+||+.++.+|..++..|+++.+++||+|+.+++
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            888999999998655 5689999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHH
Q 014486          351 GIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFM  408 (423)
Q Consensus       351 Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~  408 (423)
                      |+|++.+..||+|++|..+.+|+||+||+||+|.+|.+++|+.+ ++..+-..|-+.|
T Consensus       676 GLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p-~q~~~a~dl~~al  732 (997)
T KOG0334|consen  676 GLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITP-DQLKYAGDLCKAL  732 (997)
T ss_pred             ccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEEeCh-HHhhhHHHHHHHH
Confidence            99999999999999999999999999999999999999999998 5555555555555

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

Probab=100.00  E-value=1.9e-50  Score=349.36  Aligned_cols=362  Identities=31%  Similarity=0.509  Sum_probs=325.2

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC-CCeEEEEEecC
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP-GQVTALVLCHT  123 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~-~~~~~lil~P~  123 (423)
                      +..|++++|+..+.+++.+.||+.|+|+|++.+|.++.+++++-.+-||||||.+|++|+++.+.... .+.++++++|+
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            67899999999999999999999999999999999999999999999999999999999999876543 55699999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                      ++|+.|..+..+++.... +++...++||.+.+++...+..+ +||+++||+++..+.-.-.+.++.+.+||+||++++.
T Consensus       100 reLa~qtlkvvkdlgrgt-~lr~s~~~ggD~~eeqf~~l~~n-pDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlf  177 (529)
T KOG0337|consen  100 RELALQTLKVVKDLGRGT-KLRQSLLVGGDSIEEQFILLNEN-PDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLF  177 (529)
T ss_pred             HHHHHHHHHHHHHhcccc-chhhhhhcccchHHHHHHHhccC-CCEEEecCceeeeeehheeccccceeeeeehhhhHHH
Confidence            999999999999998776 88999999999999998888766 6999999999998777767889999999999999999


Q ss_pred             ccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHH
Q 014486          204 ESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLL  283 (423)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll  283 (423)
                      + .+|...+..++..++...|.+++|||+|+.+..+.+.-+..|..+.++.+.... ......+..+...+|...|..++
T Consensus       178 e-mgfqeql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkis-e~lk~~f~~~~~a~K~aaLl~il  255 (529)
T KOG0337|consen  178 E-MGFQEQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKIS-ELLKVRFFRVRKAEKEAALLSIL  255 (529)
T ss_pred             h-hhhHHHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcc-hhhhhheeeeccHHHHHHHHHHH
Confidence            8 899999999999999999999999999999999999999999888766555433 34455567777888888877777


Q ss_pred             Hhhc-CCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE
Q 014486          284 DALD-FNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN  362 (423)
Q Consensus       284 ~~~~-~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~  362 (423)
                      .... ..+++||+.+..+++.+...|++.|+.+..++|.+.+..|..-+..|+.++..+||.|+.+++|+|+|-.+.||+
T Consensus       256 ~~~~~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldnvin  335 (529)
T KOG0337|consen  256 GGRIKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDNVIN  335 (529)
T ss_pred             hccccccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhccCCCcccccccc
Confidence            6553 367999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcc
Q 014486          363 YDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLL  411 (423)
Q Consensus       363 ~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  411 (423)
                      |+.|.+...|.||+||+.|+|..|..+.++.+ .+..++-.|.-.++..
T Consensus       336 yd~p~~~klFvhRVgr~aragrtg~aYs~V~~-~~~~yl~DL~lflgr~  383 (529)
T KOG0337|consen  336 YDFPPDDKLFVHRVGRVARAGRTGRAYSLVAS-TDDPYLLDLQLFLGRP  383 (529)
T ss_pred             ccCCCCCceEEEEecchhhccccceEEEEEec-ccchhhhhhhhhcCCc
Confidence            99999999999999999999999999999986 4555566666666643

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=100.00  E-value=1.8e-48  Score=380.15  Aligned_cols=326  Identities=18%  Similarity=0.267  Sum_probs=254.9

Q ss_pred             CCHHHHHHHHh-CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHH
Q 014486           53 LKPELLRAIVD-SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQIC  131 (423)
Q Consensus        53 l~~~~~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  131 (423)
                      ......+.|++ +||..|+|+|+++++.++.|+++++.+|||+|||++|++|++....      .+||++|+++|+.|+.
T Consensus         9 ~~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~~g------~tlVisPl~sL~~dqv   82 (607)
T PRK11057          9 LESLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLDG------LTLVVSPLISLMKDQV   82 (607)
T ss_pred             chhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHcCC------CEEEEecHHHHHHHHH
Confidence            33444455555 4999999999999999999999999999999999999999986521      7899999999999999


Q ss_pred             HHHHHHhccCCCceEEEEEcCcchHHHHH---HHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc-CC
Q 014486          132 HEFERFSTYLPDIKVAVFYGGVNIKIHKD---LLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES-LD  207 (423)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~-~~  207 (423)
                      +.++..     ++....+.++........   .+.++..+++++||+++........+...++++||+||||++..| .+
T Consensus        83 ~~l~~~-----gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~  157 (607)
T PRK11057         83 DQLLAN-----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHD  157 (607)
T ss_pred             HHHHHc-----CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCc
Confidence            888764     567777777766554332   344566799999999987422112233457899999999999875 45


Q ss_pred             cHHHHHHH---HHhCCCCceEEEEeccCCccHHHHHHHhcc--CCceeeeccccccccccceEEEEEeChHHHHHHHHHH
Q 014486          208 MRRDVQEI---FKMTPHDKQVMMFSATLSKEIRPVCKKFMQ--DPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDL  282 (423)
Q Consensus       208 ~~~~~~~~---~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l  282 (423)
                      |+..+..+   ...+ +..+++++|||+++.....+...+.  .+. +......   .+.+  .+.......+...+..+
T Consensus       158 fr~~y~~L~~l~~~~-p~~~~v~lTAT~~~~~~~di~~~l~l~~~~-~~~~~~~---r~nl--~~~v~~~~~~~~~l~~~  230 (607)
T PRK11057        158 FRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPL-IQISSFD---RPNI--RYTLVEKFKPLDQLMRY  230 (607)
T ss_pred             ccHHHHHHHHHHHhC-CCCcEEEEecCCChhHHHHHHHHhCCCCeE-EEECCCC---CCcc--eeeeeeccchHHHHHHH
Confidence            77665444   3333 4678999999999876654433332  232 2221111   1111  12222223344556667


Q ss_pred             HHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE
Q 014486          283 LDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN  362 (423)
Q Consensus       283 l~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~  362 (423)
                      +....++++||||+++++++.+++.|+..|+.+..+|+++++.+|..+++.|+.|+++|||||+++++|+|+|++++||+
T Consensus       231 l~~~~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~  310 (607)
T PRK11057        231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVH  310 (607)
T ss_pred             HHhcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEE
Confidence            77777789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCcchhhhcccccCCCCCceEEEEEecCcc
Q 014486          363 YDMPDSADTYLHRVGRAGRFGTKGLAITFVSSAS  396 (423)
Q Consensus       363 ~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  396 (423)
                      |++|.|...|.||+||+||.|.+|.+++|+++.+
T Consensus       311 ~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d  344 (607)
T PRK11057        311 FDIPRNIESYYQETGRAGRDGLPAEAMLFYDPAD  344 (607)
T ss_pred             eCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHH
Confidence            9999999999999999999999999999998754

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=100.00  E-value=7.2e-48  Score=377.34  Aligned_cols=321  Identities=22%  Similarity=0.296  Sum_probs=257.1

Q ss_pred             HHHHh-CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           59 RAIVD-SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        59 ~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      +.|++ +||.+++|+|.++++.++.|+++++++|||+|||++|++|++...      ..++|++|+++|+.|+.+.++.+
T Consensus         3 ~~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~~------g~~lVisPl~sL~~dq~~~l~~~   76 (591)
T TIGR01389         3 QVLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLLK------GLTVVISPLISLMKDQVDQLRAA   76 (591)
T ss_pred             HHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHcC------CcEEEEcCCHHHHHHHHHHHHHc
Confidence            34554 599999999999999999999999999999999999999988542      17899999999999999888774


Q ss_pred             hccCCCceEEEEEcCcchHHHHH---HHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc-CCcHHHHH
Q 014486          138 STYLPDIKVAVFYGGVNIKIHKD---LLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES-LDMRRDVQ  213 (423)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~-~~~~~~~~  213 (423)
                           ++.+..++++.+......   .+..+..+|+++||+++........+...++++||+||||++..| .+|+..+.
T Consensus        77 -----gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~  151 (591)
T TIGR01389        77 -----GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQ  151 (591)
T ss_pred             -----CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHH
Confidence                 678888888876654433   344566899999999986533333345568899999999999875 46777766


Q ss_pred             HHH---HhCCCCceEEEEeccCCccHHHHHHHhccCC-ceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCC
Q 014486          214 EIF---KMTPHDKQVMMFSATLSKEIRPVCKKFMQDP-MEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFN  289 (423)
Q Consensus       214 ~~~---~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~  289 (423)
                      .+.   ..++ ..+++++|||++......+...+..+ ........   ....+  .+.......+...+.+++....+.
T Consensus       152 ~l~~l~~~~~-~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~~~~---~r~nl--~~~v~~~~~~~~~l~~~l~~~~~~  225 (591)
T TIGR01389       152 RLGSLAERFP-QVPRIALTATADAETRQDIRELLRLADANEFITSF---DRPNL--RFSVVKKNNKQKFLLDYLKKHRGQ  225 (591)
T ss_pred             HHHHHHHhCC-CCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEecCC---CCCCc--EEEEEeCCCHHHHHHHHHHhcCCC
Confidence            554   3344 44599999999988776665554322 11222111   11222  222223334556677777777778


Q ss_pred             cEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCc
Q 014486          290 QVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSA  369 (423)
Q Consensus       290 ~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~  369 (423)
                      ++||||++++.++.+++.|...|+++..+|++|+..+|..+++.|.+|+++|||||+++++|+|+|++++||++++|.|+
T Consensus       226 ~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~  305 (591)
T TIGR01389       226 SGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNL  305 (591)
T ss_pred             CEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhhhcccccCCCCCceEEEEEecCcc
Q 014486          370 DTYLHRVGRAGRFGTKGLAITFVSSAS  396 (423)
Q Consensus       370 ~~~~Q~~GR~~R~g~~~~~~~~~~~~~  396 (423)
                      ..|.|++||+||.|+++.+++++++.+
T Consensus       306 ~~y~Q~~GRaGR~G~~~~~il~~~~~d  332 (591)
T TIGR01389       306 ESYYQEAGRAGRDGLPAEAILLYSPAD  332 (591)
T ss_pred             HHHhhhhccccCCCCCceEEEecCHHH
Confidence            999999999999999999999987643

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.

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

Probab=100.00  E-value=4.4e-48  Score=349.27  Aligned_cols=366  Identities=31%  Similarity=0.413  Sum_probs=302.6

Q ss_pred             cccCCCCcC----CCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC-----C
Q 014486           42 GIHSSGFRD----FLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN-----P  112 (423)
Q Consensus        42 ~~~~~~~~~----~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~-----~  112 (423)
                      +....+|.+    |..++.+++++...+|..|+|+|.+++|.++.+.+++.|+|||+|||++|.+|++.++...     .
T Consensus       128 ~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~  207 (593)
T KOG0344|consen  128 PPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHK  207 (593)
T ss_pred             CCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCc
Confidence            333445654    7788999999999999999999999999999999999999999999999999999876532     4


Q ss_pred             CCeEEEEEecChHHHHHHHHHHHHHh--ccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC--CCC
Q 014486          113 GQVTALVLCHTRELAYQICHEFERFS--TYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD--LSL  188 (423)
Q Consensus       113 ~~~~~lil~P~~~L~~q~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~--~~~  188 (423)
                      .+.+++|+.|+++|+.|++.++.++.  ... +.....+............+....++++++||-++...+....  ..+
T Consensus       208 ~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t-~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl  286 (593)
T KOG0344|consen  208 VGLRALILSPTRELAAQIYREMRKYSIDEGT-SLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDL  286 (593)
T ss_pred             cceEEEEecchHHHHHHHHHHHHhcCCCCCC-chhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchh
Confidence            55689999999999999999999886  222 2333333322221222222222336999999999999888765  678


Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCC-CCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEE
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTP-HDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHY  267 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~-~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  267 (423)
                      ..+.++|+||+|.+.+...|...+..++..+. ++..+-++|||.+..+..+++.....+..+.+.........-.....
T Consensus       287 ~~V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~~sa~~~V~Qelv  366 (593)
T KOG0344|consen  287 SKVEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVGLRNSANETVDQELV  366 (593)
T ss_pred             heeeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEecchhHhhhhhhhhe
Confidence            99999999999999984378888888877664 46677889999999999999998888877766555444333333344


Q ss_pred             EEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHH-HhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcC
Q 014486          268 IKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLL-VECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD  346 (423)
Q Consensus       268 ~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L-~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~  346 (423)
                      +...+..|...+.+++...-.-+++||+.+.+.|..+...| .-.++.+..+||..++.+|...+++|+.|++++||||+
T Consensus       367 F~gse~~K~lA~rq~v~~g~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTd  446 (593)
T KOG0344|consen  367 FCGSEKGKLLALRQLVASGFKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTD  446 (593)
T ss_pred             eeecchhHHHHHHHHHhccCCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehh
Confidence            55677888999999998887789999999999999999999 77799999999999999999999999999999999999


Q ss_pred             ccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHh
Q 014486          347 LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       347 ~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                      ++++|+|+.++++||+||.|.+...|+||+||+||+|+.|.++.||+. .+...+..+.+.+.
T Consensus       447 ll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd-~d~~~ir~iae~~~  508 (593)
T KOG0344|consen  447 LLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTD-QDMPRIRSIAEVME  508 (593)
T ss_pred             hhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEecc-ccchhhhhHHHHHH
Confidence            999999999999999999999999999999999999999999999986 66666777776665

>PRK13767 ATP-dependent helicase; Provisional

Probab=100.00  E-value=7.1e-46  Score=373.95  Aligned_cols=340  Identities=23%  Similarity=0.304  Sum_probs=246.3

Q ss_pred             CCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC------CCCeEEEEEecChHH
Q 014486           53 LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN------PGQVTALVLCHTREL  126 (423)
Q Consensus        53 l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~------~~~~~~lil~P~~~L  126 (423)
                      +++.+.+.+.+ +|..|+|+|+++++.++.|+++++++|||||||++|++|++..+...      ..++++||++|+++|
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            45666666555 78999999999999999999999999999999999999999765421      234689999999999


Q ss_pred             HHHHHHHHHHH-------h----ccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCC--CCCCccE
Q 014486          127 AYQICHEFERF-------S----TYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDL--SLKNVRH  193 (423)
Q Consensus       127 ~~q~~~~~~~~-------~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~--~~~~~~~  193 (423)
                      +.|+++.+...       .    ...+++++...+|+.......+.+.+. ++|+|+||++|..++....+  .+.++++
T Consensus        97 a~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~-p~IlVtTPE~L~~ll~~~~~~~~l~~l~~  175 (876)
T PRK13767         97 NNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKP-PHILITTPESLAILLNSPKFREKLRTVKW  175 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCC-CCEEEecHHHHHHHhcChhHHHHHhcCCE
Confidence            99998866532       2    223477899999998877776666655 69999999999887765443  4688999


Q ss_pred             EEEcCcchhhccCCc----HHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccC-----Cceeeeccccccccccce
Q 014486          194 FILDECDKMLESLDM----RRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQD-----PMEIYVDDEAKLTLHGLV  264 (423)
Q Consensus       194 vVvDE~h~~~~~~~~----~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~  264 (423)
                      ||+||+|.+.+ ...    ...+.++....+...|++++|||+++. ..........     +..+.+..........+.
T Consensus       176 VVIDE~H~l~~-~~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~~-~~va~~L~~~~~~~~~r~~~iv~~~~~k~~~i~  253 (876)
T PRK13767        176 VIVDEIHSLAE-NKRGVHLSLSLERLEELAGGEFVRIGLSATIEPL-EEVAKFLVGYEDDGEPRDCEIVDARFVKPFDIK  253 (876)
T ss_pred             EEEechhhhcc-CccHHHHHHHHHHHHHhcCCCCeEEEEecccCCH-HHHHHHhcCccccCCCCceEEEccCCCccceEE
Confidence            99999999985 222    233455555555678999999999762 2222222111     111111110000000000


Q ss_pred             E-----EEEEeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhC------CCCeEEEcCCCCHHHHHHHH
Q 014486          265 Q-----HYIKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVEC------NFPSICIHSGMSQEERLTRY  331 (423)
Q Consensus       265 ~-----~~~~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~------~~~~~~~~~~~~~~~r~~~~  331 (423)
                      .     .............+...+...  ..+++||||++++.++.++..|+..      +..+..+||++++.+|..++
T Consensus       254 v~~p~~~l~~~~~~~~~~~l~~~L~~~i~~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve  333 (876)
T PRK13767        254 VISPVDDLIHTPAEEISEALYETLHELIKEHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVE  333 (876)
T ss_pred             EeccCccccccccchhHHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHH
Confidence            0     000011111112222222221  3478999999999999999999873      46788999999999999999


Q ss_pred             HhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCC-CCceEEEEEecCcc
Q 014486          332 KGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRF-GTKGLAITFVSSAS  396 (423)
Q Consensus       332 ~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~-g~~~~~~~~~~~~~  396 (423)
                      +.|++|++++||||+++++|+|+|++++||+++.|.++..|+||+||+||. |..+.+.++....+
T Consensus       334 ~~fk~G~i~vLVaTs~Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~~~~  399 (876)
T PRK13767        334 EKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVVDRD  399 (876)
T ss_pred             HHHHcCCCeEEEECChHHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEcCch
Confidence            999999999999999999999999999999999999999999999999986 44455555544433

>PRK02362 ski2-like helicase; Provisional

Probab=100.00  E-value=6.4e-46  Score=371.29  Aligned_cols=335  Identities=21%  Similarity=0.304  Sum_probs=251.8

Q ss_pred             CCcCCCCCHHHHHHHHhCCCCCCChhhhhcccc-cccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           47 GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQ-AILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        47 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~-~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      .|+++++++.+.+.+.+.|+..|+|+|.++++. +..++++++++|||||||+++.++++..+..+   .+++|++|+++
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 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIARG---GKALYIVPLRA   78 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhcC---CcEEEEeChHH
Confidence            478899999999999999999999999999998 67799999999999999999999999887643   38999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~  205 (423)
                      |+.|+++.++++.. . ++++..++|+......  .+  +.++|+|+||+++..++++....+.++++||+||+|.+.+ 
T Consensus        79 La~q~~~~~~~~~~-~-g~~v~~~tGd~~~~~~--~l--~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d-  151 (737)
T PRK02362         79 LASEKFEEFERFEE-L-GVRVGISTGDYDSRDE--WL--GDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDS-  151 (737)
T ss_pred             HHHHHHHHHHHhhc-C-CCEEEEEeCCcCcccc--cc--CCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCC-
Confidence            99999999998753 2 7899999998754332  12  2369999999999998887666678999999999999876 


Q ss_pred             CCcHHHHHHHHH---hCCCCceEEEEeccCCccHHHHHHHhccC-------Cceee--eccccccccccceEEEEEeCh-
Q 014486          206 LDMRRDVQEIFK---MTPHDKQVMMFSATLSKEIRPVCKKFMQD-------PMEIY--VDDEAKLTLHGLVQHYIKLSE-  272 (423)
Q Consensus       206 ~~~~~~~~~~~~---~~~~~~~~v~~SAT~~~~~~~~~~~~~~~-------~~~~~--~~~~~~~~~~~~~~~~~~~~~-  272 (423)
                      ..+...+..+..   ......|+|++|||+++. ..+.......       |..+.  +.......... ......... 
T Consensus       152 ~~rg~~le~il~rl~~~~~~~qii~lSATl~n~-~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~-~~~~~~~~~~  229 (737)
T PRK02362        152 ANRGPTLEVTLAKLRRLNPDLQVVALSATIGNA-DELADWLDAELVDSEWRPIDLREGVFYGGAIHFDD-SQREVEVPSK  229 (737)
T ss_pred             CcchHHHHHHHHHHHhcCCCCcEEEEcccCCCH-HHHHHHhCCCcccCCCCCCCCeeeEecCCeecccc-ccccCCCccc
Confidence            456555554433   345678999999999863 2222222111       11100  00000000000 000010011 


Q ss_pred             HHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC------------------------------------CCCeE
Q 014486          273 LEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC------------------------------------NFPSI  316 (423)
Q Consensus       273 ~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~------------------------------------~~~~~  316 (423)
                      ......+.+.+.  .++++||||++++.+..+++.|...                                    ...+.
T Consensus       230 ~~~~~~~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva  307 (737)
T PRK02362        230 DDTLNLVLDTLE--EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAA  307 (737)
T ss_pred             hHHHHHHHHHHH--cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEE
Confidence            112222222222  4689999999999998888777542                                    13577


Q ss_pred             EEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE----cc-----CCCCcchhhhcccccCCCCCc--
Q 014486          317 CIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN----YD-----MPDSADTYLHRVGRAGRFGTK--  385 (423)
Q Consensus       317 ~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~----~~-----~~~s~~~~~Q~~GR~~R~g~~--  385 (423)
                      .+|+++++.+|..+++.|++|.++|||||+++++|+|+|..++||.    |+     .|.++.+|.||+|||||.|.+  
T Consensus       308 ~hHagl~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~  387 (737)
T PRK02362        308 FHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPY  387 (737)
T ss_pred             eecCCCCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCC
Confidence            8999999999999999999999999999999999999999999986    55     588999999999999999865  


Q ss_pred             eEEEEEecCc
Q 014486          386 GLAITFVSSA  395 (423)
Q Consensus       386 ~~~~~~~~~~  395 (423)
                      |.+++++.+.
T Consensus       388 G~~ii~~~~~  397 (737)
T PRK02362        388 GEAVLLAKSY  397 (737)
T ss_pred             ceEEEEecCc
Confidence            8888888653

>PRK00254 ski2-like helicase; Provisional

Probab=100.00  E-value=8.8e-45  Score=362.19  Aligned_cols=336  Identities=19%  Similarity=0.254  Sum_probs=253.9

Q ss_pred             CCcCCCCCHHHHHHHHhCCCCCCChhhhhcccc-cccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           47 GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQ-AILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        47 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~-~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      .|+++++++.+.+.+.+.|+..|+|+|.++++. ++.++++++++|||||||+++.++++..+...+  .++||++|+++
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 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLREG--GKAVYLVPLKA   79 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhcC--CeEEEEeChHH
Confidence            477889999999999999999999999999986 788999999999999999999999998765432  38999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~  205 (423)
                      |+.|+++.++.+.. . ++++..++|+......  .+  +.++|+|+||+++..+++.....+.++++||+||+|.+.+ 
T Consensus        80 La~q~~~~~~~~~~-~-g~~v~~~~Gd~~~~~~--~~--~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~-  152 (720)
T PRK00254         80 LAEEKYREFKDWEK-L-GLRVAMTTGDYDSTDE--WL--GKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGS-  152 (720)
T ss_pred             HHHHHHHHHHHHhh-c-CCEEEEEeCCCCCchh--hh--ccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCC-
Confidence            99999999987643 3 7899999998764322  12  2369999999999988887666688999999999999976 


Q ss_pred             CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeCh-------HHHHHH
Q 014486          206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE-------LEKNRK  278 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~  278 (423)
                      ..+...+..+...+....|+|++|||+++. ..+.. ++..........+...........+.....       ......
T Consensus       153 ~~rg~~le~il~~l~~~~qiI~lSATl~n~-~~la~-wl~~~~~~~~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  230 (720)
T PRK00254        153 YDRGATLEMILTHMLGRAQILGLSATVGNA-EELAE-WLNAELVVSDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESL  230 (720)
T ss_pred             ccchHHHHHHHHhcCcCCcEEEEEccCCCH-HHHHH-HhCCccccCCCCCCcceeeEecCCeeeccCcchhcchHHHHHH
Confidence            567788888888888889999999999863 33433 333221111000000000000001111111       111122


Q ss_pred             HHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC---------------------------------CCCeEEEcCCCCHH
Q 014486          279 LNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC---------------------------------NFPSICIHSGMSQE  325 (423)
Q Consensus       279 l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~---------------------------------~~~~~~~~~~~~~~  325 (423)
                      +.+.++  .++++||||++++.+..++..|...                                 ...+..+|+++++.
T Consensus       231 ~~~~i~--~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~  308 (720)
T PRK00254        231 VYDAVK--KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRT  308 (720)
T ss_pred             HHHHHH--hCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHH
Confidence            333343  3578999999999988776555321                                 23588899999999


Q ss_pred             HHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE-------ccCCC-CcchhhhcccccCCCC--CceEEEEEecCc
Q 014486          326 ERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN-------YDMPD-SADTYLHRVGRAGRFG--TKGLAITFVSSA  395 (423)
Q Consensus       326 ~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~-------~~~~~-s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~  395 (423)
                      +|..+++.|++|.++|||||+++++|+|+|..++||.       ++.|. ++.+|.||+|||||.|  ..|.+++++.+.
T Consensus       309 eR~~ve~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~  388 (720)
T PRK00254        309 ERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTE  388 (720)
T ss_pred             HHHHHHHHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCc
Confidence            9999999999999999999999999999999999984       34333 4668999999999975  568899888754

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

Probab=100.00  E-value=2e-44  Score=347.48  Aligned_cols=335  Identities=26%  Similarity=0.322  Sum_probs=268.3

Q ss_pred             CCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC-----CCCeEEEEEecChHHH
Q 014486           53 LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN-----PGQVTALVLCHTRELA  127 (423)
Q Consensus        53 l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~-----~~~~~~lil~P~~~L~  127 (423)
                      +++.+.+.+... |..|||.|.++++.+..|+|+++.||||||||+++++|++..+...     ..+..||||+|.++|.
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            678899999888 9999999999999999999999999999999999999999887655     2346899999999999


Q ss_pred             HHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC--CCCCCccEEEEcCcchhhcc
Q 014486          128 YQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD--LSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       128 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~--~~~~~~~~vVvDE~h~~~~~  205 (423)
                      ..+..++..+.... |+.+.+.+|++...+..+...+. |+|+++||++|.-++....  ..+.++++||+||.|.+.+.
T Consensus        87 ~Di~~rL~~~~~~~-G~~v~vRhGDT~~~er~r~~~~P-PdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~s  164 (814)
T COG1201          87 NDIRRRLEEPLREL-GIEVAVRHGDTPQSEKQKMLKNP-PHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAES  164 (814)
T ss_pred             HHHHHHHHHHHHHc-CCccceecCCCChHHhhhccCCC-CcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhcc
Confidence            99999999998876 99999999999988877777776 7999999999988776543  34789999999999999753


Q ss_pred             ---CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccC--CceeeeccccccccccceEEEE-----EeChHHH
Q 014486          206 ---LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQD--PMEIYVDDEAKLTLHGLVQHYI-----KLSELEK  275 (423)
Q Consensus       206 ---~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~  275 (423)
                         ....-.+.++....+ ..|.|++|||..+. ....+.....  +..+......+...-.+.....     .......
T Consensus       165 KRG~~Lsl~LeRL~~l~~-~~qRIGLSATV~~~-~~varfL~g~~~~~~Iv~~~~~k~~~i~v~~p~~~~~~~~~~~~~~  242 (814)
T COG1201         165 KRGVQLALSLERLRELAG-DFQRIGLSATVGPP-EEVAKFLVGFGDPCEIVDVSAAKKLEIKVISPVEDLIYDEELWAAL  242 (814)
T ss_pred             ccchhhhhhHHHHHhhCc-ccEEEeehhccCCH-HHHHHHhcCCCCceEEEEcccCCcceEEEEecCCccccccchhHHH
Confidence               223445666666666 89999999998743 3444444443  2233222211110000000000     0011223


Q ss_pred             HHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCC-CCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCC
Q 014486          276 NRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECN-FPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDI  354 (423)
Q Consensus       276 ~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~  354 (423)
                      ...+.++++.+  ..+|||+|++..++.+...|+..+ .++...||.++...|..+.++|++|+.+.+|||+.++-|||+
T Consensus       243 ~~~i~~~v~~~--~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDi  320 (814)
T COG1201         243 YERIAELVKKH--RTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDI  320 (814)
T ss_pred             HHHHHHHHhhc--CcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhcccc
Confidence            45566666665  489999999999999999999987 788899999999999999999999999999999999999999


Q ss_pred             CCCCEEEEccCCCCcchhhhcccccCC-CCCceEEEEEecC
Q 014486          355 ERVNIVINYDMPDSADTYLHRVGRAGR-FGTKGLAITFVSS  394 (423)
Q Consensus       355 ~~~~~vi~~~~~~s~~~~~Q~~GR~~R-~g~~~~~~~~~~~  394 (423)
                      .+++.||+++.|+++..+.||+||+|+ .|...+++++..+
T Consensus       321 G~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         321 GDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             CCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecC
Confidence            999999999999999999999999996 5666777777765

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

Probab=100.00  E-value=2.4e-44  Score=334.94  Aligned_cols=324  Identities=21%  Similarity=0.283  Sum_probs=256.8

Q ss_pred             HHHHh-CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           59 RAIVD-SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        59 ~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      ..|.+ +|+..+++-|.++|..++.++++++..|||.|||++|.+|++-.-.      .+|||+|..+|...+.+.++..
T Consensus         7 ~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~~G------~TLVVSPLiSLM~DQV~~l~~~   80 (590)
T COG0514           7 QVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLLEG------LTLVVSPLISLMKDQVDQLEAA   80 (590)
T ss_pred             HHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhcCC------CEEEECchHHHHHHHHHHHHHc
Confidence            34444 3899999999999999999999999999999999999999988722      7899999999999999888875


Q ss_pred             hccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc-CCcHHHHH
Q 014486          138 STYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES-LDMRRDVQ  213 (423)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~-~~~~~~~~  213 (423)
                           ++.+..+.+..+..+..   ..+..+..++++.+|+++..-.....+.-..+.+++|||||+++.| ++|++.+.
T Consensus        81 -----Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~  155 (590)
T COG0514          81 -----GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYR  155 (590)
T ss_pred             -----CceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhHH
Confidence                 67888888876655544   3445577899999999886532222223456789999999999997 67998887


Q ss_pred             HHHHhCCC--CceEEEEeccCCccHHHHHHHhccCCc-eeeeccccccccccceEEEEEe-ChHHHHHHHHHHHHhhcCC
Q 014486          214 EIFKMTPH--DKQVMMFSATLSKEIRPVCKKFMQDPM-EIYVDDEAKLTLHGLVQHYIKL-SELEKNRKLNDLLDALDFN  289 (423)
Q Consensus       214 ~~~~~~~~--~~~~v~~SAT~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~ll~~~~~~  289 (423)
                      .+......  +.+++.+|||.++.+...+...+.... .++......   +++....... ....+...+.+ +.....+
T Consensus       156 ~lg~l~~~~~~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~sfdR---pNi~~~v~~~~~~~~q~~fi~~-~~~~~~~  231 (590)
T COG0514         156 RLGRLRAGLPNPPVLALTATATPRVRDDIREQLGLQDANIFRGSFDR---PNLALKVVEKGEPSDQLAFLAT-VLPQLSK  231 (590)
T ss_pred             HHHHHHhhCCCCCEEEEeCCCChHHHHHHHHHhcCCCcceEEecCCC---chhhhhhhhcccHHHHHHHHHh-hccccCC
Confidence            77543322  678999999999988877666554322 233222221   2221111111 12223332222 1244557


Q ss_pred             cEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCc
Q 014486          290 QVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSA  369 (423)
Q Consensus       290 ~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~  369 (423)
                      +.||||.+++.++.+++.|...|+.+..||++|+..+|..+.+.|..++++|+|||.++++|||.|++++||||++|.|+
T Consensus       232 ~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~  311 (590)
T COG0514         232 SGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSI  311 (590)
T ss_pred             CeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCCCH
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhhhcccccCCCCCceEEEEEecCccc
Q 014486          370 DTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       370 ~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      +.|.|-+|||||.|.+..+++++++.+.
T Consensus       312 EsYyQE~GRAGRDG~~a~aill~~~~D~  339 (590)
T COG0514         312 ESYYQETGRAGRDGLPAEAILLYSPEDI  339 (590)
T ss_pred             HHHHHHHhhccCCCCcceEEEeeccccH
Confidence            9999999999999999999999997553

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=100.00  E-value=5.4e-43  Score=349.24  Aligned_cols=324  Identities=21%  Similarity=0.201  Sum_probs=247.8

Q ss_pred             CCCCHHHHHHHHh-CCCCCCChhhhhcccccccC------CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           51 FLLKPELLRAIVD-SGFEHPSEVQHECIPQAILG------MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        51 ~~l~~~~~~~l~~-~~~~~~~~~Q~~~i~~~~~~------~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      ++.+...++.+.+ .+| .||+.|.++++.++.+      .+.+++||||+|||.+++.+++..+..+   .+++|++||
T Consensus       434 ~~~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~g---~qvlvLvPT  509 (926)
T TIGR00580       434 FPPDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDG---KQVAVLVPT  509 (926)
T ss_pred             CCCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHhC---CeEEEEeCc
Confidence            4455566666666 488 5999999999999885      6899999999999999999988876543   389999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcc
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECD  200 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h  200 (423)
                      ++||.|+++.++++.... ++++..++|+.+..+..   ..+.++.++|+|+||..+     .....+.+++++|+||+|
T Consensus       510 ~~LA~Q~~~~f~~~~~~~-~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll-----~~~v~f~~L~llVIDEah  583 (926)
T TIGR00580       510 TLLAQQHFETFKERFANF-PVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLL-----QKDVKFKDLGLLIIDEEQ  583 (926)
T ss_pred             HHHHHHHHHHHHHHhccC-CcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHh-----hCCCCcccCCEEEeeccc
Confidence            999999999999887665 67888888877654433   345566689999999533     245678899999999999


Q ss_pred             hhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHH
Q 014486          201 KMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLN  280 (423)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  280 (423)
                      ++..      .....+..++...++++||||+.+...........++..+...+...   ..+...+...........+.
T Consensus       584 rfgv------~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~R---~~V~t~v~~~~~~~i~~~i~  654 (926)
T TIGR00580       584 RFGV------KQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDR---LPVRTFVMEYDPELVREAIR  654 (926)
T ss_pred             ccch------hHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCCCc---cceEEEEEecCHHHHHHHHH
Confidence            8632      22334455667889999999987765554433344444443332221   11222222222111111111


Q ss_pred             HHHHhhcCCcEEEEEcChhhHHHHHHHHHhC--CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCC
Q 014486          281 DLLDALDFNQVVIFVKSVSRAAELNKLLVEC--NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVN  358 (423)
Q Consensus       281 ~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~  358 (423)
                      .-+  ..+++++|||++++.++.+++.|+..  ++++..+||+|++.+|..++.+|++|+.+|||||+++++|+|+|+++
T Consensus       655 ~el--~~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~  732 (926)
T TIGR00580       655 REL--LRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNAN  732 (926)
T ss_pred             HHH--HcCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCC
Confidence            111  24578999999999999999999985  78899999999999999999999999999999999999999999999


Q ss_pred             EEEEccCCC-CcchhhhcccccCCCCCceEEEEEecCc
Q 014486          359 IVINYDMPD-SADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       359 ~vi~~~~~~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      +||+++.|. +..+|.|++||+||.|+.|.|++++.+.
T Consensus       733 ~VIi~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~  770 (926)
T TIGR00580       733 TIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQ  770 (926)
T ss_pred             EEEEecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCc
Confidence            999999865 6778999999999999999999998653

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

>PRK01172 ski2-like helicase; Provisional

Probab=100.00  E-value=5.1e-43  Score=348.28  Aligned_cols=333  Identities=21%  Similarity=0.307  Sum_probs=244.2

Q ss_pred             CCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           47 GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        47 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      .|+++++++.+.+.+.+.+|. |+++|.++++.+..++++++++|||||||+++.++++..+..+   .+++|++|+++|
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            467889999999999999986 9999999999999999999999999999999999998876543   289999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccC
Q 014486          127 AYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESL  206 (423)
Q Consensus       127 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~  206 (423)
                      +.|+++.++++.. . +.++...+|+......  .+ .. ++|+|+||+++..++.+....+.++++||+||+|.+.+ .
T Consensus        78 a~q~~~~~~~l~~-~-g~~v~~~~G~~~~~~~--~~-~~-~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d-~  150 (674)
T PRK01172         78 AMEKYEELSRLRS-L-GMRVKISIGDYDDPPD--FI-KR-YDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGD-E  150 (674)
T ss_pred             HHHHHHHHHHHhh-c-CCeEEEEeCCCCCChh--hh-cc-CCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccC-C
Confidence            9999999987643 2 6788888887654322  12 22 59999999999988887666688999999999999876 4


Q ss_pred             CcHHHHHHHH---HhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccc-cc---eEEEEEeChHHHHHHH
Q 014486          207 DMRRDVQEIF---KMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLH-GL---VQHYIKLSELEKNRKL  279 (423)
Q Consensus       207 ~~~~~~~~~~---~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~---~~~~~~~~~~~~~~~l  279 (423)
                      .+...+..+.   ...++..|+|++|||+++. ..+.+ ++.... +..... ..+.. .+   ...+.. ........+
T Consensus       151 ~rg~~le~ll~~~~~~~~~~riI~lSATl~n~-~~la~-wl~~~~-~~~~~r-~vpl~~~i~~~~~~~~~-~~~~~~~~~  225 (674)
T PRK01172        151 DRGPTLETVLSSARYVNPDARILALSATVSNA-NELAQ-WLNASL-IKSNFR-PVPLKLGILYRKRLILD-GYERSQVDI  225 (674)
T ss_pred             CccHHHHHHHHHHHhcCcCCcEEEEeCccCCH-HHHHH-HhCCCc-cCCCCC-CCCeEEEEEecCeeeec-ccccccccH
Confidence            5554444443   3456688999999999763 33333 332211 100000 00000 00   000000 000011112


Q ss_pred             HHHHHh--hcCCcEEEEEcChhhHHHHHHHHHhC-------------------------CCCeEEEcCCCCHHHHHHHHH
Q 014486          280 NDLLDA--LDFNQVVIFVKSVSRAAELNKLLVEC-------------------------NFPSICIHSGMSQEERLTRYK  332 (423)
Q Consensus       280 ~~ll~~--~~~~~~ivf~~~~~~~~~l~~~L~~~-------------------------~~~~~~~~~~~~~~~r~~~~~  332 (423)
                      ..++..  ..++++||||++++.+..+++.|...                         ...+..+|+++++.+|..+++
T Consensus       226 ~~~i~~~~~~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~  305 (674)
T PRK01172        226 NSLIKETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEE  305 (674)
T ss_pred             HHHHHHHHhCCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHH
Confidence            333332  24679999999999999998888653                         124677899999999999999


Q ss_pred             hhhcCCccEEEEcCccccCCCCCCCCEEEEccC---------CCCcchhhhcccccCCCCC--ceEEEEEecCcc
Q 014486          333 GFKEGNKRILVATDLVGRGIDIERVNIVINYDM---------PDSADTYLHRVGRAGRFGT--KGLAITFVSSAS  396 (423)
Q Consensus       333 ~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~---------~~s~~~~~Q~~GR~~R~g~--~~~~~~~~~~~~  396 (423)
                      .|++|.++|||||+++++|+|+|+.. ||+.+.         |.++.+|.||+|||||.|.  .|.+++++....
T Consensus       306 ~f~~g~i~VLvaT~~la~Gvnipa~~-VII~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~  379 (674)
T PRK01172        306 MFRNRYIKVIVATPTLAAGVNLPARL-VIVRDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPA  379 (674)
T ss_pred             HHHcCCCeEEEecchhhccCCCcceE-EEEcCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCcc
Confidence            99999999999999999999999864 454432         4577889999999999985  567777765443

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

Probab=100.00  E-value=3.5e-42  Score=333.89  Aligned_cols=316  Identities=21%  Similarity=0.260  Sum_probs=235.7

Q ss_pred             CCCCCCChhhhhcccccccCC-ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEE-EecChHHHHHHHHHHHHHhccC
Q 014486           64 SGFEHPSEVQHECIPQAILGM-DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV-LCHTRELAYQICHEFERFSTYL  141 (423)
Q Consensus        64 ~~~~~~~~~Q~~~i~~~~~~~-~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~li-l~P~~~L~~q~~~~~~~~~~~~  141 (423)
                      .||. |+|+|.++++.++.|+ ++++.+|||||||.++.++++... .....++.|| ++|+++|+.|+++.+.++....
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~~-~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l   89 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAVE-IGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERL   89 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhcccc-ccccccceEEEeCchHHHHHHHHHHHHHHHHHh
Confidence            3886 9999999999999998 577889999999997665555432 2233345555 6799999999999999988754


Q ss_pred             C----------------------CceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHH-HHhcC--------CC---C
Q 014486          142 P----------------------DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA-LARDK--------DL---S  187 (423)
Q Consensus       142 ~----------------------~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~-~~~~~--------~~---~  187 (423)
                      +                      .+++..++||.+...+...+..+ ++|+|+|++.+.. .+.++        .+   .
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~-p~IIVgT~D~i~sr~L~~gYg~~~~~~pi~ag~  168 (844)
T TIGR02621        90 PDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHR-PAVIVGTVDMIGSRLLFSGYGCGFKSRPLHAGF  168 (844)
T ss_pred             cccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCC-CcEEEECHHHHcCCccccccccccccccchhhh
Confidence            2                      47899999999998888888776 6999999765543 11100        01   2


Q ss_pred             CCCccEEEEcCcchhhccCCcHHHHHHHHHhC--CCC---ceEEEEeccCCccHHHHHHHhccCCceeeecccccccccc
Q 014486          188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMT--PHD---KQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHG  262 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~--~~~---~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (423)
                      +.+++++|+||||  +. .+|...+..+...+  ++.   .|+++||||++.+.......+...+..+.+... ......
T Consensus       169 L~~v~~LVLDEAD--Ld-~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~~-~l~a~k  244 (844)
T TIGR02621       169 LGQDALIVHDEAH--LE-PAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLKK-RLAAKK  244 (844)
T ss_pred             hccceEEEEehhh--hc-cccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeecccc-cccccc
Confidence            5789999999999  34 68999999999864  332   699999999998887776666666654443221 122222


Q ss_pred             ceEEEEEeChHHHHHHHHHHH---HhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHH-----HHHHhh
Q 014486          263 LVQHYIKLSELEKNRKLNDLL---DALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERL-----TRYKGF  334 (423)
Q Consensus       263 ~~~~~~~~~~~~~~~~l~~ll---~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~-----~~~~~f  334 (423)
                      +.+ +.......+...+...+   ....++++||||++++.++.+++.|+..++  ..+||+|++.+|.     .+++.|
T Consensus       245 i~q-~v~v~~e~Kl~~lv~~L~~ll~e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~F  321 (844)
T TIGR02621       245 IVK-LVPPSDEKFLSTMVKELNLLMKDSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNRF  321 (844)
T ss_pred             eEE-EEecChHHHHHHHHHHHHHHHhhCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHHH
Confidence            233 33444433332222221   123457899999999999999999998876  8999999999999     788999


Q ss_pred             hc----CC-------ccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCce-EEEEEe
Q 014486          335 KE----GN-------KRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKG-LAITFV  392 (423)
Q Consensus       335 ~~----~~-------~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~-~~~~~~  392 (423)
                      ++    +.       ..|||||+++++|+|++. ++||++..|  ...|+||+||+||.|+.+ ..+.++
T Consensus       322 k~~~~~g~~~~~~~g~~ILVATdVaerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv  388 (844)
T TIGR02621       322 LPQMLSGSRARPQQGTVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVV  388 (844)
T ss_pred             hccccccccccccccceEEeccchhhhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEE
Confidence            87    43       679999999999999986 888887655  589999999999999853 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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=100.00  E-value=4.9e-42  Score=349.53  Aligned_cols=317  Identities=20%  Similarity=0.193  Sum_probs=245.7

Q ss_pred             HHHHHHHhCCCCCCChhhhhcccccccC------CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHH
Q 014486           56 ELLRAIVDSGFEHPSEVQHECIPQAILG------MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQ  129 (423)
Q Consensus        56 ~~~~~l~~~~~~~~~~~Q~~~i~~~~~~------~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  129 (423)
                      ...+.....+| .||+.|.++++.++.+      .+.+++++||+|||.+++.++......   +.+++|++||++||.|
T Consensus       589 ~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~---g~qvlvLvPT~eLA~Q  664 (1147)
T PRK10689        589 QYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVEN---HKQVAVLVPTTLLAQQ  664 (1147)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHH
Confidence            34445556688 7999999999999986      789999999999999988777665543   3389999999999999


Q ss_pred             HHHHHHHHhccCCCceEEEEEcCcchHHHHHHH---hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccC
Q 014486          130 ICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL---KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESL  206 (423)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~  206 (423)
                      +++.+++..... ++++..++++.+..++...+   .++.++|+|+||+.+.     ....+.+++++|+||+|++..  
T Consensus       665 ~~~~f~~~~~~~-~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~-----~~v~~~~L~lLVIDEahrfG~--  736 (1147)
T PRK10689        665 HYDNFRDRFANW-PVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQ-----SDVKWKDLGLLIVDEEHRFGV--  736 (1147)
T ss_pred             HHHHHHHhhccC-CceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHh-----CCCCHhhCCEEEEechhhcch--
Confidence            999999876555 57888888888776665443   3466899999997442     345678899999999998732  


Q ss_pred             CcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeCh-HHHHHHHHHHHHh
Q 014486          207 DMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE-LEKNRKLNDLLDA  285 (423)
Q Consensus       207 ~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~ll~~  285 (423)
                      ..    ...++.++.+.|++++|||+.+....+....+.++..+...+....   .+......... ..+...+.++.  
T Consensus       737 ~~----~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~r~---~v~~~~~~~~~~~~k~~il~el~--  807 (1147)
T PRK10689        737 RH----KERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRL---AVKTFVREYDSLVVREAILREIL--  807 (1147)
T ss_pred             hH----HHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCCCC---CceEEEEecCcHHHHHHHHHHHh--
Confidence            22    2334566778999999999988777766666666665554333221   12222222221 12222233332  


Q ss_pred             hcCCcEEEEEcChhhHHHHHHHHHhC--CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEc
Q 014486          286 LDFNQVVIFVKSVSRAAELNKLLVEC--NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINY  363 (423)
Q Consensus       286 ~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~  363 (423)
                       .+++++|||++++.++.+++.|+..  +.++..+||+|++.+|.+++.+|++|+.+|||||+++++|+|+|++++||..
T Consensus       808 -r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi~  886 (1147)
T PRK10689        808 -RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIE  886 (1147)
T ss_pred             -cCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEEe
Confidence             3578999999999999999999887  7889999999999999999999999999999999999999999999999965


Q ss_pred             cCC-CCcchhhhcccccCCCCCceEEEEEecC
Q 014486          364 DMP-DSADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       364 ~~~-~s~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                      +.. .+..+|.|++||+||.|+.|.|++++.+
T Consensus       887 ~ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~  918 (1147)
T PRK10689        887 RADHFGLAQLHQLRGRVGRSHHQAYAWLLTPH  918 (1147)
T ss_pred             cCCCCCHHHHHHHhhccCCCCCceEEEEEeCC
Confidence            543 4667899999999999999999998864

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=100.00  E-value=1.5e-41  Score=334.88  Aligned_cols=320  Identities=20%  Similarity=0.257  Sum_probs=236.6

Q ss_pred             HHHHHHHHh-CCCCCCChhhhhcccccccC------CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHH
Q 014486           55 PELLRAIVD-SGFEHPSEVQHECIPQAILG------MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELA  127 (423)
Q Consensus        55 ~~~~~~l~~-~~~~~~~~~Q~~~i~~~~~~------~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~  127 (423)
                      ..+.+.+.+ .+| .||++|+++++.+..+      .+.+++||||||||++|+++++..+..   +.+++|++||++||
T Consensus       248 ~~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~---g~q~lilaPT~~LA  323 (681)
T PRK10917        248 GELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA---GYQAALMAPTEILA  323 (681)
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEeccHHHH
Confidence            344444444 477 6999999999999886      379999999999999999999887754   33899999999999


Q ss_pred             HHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          128 YQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       128 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      .|+++.++++.... ++++..++|+.+.....   ..+.++.++|+|+||+.+..     ...+.++++||+||+|++..
T Consensus       324 ~Q~~~~l~~l~~~~-~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~v~~~~l~lvVIDE~Hrfg~  397 (681)
T PRK10917        324 EQHYENLKKLLEPL-GIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD-----DVEFHNLGLVIIDEQHRFGV  397 (681)
T ss_pred             HHHHHHHHHHHhhc-CcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc-----cchhcccceEEEechhhhhH
Confidence            99999999998765 78999999998764443   44556778999999987642     34578899999999998742


Q ss_pred             cCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHH
Q 014486          205 SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLD  284 (423)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~  284 (423)
                        ..+.    .+......+++++||||+.+...............+...+.   ....+......  ...+...+..+.+
T Consensus       398 --~qr~----~l~~~~~~~~iL~~SATp~prtl~~~~~g~~~~s~i~~~p~---~r~~i~~~~~~--~~~~~~~~~~i~~  466 (681)
T PRK10917        398 --EQRL----ALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPP---GRKPITTVVIP--DSRRDEVYERIRE  466 (681)
T ss_pred             --HHHH----HHHhcCCCCCEEEEeCCCCHHHHHHHHcCCCceEEEecCCC---CCCCcEEEEeC--cccHHHHHHHHHH
Confidence              2222    22333456889999999876544332211111111111111   11112222222  2222222222222


Q ss_pred             h-hcCCcEEEEEcChh--------hHHHHHHHHHhC--CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCC
Q 014486          285 A-LDFNQVVIFVKSVS--------RAAELNKLLVEC--NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGID  353 (423)
Q Consensus       285 ~-~~~~~~ivf~~~~~--------~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld  353 (423)
                      . ..+++++|||+.++        .+..+++.|...  ++++..+||+|++.+|..+++.|++|+.+|||||+++++|+|
T Consensus       467 ~~~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiD  546 (681)
T PRK10917        467 EIAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVD  546 (681)
T ss_pred             HHHcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcc
Confidence            2 24578999999654        455667777765  468999999999999999999999999999999999999999


Q ss_pred             CCCCCEEEEccCCC-CcchhhhcccccCCCCCceEEEEEecCc
Q 014486          354 IERVNIVINYDMPD-SADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       354 ~~~~~~vi~~~~~~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      +|++++||+++.|. +..++.|++||+||.|.+|.|+++++..
T Consensus       547 ip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~~  589 (681)
T PRK10917        547 VPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDP  589 (681)
T ss_pred             cCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECCC
Confidence            99999999999987 5788999999999999999999999633

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

Probab=100.00  E-value=4.1e-42  Score=306.03  Aligned_cols=335  Identities=21%  Similarity=0.298  Sum_probs=250.5

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      +.-++|.||.......+.+ +.+++.|||.|||+++++.+...+...++  ++|+++||+.|+.|.+..+.++... |.-
T Consensus        12 ~~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~--kvlfLAPTKPLV~Qh~~~~~~v~~i-p~~   87 (542)
T COG1111          12 NTIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGG--KVLFLAPTKPLVLQHAEFCRKVTGI-PED   87 (542)
T ss_pred             ccccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCC--eEEEecCCchHHHHHHHHHHHHhCC-Chh
Confidence            3447899999988877776 89999999999999999988888877665  8999999999999999999998755 356


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCce
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQ  224 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~  224 (423)
                      .+..++|.....+....+.++  +|+|+||+.+.+-+..+.+++.++.++|+||||+..++ .....+.+.+....+++.
T Consensus        88 ~i~~ltGev~p~~R~~~w~~~--kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGn-yAYv~Va~~y~~~~k~~~  164 (542)
T COG1111          88 EIAALTGEVRPEEREELWAKK--KVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGN-YAYVFVAKEYLRSAKNPL  164 (542)
T ss_pred             heeeecCCCChHHHHHHHhhC--CEEEeccHHHHhHHhcCccChHHceEEEechhhhccCc-chHHHHHHHHHHhccCce
Confidence            788999998888787777776  99999999999988999999999999999999999873 444455555555566778


Q ss_pred             EEEEeccCCccHHHHH---HHhccCCceeeeccc----------------------------------------------
Q 014486          225 VMMFSATLSKEIRPVC---KKFMQDPMEIYVDDE----------------------------------------------  255 (423)
Q Consensus       225 ~v~~SAT~~~~~~~~~---~~~~~~~~~~~~~~~----------------------------------------------  255 (423)
                      ++++||||..+.....   +.+....+.+.....                                              
T Consensus       165 ilgLTASPGs~~ekI~eV~~nLgIe~vevrTE~d~DV~~Yv~~~kve~ikV~lp~e~~~ir~~l~~~l~~~Lk~L~~~g~  244 (542)
T COG1111         165 ILGLTASPGSDLEKIQEVVENLGIEKVEVRTEEDPDVRPYVKKIKVEWIKVDLPEEIKEIRDLLRDALKPRLKPLKELGV  244 (542)
T ss_pred             EEEEecCCCCCHHHHHHHHHhCCcceEEEecCCCccHHHhhccceeEEEeccCcHHHHHHHHHHHHHHHHHHHHHHHcCc
Confidence            9999999854432211   111111111110000                                              


Q ss_pred             ----c---c-----------------------------------------------------------ccc--c-----c
Q 014486          256 ----A---K-----------------------------------------------------------LTL--H-----G  262 (423)
Q Consensus       256 ----~---~-----------------------------------------------------------~~~--~-----~  262 (423)
                          .   .                                                           ...  .     .
T Consensus       245 ~~~~~~~~~kdl~~~~~~~~~~a~~~~~~~~~~l~~~a~~~kl~~a~elletqGi~~~~~Yl~~l~e~~~~~~sk~a~~l  324 (542)
T COG1111         245 IESSSPVSKKDLLELRQIRLIMAKNEDSDKFRLLSVLAEAIKLAHALELLETQGIRPFYQYLEKLEEEATKGGSKAAKSL  324 (542)
T ss_pred             eeccCcccHhHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHhcccchHHHHHH
Confidence                0   0                                                           000  0     0


Q ss_pred             ------------ceEEEEEeChHHHHHHHHHHHH----hhcCCcEEEEEcChhhHHHHHHHHHhCCCCeE-EE-------
Q 014486          263 ------------LVQHYIKLSELEKNRKLNDLLD----ALDFNQVVIFVKSVSRAAELNKLLVECNFPSI-CI-------  318 (423)
Q Consensus       263 ------------~~~~~~~~~~~~~~~~l~~ll~----~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~-~~-------  318 (423)
                                  ............|...+.++++    ..+..++|||++.+++|+.+.+.|...+..+. .+       
T Consensus       325 ~~d~~~~~al~~~~~~~~~~v~HPKl~~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r~  404 (542)
T COG1111         325 LADPYFKRALRLLIRADESGVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASRE  404 (542)
T ss_pred             hcChhhHHHHHHHHHhccccCCCccHHHHHHHHHHHHhcCCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeeccccc
Confidence                        0000000001112223333332    22456899999999999999999999987774 22       


Q ss_pred             -cCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCc--
Q 014486          319 -HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSA--  395 (423)
Q Consensus       319 -~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~--  395 (423)
                       ..+|++.++.++++.|+.|+.+|||||+++++|+|+|.++.||+|++..|+-.++||.||+||. ++|.+++++...  
T Consensus       405 ~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~gtr  483 (542)
T COG1111         405 GDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEGTR  483 (542)
T ss_pred             cccccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecCch
Confidence             2579999999999999999999999999999999999999999999999999999999999997 788999998876  


Q ss_pred             ccHHHHHHHHHH
Q 014486          396 SDSDILNQVSKF  407 (423)
Q Consensus       396 ~~~~~~~~~~~~  407 (423)
                      ++..++.++++.
T Consensus       484 deayy~~s~rke  495 (542)
T COG1111         484 DEAYYYSSRRKE  495 (542)
T ss_pred             HHHHHHHHHHHH
Confidence            444444444443

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=100.00  E-value=1.4e-41  Score=333.04  Aligned_cols=319  Identities=20%  Similarity=0.253  Sum_probs=234.1

Q ss_pred             HHHHHHhCCCCCCChhhhhcccccccC------CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           57 LLRAIVDSGFEHPSEVQHECIPQAILG------MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        57 ~~~~l~~~~~~~~~~~Q~~~i~~~~~~------~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      +.+.+...+| +||+.|+++++.++.+      .+.+++||||||||++|+++++..+..+   .+++|++||++||.|+
T Consensus       225 ~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~g---~qvlilaPT~~LA~Q~  300 (630)
T TIGR00643       225 LTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAG---YQVALMAPTEILAEQH  300 (630)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHcC---CcEEEECCHHHHHHHH
Confidence            3455566688 7999999999999875      2579999999999999999998877643   3899999999999999


Q ss_pred             HHHHHHHhccCCCceEEEEEcCcchHHH---HHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCC
Q 014486          131 CHEFERFSTYLPDIKVAVFYGGVNIKIH---KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLD  207 (423)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~  207 (423)
                      ++.+++++... ++++..++|+......   ...+.++.++|+|+||..+..     ...+.++++||+||+|++..  .
T Consensus       301 ~~~~~~l~~~~-gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~fg~--~  372 (630)
T TIGR00643       301 YNSLRNLLAPL-GIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRFGV--E  372 (630)
T ss_pred             HHHHHHHhccc-CcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhccH--H
Confidence            99999988765 7899999999876553   344556778999999987753     35678899999999998643  2


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhh-
Q 014486          208 MRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDAL-  286 (423)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~-  286 (423)
                      .+..+...... ...++++++|||+.+.......  ........+... ......+.....  ....+...+..+.+.. 
T Consensus       373 qr~~l~~~~~~-~~~~~~l~~SATp~prtl~l~~--~~~l~~~~i~~~-p~~r~~i~~~~~--~~~~~~~~~~~i~~~l~  446 (630)
T TIGR00643       373 QRKKLREKGQG-GFTPHVLVMSATPIPRTLALTV--YGDLDTSIIDEL-PPGRKPITTVLI--KHDEKDIVYEFIEEEIA  446 (630)
T ss_pred             HHHHHHHhccc-CCCCCEEEEeCCCCcHHHHHHh--cCCcceeeeccC-CCCCCceEEEEe--CcchHHHHHHHHHHHHH
Confidence            22222221111 1257899999998765433321  111111111110 011111222222  2222222222233332 


Q ss_pred             cCCcEEEEEcChh--------hHHHHHHHHHhC--CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCC
Q 014486          287 DFNQVVIFVKSVS--------RAAELNKLLVEC--NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIER  356 (423)
Q Consensus       287 ~~~~~ivf~~~~~--------~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~  356 (423)
                      .+++++|||+..+        .+..+++.|...  ++++..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|+
T Consensus       447 ~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GvDiP~  526 (630)
T TIGR00643       447 KGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN  526 (630)
T ss_pred             hCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecCcccCC
Confidence            4578999998763        455667777653  678999999999999999999999999999999999999999999


Q ss_pred             CCEEEEccCCC-CcchhhhcccccCCCCCceEEEEEec
Q 014486          357 VNIVINYDMPD-SADTYLHRVGRAGRFGTKGLAITFVS  393 (423)
Q Consensus       357 ~~~vi~~~~~~-s~~~~~Q~~GR~~R~g~~~~~~~~~~  393 (423)
                      +++||+++.|. +..++.|++||+||.|++|.|++++.
T Consensus       527 v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       527 ATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             CcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEEC
Confidence            99999999986 67889999999999999999999984

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=100.00  E-value=2.3e-40  Score=338.99  Aligned_cols=321  Identities=21%  Similarity=0.283  Sum_probs=229.7

Q ss_pred             EEccCCCcchhHHHHHHhhccCCC----------CCCeEEEEEecChHHHHHHHHHHHHHh-----------ccCCCceE
Q 014486           88 CQAKSGMGKTAVFVLSTLQQTEPN----------PGQVTALVLCHTRELAYQICHEFERFS-----------TYLPDIKV  146 (423)
Q Consensus        88 i~~~tGsGKT~~~~~~~~~~~~~~----------~~~~~~lil~P~~~L~~q~~~~~~~~~-----------~~~~~~~~  146 (423)
                      |++|||||||++|++|++..+...          ..+.++|||+|+++|+.|+.++++...           ....++++
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            579999999999999999876532          234689999999999999999887522           12247899


Q ss_pred             EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC-CCCCCCccEEEEcCcchhhcc---CCcHHHHHHHHHhCCCC
Q 014486          147 AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK-DLSLKNVRHFILDECDKMLES---LDMRRDVQEIFKMTPHD  222 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~-~~~~~~~~~vVvDE~h~~~~~---~~~~~~~~~~~~~~~~~  222 (423)
                      ...+|+.+..++.+.+.+. ++|+|+||++|..++.+. ...+.++++|||||+|.+.+.   ..+...+.++...++..
T Consensus        81 ~vrtGDt~~~eR~rll~~p-pdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~~~  159 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNP-PDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLHTS  159 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCC-CCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhCCCC
Confidence            9999999988877766655 699999999998877643 346899999999999999862   12455677777777788


Q ss_pred             ceEEEEeccCCccHHHHHHHhccC-CceeeeccccccccccceEEEEEeChHH-----------------H----HHHHH
Q 014486          223 KQVMMFSATLSKEIRPVCKKFMQD-PMEIYVDDEAKLTLHGLVQHYIKLSELE-----------------K----NRKLN  280 (423)
Q Consensus       223 ~~~v~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~----~~~l~  280 (423)
                      .|+|++|||+++. ..+.+.+... +..+... ..... ..+ ...+......                 .    .....
T Consensus       160 ~QrIgLSATI~n~-eevA~~L~g~~pv~Iv~~-~~~r~-~~l-~v~vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~  235 (1490)
T PRK09751        160 AQRIGLSATVRSA-SDVAAFLGGDRPVTVVNP-PAMRH-PQI-RIVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIET  235 (1490)
T ss_pred             CeEEEEEeeCCCH-HHHHHHhcCCCCEEEECC-CCCcc-cce-EEEEecCchhhccccccccccccchhhhhhhhHHHHH
Confidence            9999999999873 4444433322 3333221 11111 111 1111111100                 0    01111


Q ss_pred             HHHHhh-cCCcEEEEEcChhhHHHHHHHHHhCC---------------------------------CCeEEEcCCCCHHH
Q 014486          281 DLLDAL-DFNQVVIFVKSVSRAAELNKLLVECN---------------------------------FPSICIHSGMSQEE  326 (423)
Q Consensus       281 ~ll~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~---------------------------------~~~~~~~~~~~~~~  326 (423)
                      .++... ..+++||||+++..++.++..|++..                                 ..+..+||++++.+
T Consensus       236 ~il~~i~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkee  315 (1490)
T PRK09751        236 GILDEVLRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQ  315 (1490)
T ss_pred             HHHHHHhcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHH
Confidence            233222 35789999999999999999887531                                 12457899999999


Q ss_pred             HHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCC-CCceEEEEEecCccc-HHHHHHH
Q 014486          327 RLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRF-GTKGLAITFVSSASD-SDILNQV  404 (423)
Q Consensus       327 r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~-g~~~~~~~~~~~~~~-~~~~~~~  404 (423)
                      |..+++.|++|++++||||+.+++|||++++++||+++.|.++.+|+||+||+||. |..+.++++..+..+ .+....+
T Consensus       316 R~~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p~~r~dlle~~~~v  395 (1490)
T PRK09751        316 RAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFPRTRRDLVDSAVIV  395 (1490)
T ss_pred             HHHHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEeCcHHHHHhhHHHH
Confidence            99999999999999999999999999999999999999999999999999999996 444555644443222 1222235


Q ss_pred             HHHHhcchh
Q 014486          405 SKFMFLLIG  413 (423)
Q Consensus       405 ~~~~~~~~~  413 (423)
                      +.++.-.++
T Consensus       396 e~~l~g~iE  404 (1490)
T PRK09751        396 ECMFAGRLE  404 (1490)
T ss_pred             HHHhcCCCC
Confidence            555554443

>PRK09401 reverse gyrase; Reviewed

Probab=100.00  E-value=1.2e-39  Score=332.94  Aligned_cols=284  Identities=24%  Similarity=0.337  Sum_probs=216.6

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      |+ .|+++|+.+++.++.|+++++.||||+|||.. .++++..+..  .+++++|++||++|+.|+++.++.+.... ++
T Consensus        78 G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~f-~l~~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~~l~~~~-~~  152 (1176)
T PRK09401         78 GS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTTF-GLVMSLYLAK--KGKKSYIIFPTRLLVEQVVEKLEKFGEKV-GC  152 (1176)
T ss_pred             CC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHHH-HHHHHHHHHh--cCCeEEEEeccHHHHHHHHHHHHHHhhhc-Cc
Confidence            66 89999999999999999999999999999964 4444443332  23489999999999999999999998765 67


Q ss_pred             eEEEEEcCcch-----HHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc----------CCcH
Q 014486          145 KVAVFYGGVNI-----KIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES----------LDMR  209 (423)
Q Consensus       145 ~~~~~~~~~~~-----~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~----------~~~~  209 (423)
                      .+..+.++.+.     ......+.++.++|+|+||++|.+++.  .+....++++|+||||+++.+          .+|.
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            77777766542     233344555668999999999998776  345567999999999999852          3563


Q ss_pred             -HHHHHHHHhCCC------------------------CceEEEEeccCCcc-HHHHHHHhccCCceeeeccccccccccc
Q 014486          210 -RDVQEIFKMTPH------------------------DKQVMMFSATLSKE-IRPVCKKFMQDPMEIYVDDEAKLTLHGL  263 (423)
Q Consensus       210 -~~~~~~~~~~~~------------------------~~~~v~~SAT~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  263 (423)
                       ..+..++..++.                        ..|++++|||+++. ...   .++..+..+.+.... ....++
T Consensus       231 ~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~---~l~~~ll~~~v~~~~-~~~rnI  306 (1176)
T PRK09401        231 EEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV---KLFRELLGFEVGSPV-FYLRNI  306 (1176)
T ss_pred             HHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH---HHhhccceEEecCcc-cccCCc
Confidence             456666655543                        67999999999864 332   112233333332221 233455


Q ss_pred             eEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhh---HHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCcc
Q 014486          264 VQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSR---AAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKR  340 (423)
Q Consensus       264 ~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~---~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  340 (423)
                      .+.+....  ++...+..+++... .++||||++.+.   ++.+++.|...|+++..+||++     .+.+++|++|+++
T Consensus       307 ~~~yi~~~--~k~~~L~~ll~~l~-~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F~~G~~~  378 (1176)
T PRK09401        307 VDSYIVDE--DSVEKLVELVKRLG-DGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVD  378 (1176)
T ss_pred             eEEEEEcc--cHHHHHHHHHHhcC-CCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHHHCCCCC
Confidence            55665544  56667778877665 589999999777   9999999999999999999999     2346999999999


Q ss_pred             EEEE----cCccccCCCCCC-CCEEEEccCCC
Q 014486          341 ILVA----TDLVGRGIDIER-VNIVINYDMPD  367 (423)
Q Consensus       341 ili~----T~~~~~Gld~~~-~~~vi~~~~~~  367 (423)
                      |||+    |++++||||+|+ +++||||+.|.
T Consensus       379 VLVatas~tdv~aRGIDiP~~IryVI~y~vP~  410 (1176)
T PRK09401        379 VLVGVASYYGVLVRGIDLPERIRYAIFYGVPK  410 (1176)
T ss_pred             EEEEecCCCCceeecCCCCcceeEEEEeCCCC
Confidence            9999    689999999999 89999999886

>PHA02653 RNA helicase NPH-II; Provisional

Probab=100.00  E-value=2.1e-39  Score=313.04  Aligned_cols=308  Identities=19%  Similarity=0.219  Sum_probs=222.0

Q ss_pred             hhhhhcccccccCCceEEEccCCCcchhHHH---------HHHhhcc---CCCCCCeEEEEEecChHHHHHHHHHHHHHh
Q 014486           71 EVQHECIPQAILGMDVICQAKSGMGKTAVFV---------LSTLQQT---EPNPGQVTALVLCHTRELAYQICHEFERFS  138 (423)
Q Consensus        71 ~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~---------~~~~~~~---~~~~~~~~~lil~P~~~L~~q~~~~~~~~~  138 (423)
                      .+|+++++.++.++++++.|+||||||.+..         ++.+..+   .......++++++|+++||.|+..++.+..
T Consensus       167 ~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~v  246 (675)
T PHA02653        167 DVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKSL  246 (675)
T ss_pred             HHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999999732         2233322   223334589999999999999999988765


Q ss_pred             cc--CCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHH
Q 014486          139 TY--LPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIF  216 (423)
Q Consensus       139 ~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~  216 (423)
                      ..  ..+..+...+||.......... .. .+++++|+...       ...+.++++||+||||++....   ..+..+.
T Consensus       247 g~~~~~g~~v~v~~Gg~~~~~~~t~~-k~-~~Ilv~T~~L~-------l~~L~~v~~VVIDEaHEr~~~~---DllL~ll  314 (675)
T PHA02653        247 GFDEIDGSPISLKYGSIPDELINTNP-KP-YGLVFSTHKLT-------LNKLFDYGTVIIDEVHEHDQIG---DIIIAVA  314 (675)
T ss_pred             CccccCCceEEEEECCcchHHhhccc-CC-CCEEEEeCccc-------ccccccCCEEEccccccCccch---hHHHHHH
Confidence            44  3456788889987632111111 23 58999997521       1246789999999999986532   2333333


Q ss_pred             HhC-CCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeC----------hHHHHHHHHHHHHh
Q 014486          217 KMT-PHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS----------ELEKNRKLNDLLDA  285 (423)
Q Consensus       217 ~~~-~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~l~~ll~~  285 (423)
                      +.. +..+|+++||||++.+...+ ..++.++..+.+...   ....+.+.+....          ...+...+..+...
T Consensus       315 k~~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~gr---t~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~  390 (675)
T PHA02653        315 RKHIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIPGG---TLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKY  390 (675)
T ss_pred             HHhhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeCCC---cCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHh
Confidence            332 33458999999999887665 567777766655432   1122233332211          11222222222222


Q ss_pred             --hcCCcEEEEEcChhhHHHHHHHHHhC--CCCeEEEcCCCCHHHHHHHHHhh-hcCCccEEEEcCccccCCCCCCCCEE
Q 014486          286 --LDFNQVVIFVKSVSRAAELNKLLVEC--NFPSICIHSGMSQEERLTRYKGF-KEGNKRILVATDLVGRGIDIERVNIV  360 (423)
Q Consensus       286 --~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f-~~~~~~ili~T~~~~~Gld~~~~~~v  360 (423)
                        ..++++|||+++..+++.+.+.|.+.  ++.+..+||++++.  .+.+++| ++|+.+|||||+++++|+|+|++++|
T Consensus       391 ~~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~V  468 (675)
T PHA02653        391 TPPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNATHV  468 (675)
T ss_pred             hcccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCeeEE
Confidence              13468999999999999999999987  68999999999975  4556777 68999999999999999999999999


Q ss_pred             EEcc---CCC---------CcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          361 INYD---MPD---------SADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       361 i~~~---~~~---------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      |+++   .|.         |.+.|.||+||+||. ++|.|+.+++....
T Consensus       469 ID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~  516 (675)
T PHA02653        469 YDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLL  516 (675)
T ss_pred             EECCCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHh
Confidence            9998   454         777899999999999 78999999987554

>PHA02558 uvsW UvsW helicase; Provisional

Probab=100.00  E-value=2e-39  Score=310.28  Aligned_cols=307  Identities=18%  Similarity=0.187  Sum_probs=218.8

Q ss_pred             CCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceE
Q 014486           67 EHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKV  146 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  146 (423)
                      ..|+++|.++++.++.++++++.+|||+|||+++...+...... . ..++||++|+++|+.||.+.++++... +...+
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~-~-~~~vLilvpt~eL~~Q~~~~l~~~~~~-~~~~~  189 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLEN-Y-EGKVLIIVPTTSLVTQMIDDFVDYRLF-PREAM  189 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhc-C-CCeEEEEECcHHHHHHHHHHHHHhccc-cccce
Confidence            48999999999999999999999999999999765432221222 2 238999999999999999999988643 23344


Q ss_pred             EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEE
Q 014486          147 AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVM  226 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v  226 (423)
                      ..+.+|....        ...+|+|+|++++.+...   ..+.++++||+||||++..     ..+..++..+++.++++
T Consensus       190 ~~i~~g~~~~--------~~~~I~VaT~qsl~~~~~---~~~~~~~~iIvDEaH~~~~-----~~~~~il~~~~~~~~~l  253 (501)
T PHA02558        190 HKIYSGTAKD--------TDAPIVVSTWQSAVKQPK---EWFDQFGMVIVDECHLFTG-----KSLTSIITKLDNCKFKF  253 (501)
T ss_pred             eEEecCcccC--------CCCCEEEeeHHHHhhchh---hhccccCEEEEEchhcccc-----hhHHHHHHhhhccceEE
Confidence            4455554321        125999999999876432   2467899999999998865     23456666666678899


Q ss_pred             EEeccCCccHHHH--HHHhccCCceeeecccc-----c---------------cccccce-EEE-----EEeChHHHHHH
Q 014486          227 MFSATLSKEIRPV--CKKFMQDPMEIYVDDEA-----K---------------LTLHGLV-QHY-----IKLSELEKNRK  278 (423)
Q Consensus       227 ~~SAT~~~~~~~~--~~~~~~~~~~~~~~~~~-----~---------------~~~~~~~-~~~-----~~~~~~~~~~~  278 (423)
                      ++|||++......  ....++. ....+....     .               ....... ..+     .......+...
T Consensus       254 GLTATp~~~~~~~~~~~~~fG~-i~~~v~~~~li~~g~l~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~l~~~~~Rn~~  332 (501)
T PHA02558        254 GLTGSLRDGKANILQYVGLFGD-IFKPVTTSQLMEEGQVTDLKINSIFLRYPDEDRVKLKGEDYQEEIKYITSHTKRNKW  332 (501)
T ss_pred             EEeccCCCccccHHHHHHhhCC-ceEEecHHHHHhCCCcCCceEEEEeccCCHHHhhhhcccchHHHHHHHhccHHHHHH
Confidence            9999997543211  1111211 111100000     0               0000000 000     00112223344


Q ss_pred             HHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEc-CccccCCCCC
Q 014486          279 LNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVAT-DLVGRGIDIE  355 (423)
Q Consensus       279 l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T-~~~~~Gld~~  355 (423)
                      +..++...  .+.+++|||.+.++++.+++.|.+.+.++..+||+++..+|..+++.|++|+..||||| +.+++|+|+|
T Consensus       333 I~~~~~~~~~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip  412 (501)
T PHA02558        333 IANLALKLAKKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIK  412 (501)
T ss_pred             HHHHHHHHHhcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceeccccccc
Confidence            44444332  35789999999999999999999999999999999999999999999999999999998 8999999999


Q ss_pred             CCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEec
Q 014486          356 RVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVS  393 (423)
Q Consensus       356 ~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~  393 (423)
                      ++++||++.++.|...|+||+||++|.+..+....+++
T Consensus       413 ~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K~~~~i~D  450 (501)
T PHA02558        413 NLHHVIFAHPSKSKIIVLQSIGRVLRKHGSKSIATVWD  450 (501)
T ss_pred             cccEEEEecCCcchhhhhhhhhccccCCCCCceEEEEE
Confidence            99999999999999999999999999876554444443

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

Probab=100.00  E-value=6.8e-39  Score=288.08  Aligned_cols=340  Identities=21%  Similarity=0.242  Sum_probs=265.2

Q ss_pred             ccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccc-cccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEe
Q 014486           43 IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQ-AILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLC  121 (423)
Q Consensus        43 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~-~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  121 (423)
                      .+....+++.+++.+..-|+..|++.+.|.|..++.+ ++.|.|.++..+|+||||++.-++-+..+..+++  +-|+++
T Consensus       191 ~~r~~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~g~--KmlfLv  268 (830)
T COG1202         191 VERVPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGK--KMLFLV  268 (830)
T ss_pred             cccccccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhCCC--eEEEEe
Confidence            3445577899999999999999999999999999976 5668999999999999999998888888776554  889999


Q ss_pred             cChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHH---HHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcC
Q 014486          122 HTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKD---LLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDE  198 (423)
Q Consensus       122 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE  198 (423)
                      |..+||.|-++.|++-.... ++++..-.|...+.....   .-.....||||+|++-+..+++.+ ..+.+++.||+||
T Consensus       269 PLVALANQKy~dF~~rYs~L-glkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg-~~lgdiGtVVIDE  346 (830)
T COG1202         269 PLVALANQKYEDFKERYSKL-GLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG-KDLGDIGTVVIDE  346 (830)
T ss_pred             hhHHhhcchHHHHHHHhhcc-cceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC-CcccccceEEeee
Confidence            99999999999998766555 778877777655443322   112244699999999999888876 6789999999999


Q ss_pred             cchhhcc-CC--cHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEe-ChHH
Q 014486          199 CDKMLES-LD--MRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL-SELE  274 (423)
Q Consensus       199 ~h~~~~~-~~--~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~  274 (423)
                      +|.+.+. .+  .-..+.++. .+-+..|+|.+|||..+. ..+++.+......+...+.      .+..+.+.. .+.+
T Consensus       347 iHtL~deERG~RLdGLI~RLr-~l~~~AQ~i~LSATVgNp-~elA~~l~a~lV~y~~RPV------plErHlvf~~~e~e  418 (830)
T COG1202         347 IHTLEDEERGPRLDGLIGRLR-YLFPGAQFIYLSATVGNP-EELAKKLGAKLVLYDERPV------PLERHLVFARNESE  418 (830)
T ss_pred             eeeccchhcccchhhHHHHHH-HhCCCCeEEEEEeecCCh-HHHHHHhCCeeEeecCCCC------ChhHeeeeecCchH
Confidence            9998762 12  222334443 444589999999999765 3455555544443322221      123333333 4778


Q ss_pred             HHHHHHHHHHhh--------cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcC
Q 014486          275 KNRKLNDLLDAL--------DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD  346 (423)
Q Consensus       275 ~~~~l~~ll~~~--------~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~  346 (423)
                      |...+..+.+..        -.+++|||++++..+..++..|...|+++.+||++++..+|..+...|.++++.++|+|.
T Consensus       419 K~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTA  498 (830)
T COG1202         419 KWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTA  498 (830)
T ss_pred             HHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehh
Confidence            888888887554        237899999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCCCCEEEE----ccCC-CCcchhhhcccccCCCC--CceEEEEEecCc
Q 014486          347 LVGRGIDIERVNIVIN----YDMP-DSADTYLHRVGRAGRFG--TKGLAITFVSSA  395 (423)
Q Consensus       347 ~~~~Gld~~~~~~vi~----~~~~-~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~  395 (423)
                      +++.|+|+|.-. ||+    .+.- -|+.+|.|+.|||||.+  ..|.|++++.+.
T Consensus       499 AL~AGVDFPASQ-VIFEsLaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg  553 (830)
T COG1202         499 ALAAGVDFPASQ-VIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPG  553 (830)
T ss_pred             hhhcCCCCchHH-HHHHHHHcccccCCHHHHHHHhcccCCCCcccCceEEEEecCC
Confidence            999999999544 443    2222 38999999999999976  458888887653

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=100.00  E-value=1.6e-38  Score=314.88  Aligned_cols=301  Identities=19%  Similarity=0.265  Sum_probs=227.2

Q ss_pred             hcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcc
Q 014486           75 ECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVN  154 (423)
Q Consensus        75 ~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~  154 (423)
                      +.+..+..++++++.||||||||+++.+++++.....   .+++|++|++++|.|+++++.+......+..+.+..++.+
T Consensus        12 ~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~~---~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~vr~~~   88 (812)
T PRK11664         12 ELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGIN---GKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMRAES   88 (812)
T ss_pred             HHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCcC---CeEEEECChHHHHHHHHHHHHHHhCcccCceEEEEecCcc
Confidence            4455666788999999999999999999999765432   2899999999999999999866544433567776666543


Q ss_pred             hHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcH-HHHHHHHHhCCCCceEEEEeccCC
Q 014486          155 IKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMR-RDVQEIFKMTPHDKQVMMFSATLS  233 (423)
Q Consensus       155 ~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~-~~~~~~~~~~~~~~~~v~~SAT~~  233 (423)
                      ..       +...+|+|+|++.|.+++.. ...++++++||+||+|...-..++. ..+..+...++++.|+++||||++
T Consensus        89 ~~-------~~~t~I~v~T~G~Llr~l~~-d~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlilmSATl~  160 (812)
T PRK11664         89 KV-------GPNTRLEVVTEGILTRMIQR-DPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMSATLD  160 (812)
T ss_pred             cc-------CCCCcEEEEChhHHHHHHhh-CCCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEEEecCCC
Confidence            21       11248999999999998875 4578999999999999742213332 234455666778899999999998


Q ss_pred             ccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHH-----HHHHHHHhhcCCcEEEEEcChhhHHHHHHHH
Q 014486          234 KEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNR-----KLNDLLDALDFNQVVIFVKSVSRAAELNKLL  308 (423)
Q Consensus       234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L  308 (423)
                      ..   .+..++.++..+......    ..+..++.......+..     .+..++.. ..+.+|||+++..+++.+++.|
T Consensus       161 ~~---~l~~~~~~~~~I~~~gr~----~pV~~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~ei~~l~~~L  232 (812)
T PRK11664        161 ND---RLQQLLPDAPVIVSEGRS----FPVERRYQPLPAHQRFDEAVARATAELLRQ-ESGSLLLFLPGVGEIQRVQEQL  232 (812)
T ss_pred             HH---HHHHhcCCCCEEEecCcc----ccceEEeccCchhhhHHHHHHHHHHHHHHh-CCCCEEEEcCCHHHHHHHHHHH
Confidence            64   234555544444332211    11333444333333322     23333332 3588999999999999999999


Q ss_pred             Hh---CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCC-----------------
Q 014486          309 VE---CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDS-----------------  368 (423)
Q Consensus       309 ~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s-----------------  368 (423)
                      .+   .++.+..+||+++..+|..++..|.+|+.+|||||+++++|+|++++++||+++.++.                 
T Consensus       233 ~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~i  312 (812)
T PRK11664        233 ASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRI  312 (812)
T ss_pred             HHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCcceeEEEee
Confidence            87   5788899999999999999999999999999999999999999999999999887753                 


Q ss_pred             -cchhhhcccccCCCCCceEEEEEecCc
Q 014486          369 -ADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       369 -~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                       ..++.||.||+||. ++|.|+.+++..
T Consensus       313 Skasa~QR~GRaGR~-~~G~cyrL~t~~  339 (812)
T PRK11664        313 SQASMTQRAGRAGRL-EPGICLHLYSKE  339 (812)
T ss_pred             chhhhhhhccccCCC-CCcEEEEecCHH
Confidence             34799999999999 689999999854

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=100.00  E-value=2.3e-38  Score=312.99  Aligned_cols=300  Identities=19%  Similarity=0.248  Sum_probs=225.7

Q ss_pred             hcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcc
Q 014486           75 ECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVN  154 (423)
Q Consensus        75 ~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~  154 (423)
                      +.+..+..+++++++|+||||||+++.+++++....   +.+++|+.|++++|.|+++++.+......+..+++...+.+
T Consensus         9 ~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~~---~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr~~~   85 (819)
T TIGR01970         9 ALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGI---GGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVRGEN   85 (819)
T ss_pred             HHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhcc---CCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEcccc
Confidence            444556667889999999999999999999987632   23899999999999999999865543333555655544432


Q ss_pred             hHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcch-hhccCCcHH-HHHHHHHhCCCCceEEEEeccC
Q 014486          155 IKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDK-MLESLDMRR-DVQEIFKMTPHDKQVMMFSATL  232 (423)
Q Consensus       155 ~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~-~~~~~~~~~-~~~~~~~~~~~~~~~v~~SAT~  232 (423)
                            .... ..+|+|+|++.|++.+.. ...+.++++||+||+|. .++ .++.. .+..+...++++.|+++||||+
T Consensus        86 ------~~s~-~t~I~v~T~G~Llr~l~~-d~~L~~v~~VIiDEaHER~L~-~Dl~L~ll~~i~~~lr~dlqlIlmSATl  156 (819)
T TIGR01970        86 ------KVSR-RTRLEVVTEGILTRMIQD-DPELDGVGALIFDEFHERSLD-ADLGLALALDVQSSLREDLKILAMSATL  156 (819)
T ss_pred             ------ccCC-CCcEEEECCcHHHHHHhh-CcccccCCEEEEeccchhhhc-cchHHHHHHHHHHhcCCCceEEEEeCCC
Confidence                  1122 259999999999998876 45789999999999995 444 45443 3345666678889999999999


Q ss_pred             CccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHH-----HHHHHHHHhhcCCcEEEEEcChhhHHHHHHH
Q 014486          233 SKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKN-----RKLNDLLDALDFNQVVIFVKSVSRAAELNKL  307 (423)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~  307 (423)
                      +...   +..++.++..+......    ..+..++......++.     ..+..++.. ..+++|||+++..+++.+++.
T Consensus       157 ~~~~---l~~~l~~~~vI~~~gr~----~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~eI~~l~~~  228 (819)
T TIGR01970       157 DGER---LSSLLPDAPVVESEGRS----FPVEIRYLPLRGDQRLEDAVSRAVEHALAS-ETGSILVFLPGQAEIRRVQEQ  228 (819)
T ss_pred             CHHH---HHHHcCCCcEEEecCcc----eeeeeEEeecchhhhHHHHHHHHHHHHHHh-cCCcEEEEECCHHHHHHHHHH
Confidence            9653   34555544444332211    1122333333322221     223333333 357899999999999999999


Q ss_pred             HHh---CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCC----------------
Q 014486          308 LVE---CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDS----------------  368 (423)
Q Consensus       308 L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s----------------  368 (423)
                      |.+   .++.+..+||++++.+|..+++.|.+|..+|||||+++++|||+|++++||+++.|+.                
T Consensus       229 L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~  308 (819)
T TIGR01970       229 LAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVR  308 (819)
T ss_pred             HHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCcccccccccccCCceeeEEE
Confidence            987   4788999999999999999999999999999999999999999999999999998863                


Q ss_pred             --cchhhhcccccCCCCCceEEEEEecCc
Q 014486          369 --ADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       369 --~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                        ..++.||.||+||. ++|.|+.+++..
T Consensus       309 iSkasa~QR~GRAGR~-~~G~cyrL~t~~  336 (819)
T TIGR01970       309 ISQASATQRAGRAGRL-EPGVCYRLWSEE  336 (819)
T ss_pred             ECHHHHHhhhhhcCCC-CCCEEEEeCCHH
Confidence              23489999999999 799999999853

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.

>PRK14701 reverse gyrase; Provisional

Probab=100.00  E-value=2.9e-38  Score=329.16  Aligned_cols=319  Identities=18%  Similarity=0.235  Sum_probs=242.5

Q ss_pred             HHHHHHh-CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHH
Q 014486           57 LLRAIVD-SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFE  135 (423)
Q Consensus        57 ~~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  135 (423)
                      ..+.+++ .|| .|+++|+.+++.+++|+++++.+|||+|||+.++++++....   .+.+++|++||++|+.|+++.++
T Consensus        68 ~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~---~g~~aLVl~PTreLa~Qi~~~l~  143 (1638)
T PRK14701         68 FEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL---KGKKCYIILPTTLLVKQTVEKIE  143 (1638)
T ss_pred             HHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh---cCCeEEEEECHHHHHHHHHHHHH
Confidence            4455665 699 699999999999999999999999999999966555544432   22389999999999999999999


Q ss_pred             HHhccCC-CceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc------
Q 014486          136 RFSTYLP-DIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES------  205 (423)
Q Consensus       136 ~~~~~~~-~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~------  205 (423)
                      .+..... ++.+..++|+.+...+.   ..+.++.++|+|+||+.+...+...  ...+++++|+||||+++.+      
T Consensus       144 ~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l--~~~~i~~iVVDEAD~ml~~~knid~  221 (1638)
T PRK14701        144 SFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM--KHLKFDFIFVDDVDAFLKASKNIDR  221 (1638)
T ss_pred             HHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH--hhCCCCEEEEECceeccccccccch
Confidence            9876542 46778888988776553   3455666899999999988765532  1267899999999999753      


Q ss_pred             ----CCcHHHHHH----HHH----------------------hCCCCce-EEEEeccCCccHHHHHHHhccCCceeeecc
Q 014486          206 ----LDMRRDVQE----IFK----------------------MTPHDKQ-VMMFSATLSKEIRPVCKKFMQDPMEIYVDD  254 (423)
Q Consensus       206 ----~~~~~~~~~----~~~----------------------~~~~~~~-~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~  254 (423)
                          .+|...+..    +..                      .+++..| .+++|||+++... . ..++..+..+.+..
T Consensus       222 ~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~~-~-~~l~~~~l~f~v~~  299 (1638)
T PRK14701        222 SLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKGD-R-VKLYRELLGFEVGS  299 (1638)
T ss_pred             hhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchhH-H-HHHhhcCeEEEecC
Confidence                367766653    221                      2244455 5779999986411 1 12334444444433


Q ss_pred             ccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhh---HHHHHHHHHhCCCCeEEEcCCCCHHHHHHHH
Q 014486          255 EAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSR---AAELNKLLVECNFPSICIHSGMSQEERLTRY  331 (423)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~---~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~  331 (423)
                      . ......+.+.++......+ ..+..+++.. +..+||||++.+.   ++.+++.|...|+++..+|++     |...+
T Consensus       300 ~-~~~lr~i~~~yi~~~~~~k-~~L~~ll~~~-g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~l  371 (1638)
T PRK14701        300 G-RSALRNIVDVYLNPEKIIK-EHVRELLKKL-GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKGF  371 (1638)
T ss_pred             C-CCCCCCcEEEEEECCHHHH-HHHHHHHHhC-CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHHH
Confidence            3 2344556666665554444 4677777766 4689999999875   589999999999999999995     88899


Q ss_pred             HhhhcCCccEEEEc----CccccCCCCCC-CCEEEEccCCC---Ccchhhhcc-------------cccCCCCCceEEEE
Q 014486          332 KGFKEGNKRILVAT----DLVGRGIDIER-VNIVINYDMPD---SADTYLHRV-------------GRAGRFGTKGLAIT  390 (423)
Q Consensus       332 ~~f~~~~~~ili~T----~~~~~Gld~~~-~~~vi~~~~~~---s~~~~~Q~~-------------GR~~R~g~~~~~~~  390 (423)
                      +.|++|+++|||||    ++++||||+|+ +++||||+.|+   +...|.|..             ||++|.|.+..++.
T Consensus       372 ~~F~~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~  451 (1638)
T PRK14701        372 DLFEEGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEGVL  451 (1638)
T ss_pred             HHHHcCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchhHH
Confidence            99999999999999    48999999998 99999999999   887776665             99999998877764


Q ss_pred             E
Q 014486          391 F  391 (423)
Q Consensus       391 ~  391 (423)
                      .
T Consensus       452 ~  452 (1638)
T PRK14701        452 D  452 (1638)
T ss_pred             H
Confidence            3

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=5.3e-38  Score=298.47  Aligned_cols=316  Identities=20%  Similarity=0.203  Sum_probs=241.6

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      |+ .|+++|..+++.++.|+  |..+.||+|||+++++|++.....+   +.++|++|++.||.|.++++..+.... ++
T Consensus       101 g~-~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~G---~~v~VvTptreLA~qdae~~~~l~~~l-Gl  173 (656)
T PRK12898        101 GQ-RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALAG---LPVHVITVNDYLAERDAELMRPLYEAL-GL  173 (656)
T ss_pred             CC-CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhcC---CeEEEEcCcHHHHHHHHHHHHHHHhhc-CC
Confidence            44 79999999999999998  9999999999999999999876644   389999999999999999999998877 89


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcCCC-------------------------CCCCccEEEEcC
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDKDL-------------------------SLKNVRHFILDE  198 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~~~-------------------------~~~~~~~vVvDE  198 (423)
                      ++.++.|+.+..  .+....+ ++|+|+|...| +++++.+..                         -...+.++||||
T Consensus       174 sv~~i~gg~~~~--~r~~~y~-~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~aIvDE  250 (656)
T PRK12898        174 TVGCVVEDQSPD--ERRAAYG-ADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHFAIVDE  250 (656)
T ss_pred             EEEEEeCCCCHH--HHHHHcC-CCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhcccccceeEeec
Confidence            999999997643  2233334 49999999877 444443311                         135578999999


Q ss_pred             cchhhcc--------------C---CcHHHHHHHHHhCCC----------------------------------------
Q 014486          199 CDKMLES--------------L---DMRRDVQEIFKMTPH----------------------------------------  221 (423)
Q Consensus       199 ~h~~~~~--------------~---~~~~~~~~~~~~~~~----------------------------------------  221 (423)
                      +|.++-+              .   .+......+...+..                                        
T Consensus       251 vDSiLiDeartpliis~~~~~~~~~~~y~~~~~~~~~l~~~~~y~~d~~~~~v~lt~~g~~~~e~~~~~l~~~~~~~~~~  330 (656)
T PRK12898        251 ADSVLIDEARTPLIISAPAKEADEAEVYRQALELAAQLKEGEDYTIDAAEKRIELTEAGRARIAELAESLPPAWRGAVRR  330 (656)
T ss_pred             ccceeeccCCCceEEECCCCCCchhHHHHHHHHHHHhcCCCCceEEECCCCeEEEcHHHHHHHHHHhCcchhhcccchHH
Confidence            9987611              0   011111111110000                                        


Q ss_pred             ----------------Cc-------------------------------------------------------------e
Q 014486          222 ----------------DK-------------------------------------------------------------Q  224 (423)
Q Consensus       222 ----------------~~-------------------------------------------------------------~  224 (423)
                                      +.                                                             +
T Consensus       331 ~~~i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~w~~GLhQaieaKE~v~i~~e~~t~a~It~q~~Fr~Y~k  410 (656)
T PRK12898        331 EELVRQALSALHLFRRDEHYIVRDGKVVIVDEFTGRVMPDRSWEDGLHQMIEAKEGCELTDPRETLARITYQRFFRRYLR  410 (656)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEECCeEEEEECCCCeECCCCCcChHHHHHHHHhcCCCCCcCceeeeeehHHHHHHhhHH
Confidence                            00                                                             5


Q ss_pred             EEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhc--CCcEEEEEcChhhHH
Q 014486          225 VMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALD--FNQVVIFVKSVSRAA  302 (423)
Q Consensus       225 ~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~--~~~~ivf~~~~~~~~  302 (423)
                      +.+||||.+.....+.+.+...+..+....+..   ......++.....+|...+.+++....  +.++||||++++.++
T Consensus       411 l~GmTGTa~~~~~El~~~y~l~vv~IPt~kp~~---r~~~~~~v~~t~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se  487 (656)
T PRK12898        411 LAGMTGTAREVAGELWSVYGLPVVRIPTNRPSQ---RRHLPDEVFLTAAAKWAAVAARVRELHAQGRPVLVGTRSVAASE  487 (656)
T ss_pred             HhcccCcChHHHHHHHHHHCCCeEEeCCCCCcc---ceecCCEEEeCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHH
Confidence            678999998877777777776665554443332   222333455667788888888887643  578999999999999


Q ss_pred             HHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCC---CCC-----EEEEccCCCCcchhhh
Q 014486          303 ELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIE---RVN-----IVINYDMPDSADTYLH  374 (423)
Q Consensus       303 ~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~---~~~-----~vi~~~~~~s~~~~~Q  374 (423)
                      .+++.|...|+++..+|+..+  +++..+..|..+...|+|||++++||+|++   ++.     +||+++.|.|...|.|
T Consensus       488 ~L~~~L~~~gi~~~~Lhg~~~--~rE~~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~h  565 (656)
T PRK12898        488 RLSALLREAGLPHQVLNAKQD--AEEAAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQ  565 (656)
T ss_pred             HHHHHHHHCCCCEEEeeCCcH--HHHHHHHHHcCCCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHH
Confidence            999999999999999999865  444555566666678999999999999999   665     9999999999999999


Q ss_pred             cccccCCCCCceEEEEEecCc
Q 014486          375 RVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       375 ~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      |+||+||.|.+|.++.|++..
T Consensus       566 r~GRTGRqG~~G~s~~~is~e  586 (656)
T PRK12898        566 LAGRCGRQGDPGSYEAILSLE  586 (656)
T ss_pred             hcccccCCCCCeEEEEEechh
Confidence            999999999999999999863

>COG1204 Superfamily II helicase [General function prediction only]

Probab=100.00  E-value=3.1e-38  Score=308.97  Aligned_cols=341  Identities=23%  Similarity=0.304  Sum_probs=246.5

Q ss_pred             CCCHHHHHHHHhCCCCCCChhhhhcccccccC-CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           52 LLKPELLRAIVDSGFEHPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        52 ~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~-~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      .+.+.+.+-+...++..+++.|+.++...+.+ +|++|++|||||||+++++.++..+...+.  +++|+||+++||.+.
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~~~--k~vYivPlkALa~Ek   92 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGG--KVVYIVPLKALAEEK   92 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhcCC--cEEEEeChHHHHHHH
Confidence            36677888888888889999999998877765 899999999999999999999998887632  899999999999999


Q ss_pred             HHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHH
Q 014486          131 CHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRR  210 (423)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~  210 (423)
                      +++++++...  ++++...+|+.....+  .+. . ++|+|+||+++..+.++......++++||+||+|.+.+. .-.+
T Consensus        93 ~~~~~~~~~~--GirV~~~TgD~~~~~~--~l~-~-~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~-~RG~  165 (766)
T COG1204          93 YEEFSRLEEL--GIRVGISTGDYDLDDE--RLA-R-YDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDR-TRGP  165 (766)
T ss_pred             HHHhhhHHhc--CCEEEEecCCcccchh--hhc-c-CCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCc-ccCc
Confidence            9999944333  8999999998775442  222 2 599999999999999988878889999999999998763 2222


Q ss_pred             HHHHH---HHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChH-------HHHHHHH
Q 014486          211 DVQEI---FKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEL-------EKNRKLN  280 (423)
Q Consensus       211 ~~~~~---~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~l~  280 (423)
                      .+..+   ........|++++|||+|+. ..++.....++......+..-.........+......       .....+.
T Consensus       166 ~lE~iv~r~~~~~~~~rivgLSATlpN~-~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~  244 (766)
T COG1204         166 VLESIVARMRRLNELIRIVGLSATLPNA-EEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALE  244 (766)
T ss_pred             eehhHHHHHHhhCcceEEEEEeeecCCH-HHHHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHHH
Confidence            22222   33334458999999999975 3344444333332122211111111112222222211       1223333


Q ss_pred             HHHHhh-cCCcEEEEEcChhhHHHHHHHHHhC-------------------------------------CCCeEEEcCCC
Q 014486          281 DLLDAL-DFNQVVIFVKSVSRAAELNKLLVEC-------------------------------------NFPSICIHSGM  322 (423)
Q Consensus       281 ~ll~~~-~~~~~ivf~~~~~~~~~l~~~L~~~-------------------------------------~~~~~~~~~~~  322 (423)
                      ..+... .+++++|||++++.+...++.+...                                     ...+..+|.++
T Consensus       245 ~v~~~~~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL  324 (766)
T COG1204         245 LVLESLAEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGL  324 (766)
T ss_pred             HHHHHHhcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCC
Confidence            333333 4579999999999998888888730                                     01345679999


Q ss_pred             CHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEE----Ecc-----CCCCcchhhhcccccCCCCC--ceEEEEE
Q 014486          323 SQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVI----NYD-----MPDSADTYLHRVGRAGRFGT--KGLAITF  391 (423)
Q Consensus       323 ~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi----~~~-----~~~s~~~~~Q~~GR~~R~g~--~~~~~~~  391 (423)
                      +..+|..+.+.|+.|.++||+||+.++.|+|+|.-+.||    .|+     .+-++.++.|+.|||||.|-  .|.++++
T Consensus       325 ~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~  404 (766)
T COG1204         325 PREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIIL  404 (766)
T ss_pred             CHHHHHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCcEEEE
Confidence            999999999999999999999999999999999666665    355     34567889999999999874  4777777


Q ss_pred             ecCcccHHHHH
Q 014486          392 VSSASDSDILN  402 (423)
Q Consensus       392 ~~~~~~~~~~~  402 (423)
                      ....++..+..
T Consensus       405 ~~~~~~~~~~~  415 (766)
T COG1204         405 ATSHDELEYLA  415 (766)
T ss_pred             ecCccchhHHH
Confidence            74444444333

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=100.00  E-value=6.2e-38  Score=290.79  Aligned_cols=298  Identities=20%  Similarity=0.258  Sum_probs=202.5

Q ss_pred             ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHH-------
Q 014486           85 DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKI-------  157 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------  157 (423)
                      ++++.+|||||||.+++++++..+... ...+++|++|+++|+.|+++.+..+...    ++..++++.....       
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~-~~~~ii~v~P~~~L~~q~~~~l~~~f~~----~~~~~~~~~~~~~~~~~~~~   75 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ-KADRVIIALPTRATINAMYRRAKELFGS----NLGLLHSSSSFKRIKEMGDS   75 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC-CCCeEEEEeehHHHHHHHHHHHHHHhCc----ccEEeeccHHHHHHhccCCc
Confidence            478999999999999999999876543 3348999999999999999999987532    3444444332110       


Q ss_pred             -----HHHHH-hc----CCCcEEEechHHHHHHHhcCCC----CC--CCccEEEEcCcchhhccCCcHHHHHHHHHhC-C
Q 014486          158 -----HKDLL-KN----ECPQIVVGTPGRILALARDKDL----SL--KNVRHFILDECDKMLESLDMRRDVQEIFKMT-P  220 (423)
Q Consensus       158 -----~~~~~-~~----~~~~ilv~T~~~l~~~~~~~~~----~~--~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-~  220 (423)
                           ..... .+    ...+|+++||+.+...+.....    .+  -..++||+||+|.+.. ..+.. +..++..+ .
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~-~~~~~-l~~~l~~l~~  153 (358)
T TIGR01587        76 EEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDE-YTLAL-ILAVLEVLKD  153 (358)
T ss_pred             hhHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCH-HHHHH-HHHHHHHHHH
Confidence                 00000 00    1247999999999886654211    11  1237899999999876 22222 44444433 3


Q ss_pred             CCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEE--EeChHHHHHHHHHHHHhh-cCCcEEEEEcC
Q 014486          221 HDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYI--KLSELEKNRKLNDLLDAL-DFNQVVIFVKS  297 (423)
Q Consensus       221 ~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~ll~~~-~~~~~ivf~~~  297 (423)
                      ...|++++|||+|..+..++......+...........  ....+.+.  ......+...+..+++.. .++++||||++
T Consensus       154 ~~~~~i~~SATlp~~l~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~~t  231 (358)
T TIGR01587       154 NDVPILLMSATLPKFLKEYAEKIGYVEFNEPLDLKEER--RFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNT  231 (358)
T ss_pred             cCCCEEEEecCchHHHHHHHhcCCCcccccCCCCcccc--ccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEECC
Confidence            46899999999997766665544332111111110000  00011111  111123344555555443 46899999999


Q ss_pred             hhhHHHHHHHHHhCCC--CeEEEcCCCCHHHHHHH----HHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcch
Q 014486          298 VSRAAELNKLLVECNF--PSICIHSGMSQEERLTR----YKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADT  371 (423)
Q Consensus       298 ~~~~~~l~~~L~~~~~--~~~~~~~~~~~~~r~~~----~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~  371 (423)
                      +++++.+++.|++.+.  .+..+||++++.+|...    ++.|++++.++||||+++++|+|++ +++||++..|  +..
T Consensus       232 ~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~vi~~~~~--~~~  308 (358)
T TIGR01587       232 VDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVMITELAP--IDS  308 (358)
T ss_pred             HHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEEEEcCCC--HHH
Confidence            9999999999988765  48899999999999764    8899999999999999999999996 7888887655  789


Q ss_pred             hhhcccccCCCCCc----eEEEEEecC
Q 014486          372 YLHRVGRAGRFGTK----GLAITFVSS  394 (423)
Q Consensus       372 ~~Q~~GR~~R~g~~----~~~~~~~~~  394 (423)
                      |+||+||+||.|+.    |.++++...
T Consensus       309 ~iqr~GR~gR~g~~~~~~~~~~v~~~~  335 (358)
T TIGR01587       309 LIQRLGRLHRYGRKNGENFEVYIITIA  335 (358)
T ss_pred             HHHHhccccCCCCCCCCCCeEEEEeec
Confidence            99999999998854    356666543

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.

>PRK13766 Hef nuclease; Provisional

Probab=100.00  E-value=6e-37  Score=310.63  Aligned_cols=324  Identities=21%  Similarity=0.310  Sum_probs=236.7

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      +..++++||+.++..++.+ ++++++|||+|||+++++++...+.. . +.++||++|+++|+.|+.+.++++.... ..
T Consensus        12 ~~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~-~-~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~-~~   87 (773)
T PRK13766         12 NTIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHK-K-GGKVLILAPTKPLVEQHAEFFRKFLNIP-EE   87 (773)
T ss_pred             CcCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHh-C-CCeEEEEeCcHHHHHHHHHHHHHHhCCC-Cc
Confidence            3447899999999887776 89999999999999998888776632 2 2389999999999999999999876432 45


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCce
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQ  224 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~  224 (423)
                      ++..++|+.........+.+  .+|+|+||+.+...+....+.+.++++||+||||++.+... ...+...+....+.++
T Consensus        88 ~v~~~~g~~~~~~r~~~~~~--~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~~~-~~~i~~~~~~~~~~~~  164 (773)
T PRK13766         88 KIVVFTGEVSPEKRAELWEK--AKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYA-YVYIAERYHEDAKNPL  164 (773)
T ss_pred             eEEEEeCCCCHHHHHHHHhC--CCEEEECHHHHHHHHHcCCCChhhCcEEEEECCcccccccc-HHHHHHHHHhcCCCCE
Confidence            78888888776554444433  49999999999887777777889999999999999876333 3344444445556778


Q ss_pred             EEEEeccCCccHHH---HHHHhccCCcee--------------------ee-----------------------------
Q 014486          225 VMMFSATLSKEIRP---VCKKFMQDPMEI--------------------YV-----------------------------  252 (423)
Q Consensus       225 ~v~~SAT~~~~~~~---~~~~~~~~~~~~--------------------~~-----------------------------  252 (423)
                      ++++||||......   .+.........+                    .+                             
T Consensus       165 il~lTaTP~~~~~~i~~~~~~L~i~~v~~~~~~~~~v~~~~~~~~v~~~~v~l~~~~~~i~~~l~~~~~~~l~~l~~~~~  244 (773)
T PRK13766        165 VLGLTASPGSDEEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRDLLNEALKDRLKKLKELGV  244 (773)
T ss_pred             EEEEEcCCCCCHHHHHHHHHhCCceEEEEcCCCChhHHhhhccceeEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence            99999998433211   111111000000                    00                             


Q ss_pred             ccccc--cc-----------cccceE------------------------------------------EE----------
Q 014486          253 DDEAK--LT-----------LHGLVQ------------------------------------------HY----------  267 (423)
Q Consensus       253 ~~~~~--~~-----------~~~~~~------------------------------------------~~----------  267 (423)
                      .....  ..           ...+..                                          ..          
T Consensus       245 ~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~y~~~l~~~~~~~~~~~~~~  324 (773)
T PRK13766        245 IVSISPDVSKKELLGLQKKLQQEIANDDSEGYEAISILAEAMKLRHAVELLETQGVEALRRYLERLREEARSSGGSKASK  324 (773)
T ss_pred             cccCCCCcCHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHhhccccCCcHHHH
Confidence            00000  00           000000                                          00          


Q ss_pred             ----------------EEeChHHHHHHHHHHHHh----hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCC------
Q 014486          268 ----------------IKLSELEKNRKLNDLLDA----LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSG------  321 (423)
Q Consensus       268 ----------------~~~~~~~~~~~l~~ll~~----~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~------  321 (423)
                                      .......|...+.+++..    .+.+++||||++...+..+.+.|...++++..+||.      
T Consensus       325 ~l~~~~~~~~~~~~~~~~~~~~pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~  404 (773)
T PRK13766        325 RLVEDPRFRKAVRKAKELDIEHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGD  404 (773)
T ss_pred             HHHhCHHHHHHHHHHHhcccCChHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEcccccccc
Confidence                            000112244445555544    456899999999999999999999999999999886      


Q ss_pred             --CCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcc
Q 014486          322 --MSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSAS  396 (423)
Q Consensus       322 --~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  396 (423)
                        +++.+|.+++..|++|+.++||+|+++++|+|+|++++||+|++|+++..|+||+||+||.|. |.+++++....
T Consensus       405 ~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~-~~v~~l~~~~t  480 (773)
T PRK13766        405 KGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEE-GRVVVLIAKGT  480 (773)
T ss_pred             CCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCC-CEEEEEEeCCC
Confidence              899999999999999999999999999999999999999999999999999999999999876 66777766433

>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=306.82  Aligned_cols=336  Identities=25%  Similarity=0.359  Sum_probs=260.2

Q ss_pred             CHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHH
Q 014486           54 KPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHE  133 (423)
Q Consensus        54 ~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~  133 (423)
                      ...+..++.+.|...|++||.+|+..+..|++++|..+||||||.+|++|+++.+...+.. ++|+|.|+++||..+.++
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            3445788999999999999999999999999999999999999999999999999887766 899999999999999999


Q ss_pred             HHHHhccCC-CceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHH-hcC---CCCCCCccEEEEcCcchhhccC--
Q 014486          134 FERFSTYLP-DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALA-RDK---DLSLKNVRHFILDECDKMLESL--  206 (423)
Q Consensus       134 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~-~~~---~~~~~~~~~vVvDE~h~~~~~~--  206 (423)
                      ++++....+ .+++..++|+....+....+.+. |+|+++||++|..++ ...   .+.+.++++||+||+|..-.-.  
T Consensus       135 l~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~p-p~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~GS  213 (851)
T COG1205         135 LRELISDLPGKVTFGRYTGDTPPEERRAIIRNP-PDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGS  213 (851)
T ss_pred             HHHHHHhCCCcceeeeecCCCChHHHHHHHhCC-CCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccchh
Confidence            999998886 68888999988777665555554 799999999998744 322   2346779999999999876521  


Q ss_pred             CcH---HHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeC------h---HH
Q 014486          207 DMR---RDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS------E---LE  274 (423)
Q Consensus       207 ~~~---~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~---~~  274 (423)
                      +..   +.+..+.+..+...|+|++|||+.... .+...+........+......  ..........+      .   ..
T Consensus       214 ~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np~-e~~~~l~~~~f~~~v~~~g~~--~~~~~~~~~~p~~~~~~~~~r~s  290 (851)
T COG1205         214 EVALLLRRLLRRLRRYGSPLQIICTSATLANPG-EFAEELFGRDFEVPVDEDGSP--RGLRYFVRREPPIRELAESIRRS  290 (851)
T ss_pred             HHHHHHHHHHHHHhccCCCceEEEEeccccChH-HHHHHhcCCcceeeccCCCCC--CCceEEEEeCCcchhhhhhcccc
Confidence            222   334444455566889999999998764 445555555544432222211  11112222222      0   12


Q ss_pred             HHHHHHHHHHhh--cCCcEEEEEcChhhHHHHH----HHHHhCC----CCeEEEcCCCCHHHHHHHHHhhhcCCccEEEE
Q 014486          275 KNRKLNDLLDAL--DFNQVVIFVKSVSRAAELN----KLLVECN----FPSICIHSGMSQEERLTRYKGFKEGNKRILVA  344 (423)
Q Consensus       275 ~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~----~~L~~~~----~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~  344 (423)
                      .......+....  ++-++|+|+.+++.++.+.    ..+...+    ..+..+++++.+.+|.++...|+.|+..++++
T Consensus       291 ~~~~~~~~~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~s  370 (851)
T COG1205         291 ALAELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIA  370 (851)
T ss_pred             hHHHHHHHHHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEec
Confidence            222333333222  4578999999999999986    4444445    56778999999999999999999999999999


Q ss_pred             cCccccCCCCCCCCEEEEccCCC-CcchhhhcccccCCCCCceEEEEEecC
Q 014486          345 TDLVGRGIDIERVNIVINYDMPD-SADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       345 T~~~~~Gld~~~~~~vi~~~~~~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                      |++++-|+|+.+++.||..+.|. +..++.|+.||+||.++.+.++++...
T Consensus       371 t~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~  421 (851)
T COG1205         371 TNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRS  421 (851)
T ss_pred             chhhhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCC
Confidence            99999999999999999999999 899999999999999988888777764

>TIGR01054 rgy reverse gyrase

Probab=100.00  E-value=2e-36  Score=309.77  Aligned_cols=293  Identities=17%  Similarity=0.290  Sum_probs=213.1

Q ss_pred             HHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHH
Q 014486           57 LLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER  136 (423)
Q Consensus        57 ~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  136 (423)
                      ..+.+.+.....|+++|+.+++.++.|+++++.+|||+|||. +.++++..+...  +++++|++||++||.|+++.++.
T Consensus        67 f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~~--g~~vLIL~PTreLa~Qi~~~l~~  143 (1171)
T TIGR01054        67 FEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAKK--GKRCYIILPTTLLVIQVAEKISS  143 (1171)
T ss_pred             HHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHhc--CCeEEEEeCHHHHHHHHHHHHHH
Confidence            334444444448999999999999999999999999999997 445555444322  34899999999999999999999


Q ss_pred             HhccCCCce---EEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc-----
Q 014486          137 FSTYLPDIK---VAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES-----  205 (423)
Q Consensus       137 ~~~~~~~~~---~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~-----  205 (423)
                      +.... ++.   +..++|+.+...+.   ..+.++.++|+|+||++|...+....  . +++++|+||||+++.+     
T Consensus       144 l~~~~-~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~--~-~~~~iVvDEaD~~L~~~k~vd  219 (1171)
T TIGR01054       144 LAEKA-GVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELG--P-KFDFIFVDDVDALLKASKNVD  219 (1171)
T ss_pred             HHHhc-CCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhc--C-CCCEEEEeChHhhhhccccHH
Confidence            88654 443   33577887765543   34555668999999999988766421  2 8899999999999863     


Q ss_pred             -----CCcHHH-HHHHH----------------------HhCCCCce--EEEEecc-CCccHHHHHHHhccCCceeeecc
Q 014486          206 -----LDMRRD-VQEIF----------------------KMTPHDKQ--VMMFSAT-LSKEIRPVCKKFMQDPMEIYVDD  254 (423)
Q Consensus       206 -----~~~~~~-~~~~~----------------------~~~~~~~~--~v~~SAT-~~~~~~~~~~~~~~~~~~~~~~~  254 (423)
                           .+|... +..++                      ..+++..|  ++++||| .|.....   .++.....+.+..
T Consensus       220 ~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~---~l~r~ll~~~v~~  296 (1171)
T TIGR01054       220 KLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRA---KLFRELLGFEVGG  296 (1171)
T ss_pred             HHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHH---HHcccccceEecC
Confidence                 345442 33322                      23344444  5678999 5655432   2233333333332


Q ss_pred             ccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcCh---hhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHH
Q 014486          255 EAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSV---SRAAELNKLLVECNFPSICIHSGMSQEERLTRY  331 (423)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~---~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~  331 (423)
                      . ......+.+.+.....  +...+..+++... .++||||++.   +.++.+++.|.+.|+++..+||+++.    .++
T Consensus       297 ~-~~~~r~I~~~~~~~~~--~~~~L~~ll~~l~-~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~----~~l  368 (1171)
T TIGR01054       297 G-SDTLRNVVDVYVEDED--LKETLLEIVKKLG-TGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK----EDY  368 (1171)
T ss_pred             c-cccccceEEEEEeccc--HHHHHHHHHHHcC-CCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH----HHH
Confidence            2 2234455555554433  2345667776654 6799999999   99999999999999999999999973    679


Q ss_pred             HhhhcCCccEEEE----cCccccCCCCCC-CCEEEEccCCC
Q 014486          332 KGFKEGNKRILVA----TDLVGRGIDIER-VNIVINYDMPD  367 (423)
Q Consensus       332 ~~f~~~~~~ili~----T~~~~~Gld~~~-~~~vi~~~~~~  367 (423)
                      +.|++|+++||||    |++++||||+|+ +++||+|+.|.
T Consensus       369 ~~Fr~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P~  409 (1171)
T TIGR01054       369 EKFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPK  409 (1171)
T ss_pred             HHHHcCCCCEEEEeccccCcccccCCCCccccEEEEECCCC
Confidence            9999999999999    489999999999 89999988764

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.

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

Probab=100.00  E-value=1.9e-37  Score=305.29  Aligned_cols=335  Identities=19%  Similarity=0.214  Sum_probs=256.3

Q ss_pred             HHHHHH-hCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHH
Q 014486           57 LLRAIV-DSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFE  135 (423)
Q Consensus        57 ~~~~l~-~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  135 (423)
                      +...+. ..|...+++-|.++|..++.|++.++.+|||.||+++|.+|++..-.      .+|||.|..+|++.+...+.
T Consensus       252 ~~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~~g------itvVISPL~SLm~DQv~~L~  325 (941)
T KOG0351|consen  252 LELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLLGG------VTVVISPLISLMQDQVTHLS  325 (941)
T ss_pred             HHHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeeccccccCC------ceEEeccHHHHHHHHHHhhh
Confidence            333333 45999999999999999999999999999999999999888776544      78999999999887765553


Q ss_pred             HHhccCCCceEEEEEcCcchHHHH---HHHhcC--CCcEEEechHHHHH--HHhcCCCCCCC---ccEEEEcCcchhhcc
Q 014486          136 RFSTYLPDIKVAVFYGGVNIKIHK---DLLKNE--CPQIVVGTPGRILA--LARDKDLSLKN---VRHFILDECDKMLES  205 (423)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~--~~~ilv~T~~~l~~--~~~~~~~~~~~---~~~vVvDE~h~~~~~  205 (423)
                      .     .++....+.++....++.   ..+.++  ..+|++.||+++..  .+......+..   +.++|+||||+...|
T Consensus       326 ~-----~~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqW  400 (941)
T KOG0351|consen  326 K-----KGIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQW  400 (941)
T ss_pred             h-----cCcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhh
Confidence            2     278888888888775443   344455  67999999998865  12222223333   778999999999988


Q ss_pred             -CCcHHHHHHHHHhCC--CCceEEEEeccCCccHHHHHHHhccCCc-eeeeccccccccccceEEEEEeChHHHHH-HHH
Q 014486          206 -LDMRRDVQEIFKMTP--HDKQVMMFSATLSKEIRPVCKKFMQDPM-EIYVDDEAKLTLHGLVQHYIKLSELEKNR-KLN  280 (423)
Q Consensus       206 -~~~~~~~~~~~~~~~--~~~~~v~~SAT~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~l~  280 (423)
                       ++|++.+..+.....  +..+++++|||.+..+...+-..+.-.. .+.....   ...++...+..-....... .+.
T Consensus       401 gHdFRp~Yk~l~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~sf---nR~NL~yeV~~k~~~~~~~~~~~  477 (941)
T KOG0351|consen  401 GHDFRPSYKRLGLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELFKSSF---NRPNLKYEVSPKTDKDALLDILE  477 (941)
T ss_pred             cccccHHHHHHHHHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCcceecccC---CCCCceEEEEeccCccchHHHHH
Confidence             788888777644332  2468999999998887765555444222 2222111   1222222222212122222 333


Q ss_pred             HHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEE
Q 014486          281 DLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIV  360 (423)
Q Consensus       281 ~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~v  360 (423)
                      ..-...+....||||.++..++.+...|+..+..+..||++|+..+|..+.+.|..++++|++||=++++|+|.|+++.|
T Consensus       478 ~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~V  557 (941)
T KOG0351|consen  478 ESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFV  557 (941)
T ss_pred             HhhhcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEE
Confidence            33344567899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHH
Q 014486          361 INYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVS  405 (423)
Q Consensus       361 i~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~  405 (423)
                      |||..|+|++.|.|.+|||||.|....|++|++..+...+.-.|.
T Consensus       558 iH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~D~~~l~~ll~  602 (941)
T KOG0351|consen  558 IHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYADISELRRLLT  602 (941)
T ss_pred             EECCCchhHHHHHHhccccCcCCCcceeEEecchhHHHHHHHHHH
Confidence            999999999999999999999999999999999875555444443

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=7.9e-37  Score=296.67  Aligned_cols=317  Identities=20%  Similarity=0.249  Sum_probs=236.5

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      |+ .|+++|..+.+.+..|+  |..+.||+|||+++++|++.....+.   .++|++|++.||.|.++.+..+.... ++
T Consensus        76 g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~G~---~v~VvTpt~~LA~qd~e~~~~l~~~l-Gl  148 (790)
T PRK09200         76 GM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALEGK---GVHLITVNDYLAKRDAEEMGQVYEFL-GL  148 (790)
T ss_pred             CC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHcCC---CeEEEeCCHHHHHHHHHHHHHHHhhc-CC
Confidence            55 89999999988888775  99999999999999999986666443   78999999999999999999999887 99


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcCC------CCCCCccEEEEcCcchhhcc------------
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDKD------LSLKNVRHFILDECDKMLES------------  205 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~~------~~~~~~~~vVvDE~h~~~~~------------  205 (423)
                      +++++.|+.+...+.+....  ++|+++||+.+ ++++....      ..+..+.++|+||||+++-+            
T Consensus       149 ~v~~i~g~~~~~~~r~~~y~--~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiLiDea~tpliisg~~  226 (790)
T PRK09200        149 TVGLNFSDIDDASEKKAIYE--ADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSILLDEAQTPLIISGKP  226 (790)
T ss_pred             eEEEEeCCCCcHHHHHHhcC--CCEEEECCccccchhHHhccccchhhhcccccceEEEeccccceeccCCCceeeeCCC
Confidence            99999999884333333333  59999999988 44444332      34578899999999988621            


Q ss_pred             ---CCcHHHHHHHHHhCCCC--------c---------------------------------------------------
Q 014486          206 ---LDMRRDVQEIFKMTPHD--------K---------------------------------------------------  223 (423)
Q Consensus       206 ---~~~~~~~~~~~~~~~~~--------~---------------------------------------------------  223 (423)
                         .........+...+...        .                                                   
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               00111111111111100        0                                                   


Q ss_pred             ----------------------------------------------------------eEEEEeccCCccHHHHHHHhcc
Q 014486          224 ----------------------------------------------------------QVMMFSATLSKEIRPVCKKFMQ  245 (423)
Q Consensus       224 ----------------------------------------------------------~~v~~SAT~~~~~~~~~~~~~~  245 (423)
                                                                                ++.+||+|...+...+.+.+..
T Consensus       307 V~~~~v~ivD~~TGr~~~gr~~s~GlhQaieaKe~v~i~~e~~t~a~It~q~~fr~Y~kl~GmTGTa~t~~~e~~~~Y~l  386 (790)
T PRK09200        307 VYDGEIVLVDRFTGRVLPGRKLQDGLHQAIEAKEGVEITEENRTMASITIQNLFRMFPKLSGMTGTAKTEEKEFFEVYNM  386 (790)
T ss_pred             EECCEEEEEECCCCcCCCCCccChHHHHHHHHhcCCCcCCCceehhhhhHHHHHHHhHHHhccCCCChHHHHHHHHHhCC
Confidence                                                                      4566777765544444333322


Q ss_pred             CCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCC
Q 014486          246 DPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMS  323 (423)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~  323 (423)
                      ...  .++...+..... ....+......|...+...+...  .+.++||||++.+.++.++..|...|+++..+|+.+.
T Consensus       387 ~v~--~IPt~kp~~r~d-~~~~i~~~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~  463 (790)
T PRK09200        387 EVV--QIPTNRPIIRID-YPDKVFVTLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNA  463 (790)
T ss_pred             cEE--ECCCCCCccccc-CCCeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCcc
Confidence            222  222222212222 22233445667888887777653  5789999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhcCCccEEEEcCccccCCCC---CCCC-----EEEEccCCCCcchhhhcccccCCCCCceEEEEEecCc
Q 014486          324 QEERLTRYKGFKEGNKRILVATDLVGRGIDI---ERVN-----IVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       324 ~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~---~~~~-----~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      +.++..+...+..|  .|+|||++++||+|+   +++.     +||++++|.|...|.||+||+||.|.+|.++.|++..
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            88888777776655  799999999999999   6898     9999999999999999999999999999999999863

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

Probab=100.00  E-value=9.6e-37  Score=287.52  Aligned_cols=319  Identities=21%  Similarity=0.295  Sum_probs=226.5

Q ss_pred             CCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCce
Q 014486           66 FEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIK  145 (423)
Q Consensus        66 ~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  145 (423)
                      ...+|.||.+.+...+ ++++||++|||+|||+++...++.++...+.+ ++++++|++.|+.|+...+..++..   ..
T Consensus        60 ~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~-KiVF~aP~~pLv~QQ~a~~~~~~~~---~~  134 (746)
T KOG0354|consen   60 NLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPKG-KVVFLAPTRPLVNQQIACFSIYLIP---YS  134 (746)
T ss_pred             cccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCcc-eEEEeeCCchHHHHHHHHHhhccCc---cc
Confidence            4489999999998888 99999999999999999999899888877765 9999999999999998777766543   34


Q ss_pred             EEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCC-CCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCce
Q 014486          146 VAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLS-LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQ  224 (423)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~-~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~  224 (423)
                      +....||.........+... .+|+|+||+.+.+-+...... ++.|.++||||||+......+...++.++.......|
T Consensus       135 ~T~~l~~~~~~~~r~~i~~s-~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~~Vmr~~l~~k~~~~q  213 (746)
T KOG0354|consen  135 VTGQLGDTVPRSNRGEIVAS-KRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYNNIMREYLDLKNQGNQ  213 (746)
T ss_pred             ceeeccCccCCCchhhhhcc-cceEEeChHhhhhhcccccccccceEEEEEEcccccccccccHHHHHHHHHHhhhcccc
Confidence            55555553322222233333 499999999999877665444 5999999999999998866777777777777666779


Q ss_pred             EEEEeccCCccHHHHHHHh---ccCCceee--------------------------------------------------
Q 014486          225 VMMFSATLSKEIRPVCKKF---MQDPMEIY--------------------------------------------------  251 (423)
Q Consensus       225 ~v~~SAT~~~~~~~~~~~~---~~~~~~~~--------------------------------------------------  251 (423)
                      ++++||||.+.........   +.. ..+.                                                  
T Consensus       214 ILgLTASpG~~~~~v~~~I~~L~as-ldvr~~ssi~~~y~~lr~~~~i~v~~~~~~~~~~~~f~~~i~p~l~~l~~~~l~  292 (746)
T KOG0354|consen  214 ILGLTASPGSKLEQVQNVIDNLCAS-LDVRTESSIKSNYEELREHVQIPVDLSLCERDIEDPFGMIIEPLLQQLQEEGLI  292 (746)
T ss_pred             EEEEecCCCccHHHHHHHHHhhhee-cccchhhhhhhhHHHHhccCcccCcHHHhhhhhhhhHHHHHHHHHHHHHhcCcc
Confidence            9999999865433211110   000 0000                                                  


Q ss_pred             -ecccc-----------ccccccc--eEE-------------------EEE-----------------------------
Q 014486          252 -VDDEA-----------KLTLHGL--VQH-------------------YIK-----------------------------  269 (423)
Q Consensus       252 -~~~~~-----------~~~~~~~--~~~-------------------~~~-----------------------------  269 (423)
                       .....           .......  .++                   -+.                             
T Consensus       293 ~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~f~~~~~~~~~~~ll~~~gir~~~~l~~~~~f~~e~~~~k~~~~~~e~~~  372 (746)
T KOG0354|consen  293 EISDKSTSYEQWVVQAEKAAAPNGPENQRNCFYALHLRKYNLALLISDGIRFVDALDYLEDFYEEVALKKYLKLELEARL  372 (746)
T ss_pred             ccccccccccchhhhhhhhhccCCCccchhhHHHHHHHHHHHHHHhhcchhhHHHHhhhhhhccccchhHHHHHHhcchh
Confidence             00000           0000000  000                   000                             


Q ss_pred             ----------------e--ChHHHHHHHHHHHH----hhcCCcEEEEEcChhhHHHHHHHHHh---CCCCeEEE------
Q 014486          270 ----------------L--SELEKNRKLNDLLD----ALDFNQVVIFVKSVSRAAELNKLLVE---CNFPSICI------  318 (423)
Q Consensus       270 ----------------~--~~~~~~~~l~~ll~----~~~~~~~ivf~~~~~~~~~l~~~L~~---~~~~~~~~------  318 (423)
                                      .  .+..|...+.+++.    ..+..++|||+.+++.|..+.+.|.+   .++++..+      
T Consensus       373 ~~~~~~~m~~~~~l~~~~~~~npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s  452 (746)
T KOG0354|consen  373 IRNFTENMNELEHLSLDPPKENPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKS  452 (746)
T ss_pred             hHHHHHHHHhhhhhhcCCCccChhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeecccc
Confidence                            0  00111222222221    12445799999999999999999884   23343333      


Q ss_pred             --cCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEec
Q 014486          319 --HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVS  393 (423)
Q Consensus       319 --~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~  393 (423)
                        ..+|++.++.++++.|++|+++|||||+++++|+|++.|+.||.||...++..++||.|| ||+. .|.++++++
T Consensus       453 ~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa~-ns~~vll~t  527 (746)
T KOG0354|consen  453 TQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRAR-NSKCVLLTT  527 (746)
T ss_pred             ccccccCHHHHHHHHHHHhCCCccEEEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-cccc-CCeEEEEEc
Confidence              248999999999999999999999999999999999999999999999999999999999 9984 467777776

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=100.00  E-value=2.3e-36  Score=290.59  Aligned_cols=319  Identities=18%  Similarity=0.182  Sum_probs=228.9

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .++|+|.+++..+..++..++.++||+|||+++++|++.....+.   .++|++|++.||.|+++++..+...+ ++++.
T Consensus        68 glrpydVQlig~l~l~~G~Iaem~TGeGKTLta~Lpa~l~aL~g~---~V~VVTpn~yLA~Rdae~m~~l~~~L-GLsv~  143 (762)
T TIGR03714        68 GMFPYDVQVLGAIVLHQGNIAEMKTGEGKTLTATMPLYLNALTGK---GAMLVTTNDYLAKRDAEEMGPVYEWL-GLTVS  143 (762)
T ss_pred             CCCccHHHHHHHHHhcCCceeEecCCcchHHHHHHHHHHHhhcCC---ceEEeCCCHHHHHHHHHHHHHHHhhc-CCcEE
Confidence            345555555555555555899999999999999999877665443   68999999999999999999998887 88988


Q ss_pred             EEEcCcc---hHHHHHHHhcCCCcEEEechHHH-HHHHhcC------CCCCCCccEEEEcCcchhhcc------------
Q 014486          148 VFYGGVN---IKIHKDLLKNECPQIVVGTPGRI-LALARDK------DLSLKNVRHFILDECDKMLES------------  205 (423)
Q Consensus       148 ~~~~~~~---~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~------~~~~~~~~~vVvDE~h~~~~~------------  205 (423)
                      ...++..   .....+....+ ++|+++||+.| ++++...      ...+..+.++|+||||.++.+            
T Consensus       144 ~~~~~s~~~~~~~~~rr~~y~-~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsILiDeartpliisg~~  222 (762)
T TIGR03714       144 LGVVDDPDEEYDANEKRKIYN-SDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVLLDSAQTPLVISGAP  222 (762)
T ss_pred             EEECCCCccccCHHHHHHhCC-CCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHhhccCcCCeeeeCCC
Confidence            8776532   22222333334 59999999999 4555322      234678999999999998621            


Q ss_pred             ---CCcHHHHHHHHHhCCCC------------------------------------------------------------
Q 014486          206 ---LDMRRDVQEIFKMTPHD------------------------------------------------------------  222 (423)
Q Consensus       206 ---~~~~~~~~~~~~~~~~~------------------------------------------------------------  222 (423)
                         .........+.+.+...                                                            
T Consensus       223 ~~~~~~y~~~~~~v~~l~~~~dy~~d~~~~~v~lt~~G~~~~e~~~~~~~l~~~~~~~~~~~i~~al~A~~~~~~d~dYi  302 (762)
T TIGR03714       223 RVQSNLYHIADTFVRTLKEDVDYIFKKDKKEVWLTDKGIEKAEQYFKIDNLYSEEYFELVRHINLALRAHYLFKRNKDYV  302 (762)
T ss_pred             ccchHHHHHHHHHHHhcCCCCCeEEEcCCCeeeecHhHHHHHHHHcCCCccCChhhHHHHHHHHHHHHHHHHHhcCCceE
Confidence               00111111111111110                                                            


Q ss_pred             ---------------------------------------------------------ceEEEEeccCCccHHHHHHHhcc
Q 014486          223 ---------------------------------------------------------KQVMMFSATLSKEIRPVCKKFMQ  245 (423)
Q Consensus       223 ---------------------------------------------------------~~~v~~SAT~~~~~~~~~~~~~~  245 (423)
                                                                               .++.+||+|...+...+.+.+..
T Consensus       303 V~~~~v~ivD~~TGr~~~gr~~~~GLhQaieaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~~~~~Ef~~iY~l  382 (762)
T TIGR03714       303 VTNGEVVLLDRITGRLLEGTKLQSGIHQAIEAKEHVELSKETRAMASITYQNLFKMFNKLSGMTGTGKVAEKEFIETYSL  382 (762)
T ss_pred             EECCEEEEEECCCCcCCCCCCcchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCChhHHHHHHHHhCC
Confidence                                                                     04667777765555555443332


Q ss_pred             CCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHh--hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCC
Q 014486          246 DPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDA--LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMS  323 (423)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~--~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~  323 (423)
                      ..  +.++...+..... ....+......|...+...+..  ..+.++||||++++.++.+...|...|+++..+|+.+.
T Consensus       383 ~v--~~IPt~kp~~r~d-~~d~i~~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~  459 (762)
T TIGR03714       383 SV--VKIPTNKPIIRID-YPDKIYATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNA  459 (762)
T ss_pred             CE--EEcCCCCCeeeee-CCCeEEECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCCh
Confidence            22  2222222222222 2223445667788878777755  35689999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhcCCccEEEEcCccccCCCCC---------CCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecC
Q 014486          324 QEERLTRYKGFKEGNKRILVATDLVGRGIDIE---------RVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       324 ~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~---------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                      +.++..+..+++.|  .|+|||++++||+|++         ++.+|+++++|..... .||.||+||.|.+|.++.|++.
T Consensus       460 ~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~  536 (762)
T TIGR03714       460 AKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSL  536 (762)
T ss_pred             HHHHHHHHHcCCCC--eEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEcc
Confidence            88887777766655  7999999999999999         8999999999987666 9999999999999999999986


Q ss_pred             ccc
Q 014486          395 ASD  397 (423)
Q Consensus       395 ~~~  397 (423)
                      .++
T Consensus       537 eD~  539 (762)
T TIGR03714       537 EDD  539 (762)
T ss_pred             chh
Confidence            433

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.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=100.00  E-value=2.4e-36  Score=290.47  Aligned_cols=307  Identities=18%  Similarity=0.183  Sum_probs=211.2

Q ss_pred             CCCChhhhhccccccc-C--CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           67 EHPSEVQHECIPQAIL-G--MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~-~--~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      ..+||||.+++..+.. +  +++++++|||+|||++.+..+....      .++|||||+..|+.||.+++.++... +.
T Consensus       254 ~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~l~------k~tLILvps~~Lv~QW~~ef~~~~~l-~~  326 (732)
T TIGR00603       254 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVK------KSCLVLCTSAVSVEQWKQQFKMWSTI-DD  326 (732)
T ss_pred             CCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHHhC------CCEEEEeCcHHHHHHHHHHHHHhcCC-CC
Confidence            3789999999999885 3  3689999999999999876554432      17899999999999999999998643 24


Q ss_pred             ceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC--------CCCCCCccEEEEcCcchhhccCCcHHHHHHH
Q 014486          144 IKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK--------DLSLKNVRHFILDECDKMLESLDMRRDVQEI  215 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~--------~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~  215 (423)
                      ..+..++|+....     . .+...|+|+|++++.....+.        .+.-..+++||+||||++..     ..++.+
T Consensus       327 ~~I~~~tg~~k~~-----~-~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA-----~~fr~i  395 (732)
T TIGR00603       327 SQICRFTSDAKER-----F-HGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPA-----AMFRRV  395 (732)
T ss_pred             ceEEEEecCcccc-----c-ccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccH-----HHHHHH
Confidence            4666677653221     1 122489999999876432211        12234688999999998743     334445


Q ss_pred             HHhCCCCceEEEEeccCCccHHH--HHHHhccCCceeeeccccccc---cccceEE-----------------------E
Q 014486          216 FKMTPHDKQVMMFSATLSKEIRP--VCKKFMQDPMEIYVDDEAKLT---LHGLVQH-----------------------Y  267 (423)
Q Consensus       216 ~~~~~~~~~~v~~SAT~~~~~~~--~~~~~~~~~~~~~~~~~~~~~---~~~~~~~-----------------------~  267 (423)
                      ...+. ....+++||||.+.-..  .+..+++ |..+.........   .......                       .
T Consensus       396 l~~l~-a~~RLGLTATP~ReD~~~~~L~~LiG-P~vye~~~~eLi~~G~LA~~~~~ev~v~~t~~~~~~yl~~~~~~k~~  473 (732)
T TIGR00603       396 LTIVQ-AHCKLGLTATLVREDDKITDLNFLIG-PKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRML  473 (732)
T ss_pred             HHhcC-cCcEEEEeecCcccCCchhhhhhhcC-CeeeecCHHHHHhCCccccceEEEEEecCCHHHHHHHHHhcchhhhH
Confidence            55543 34579999999753221  1222222 2111110000000   0000000                       0


Q ss_pred             EEeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcC-CccEEEE
Q 014486          268 IKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEG-NKRILVA  344 (423)
Q Consensus       268 ~~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~ili~  344 (423)
                      .......|...+..+++.+  ++.++||||.+...+..+++.|.     +..+||.+++.+|..+++.|+.+ .+++||+
T Consensus       474 l~~~np~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L~-----~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~  548 (732)
T TIGR00603       474 LYVMNPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQQERMQILQNFQHNPKVNTIFL  548 (732)
T ss_pred             HhhhChHHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHcC-----CceEECCCCHHHHHHHHHHHHhCCCccEEEE
Confidence            0111223445555566554  67899999999999998888773     45689999999999999999875 7899999


Q ss_pred             cCccccCCCCCCCCEEEEccCC-CCcchhhhcccccCCCCCceEE-------EEEecCcccH
Q 014486          345 TDLVGRGIDIERVNIVINYDMP-DSADTYLHRVGRAGRFGTKGLA-------ITFVSSASDS  398 (423)
Q Consensus       345 T~~~~~Gld~~~~~~vi~~~~~-~s~~~~~Q~~GR~~R~g~~~~~-------~~~~~~~~~~  398 (423)
                      |+++++|+|+|++++||+++.| .|..+|+||+||++|.+..|.+       +.|++.+...
T Consensus       549 SkVgdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E  610 (732)
T TIGR00603       549 SKVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQE  610 (732)
T ss_pred             ecccccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchH
Confidence            9999999999999999999987 5999999999999998765553       6677654433

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).

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=100.00  E-value=5.2e-36  Score=286.31  Aligned_cols=318  Identities=20%  Similarity=0.240  Sum_probs=237.2

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      |+ .|++.|..+...+..|+  +..++||+|||+++++|++.....+.   .+.|++|+..||.|.++++..+.... ++
T Consensus        54 g~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~---~V~VvTpt~~LA~qdae~~~~l~~~L-GL  126 (745)
T TIGR00963        54 GM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALTGK---GVHVVTVNDYLAQRDAEWMGQVYRFL-GL  126 (745)
T ss_pred             CC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHhCC---CEEEEcCCHHHHHHHHHHHHHHhccC-CC
Confidence            44 78899998888777665  99999999999999999964444332   68999999999999999999999887 89


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcC------CCCCCCccEEEEcCcchhhccCC----------
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDK------DLSLKNVRHFILDECDKMLESLD----------  207 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~------~~~~~~~~~vVvDE~h~~~~~~~----------  207 (423)
                      ++..+.|+.+.......+.   ++|+++||..| +++++.+      ...+..++++|+||+|+++-+..          
T Consensus       127 sv~~i~g~~~~~~r~~~y~---~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LIDeaRtpLiisg~~  203 (745)
T TIGR00963       127 SVGLILSGMSPEERREAYA---CDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILIDEARTPLIISGPA  203 (745)
T ss_pred             eEEEEeCCCCHHHHHHhcC---CCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhHHhhhhHHhhcCCC
Confidence            9999999988655444332   59999999999 8888765      24578899999999998863100          


Q ss_pred             -----cHHHHHHHHHhCCCC------------------------------------------------------------
Q 014486          208 -----MRRDVQEIFKMTPHD------------------------------------------------------------  222 (423)
Q Consensus       208 -----~~~~~~~~~~~~~~~------------------------------------------------------------  222 (423)
                           .......+.+.+...                                                            
T Consensus       204 ~~~~~ly~~a~~i~r~L~~~~dy~~de~~k~v~Lt~~G~~~~e~~~~~~~ly~~~~~~~~~~i~~Al~A~~l~~~d~dYi  283 (745)
T TIGR00963       204 EKSTELYLQANRFAKALEKEVHYEVDEKNRAVLLTEKGIKKAEDLLGVDNLYDLENSPLIHYINNALKAKELFEKDVDYI  283 (745)
T ss_pred             CCchHHHHHHHHHHHhhccCCCeEEecCCCceeECHHHHHHHHHHcCCccccChhhhHHHHHHHHHHHHHHHHhcCCcEE
Confidence                 000000111111000                                                            


Q ss_pred             ---------------------------------------------------------ceEEEEeccCCccHHHHHHHhcc
Q 014486          223 ---------------------------------------------------------KQVMMFSATLSKEIRPVCKKFMQ  245 (423)
Q Consensus       223 ---------------------------------------------------------~~~v~~SAT~~~~~~~~~~~~~~  245 (423)
                                                                               .++.+||+|...+...+.+.+..
T Consensus       284 V~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       284 VRDGEVVIVDEFTGRIMEGRRWSDGLHQAIEAKEGVEIQNENQTLATITYQNFFRLYEKLSGMTGTAKTEEEEFEKIYNL  363 (745)
T ss_pred             EECCEEEEEECCCCcCCCCCccchHHHHHHHHhcCCCcCCCceeeeeeeHHHHHhhCchhhccCCCcHHHHHHHHHHhCC
Confidence                                                                     04566777766554444444433


Q ss_pred             CCceeeeccccccccccceEEEEEeChHHHHHHHHHHHH--hhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCC
Q 014486          246 DPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLD--ALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMS  323 (423)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~--~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~  323 (423)
                      ....+  +...+....... ..+.....+|...+.+.+.  ...+.++||||++++.++.+++.|.+.|+++..+|+.  
T Consensus       364 ~vv~I--Ptnkp~~R~d~~-d~i~~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--  438 (745)
T TIGR00963       364 EVVVV--PTNRPVIRKDLS-DLVYKTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--  438 (745)
T ss_pred             CEEEe--CCCCCeeeeeCC-CeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--
Confidence            33222  222221222212 2233345556666655552  2357899999999999999999999999999999998  


Q ss_pred             HHHHHHHHHhhhcCCccEEEEcCccccCCCCCC-------CCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcc
Q 014486          324 QEERLTRYKGFKEGNKRILVATDLVGRGIDIER-------VNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSAS  396 (423)
Q Consensus       324 ~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~-------~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  396 (423)
                      +.+|+..+..|..+...|+|||++++||+|++.       ..+||+++.|.|...+.|+.||+||.|.+|.+..|++..+
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            778999999999999999999999999999998       5699999999999999999999999999999999998654


Q ss_pred             c
Q 014486          397 D  397 (423)
Q Consensus       397 ~  397 (423)
                      +
T Consensus       519 ~  519 (745)
T TIGR00963       519 N  519 (745)
T ss_pred             H
Confidence            3

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=100.00  E-value=1.3e-35  Score=271.81  Aligned_cols=293  Identities=17%  Similarity=0.174  Sum_probs=200.9

Q ss_pred             hhhhcccccccCCc--eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccC---CCceE
Q 014486           72 VQHECIPQAILGMD--VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYL---PDIKV  146 (423)
Q Consensus        72 ~Q~~~i~~~~~~~~--~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~---~~~~~  146 (423)
                      ||.++++.+..+.+  +++++|||+|||.+++++++...      .++++++|+++|+.|+++.++++....   .+..+
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~~------~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v   74 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHGE------NDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNL   74 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHcC------CCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCceE
Confidence            69999999998864  78999999999999999988532      268999999999999999999887443   24566


Q ss_pred             EEEEcCcchH--HH-----------------HHHHhcCCCcEEEechHHHHHHHhcCC-----C---CCCCccEEEEcCc
Q 014486          147 AVFYGGVNIK--IH-----------------KDLLKNECPQIVVGTPGRILALARDKD-----L---SLKNVRHFILDEC  199 (423)
Q Consensus       147 ~~~~~~~~~~--~~-----------------~~~~~~~~~~ilv~T~~~l~~~~~~~~-----~---~~~~~~~vVvDE~  199 (423)
                      ..+.|.....  ..                 ........+.|+++||+.|..++....     .   .+.++++||+||+
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            6666652211  00                 111222357899999999976654321     1   2478999999999


Q ss_pred             chhhccCC----cHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHh--ccCCceeeecc----c-------cc-----
Q 014486          200 DKMLESLD----MRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKF--MQDPMEIYVDD----E-------AK-----  257 (423)
Q Consensus       200 h~~~~~~~----~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~--~~~~~~~~~~~----~-------~~-----  257 (423)
                      |.+..+..    +......+........+++++|||+++.+...+...  ...+.......    .       ..     
T Consensus       155 H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~v~g~~~~~~~~~~~~~~~~~~~~  234 (357)
T TIGR03158       155 HLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEADNKTQSF  234 (357)
T ss_pred             cccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCceeeeecCcccccCCChhhhcccccccc
Confidence            99864211    111233333333445789999999998877777654  33332111111    0       00     


Q ss_pred             -cccccceEEEEEeChHHHHHHHHHHHH-------hhcCCcEEEEEcChhhHHHHHHHHHhCC--CCeEEEcCCCCHHHH
Q 014486          258 -LTLHGLVQHYIKLSELEKNRKLNDLLD-------ALDFNQVVIFVKSVSRAAELNKLLVECN--FPSICIHSGMSQEER  327 (423)
Q Consensus       258 -~~~~~~~~~~~~~~~~~~~~~l~~ll~-------~~~~~~~ivf~~~~~~~~~l~~~L~~~~--~~~~~~~~~~~~~~r  327 (423)
                       ...+.+...+.. ....+...+..+++       ..+++++||||++.+.++.+++.|++.+  +.+..+||.+++.+|
T Consensus       235 ~~~~~~i~~~~~~-~~~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R  313 (357)
T TIGR03158       235 RPVLPPVELELIP-APDFKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDR  313 (357)
T ss_pred             ceeccceEEEEEe-CCchhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHH
Confidence             000122222222 22223333322222       2356799999999999999999999864  567889999999988


Q ss_pred             HHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccC
Q 014486          328 LTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAG  380 (423)
Q Consensus       328 ~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~  380 (423)
                      .+.      ++.+|||||+++++|+|++.. +|| ++ |.++..|+||+||+|
T Consensus       314 ~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       314 ERA------MQFDILLGTSTVDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             HHh------ccCCEEEEecHHhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence            755      367999999999999999976 566 44 889999999999997

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.

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

Probab=100.00  E-value=9.8e-37  Score=264.91  Aligned_cols=328  Identities=16%  Similarity=0.251  Sum_probs=240.9

Q ss_pred             HHHHHHHhC-CCCCC-Chhhhhccccccc-CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHH
Q 014486           56 ELLRAIVDS-GFEHP-SEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICH  132 (423)
Q Consensus        56 ~~~~~l~~~-~~~~~-~~~Q~~~i~~~~~-~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~  132 (423)
                      .+.++|++. |+..+ ++.|.+++..+.. .+++.+++|||+||+++|.+|.+..-.      .+||++|..+|...+.+
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~~g------ITIV~SPLiALIkDQiD   79 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVHGG------ITIVISPLIALIKDQID   79 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHhCC------eEEEehHHHHHHHHHHH
Confidence            456777764 66543 7899999988887 478999999999999999999887644      78999999999998888


Q ss_pred             HHHHHhccCCCceEEEEEcCcchHHHHHHH---h--cCCCcEEEechHHHHH-----HHhcCCCCCCCccEEEEcCcchh
Q 014486          133 EFERFSTYLPDIKVAVFYGGVNIKIHKDLL---K--NECPQIVVGTPGRILA-----LARDKDLSLKNVRHFILDECDKM  202 (423)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~--~~~~~ilv~T~~~l~~-----~~~~~~~~~~~~~~vVvDE~h~~  202 (423)
                      -+.++     .+++..+.+..+..+..+.+   .  +....+++.||+.-..     +++ ....-..+.++|+||||+.
T Consensus        80 HL~~L-----KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn-~L~~r~~L~Y~vVDEAHCV  153 (641)
T KOG0352|consen   80 HLKRL-----KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLN-GLANRDVLRYIVVDEAHCV  153 (641)
T ss_pred             HHHhc-----CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHH-HHhhhceeeeEEechhhhH
Confidence            77665     34444444444444333322   1  2335799999986432     222 1223355789999999999


Q ss_pred             hcc-CCcHHHHHHHHHh--CCCCceEEEEeccCCccHHHHHHH--hccCCceeeecccccccc--ccceEEEEEeChHHH
Q 014486          203 LES-LDMRRDVQEIFKM--TPHDKQVMMFSATLSKEIRPVCKK--FMQDPMEIYVDDEAKLTL--HGLVQHYIKLSELEK  275 (423)
Q Consensus       203 ~~~-~~~~~~~~~~~~~--~~~~~~~v~~SAT~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~  275 (423)
                      ..| ++|++++.++-..  .-.+.+.+.+|||..+.+.+.+-.  .+.+|.-++-.+.-..+.  ......++    .+-
T Consensus       154 SQWGHDFRPDYL~LG~LRS~~~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~FR~NLFYD~~~K~~I----~D~  229 (641)
T KOG0352|consen  154 SQWGHDFRPDYLTLGSLRSVCPGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTFRDNLFYDNHMKSFI----TDC  229 (641)
T ss_pred             hhhccccCcchhhhhhHHhhCCCCceEEeecccChhHHHHHHHHHhhcCcHHhccCcchhhhhhHHHHHHHHh----hhH
Confidence            987 7888887666432  223667999999999887765433  345665554333221110  00000000    111


Q ss_pred             HHHHHHHHHhh-------------cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEE
Q 014486          276 NRKLNDLLDAL-------------DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRIL  342 (423)
Q Consensus       276 ~~~l~~ll~~~-------------~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~il  342 (423)
                      ...|.++....             ..+-.||||.+++.+++++..|.-+|+++..||.++...+|.++.+.|.++++.|+
T Consensus       230 ~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI  309 (641)
T KOG0352|consen  230 LTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVI  309 (641)
T ss_pred             hHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEE
Confidence            12233332221             11347999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHH
Q 014486          343 VATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSD  399 (423)
Q Consensus       343 i~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~  399 (423)
                      ++|...++|+|-|++++||||++|.++.-|.|..||+||.|.+..|-++|+-.+...
T Consensus       310 ~AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~  366 (641)
T KOG0352|consen  310 AATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGRDGKRSYCRLYYSRQDKNA  366 (641)
T ss_pred             EEEeccccccCCcceeEEEecCchhhhHHHHHhccccccCCCccceeeeecccchHH
Confidence            999999999999999999999999999999999999999999999999998554443

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

Probab=100.00  E-value=5.9e-36  Score=256.74  Aligned_cols=338  Identities=20%  Similarity=0.245  Sum_probs=259.1

Q ss_pred             CCCCcCCCCCHHHHHHHHhC-CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           45 SSGFRDFLLKPELLRAIVDS-GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~-~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      .+.-++|+++....+.|+.. ..+.+||.|..+|+..+.+.++++..|||.||+++|.+|++-.-.      .+||++|.
T Consensus        70 awdkd~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~adg------~alvi~pl  143 (695)
T KOG0353|consen   70 AWDKDDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCADG------FALVICPL  143 (695)
T ss_pred             ccccCCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhcCC------ceEeechh
Confidence            34557899999988888765 777899999999999999999999999999999999999886644      78999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHH---HH--hcCCCcEEEechHHHHH---HHh--cCCCCCCCccE
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKD---LL--KNECPQIVVGTPGRILA---LAR--DKDLSLKNVRH  193 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~--~~~~~~ilv~T~~~l~~---~~~--~~~~~~~~~~~  193 (423)
                      ..|++.+.-.++.+     ++....+..+.+.++-..   .+  .+....+++.||+.+..   ++.  ...+....+++
T Consensus       144 islmedqil~lkql-----gi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~  218 (695)
T KOG0353|consen  144 ISLMEDQILQLKQL-----GIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKL  218 (695)
T ss_pred             HHHHHHHHHHHHHh-----CcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEE
Confidence            99999888778776     455545544444333221   12  22456899999998754   111  12234566889


Q ss_pred             EEEcCcchhhcc-CCcHHHHHHH--HHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEe
Q 014486          194 FILDECDKMLES-LDMRRDVQEI--FKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL  270 (423)
Q Consensus       194 vVvDE~h~~~~~-~~~~~~~~~~--~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (423)
                      |.+||+|+...| ++|++.+..+  +++.-+..+++++|||.+..+....+..+.....+.....-  ..+++......-
T Consensus       219 iaidevhccsqwghdfr~dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~il~ie~~~tf~a~f--nr~nl~yev~qk  296 (695)
T KOG0353|consen  219 IAIDEVHCCSQWGHDFRPDYKALGILKRQFKGAPIIGLTATATNHVLDDAKDILCIEAAFTFRAGF--NRPNLKYEVRQK  296 (695)
T ss_pred             EeecceeehhhhCcccCcchHHHHHHHHhCCCCceeeeehhhhcchhhHHHHHHhHHhhheeeccc--CCCCceeEeeeC
Confidence            999999999887 6787765543  45545577899999999988877776655433333222211  112222222222


Q ss_pred             C--hHHHHHHHHHHHHhh-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc
Q 014486          271 S--ELEKNRKLNDLLDAL-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL  347 (423)
Q Consensus       271 ~--~~~~~~~l~~ll~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~  347 (423)
                      +  +.+-.+.+..+++.. .+...||||-+++.++.+...|+..|+.+-.||..+.+.++..+.+.|..|+++|+|+|-+
T Consensus       297 p~n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatva  376 (695)
T KOG0353|consen  297 PGNEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVA  376 (695)
T ss_pred             CCChHHHHHHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEee
Confidence            2  222334444444332 4567899999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCCCCEEEEccCCCCcchhhh-------------------------------------------cccccCCCCC
Q 014486          348 VGRGIDIERVNIVINYDMPDSADTYLH-------------------------------------------RVGRAGRFGT  384 (423)
Q Consensus       348 ~~~Gld~~~~~~vi~~~~~~s~~~~~Q-------------------------------------------~~GR~~R~g~  384 (423)
                      .++|+|-|++++|||..+|+|+..|.|                                           ..||+||.+.
T Consensus       377 fgmgidkpdvrfvihhsl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~  456 (695)
T KOG0353|consen  377 FGMGIDKPDVRFVIHHSLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDM  456 (695)
T ss_pred             ecccCCCCCeeEEEecccchhHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeecchhccccccCCC
Confidence            999999999999999999999999999                                           6799999999


Q ss_pred             ceEEEEEecCc
Q 014486          385 KGLAITFVSSA  395 (423)
Q Consensus       385 ~~~~~~~~~~~  395 (423)
                      +..|+++|.-.
T Consensus       457 ~a~cilyy~~~  467 (695)
T KOG0353|consen  457 KADCILYYGFA  467 (695)
T ss_pred             cccEEEEechH
Confidence            99999998753

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

Probab=100.00  E-value=1.2e-35  Score=258.75  Aligned_cols=276  Identities=29%  Similarity=0.495  Sum_probs=217.0

Q ss_pred             eEEEEEecChHHHHHHHHHHHHHhccC--CCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          115 VTALVLCHTRELAYQICHEFERFSTYL--PDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       115 ~~~lil~P~~~L~~q~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      |.++|+-|+++|++|....+++|-...  |.++...+.||...+.+.+.+.++ .+|+|+||.++...+....+.+..++
T Consensus       287 p~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g-~~ivvGtpgRl~~~is~g~~~lt~cr  365 (725)
T KOG0349|consen  287 PEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDG-THIVVGTPGRLLQPISKGLVTLTHCR  365 (725)
T ss_pred             cceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcC-ceeeecCchhhhhhhhccceeeeeeE
Confidence            568999999999999999887775443  455666888888889999999998 59999999999999999999999999


Q ss_pred             EEEEcCcchhhccCCcHHHHHHHHHhCCC------CceEEEEeccCCc-cHHHHHHHhccCCceeeeccccccccccceE
Q 014486          193 HFILDECDKMLESLDMRRDVQEIFKMTPH------DKQVMMFSATLSK-EIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQ  265 (423)
Q Consensus       193 ~vVvDE~h~~~~~~~~~~~~~~~~~~~~~------~~~~v~~SAT~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (423)
                      ++|+||++.++. .++...+.++...+++      ..|.+.+|||+.. ++..+.+..++.|..+.+..+...+  ...+
T Consensus       366 FlvlDead~lL~-qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vp--etvH  442 (725)
T KOG0349|consen  366 FLVLDEADLLLG-QGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVP--ETVH  442 (725)
T ss_pred             EEEecchhhhhh-cccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccccccc--hhhc
Confidence            999999999988 6888888888777654      4689999999753 3344444555555444433222111  0011


Q ss_pred             EEEEeC-------------------------------hHH---------HHHHHHHHHHhhcCCcEEEEEcChhhHHHHH
Q 014486          266 HYIKLS-------------------------------ELE---------KNRKLNDLLDALDFNQVVIFVKSVSRAAELN  305 (423)
Q Consensus       266 ~~~~~~-------------------------------~~~---------~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~  305 (423)
                      ++....                               ..+         |.+.-...++.+...+.||||.+...++.+.
T Consensus       443 hvv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLe  522 (725)
T KOG0349|consen  443 HVVKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLE  522 (725)
T ss_pred             cceeecCCccCccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhhccCceEEEEeccccchHHH
Confidence            111000                               000         1111222334456678999999999999999


Q ss_pred             HHHHhCC---CCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCC
Q 014486          306 KLLVECN---FPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRF  382 (423)
Q Consensus       306 ~~L~~~~---~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~  382 (423)
                      +++.+.|   +.++++|++..+.+|.+.++.|+.+..+.||||+++++|+|+.++-++|++.+|.+...|+||+||+||+
T Consensus       523 r~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgra  602 (725)
T KOG0349|consen  523 RMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRA  602 (725)
T ss_pred             HHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEecCcccchhhhhhhccchh
Confidence            9998875   6899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceEEEEEecC
Q 014486          383 GTKGLAITFVSS  394 (423)
Q Consensus       383 g~~~~~~~~~~~  394 (423)
                      ..-|.++.++..
T Consensus       603 ermglaislvat  614 (725)
T KOG0349|consen  603 ERMGLAISLVAT  614 (725)
T ss_pred             hhcceeEEEeec
Confidence            888888888764

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=100.00  E-value=7.1e-34  Score=282.83  Aligned_cols=334  Identities=16%  Similarity=0.161  Sum_probs=220.5

Q ss_pred             CCChhhhhcccccccC--CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCce
Q 014486           68 HPSEVQHECIPQAILG--MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIK  145 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~--~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  145 (423)
                      .|.|||..++..++..  ..++++.++|.|||..+.+.+...+..+... ++|||||. .|..||..++.+..    ++.
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g~~~-rvLIVvP~-sL~~QW~~El~~kF----~l~  225 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTGRAE-RVLILVPE-TLQHQWLVEMLRRF----NLR  225 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcCCCC-cEEEEcCH-HHHHHHHHHHHHHh----CCC
Confidence            6899999998776653  4699999999999998876555544443333 89999997 79999999987654    455


Q ss_pred             EEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHh-cCCCCCCCccEEEEcCcchhhccCC-cHHHHHHHHHhCC
Q 014486          146 VAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALAR-DKDLSLKNVRHFILDECDKMLESLD-MRRDVQEIFKMTP  220 (423)
Q Consensus       146 ~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~-~~~~~~~~~~~vVvDE~h~~~~~~~-~~~~~~~~~~~~~  220 (423)
                      +..+.++.......   ..+.  ..+++|+|++.+...-. ...+.-..+++||+||||++....+ ....+..+.....
T Consensus       226 ~~i~~~~~~~~~~~~~~~pf~--~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~~La~  303 (956)
T PRK04914        226 FSLFDEERYAEAQHDADNPFE--TEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAE  303 (956)
T ss_pred             eEEEcCcchhhhcccccCccc--cCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHHHHHhh
Confidence            55554432211100   1111  24899999998764111 1112234789999999999973211 1222333333333


Q ss_pred             CCceEEEEeccCCcc-------------------HHHHH------------------------------HHhccCC----
Q 014486          221 HDKQVMMFSATLSKE-------------------IRPVC------------------------------KKFMQDP----  247 (423)
Q Consensus       221 ~~~~~v~~SAT~~~~-------------------~~~~~------------------------------~~~~~~~----  247 (423)
                      +...++++||||-..                   ...+.                              ..++...    
T Consensus       304 ~~~~~LLLTATP~q~~~~e~falL~lLdP~~f~~~~~F~~e~~~~~~~a~~v~~l~~~~~~~~~~~~~l~~ll~~~~~~~  383 (956)
T PRK04914        304 VIPGVLLLTATPEQLGQESHFARLRLLDPDRFHDYEAFVEEQQQYRPVADAVQALLAGEKLSDDALNALGELLGEQDIEP  383 (956)
T ss_pred             ccCCEEEEEcCcccCCcHHHHHhhhhhCCCcCCCHHHHHHHHHhhHHHHHHHHHHhcCCcCCHHHHHHHHHHhcccchhH
Confidence            455789999997210                   00000                              0000000    


Q ss_pred             -----------------------------ceeeecccc---ccccccceEEE-E--------------------------
Q 014486          248 -----------------------------MEIYVDDEA---KLTLHGLVQHY-I--------------------------  268 (423)
Q Consensus       248 -----------------------------~~~~~~~~~---~~~~~~~~~~~-~--------------------------  268 (423)
                                                   ..+.+....   ..........+ .                          
T Consensus       384 l~~~~~~~~~~~~~~~~~~i~~L~d~hg~~rvm~RntR~~v~~fp~R~~~~~~l~~~~~y~~~~~~~~~~~~~~~l~pe~  463 (956)
T PRK04914        384 LLQAANSDSEEAQAARQELISELLDRHGTGRVLFRNTRAAVKGFPKRELHPIPLPLPEQYQTAIKVSLEARARDMLYPEQ  463 (956)
T ss_pred             HHhhhcccccccHHHHHHHHHHHHhhcCcceEEEeccHHhhcCCCcCceeEeecCCCHHHHHHHHHhHHHHHHhhcCHHH
Confidence                                         000000000   00000000000 0                          


Q ss_pred             ----------EeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHH-hCCCCeEEEcCCCCHHHHHHHHHhhhcC
Q 014486          269 ----------KLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLV-ECNFPSICIHSGMSQEERLTRYKGFKEG  337 (423)
Q Consensus       269 ----------~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~-~~~~~~~~~~~~~~~~~r~~~~~~f~~~  337 (423)
                                ......|...+.++++.....|+||||++...+..+.+.|+ ..|+++..+||+++..+|.++++.|+++
T Consensus       464 ~~~~~~~~~~~~~~d~Ki~~L~~~L~~~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~  543 (956)
T PRK04914        464 IYQEFEDNATWWNFDPRVEWLIDFLKSHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADE  543 (956)
T ss_pred             HHHHHhhhhhccccCHHHHHHHHHHHhcCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcC
Confidence                      00112344567777777778899999999999999999994 6699999999999999999999999974


Q ss_pred             --CccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhc
Q 014486          338 --NKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFL  410 (423)
Q Consensus       338 --~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (423)
                        ..+|||||+++++|+|++.+++||+||+|++|..|.||+||++|.|+++.+.+++.. .+......|.+.+..
T Consensus       544 ~~~~~VLIsTdvgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~-~~~t~~e~i~~~~~~  617 (956)
T PRK04914        544 EDGAQVLLCSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPY-LEGTAQERLFRWYHE  617 (956)
T ss_pred             CCCccEEEechhhccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEcc-CCCCHHHHHHHHHhh
Confidence              589999999999999999999999999999999999999999999999887666543 333334444444443

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

Probab=100.00  E-value=1.4e-34  Score=276.38  Aligned_cols=331  Identities=22%  Similarity=0.299  Sum_probs=230.3

Q ss_pred             CCCCCCChhhhhccccccc-CCceEEEccCCCcchhHHHHHHhhccCC-------CCCCeEEEEEecChHHHHHHHHHHH
Q 014486           64 SGFEHPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQTEP-------NPGQVTALVLCHTRELAYQICHEFE  135 (423)
Q Consensus        64 ~~~~~~~~~Q~~~i~~~~~-~~~~ii~~~tGsGKT~~~~~~~~~~~~~-------~~~~~~~lil~P~~~L~~q~~~~~~  135 (423)
                      ++|..++.+|..++|..+. +.|.+||||||+|||.++++.|+..+..       ..+..|++||+|+++||.++.+.+.
T Consensus       106 f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~  185 (1230)
T KOG0952|consen  106 FSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFS  185 (1230)
T ss_pred             ccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHh
Confidence            3678899999999999887 5789999999999999999999986653       2345699999999999999998887


Q ss_pred             HHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC---CCCCCccEEEEcCcchhhccCCc--HH
Q 014486          136 RFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD---LSLKNVRHFILDECDKMLESLDM--RR  210 (423)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~---~~~~~~~~vVvDE~h~~~~~~~~--~~  210 (423)
                      +-...+ ++.+..++|+.......  +..  .+|+|+||+++.-.-++..   ..++.+++||+||+|.+-++.+.  ..
T Consensus       186 kkl~~~-gi~v~ELTGD~ql~~te--i~~--tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~RGpvlEt  260 (1230)
T KOG0952|consen  186 KKLAPL-GISVRELTGDTQLTKTE--IAD--TQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDDRGPVLET  260 (1230)
T ss_pred             hhcccc-cceEEEecCcchhhHHH--HHh--cCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCcccchHHH
Confidence            666555 89999999998766554  222  4999999999854333322   23578999999999998764321  11


Q ss_pred             ---HHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCce--eeeccccccccccceEEEEEeChH---H--------
Q 014486          211 ---DVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPME--IYVDDEAKLTLHGLVQHYIKLSEL---E--------  274 (423)
Q Consensus       211 ---~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~---~--------  274 (423)
                         +..+.........++|++|||+|+- .+.+.....++..  ++.+...  .+..+.+.++-.+..   .        
T Consensus       261 iVaRtlr~vessqs~IRivgLSATlPN~-eDvA~fL~vn~~~glfsFd~~y--RPvpL~~~~iG~k~~~~~~~~~~~d~~  337 (1230)
T KOG0952|consen  261 IVARTLRLVESSQSMIRIVGLSATLPNY-EDVARFLRVNPYAGLFSFDQRY--RPVPLTQGFIGIKGKKNRQQKKNIDEV  337 (1230)
T ss_pred             HHHHHHHHHHhhhhheEEEEeeccCCCH-HHHHHHhcCCCccceeeecccc--cccceeeeEEeeecccchhhhhhHHHH
Confidence               1222223344577899999999975 3344443333221  2222221  112222222222111   1        


Q ss_pred             HHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC----C-------------------CCeEEEcCCCCHHHHHHHH
Q 014486          275 KNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC----N-------------------FPSICIHSGMSQEERLTRY  331 (423)
Q Consensus       275 ~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~----~-------------------~~~~~~~~~~~~~~r~~~~  331 (423)
                      ....+.+++.  ++.+++|||++++.....++.|.+.    |                   ......|.+|...+|.-+.
T Consensus       338 ~~~kv~e~~~--~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E  415 (1230)
T KOG0952|consen  338 CYDKVVEFLQ--EGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVE  415 (1230)
T ss_pred             HHHHHHHHHH--cCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHH
Confidence            1122233322  4678999999999998888888663    1                   1244578999999999999


Q ss_pred             HhhhcCCccEEEEcCccccCCCCCCCCEEEE----ccCCC------CcchhhhcccccCCC--CCceEEEEEecCcccHH
Q 014486          332 KGFKEGNKRILVATDLVGRGIDIERVNIVIN----YDMPD------SADTYLHRVGRAGRF--GTKGLAITFVSSASDSD  399 (423)
Q Consensus       332 ~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~----~~~~~------s~~~~~Q~~GR~~R~--g~~~~~~~~~~~~~~~~  399 (423)
                      +.|..|.++||+||..+++|+|+|+-..+|-    |+..+      ++-+..|..|||||.  +..|.++++.+.+.-+.
T Consensus       416 ~~F~~G~i~vL~cTaTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~~  495 (1230)
T KOG0952|consen  416 KEFKEGHIKVLCCTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLDH  495 (1230)
T ss_pred             HHHhcCCceEEEecceeeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHHHH
Confidence            9999999999999999999999996554443    22222      344568999999995  56788888777544444


Q ss_pred             HHHHH
Q 014486          400 ILNQV  404 (423)
Q Consensus       400 ~~~~~  404 (423)
                      +...|
T Consensus       496 Y~sLl  500 (1230)
T KOG0952|consen  496 YESLL  500 (1230)
T ss_pred             HHHHH
Confidence            44443

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

Probab=100.00  E-value=5e-33  Score=260.89  Aligned_cols=291  Identities=20%  Similarity=0.250  Sum_probs=203.3

Q ss_pred             CCChhhhhccccccc----CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           68 HPSEVQHECIPQAIL----GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      .|++||++++..+..    ++.+++.+|||+|||.+++..+.....      ++|||||+.+|+.||.+.+..+...  .
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~~------~~Lvlv~~~~L~~Qw~~~~~~~~~~--~  107 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKR------STLVLVPTKELLDQWAEALKKFLLL--N  107 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhcC------CEEEEECcHHHHHHHHHHHHHhcCC--c
Confidence            799999999999998    788999999999999987665554443      4899999999999999777766532  1


Q ss_pred             ceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCc
Q 014486          144 IKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK  223 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~  223 (423)
                      ..+..+.|+......        ..|.|+|.+++........+....+.+||+||||++..     .....+...+....
T Consensus       108 ~~~g~~~~~~~~~~~--------~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a-----~~~~~~~~~~~~~~  174 (442)
T COG1061         108 DEIGIYGGGEKELEP--------AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPA-----PSYRRILELLSAAY  174 (442)
T ss_pred             cccceecCceeccCC--------CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCc-----HHHHHHHHhhhccc
Confidence            134444444322110        26999999999874211223334789999999998764     22333333333333


Q ss_pred             eEEEEeccCCccHHHH---HHHhccCCceeeeccccccc---cccceEEEEEe---------------------------
Q 014486          224 QVMMFSATLSKEIRPV---CKKFMQDPMEIYVDDEAKLT---LHGLVQHYIKL---------------------------  270 (423)
Q Consensus       224 ~~v~~SAT~~~~~~~~---~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~---------------------------  270 (423)
                      .++++||||++.....   +....+ +..+.........   ........+..                           
T Consensus       175 ~~LGLTATp~R~D~~~~~~l~~~~g-~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~~~~~~~~~~~~~  253 (442)
T COG1061         175 PRLGLTATPEREDGGRIGDLFDLIG-PIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTL  253 (442)
T ss_pred             ceeeeccCceeecCCchhHHHHhcC-CeEeecCHHHHHhCCCccceEEEEEEeccchHHHHHhhhhhhhhhhhhhhhhhh
Confidence            3899999987543111   111111 1111111000000   00000000011                           


Q ss_pred             -----------ChHHHHHHHHHHHHhh-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCC
Q 014486          271 -----------SELEKNRKLNDLLDAL-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN  338 (423)
Q Consensus       271 -----------~~~~~~~~l~~ll~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~  338 (423)
                                 ....+...+..++..+ ...+++||+.+..++..++..+...+. +..+.+.++..+|..+++.|+.|.
T Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~  332 (442)
T COG1061         254 RAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGG  332 (442)
T ss_pred             hHHHHHHHHhhccHHHHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCC
Confidence                       0111222333333333 367999999999999999999998887 889999999999999999999999


Q ss_pred             ccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCC
Q 014486          339 KRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR  381 (423)
Q Consensus       339 ~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R  381 (423)
                      +++|+++.++.+|+|+|+++++|...+..|+..|+||+||.-|
T Consensus       333 ~~~lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR  375 (442)
T COG1061         333 IKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLR  375 (442)
T ss_pred             CCEEEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHhhhhcc
Confidence            9999999999999999999999999999999999999999999

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

Probab=100.00  E-value=1.3e-31  Score=249.41  Aligned_cols=327  Identities=20%  Similarity=0.261  Sum_probs=244.7

Q ss_pred             CCCCCHHHHHHH-HhCCCCCCChhhhhcccccccC------CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           50 DFLLKPELLRAI-VDSGFEHPSEVQHECIPQAILG------MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        50 ~~~l~~~~~~~l-~~~~~~~~~~~Q~~~i~~~~~~------~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      .++.+..+++.+ ...+| +||..|++++..+...      .+-+++|..|||||++++++++.....+.   ++...+|
T Consensus       244 ~~~~~~~l~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~---Q~ALMAP  319 (677)
T COG1200         244 PLPANGELLAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGY---QAALMAP  319 (677)
T ss_pred             CCCccHHHHHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcCC---eeEEecc
Confidence            344555555555 44577 7999999999998873      34799999999999999999988877654   8999999


Q ss_pred             ChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHH---HHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCc
Q 014486          123 TRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKI---HKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDEC  199 (423)
Q Consensus       123 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~  199 (423)
                      |.-||.|.++.+.++.... ++++..++|...-..   ....+.+|..+|+|+|..-+.     ....++++.+||+||=
T Consensus       320 TEILA~QH~~~~~~~l~~~-~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQ-----d~V~F~~LgLVIiDEQ  393 (677)
T COG1200         320 TEILAEQHYESLRKWLEPL-GIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQ-----DKVEFHNLGLVIIDEQ  393 (677)
T ss_pred             HHHHHHHHHHHHHHHhhhc-CCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhh-----cceeecceeEEEEecc
Confidence            9999999999999999887 799999999775443   345567788999999976554     4677899999999999


Q ss_pred             chhhccCCcHHHHHHHHHhCCC-CceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHH
Q 014486          200 DKMLESLDMRRDVQEIFKMTPH-DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRK  278 (423)
Q Consensus       200 h~~~~~~~~~~~~~~~~~~~~~-~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  278 (423)
                      |++.-    ..  +..+..... .+-++.|||||-+....+.  .+.+ ..++...+-+.....+....+  +...+...
T Consensus       394 HRFGV----~Q--R~~L~~KG~~~Ph~LvMTATPIPRTLAlt--~fgD-ldvS~IdElP~GRkpI~T~~i--~~~~~~~v  462 (677)
T COG1200         394 HRFGV----HQ--RLALREKGEQNPHVLVMTATPIPRTLALT--AFGD-LDVSIIDELPPGRKPITTVVI--PHERRPEV  462 (677)
T ss_pred             ccccH----HH--HHHHHHhCCCCCcEEEEeCCCchHHHHHH--Hhcc-ccchhhccCCCCCCceEEEEe--ccccHHHH
Confidence            98743    22  222333333 5678999999876554432  2222 223333333333333333333  33333334


Q ss_pred             HHHHHHhh-cCCcEEEEEcChhhH--------HHHHHHHHhC--CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc
Q 014486          279 LNDLLDAL-DFNQVVIFVKSVSRA--------AELNKLLVEC--NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL  347 (423)
Q Consensus       279 l~~ll~~~-~~~~~ivf~~~~~~~--------~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~  347 (423)
                      +..+.+.. .++++.|.|+-+++.        ..+++.|+..  ++++..+||.|+..++.+++.+|++|+++|||||.+
T Consensus       463 ~e~i~~ei~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTV  542 (677)
T COG1200         463 YERIREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTV  542 (677)
T ss_pred             HHHHHHHHHcCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeE
Confidence            44443333 467899999887654        4556666643  566889999999999999999999999999999999


Q ss_pred             cccCCCCCCCCEEEEccCC-CCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          348 VGRGIDIERVNIVINYDMP-DSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       348 ~~~Gld~~~~~~vi~~~~~-~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      ++.|+|+|+++++|+.+.- ...+++.|-.||+||.+.++.|++++.+...
T Consensus       543 IEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~~  593 (677)
T COG1200         543 IEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPLS  593 (677)
T ss_pred             EEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCCC
Confidence            9999999999998887754 4788999999999999999999999987663

>PRK05580 primosome assembly protein PriA; Validated

Probab=100.00  E-value=3.6e-31  Score=260.27  Aligned_cols=309  Identities=21%  Similarity=0.220  Sum_probs=213.1

Q ss_pred             CCChhhhhcccccccC---CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           68 HPSEVQHECIPQAILG---MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~---~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      .|+++|+++++.+..+   +++++.++||||||.+|+.++...+..+   .++||++|+++|+.|+.+.+++..    +.
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g---~~vLvLvPt~~L~~Q~~~~l~~~f----g~  216 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQG---KQALVLVPEIALTPQMLARFRARF----GA  216 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHcC---CeEEEEeCcHHHHHHHHHHHHHHh----CC
Confidence            5899999999999874   6799999999999999988776665542   289999999999999999998754    46


Q ss_pred             eEEEEEcCcchHHHHH---HHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCC----c-HHHHHHHH
Q 014486          145 KVAVFYGGVNIKIHKD---LLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLD----M-RRDVQEIF  216 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~---~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~----~-~~~~~~~~  216 (423)
                      ++..++|+.+..+...   .+.++.++|+|+|+..++       ..+.++++||+||+|....+..    + .+.+. +.
T Consensus       217 ~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-------~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va-~~  288 (679)
T PRK05580        217 PVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-------LPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLA-VV  288 (679)
T ss_pred             CEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-------ccccCCCEEEEECCCccccccCcCCCCcHHHHH-HH
Confidence            8889999887654443   344566799999998764       3578899999999997653211    1 12222 33


Q ss_pred             HhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccc-cccccceEEEEEeChHH-------HHHHHHHHH-Hhh-
Q 014486          217 KMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAK-LTLHGLVQHYIKLSELE-------KNRKLNDLL-DAL-  286 (423)
Q Consensus       217 ~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~-------~~~~l~~ll-~~~-  286 (423)
                      .....+.+++++|||++.+....+..  +....+....... ...+  ....+......       -...+.+.+ +.+ 
T Consensus       289 ra~~~~~~~il~SATps~~s~~~~~~--g~~~~~~l~~r~~~~~~p--~v~~id~~~~~~~~~~~~ls~~l~~~i~~~l~  364 (679)
T PRK05580        289 RAKLENIPVVLGSATPSLESLANAQQ--GRYRLLRLTKRAGGARLP--EVEIIDMRELLRGENGSFLSPPLLEAIKQRLE  364 (679)
T ss_pred             HhhccCCCEEEEcCCCCHHHHHHHhc--cceeEEEeccccccCCCC--eEEEEechhhhhhcccCCCCHHHHHHHHHHHH
Confidence            33456789999999988655443321  1111111111100 0011  11111111100       001222222 222 


Q ss_pred             cCCcEEEEEcChh------------------------------------------------------------hHHHHHH
Q 014486          287 DFNQVVIFVKSVS------------------------------------------------------------RAAELNK  306 (423)
Q Consensus       287 ~~~~~ivf~~~~~------------------------------------------------------------~~~~l~~  306 (423)
                      .++++|||++.+.                                                            -.+.+.+
T Consensus       365 ~g~qvll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~g~G~e~~~e  444 (679)
T PRK05580        365 RGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTERLEE  444 (679)
T ss_pred             cCCeEEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccHHHHHH
Confidence            2457888876521                                                            3456777


Q ss_pred             HHHhC--CCCeEEEcCCCC--HHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccC--CCC----------cc
Q 014486          307 LLVEC--NFPSICIHSGMS--QEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDM--PDS----------AD  370 (423)
Q Consensus       307 ~L~~~--~~~~~~~~~~~~--~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~--~~s----------~~  370 (423)
                      .|++.  +.++..+|++++  ..++..+++.|++|+.+|||+|+++++|+|+|++++|+.++.  +-+          ..
T Consensus       445 ~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfra~Er~~~  524 (679)
T PRK05580        445 ELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASERTFQ  524 (679)
T ss_pred             HHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccchHHHHHH
Confidence            77765  678889999986  467889999999999999999999999999999999965543  322          25


Q ss_pred             hhhhcccccCCCCCceEEEEEecCc
Q 014486          371 TYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       371 ~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      .|.|++||+||.+..|.+++.....
T Consensus       525 ~l~q~~GRagR~~~~g~viiqT~~p  549 (679)
T PRK05580        525 LLTQVAGRAGRAEKPGEVLIQTYHP  549 (679)
T ss_pred             HHHHHHhhccCCCCCCEEEEEeCCC
Confidence            6899999999999999999766543

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=100.00  E-value=6.8e-32  Score=272.42  Aligned_cols=297  Identities=20%  Similarity=0.268  Sum_probs=197.6

Q ss_pred             hhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh----HHHHHHHHHHHHHhccCCCceEEE
Q 014486           73 QHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR----ELAYQICHEFERFSTYLPDIKVAV  148 (423)
Q Consensus        73 Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~----~L~~q~~~~~~~~~~~~~~~~~~~  148 (423)
                      ..+.+..+..++.++++|+||||||++... ++.....+.. ..+++..|.+    +||.++++++..-.    +-.+++
T Consensus        79 r~~Il~ai~~~~VviI~GeTGSGKTTqlPq-~lle~g~g~~-g~I~~TQPRRlAArsLA~RVA~El~~~l----G~~VGY  152 (1294)
T PRK11131         79 KQDILEAIRDHQVVIVAGETGSGKTTQLPK-ICLELGRGVK-GLIGHTQPRRLAARTVANRIAEELETEL----GGCVGY  152 (1294)
T ss_pred             HHHHHHHHHhCCeEEEECCCCCCHHHHHHH-HHHHcCCCCC-CceeeCCCcHHHHHHHHHHHHHHHhhhh----cceece
Confidence            344555555666789999999999996332 3332222221 2445556754    66666666665422    112221


Q ss_pred             EEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcch-hhccCCcHHH-HHHHHHhCCCCceEE
Q 014486          149 FYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDK-MLESLDMRRD-VQEIFKMTPHDKQVM  226 (423)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~-~~~~~~~~~~-~~~~~~~~~~~~~~v  226 (423)
                           ...... ...+ ..+|+|+|++.|+..+.... .+.++++||+||||. .++ .+|... +..+... .++.|+|
T Consensus       153 -----~vrf~~-~~s~-~t~I~v~TpG~LL~~l~~d~-~Ls~~~~IIIDEAHERsLn-~DfLLg~Lk~lL~~-rpdlKvI  222 (1294)
T PRK11131        153 -----KVRFND-QVSD-NTMVKLMTDGILLAEIQQDR-LLMQYDTIIIDEAHERSLN-IDFILGYLKELLPR-RPDLKVI  222 (1294)
T ss_pred             -----eecCcc-ccCC-CCCEEEEChHHHHHHHhcCC-ccccCcEEEecCccccccc-cchHHHHHHHhhhc-CCCceEE
Confidence                 111111 1122 36999999999999887543 489999999999995 555 666543 3333322 3468999


Q ss_pred             EEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeCh------HHHHHHHHHHHH---hhcCCcEEEEEcC
Q 014486          227 MFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE------LEKNRKLNDLLD---ALDFNQVVIFVKS  297 (423)
Q Consensus       227 ~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~l~~ll~---~~~~~~~ivf~~~  297 (423)
                      ++|||++..  .+.+.+...+ .+.+....   . .+...+.....      .+....+...+.   ....+.+|||+++
T Consensus       223 LmSATid~e--~fs~~F~~ap-vI~V~Gr~---~-pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFLpg  295 (1294)
T PRK11131        223 ITSATIDPE--RFSRHFNNAP-IIEVSGRT---Y-PVEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFMSG  295 (1294)
T ss_pred             EeeCCCCHH--HHHHHcCCCC-EEEEcCcc---c-cceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEcCC
Confidence            999999753  4444444434 33333221   1 12223332221      122222222222   2356889999999


Q ss_pred             hhhHHHHHHHHHhCCCC---eEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccC---------
Q 014486          298 VSRAAELNKLLVECNFP---SICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDM---------  365 (423)
Q Consensus       298 ~~~~~~l~~~L~~~~~~---~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~---------  365 (423)
                      ..+++.+++.|...+++   +..+||++++.+|..+++.  .|..+|||||+++++|+|+|++++||+++.         
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            99999999999988765   6689999999999999876  477899999999999999999999999863         


Q ss_pred             ------C---CCcchhhhcccccCCCCCceEEEEEecCc
Q 014486          366 ------P---DSADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       366 ------~---~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                            |   .|..+|.||+||+||. .+|.|+.+++..
T Consensus       374 ~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~  411 (1294)
T PRK11131        374 TKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSED  411 (1294)
T ss_pred             cCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHH
Confidence                  3   3457899999999999 689999999853

>PRK09694 helicase Cas3; Provisional

Probab=100.00  E-value=5.1e-31  Score=260.94  Aligned_cols=312  Identities=21%  Similarity=0.226  Sum_probs=203.2

Q ss_pred             CCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhcc-CCCce
Q 014486           67 EHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTY-LPDIK  145 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~-~~~~~  145 (423)
                      .+|+|+|+.+.........++|.+|||+|||.+++.++...+..++ ..+++|..||++++.++++++.++... ++..+
T Consensus       285 ~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~~~-~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~~  363 (878)
T PRK09694        285 YQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQGL-ADSIIFALPTQATANAMLSRLEALASKLFPSPN  363 (878)
T ss_pred             CCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHhCC-CCeEEEECcHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            3799999987544334566899999999999998887665444333 338999999999999999999875432 23446


Q ss_pred             EEEEEcCcchHHHH---------------------HHHh---c--CCCcEEEechHHHHH-HHhcCCCCCCC----ccEE
Q 014486          146 VAVFYGGVNIKIHK---------------------DLLK---N--ECPQIVVGTPGRILA-LARDKDLSLKN----VRHF  194 (423)
Q Consensus       146 ~~~~~~~~~~~~~~---------------------~~~~---~--~~~~ilv~T~~~l~~-~~~~~~~~~~~----~~~v  194 (423)
                      +...+|........                     ..+.   +  --..|+|||.+.++. .+......+..    -++|
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            77777765422110                     0011   0  014899999998875 33222112222    2489


Q ss_pred             EEcCcchhhccCCcHHHHHHHHHhC-CCCceEEEEeccCCccHHHHHHHhccCCce---------eeeccc---ccc--c
Q 014486          195 ILDECDKMLESLDMRRDVQEIFKMT-PHDKQVMMFSATLSKEIRPVCKKFMQDPME---------IYVDDE---AKL--T  259 (423)
Q Consensus       195 VvDE~h~~~~~~~~~~~~~~~~~~~-~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~---------~~~~~~---~~~--~  259 (423)
                      ||||+|.+..  .....+..+++.+ ....++|+||||+|......+...+.....         +.....   ...  .
T Consensus       444 IiDEVHAyD~--ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L~~a~~~~~~~~~~~~YPlvt~~~~~~~~~~~~~  521 (878)
T PRK09694        444 IVDEVHAYDA--YMYGLLEAVLKAQAQAGGSVILLSATLPATLKQKLLDTYGGHDPVELSSAYPLITWRGVNGAQRFDLS  521 (878)
T ss_pred             EEechhhCCH--HHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhccccccccccccccccccccccceeeecc
Confidence            9999998743  3444555555543 235679999999998876544332221100         000000   000  0


Q ss_pred             cc---cceEEEEEe-----Ch-HHHHHHHHHHHHh-hcCCcEEEEEcChhhHHHHHHHHHhCC---CCeEEEcCCCCHHH
Q 014486          260 LH---GLVQHYIKL-----SE-LEKNRKLNDLLDA-LDFNQVVIFVKSVSRAAELNKLLVECN---FPSICIHSGMSQEE  326 (423)
Q Consensus       260 ~~---~~~~~~~~~-----~~-~~~~~~l~~ll~~-~~~~~~ivf~~~~~~~~~l~~~L~~~~---~~~~~~~~~~~~~~  326 (423)
                      ..   ......+.+     .. ......+..+++. ..+++++||||+++.++.+++.|++.+   .++..+||.++..+
T Consensus       522 ~~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~d  601 (878)
T PRK09694        522 AHPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAANAGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLND  601 (878)
T ss_pred             ccccccCcceEEEEEeeccccccCHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHH
Confidence            00   000111111     11 1112233334433 245789999999999999999999764   57899999999999


Q ss_pred             HH----HHHHhh-hcCC---ccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCC
Q 014486          327 RL----TRYKGF-KEGN---KRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGT  384 (423)
Q Consensus       327 r~----~~~~~f-~~~~---~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~  384 (423)
                      |.    ++++.| ++|+   ..|||+|+++++|+|+ +++++|....|  +..++||+||++|.+.
T Consensus       602 R~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        602 RREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             HHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            94    567788 5565   4799999999999999 57988887777  6789999999999875

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=100.00  E-value=6.3e-31  Score=262.71  Aligned_cols=333  Identities=19%  Similarity=0.219  Sum_probs=222.2

Q ss_pred             CCChhhhhcccccc----cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           68 HPSEVQHECIPQAI----LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~----~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      ++++||..++..++    .+.++|++.++|.|||+..+..+.......+....+|||||. ++..||.+++.+|+   |.
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~---p~  244 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFC---PV  244 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHC---CC
Confidence            68999999998876    367899999999999998654433322222222268999996 67788999998876   56


Q ss_pred             ceEEEEEcCcchHHHH--HHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCC
Q 014486          144 IKVAVFYGGVNIKIHK--DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPH  221 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~--~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~  221 (423)
                      +++..++|........  ..+..+.++|+|+|++.+.....  .+.-..+.+||+||||++.+.   .....+....+. 
T Consensus       245 l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~--~L~k~~W~~VIvDEAHrIKN~---~Sklskalr~L~-  318 (1033)
T PLN03142        245 LRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKT--ALKRFSWRYIIIDEAHRIKNE---NSLLSKTMRLFS-  318 (1033)
T ss_pred             CceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHH--HhccCCCCEEEEcCccccCCH---HHHHHHHHHHhh-
Confidence            7888888865433221  22333557999999999876332  222346789999999999762   233344444444 


Q ss_pred             CceEEEEeccCCcc-HH---HHHHHhccC--------------------------------Cceeeec-cccccccccce
Q 014486          222 DKQVMMFSATLSKE-IR---PVCKKFMQD--------------------------------PMEIYVD-DEAKLTLHGLV  264 (423)
Q Consensus       222 ~~~~v~~SAT~~~~-~~---~~~~~~~~~--------------------------------~~~~~~~-~~~~~~~~~~~  264 (423)
                      ....+++||||-.. ..   .++......                                |..+... .......+...
T Consensus       319 a~~RLLLTGTPlqNnl~ELwsLL~FL~P~~f~s~~~F~~~f~~~~~~~~~e~i~~L~~~L~pf~LRR~KsdV~~~LPpK~  398 (1033)
T PLN03142        319 TNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQQEVVQQLHKVLRPFLLRRLKSDVEKGLPPKK  398 (1033)
T ss_pred             cCcEEEEecCCCCCCHHHHHHHHhcCCCCcCCCHHHHHHHHccccccchHHHHHHHHHHhhHHHhhhhHHHHhhhCCCce
Confidence            33468999997321 11   111100000                                0000000 00000000000


Q ss_pred             EEEEEe---------------------------------------------------------------ChHHHHHHHHH
Q 014486          265 QHYIKL---------------------------------------------------------------SELEKNRKLND  281 (423)
Q Consensus       265 ~~~~~~---------------------------------------------------------------~~~~~~~~l~~  281 (423)
                      ...+.+                                                               ....|...+..
T Consensus       399 e~iv~v~LS~~Qk~lY~~ll~k~~~~l~~g~~~~~LlnilmqLRk~cnHP~L~~~~ep~~~~~~~e~lie~SgKl~lLdk  478 (1033)
T PLN03142        399 ETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGEHLVENSGKMVLLDK  478 (1033)
T ss_pred             eEEEeeCCCHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCHHhhhcccccCcccchhHHhhhhhHHHHHHH
Confidence            000000                                                               11223334444


Q ss_pred             HHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCC---ccEEEEcCccccCCCCCC
Q 014486          282 LLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN---KRILVATDLVGRGIDIER  356 (423)
Q Consensus       282 ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~---~~ili~T~~~~~Gld~~~  356 (423)
                      ++..+  .+.++|||+......+.+.+.|...++.+..++|+++..+|..+++.|+++.   ..+|++|.+++.|||+..
T Consensus       479 LL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAGGlGINLt~  558 (1033)
T PLN03142        479 LLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLAT  558 (1033)
T ss_pred             HHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccccccCCchhh
Confidence            44433  4579999999999999999999999999999999999999999999997643   357889999999999999


Q ss_pred             CCEEEEccCCCCcchhhhcccccCCCCCceEEEE--EecC-cccHHHHHHHHHHHhc
Q 014486          357 VNIVINYDMPDSADTYLHRVGRAGRFGTKGLAIT--FVSS-ASDSDILNQVSKFMFL  410 (423)
Q Consensus       357 ~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~--~~~~-~~~~~~~~~~~~~~~~  410 (423)
                      +++||+||++|+|....|++||++|.||+..|.+  |+.. ..+..++....++++.
T Consensus       559 Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~gTIEEkIlera~~Kl~L  615 (1033)
T PLN03142        559 ADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLAL  615 (1033)
T ss_pred             CCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCCcHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999866544  3443 3456666666666654

>cd00268 DEADc DEAD-box helicases

Probab=100.00  E-value=3e-31  Score=226.24  Aligned_cols=200  Identities=42%  Similarity=0.737  Sum_probs=178.7

Q ss_pred             CcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC--CCCeEEEEEecChH
Q 014486           48 FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN--PGQVTALVLCHTRE  125 (423)
Q Consensus        48 ~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~--~~~~~~lil~P~~~  125 (423)
                      |.++++++.+.+.|.+.|+..|+++|+++++.+..++++++.+|||+|||++++++++..+...  ..+++++|++|+++
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            6789999999999999999999999999999999999999999999999999999999887776  45669999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~  205 (423)
                      |+.|+.+.++.+.... ++++..++|+.........+..+ .+|+|+||+.+..++......+.+++++|+||+|.+.+ 
T Consensus        81 L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~-~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~-  157 (203)
T cd00268          81 LALQIAEVARKLGKHT-NLKVVVIYGGTSIDKQIRKLKRG-PHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLD-  157 (203)
T ss_pred             HHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhcCC-CCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhc-
Confidence            9999999999987664 78889999998877776666544 59999999999998888888889999999999999886 


Q ss_pred             CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCcee
Q 014486          206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEI  250 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~  250 (423)
                      ..+...+..+...++...|++++|||+++.....+..++..+..+
T Consensus       158 ~~~~~~~~~~~~~l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         158 MGFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             cChHHHHHHHHHhCCcccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            678888999999998899999999999999888888888777543

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.

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

Probab=100.00  E-value=3e-31  Score=251.16  Aligned_cols=309  Identities=21%  Similarity=0.267  Sum_probs=224.2

Q ss_pred             CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           64 SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        64 ~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      .+| .|-.+|++||.++.+|.+++|+|+|.+|||+++-.++...-.+..   +++|.+|-++|..|-++.|+.-..    
T Consensus       294 ~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~h~T---R~iYTSPIKALSNQKfRDFk~tF~----  365 (1248)
T KOG0947|consen  294 YPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQKHMT---RTIYTSPIKALSNQKFRDFKETFG----  365 (1248)
T ss_pred             CCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHhhcc---ceEecchhhhhccchHHHHHHhcc----
Confidence            355 789999999999999999999999999999987665554433322   899999999999998888876543    


Q ss_pred             ceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCc
Q 014486          144 IKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK  223 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~  223 (423)
                       .++.++|+..++.+        ..++|+|.+.|..++-++..-+.++.+||+||+|.+.+ ..-.-.+..+.-++|++.
T Consensus       366 -DvgLlTGDvqinPe--------AsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND-~eRGvVWEEViIMlP~HV  435 (1248)
T KOG0947|consen  366 -DVGLLTGDVQINPE--------ASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYIND-VERGVVWEEVIIMLPRHV  435 (1248)
T ss_pred             -ccceeecceeeCCC--------cceEeehHHHHHHHHhcccchhhccceEEEeeeeeccc-ccccccceeeeeeccccc
Confidence             23388888766543        58999999999998888887889999999999999977 677778889999999999


Q ss_pred             eEEEEeccCCccHHHHHHHhcc-CCceeeeccccccccccceEEEEEeC-------------------------------
Q 014486          224 QVMMFSATLSKEIRPVCKKFMQ-DPMEIYVDDEAKLTLHGLVQHYIKLS-------------------------------  271 (423)
Q Consensus       224 ~~v~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------------  271 (423)
                      ++|++|||.|+... ++.+... ....+++......+.+.  .+++...                               
T Consensus       436 ~~IlLSATVPN~~E-FA~WIGRtK~K~IyViST~kRPVPL--Eh~l~t~~~l~kiidq~g~fl~~~~~~a~~~~~~~ak~  512 (1248)
T KOG0947|consen  436 NFILLSATVPNTLE-FADWIGRTKQKTIYVISTSKRPVPL--EHYLYTKKSLFKIIDQNGIFLLKGIKDAKDSLKKEAKF  512 (1248)
T ss_pred             eEEEEeccCCChHH-HHHHhhhccCceEEEEecCCCccce--EEEEEeccceehhhcccchhhhhcchhhhhhhcccccc
Confidence            99999999998643 3322211 11112211111111000  0000000                               


Q ss_pred             -----------------------------------hHHH---HHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCC
Q 014486          272 -----------------------------------ELEK---NRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNF  313 (423)
Q Consensus       272 -----------------------------------~~~~---~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~  313 (423)
                                                         ...+   ...+...+....-=++||||-+++.|+..++.|...++
T Consensus       513 ~~~~~~~~~~~rgs~~~ggk~~~~~g~~r~~~~~~nrr~~~~~l~lin~L~k~~lLP~VvFvFSkkrCde~a~~L~~~nL  592 (1248)
T KOG0947|consen  513 VDVEKSDARGGRGSQKRGGKTNYHNGGSRGSGIGKNRRKQPTWLDLINHLRKKNLLPVVVFVFSKKRCDEYADYLTNLNL  592 (1248)
T ss_pred             cccccccccccccccccCCcCCCCCCCcccccccccccccchHHHHHHHHhhcccCceEEEEEccccHHHHHHHHhccCc
Confidence                                               0000   12222233333345799999999999999999876321


Q ss_pred             ---------------------------------------CeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCC
Q 014486          314 ---------------------------------------PSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDI  354 (423)
Q Consensus       314 ---------------------------------------~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~  354 (423)
                                                             .+.+.||++=+--++-+.--|..|-++||+||..+++|+|.
T Consensus       593 ~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivKE~VE~LFqrGlVKVLFATETFAMGVNM  672 (1248)
T KOG0947|consen  593 TDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVKEVVELLFQRGLVKVLFATETFAMGVNM  672 (1248)
T ss_pred             ccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHHHHHHHHHHHhcCceEEEeehhhhhhhcCC
Confidence                                                   35567899888888888889999999999999999999999


Q ss_pred             CCCCEEEEccCCC---------CcchhhhcccccCCCCC--ceEEEEEecC
Q 014486          355 ERVNIVINYDMPD---------SADTYLHRVGRAGRFGT--KGLAITFVSS  394 (423)
Q Consensus       355 ~~~~~vi~~~~~~---------s~~~~~Q~~GR~~R~g~--~~~~~~~~~~  394 (423)
                      |.-++|+ -...+         .|.+|.|++|||||.|-  +|.++++...
T Consensus       673 PARtvVF-~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~  722 (1248)
T KOG0947|consen  673 PARTVVF-SSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKD  722 (1248)
T ss_pred             CceeEEe-eehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecC
Confidence            9555444 33322         68899999999999985  4666666543

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.98  E-value=1.2e-30  Score=264.47  Aligned_cols=298  Identities=18%  Similarity=0.247  Sum_probs=202.3

Q ss_pred             hcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCc-
Q 014486           75 ECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGV-  153 (423)
Q Consensus        75 ~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~-  153 (423)
                      +.+..+..++.++|+|+||||||......++... .+ ...++++..|.+.-|..++.++.+....    .++...|.. 
T Consensus        74 ~Il~~l~~~~vvii~g~TGSGKTTqlPq~lle~~-~~-~~~~I~~tQPRRlAA~svA~RvA~elg~----~lG~~VGY~v  147 (1283)
T TIGR01967        74 DIAEAIAENQVVIIAGETGSGKTTQLPKICLELG-RG-SHGLIGHTQPRRLAARTVAQRIAEELGT----PLGEKVGYKV  147 (1283)
T ss_pred             HHHHHHHhCceEEEeCCCCCCcHHHHHHHHHHcC-CC-CCceEecCCccHHHHHHHHHHHHHHhCC----CcceEEeeEE
Confidence            4445555567789999999999996544343322 12 2226777789998888888777665432    333333321 


Q ss_pred             chHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcch-hhccCCcHHH-HHHHHHhCCCCceEEEEecc
Q 014486          154 NIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDK-MLESLDMRRD-VQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       154 ~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~-~~~~~~~~~~-~~~~~~~~~~~~~~v~~SAT  231 (423)
                      .....   . +....|.++|++.|+..+.... .+.++++||+||+|. .++ .++... +..+... .++.|+|+||||
T Consensus       148 R~~~~---~-s~~T~I~~~TdGiLLr~l~~d~-~L~~~~~IIIDEaHERsL~-~D~LL~lLk~il~~-rpdLKlIlmSAT  220 (1283)
T TIGR01967       148 RFHDQ---V-SSNTLVKLMTDGILLAETQQDR-FLSRYDTIIIDEAHERSLN-IDFLLGYLKQLLPR-RPDLKIIITSAT  220 (1283)
T ss_pred             cCCcc---c-CCCceeeeccccHHHHHhhhCc-ccccCcEEEEcCcchhhcc-chhHHHHHHHHHhh-CCCCeEEEEeCC
Confidence            11111   1 2225899999999999776543 478999999999995 555 566554 4455433 457899999999


Q ss_pred             CCccHHHHHHHhccCCceeeeccccccccccceEEEEEeC------hHHHHHHHHHHHHh---hcCCcEEEEEcChhhHH
Q 014486          232 LSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS------ELEKNRKLNDLLDA---LDFNQVVIFVKSVSRAA  302 (423)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~l~~ll~~---~~~~~~ivf~~~~~~~~  302 (423)
                      ++.  ..+.+.+...+ .+.+....   .+ +...+....      ..+....+...+..   ...+.+|||+++..++.
T Consensus       221 ld~--~~fa~~F~~ap-vI~V~Gr~---~P-Vev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~~EI~  293 (1283)
T TIGR01967       221 IDP--ERFSRHFNNAP-IIEVSGRT---YP-VEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPGEREIR  293 (1283)
T ss_pred             cCH--HHHHHHhcCCC-EEEECCCc---cc-ceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCCHHHHH
Confidence            974  34444444333 23332211   11 112222111      11222333333322   24588999999999999


Q ss_pred             HHHHHHHhCCC---CeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCC------------
Q 014486          303 ELNKLLVECNF---PSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPD------------  367 (423)
Q Consensus       303 ~l~~~L~~~~~---~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~------------  367 (423)
                      .+.+.|.+.+.   .+..+||+++..+|..+++.+  +..+|||||+++++|+|+|++++||+++.++            
T Consensus       294 ~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~~  371 (1283)
T TIGR01967       294 DAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQR  371 (1283)
T ss_pred             HHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeCCCccccccccccCccc
Confidence            99999987654   477899999999999997654  2468999999999999999999999998543            


Q ss_pred             ------CcchhhhcccccCCCCCceEEEEEecCc
Q 014486          368 ------SADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       368 ------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                            |..++.||.||+||.| +|.|+.+++..
T Consensus       372 L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~  404 (1283)
T TIGR01967       372 LPIEPISQASANQRKGRCGRVA-PGICIRLYSEE  404 (1283)
T ss_pred             cCCccCCHHHHHHHhhhhCCCC-CceEEEecCHH
Confidence                  5578999999999997 89999999854

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.

>TIGR00595 priA primosomal protein N'

Probab=99.98  E-value=1.8e-30  Score=246.54  Aligned_cols=290  Identities=21%  Similarity=0.214  Sum_probs=192.5

Q ss_pred             EEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHh
Q 014486           87 ICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLK  163 (423)
Q Consensus        87 ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~  163 (423)
                      ++.||||||||.+|+..+...+..++   ++||++|+++|+.|+++.+++..    +.++..++++.+..+..   ..+.
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~g~---~vLvlvP~i~L~~Q~~~~l~~~f----~~~v~vlhs~~~~~er~~~~~~~~   73 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGK---SVLVLVPEIALTPQMIQRFKYRF----GSQVAVLHSGLSDSEKLQAWRKVK   73 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcCC---eEEEEeCcHHHHHHHHHHHHHHh----CCcEEEEECCCCHHHHHHHHHHHH
Confidence            47899999999999766555443322   89999999999999999998764    45788889887655443   3344


Q ss_pred             cCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccC----Cc-HHHHHHHHHhCCCCceEEEEeccCCccHHH
Q 014486          164 NECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESL----DM-RRDVQEIFKMTPHDKQVMMFSATLSKEIRP  238 (423)
Q Consensus       164 ~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~----~~-~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~  238 (423)
                      ++..+|+|+|+..++       ..+.++++|||||.|....+.    .+ .+.+..... ...+.+++++||||..+...
T Consensus        74 ~g~~~IVVGTrsalf-------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra-~~~~~~vil~SATPsles~~  145 (505)
T TIGR00595        74 NGEILVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRA-KKFNCPVVLGSATPSLESYH  145 (505)
T ss_pred             cCCCCEEECChHHHc-------CcccCCCEEEEECCCccccccccCCCCcHHHHHHHHH-HhcCCCEEEEeCCCCHHHHH
Confidence            566799999998774       357889999999999875321    11 122333333 33577899999998765444


Q ss_pred             HHHHhccCCceeeeccccccccccceEEEEEeChHH----HHHHHHHHH-Hhh-cCCcEEEEEcChhh------------
Q 014486          239 VCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE----KNRKLNDLL-DAL-DFNQVVIFVKSVSR------------  300 (423)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~l~~ll-~~~-~~~~~ivf~~~~~~------------  300 (423)
                      .+..  +....+....... .........+......    -...+.+.+ +.. .++++|||+|++..            
T Consensus       146 ~~~~--g~~~~~~l~~r~~-~~~~p~v~vid~~~~~~~~~ls~~l~~~i~~~l~~g~qvLvflnrrGya~~~~C~~Cg~~  222 (505)
T TIGR00595       146 NAKQ--KAYRLLVLTRRVS-GRKPPEVKLIDMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYI  222 (505)
T ss_pred             HHhc--CCeEEeechhhhc-CCCCCeEEEEecccccccCCccHHHHHHHHHHHHcCCcEEEEEeCCcCCCeeEhhhCcCc
Confidence            3321  1111111111000 0000011111111111    011222222 223 24689999766432            


Q ss_pred             ------------------------------------------------HHHHHHHHHhC--CCCeEEEcCCCCHHHH--H
Q 014486          301 ------------------------------------------------AAELNKLLVEC--NFPSICIHSGMSQEER--L  328 (423)
Q Consensus       301 ------------------------------------------------~~~l~~~L~~~--~~~~~~~~~~~~~~~r--~  328 (423)
                                                                      .+.+.+.|++.  +.++..+|++++...+  .
T Consensus       223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~  302 (505)
T TIGR00595       223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHE  302 (505)
T ss_pred             cCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHHHHHHhhCCCCcEEEEecccccCccHHH
Confidence                                                            46777777776  6788999999876655  8


Q ss_pred             HHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCC------------CcchhhhcccccCCCCCceEEEEEecC
Q 014486          329 TRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPD------------SADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       329 ~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~------------s~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                      .+++.|++|+.+|||+|+++++|+|+|++++|+.++...            ....+.|++||+||.++.|.+++....
T Consensus       303 ~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra~E~~~~ll~q~~GRagR~~~~g~viiqt~~  380 (505)
T TIGR00595       303 ALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYN  380 (505)
T ss_pred             HHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccchHHHHHHHHHHHHhccCCCCCCCEEEEEeCC
Confidence            899999999999999999999999999999986544321            235689999999999999998865543

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).

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=6.2e-30  Score=248.22  Aligned_cols=316  Identities=19%  Similarity=0.231  Sum_probs=227.9

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .|++.|--+--.+  +..-|..++||+|||+++++|++..+..+.   .++|++|++.||.|.++++..+.... ++++.
T Consensus        82 ~~ydvQliGg~~L--h~G~Iaem~TGeGKTL~a~Lpa~~~al~G~---~V~VvTpn~yLA~qd~e~m~~l~~~l-GLtv~  155 (896)
T PRK13104         82 RHFDVQLIGGMVL--HEGNIAEMRTGEGKTLVATLPAYLNAISGR---GVHIVTVNDYLAKRDSQWMKPIYEFL-GLTVG  155 (896)
T ss_pred             CcchHHHhhhhhh--ccCccccccCCCCchHHHHHHHHHHHhcCC---CEEEEcCCHHHHHHHHHHHHHHhccc-CceEE
Confidence            5677776654444  445699999999999999999997766443   68999999999999999999998887 89999


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcC-CCCC-----CCccEEEEcCcchhhcc---------------
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDK-DLSL-----KNVRHFILDECDKMLES---------------  205 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~-~~~~-----~~~~~vVvDE~h~~~~~---------------  205 (423)
                      ++.|+.+.......+  . ++|+++||+.| +++++.+ .+.+     ..+.++|+||||.++-+               
T Consensus       156 ~i~gg~~~~~r~~~y--~-~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiLIDeArtPLIISg~~~~~  232 (896)
T PRK13104        156 VIYPDMSHKEKQEAY--K-ADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSILIDEARTPLIISGAAEDS  232 (896)
T ss_pred             EEeCCCCHHHHHHHh--C-CCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhhhhccCCceeeeCCCccc
Confidence            999998777665444  2 59999999999 8888766 2333     58899999999988621               


Q ss_pred             CCcHHHHHHHHHhCCC--------------Cc------------------------------------------------
Q 014486          206 LDMRRDVQEIFKMTPH--------------DK------------------------------------------------  223 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~--------------~~------------------------------------------------  223 (423)
                      .........+...+..              ..                                                
T Consensus       233 ~~~y~~~~~~v~~l~~~~~~~~~~dy~idek~~~v~Lte~G~~~~e~~~~~~~il~~~~~l~~~~~~~~~~~i~~aL~A~  312 (896)
T PRK13104        233 SELYIKINSLIPQLKKQEEEGDEGDYTIDEKQKQAHLTDAGHLHIEELLTKAKLLDPGESLYHASNIMLMHHVNAALKAH  312 (896)
T ss_pred             hHHHHHHHHHHHHHHhccccCCCCCEEEEcCCCceEEchHHHHHHHHHHHhCCccCCcccccCchhhhHHHHHHHHHHHH
Confidence            0011111111111110              00                                                


Q ss_pred             --------------------------------------------------------------------eEEEEeccCCcc
Q 014486          224 --------------------------------------------------------------------QVMMFSATLSKE  235 (423)
Q Consensus       224 --------------------------------------------------------------------~~v~~SAT~~~~  235 (423)
                                                                                          ++-+||+|...+
T Consensus       313 ~lf~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQaiEaKE~v~i~~e~~t~AsIT~Qn~Fr~Y~kLsGMTGTa~te  392 (896)
T PRK13104        313 AMFHRDIDYIVKDNQVVIVDEHTGRTMPGRRWSEGLHQAVEAKEGVPIQNENQTLASITFQNFFRMYNKLSGMTGTADTE  392 (896)
T ss_pred             HHhcCCCceEEECCEEEEEECCCCCcCCCCCcChHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhccCCCCChhH
Confidence                                                                                233444444443


Q ss_pred             HHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHh--hcCCcEEEEEcChhhHHHHHHHHHhCCC
Q 014486          236 IRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDA--LDFNQVVIFVKSVSRAAELNKLLVECNF  313 (423)
Q Consensus       236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~--~~~~~~ivf~~~~~~~~~l~~~L~~~~~  313 (423)
                      ...+.+.+......+..  ..+..... ....+......|...+.+-+..  ..+.|+||||++++.++.+++.|...|+
T Consensus       393 ~~Ef~~iY~l~Vv~IPt--nkp~~R~d-~~d~v~~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~~L~~~gi  469 (896)
T PRK13104        393 AYEFQQIYNLEVVVIPT--NRSMIRKD-EADLVYLTQADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQLLKKENI  469 (896)
T ss_pred             HHHHHHHhCCCEEECCC--CCCcceec-CCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCC
Confidence            33333333322222211  11111111 1223344556666666555532  3568999999999999999999999999


Q ss_pred             CeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCC--------------------------------------
Q 014486          314 PSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIE--------------------------------------  355 (423)
Q Consensus       314 ~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~--------------------------------------  355 (423)
                      ++..+|+.+.+.++..+.+.|+.|.  |+|||++++||+|+.                                      
T Consensus       470 ~h~vLnak~~q~Ea~iia~Ag~~G~--VtIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~  547 (896)
T PRK13104        470 KHQVLNAKFHEKEAQIIAEAGRPGA--VTIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVIAA  547 (896)
T ss_pred             CeEeecCCCChHHHHHHHhCCCCCc--EEEeccCccCCcceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHHHc
Confidence            9999999999999999999999995  999999999999986                                      


Q ss_pred             CCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          356 RVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       356 ~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      +--|||-...+.|-.--.|-.||+||.|.+|..-.|++-.++
T Consensus       548 GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD~  589 (896)
T PRK13104        548 GGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDN  589 (896)
T ss_pred             CCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcH
Confidence            223688888888888889999999999999999999986443

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

Probab=99.97  E-value=2.6e-30  Score=250.62  Aligned_cols=329  Identities=24%  Similarity=0.315  Sum_probs=231.2

Q ss_pred             HHHHHHHHhCCCCCCChhhhhcccccccC-CceEEEccCCCcchhHHHHHHhhccCCCC--------CCeEEEEEecChH
Q 014486           55 PELLRAIVDSGFEHPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFVLSTLQQTEPNP--------GQVTALVLCHTRE  125 (423)
Q Consensus        55 ~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~-~~~ii~~~tGsGKT~~~~~~~~~~~~~~~--------~~~~~lil~P~~~  125 (423)
                      .+-..++.  |...++++|....+..+.+ .++++|||||+|||.++++.+++.+..+.        ...+++|++|..+
T Consensus       298 ~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKa  375 (1674)
T KOG0951|consen  298 KWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKA  375 (1674)
T ss_pred             chhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHH
Confidence            33344443  5567999999999988886 56999999999999999999998765543        2348999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCC-C-CCCccEEEEcCcchhh
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDL-S-LKNVRHFILDECDKML  203 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~-~-~~~~~~vVvDE~h~~~  203 (423)
                      |++.|...+.+....+ +++|.-.+|+........  . + .+|+||||+.+.-+-++... . .+-++++|+||.|.+-
T Consensus       376 LvqE~VgsfSkRla~~-GI~V~ElTgD~~l~~~qi--e-e-TqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLh  450 (1674)
T KOG0951|consen  376 LVQEMVGSFSKRLAPL-GITVLELTGDSQLGKEQI--E-E-TQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLH  450 (1674)
T ss_pred             HHHHHHHHHHhhcccc-CcEEEEecccccchhhhh--h-c-ceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhcc
Confidence            9999999888877777 899999999866433221  1 2 49999999998554443221 1 3467899999999885


Q ss_pred             ccCCc--HHHHHHHHHh---CCCCceEEEEeccCCccHHHHHHHhccCCce-eeeccccccccccceEEEEEeCh--HHH
Q 014486          204 ESLDM--RRDVQEIFKM---TPHDKQVMMFSATLSKEIRPVCKKFMQDPME-IYVDDEAKLTLHGLVQHYIKLSE--LEK  275 (423)
Q Consensus       204 ~~~~~--~~~~~~~~~~---~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~--~~~  275 (423)
                      ++.+.  .....+..+.   -....+++++|||+|+.. +.......++.. ++.+....  ...+.+.++-+.+  ..+
T Consensus       451 DdRGpvLESIVaRt~r~ses~~e~~RlVGLSATLPNy~-DV~~Fl~v~~~glf~fd~syR--pvPL~qq~Igi~ek~~~~  527 (1674)
T KOG0951|consen  451 DDRGPVLESIVARTFRRSESTEEGSRLVGLSATLPNYE-DVASFLRVDPEGLFYFDSSYR--PVPLKQQYIGITEKKPLK  527 (1674)
T ss_pred             cccchHHHHHHHHHHHHhhhcccCceeeeecccCCchh-hhHHHhccCcccccccCcccC--cCCccceEeccccCCchH
Confidence            53222  2222233222   233678999999999753 222222222222 22322222  2223334433322  222


Q ss_pred             H------HHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHh-------------------------------------CC
Q 014486          276 N------RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVE-------------------------------------CN  312 (423)
Q Consensus       276 ~------~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~-------------------------------------~~  312 (423)
                      .      ....++++....+++|||+.++++....++.+++                                     ..
T Consensus       528 ~~qamNe~~yeKVm~~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLp  607 (1674)
T KOG0951|consen  528 RFQAMNEACYEKVLEHAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLP  607 (1674)
T ss_pred             HHHHHHHHHHHHHHHhCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhh
Confidence            2      2344566777789999999999988877777763                                     13


Q ss_pred             CCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE----ccC------CCCcchhhhcccccCCC
Q 014486          313 FPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN----YDM------PDSADTYLHRVGRAGRF  382 (423)
Q Consensus       313 ~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~----~~~------~~s~~~~~Q~~GR~~R~  382 (423)
                      +...+.|.+|++.+|..+.+.|.+|.++|+++|..+++|+|+|.-+++|-    |++      +.++.+..||.||+||.
T Consensus       608 ygfaIHhAGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp  687 (1674)
T KOG0951|consen  608 YGFAIHHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRP  687 (1674)
T ss_pred             ccceeeccCCCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCC
Confidence            56778899999999999999999999999999999999999997776662    444      34788999999999997


Q ss_pred             C--CceEEEEEec
Q 014486          383 G--TKGLAITFVS  393 (423)
Q Consensus       383 g--~~~~~~~~~~  393 (423)
                      +  +.|..+++..
T Consensus       688 ~~D~~gegiiit~  700 (1674)
T KOG0951|consen  688 QYDTCGEGIIITD  700 (1674)
T ss_pred             ccCcCCceeeccC
Confidence            5  3466665544

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=1.4e-29  Score=245.65  Aligned_cols=318  Identities=20%  Similarity=0.230  Sum_probs=237.6

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      |+ .|++.|--+.-.+..|  -|..+.||+|||+++.+|++.....+.   .+-|++|+..||.|.++.+..+.... ++
T Consensus        79 g~-~~~dvQlig~l~L~~G--~Iaem~TGeGKTLva~lpa~l~aL~G~---~V~IvTpn~yLA~rd~e~~~~l~~~L-Gl  151 (830)
T PRK12904         79 GM-RHFDVQLIGGMVLHEG--KIAEMKTGEGKTLVATLPAYLNALTGK---GVHVVTVNDYLAKRDAEWMGPLYEFL-GL  151 (830)
T ss_pred             CC-CCCccHHHhhHHhcCC--chhhhhcCCCcHHHHHHHHHHHHHcCC---CEEEEecCHHHHHHHHHHHHHHHhhc-CC
Confidence            44 7888888776665554  599999999999999999974444333   46699999999999999999998887 99


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcCCC------CCCCccEEEEcCcchhhcc------------
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDKDL------SLKNVRHFILDECDKMLES------------  205 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~~~------~~~~~~~vVvDE~h~~~~~------------  205 (423)
                      ++.++.|+.+...+...+.   ++|+++|+..| +++++....      ....+.++|+||||.++-+            
T Consensus       152 sv~~i~~~~~~~er~~~y~---~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiLIDeArtpLiiSg~~  228 (830)
T PRK12904        152 SVGVILSGMSPEERREAYA---ADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSILIDEARTPLIISGPA  228 (830)
T ss_pred             eEEEEcCCCCHHHHHHhcC---CCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhheeccCCCceeeECCC
Confidence            9999999988776666543   59999999999 888876542      3578899999999988621            


Q ss_pred             ---CCcHHHHHHHHHhCCCC--------c---------------------------------------------------
Q 014486          206 ---LDMRRDVQEIFKMTPHD--------K---------------------------------------------------  223 (423)
Q Consensus       206 ---~~~~~~~~~~~~~~~~~--------~---------------------------------------------------  223 (423)
                         .........+...+...        .                                                   
T Consensus       229 ~~~~~~y~~~~~~v~~l~~~~dy~vde~~~~v~lte~G~~~~e~~~~~~~ly~~~~~~~~~~i~~AL~A~~l~~~d~dYi  308 (830)
T PRK12904        229 EDSSELYKRANKIVPTLEKEGDYTVDEKSRTVGLTEEGIEKAEKLLGIENLYDPENIALVHHLNQALRAHELFKRDVDYI  308 (830)
T ss_pred             CcccHHHHHHHHHHHhcCCCCCeEEEcCCCeeeECHHHHHHHHHHhCCccccChhhhHHHHHHHHHHHHHHHHhcCCcEE
Confidence               01111122222222110        0                                                   


Q ss_pred             ----------------------------------------------------------eEEEEeccCCccHHHHHHHhcc
Q 014486          224 ----------------------------------------------------------QVMMFSATLSKEIRPVCKKFMQ  245 (423)
Q Consensus       224 ----------------------------------------------------------~~v~~SAT~~~~~~~~~~~~~~  245 (423)
                                                                                ++.+||+|...+...+.+.+..
T Consensus       309 V~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        309 VKDGEVVIVDEFTGRLMPGRRYSDGLHQAIEAKEGVKIQNENQTLASITFQNYFRMYEKLAGMTGTADTEAEEFREIYNL  388 (830)
T ss_pred             EECCEEEEEECCCCccCCCCccchHHHHHHHHhcCCCCCCCceeeeeeeHHHHHHhcchhcccCCCcHHHHHHHHHHhCC
Confidence                                                                      4566777776554444444433


Q ss_pred             CCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHh--hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCC
Q 014486          246 DPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDA--LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMS  323 (423)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~--~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~  323 (423)
                      ....+..  ..+..... ....+.....+|...+.+.+..  ..+.++||||++++.++.+++.|.+.|+++..+|+.  
T Consensus       389 ~vv~IPt--nkp~~r~d-~~d~i~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--  463 (830)
T PRK12904        389 DVVVIPT--NRPMIRID-HPDLIYKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--  463 (830)
T ss_pred             CEEEcCC--CCCeeeee-CCCeEEECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--
Confidence            3322222  21111111 1223444666778888887755  567899999999999999999999999999999996  


Q ss_pred             HHHHHHHHHhhhcCCccEEEEcCccccCCCCCC--------------------------------------CCEEEEccC
Q 014486          324 QEERLTRYKGFKEGNKRILVATDLVGRGIDIER--------------------------------------VNIVINYDM  365 (423)
Q Consensus       324 ~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~--------------------------------------~~~vi~~~~  365 (423)
                      +.+|+..+..|..+...|+|||++++||+|++-                                      --|||....
T Consensus       464 q~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTer  543 (830)
T PRK12904        464 NHEREAEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTER  543 (830)
T ss_pred             hHHHHHHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEeccc
Confidence            778999999999999999999999999999863                                      236888888


Q ss_pred             CCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          366 PDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       366 ~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      +.|-.--.|-.||+||.|.+|.+-.|++-.++
T Consensus       544 hesrRid~QlrGRagRQGdpGss~f~lSleD~  575 (830)
T PRK12904        544 HESRRIDNQLRGRSGRQGDPGSSRFYLSLEDD  575 (830)
T ss_pred             CchHHHHHHhhcccccCCCCCceeEEEEcCcH
Confidence            99998899999999999999999999986444

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=1.5e-29  Score=244.44  Aligned_cols=318  Identities=19%  Similarity=0.211  Sum_probs=229.0

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      |+ .|++.|--+.-.+..|+  |..+.||+|||+++.+|++.....+.   .+-+++|+.-||.|-++.+..+...+ ++
T Consensus        78 g~-~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~G~---~v~vvT~neyLA~Rd~e~~~~~~~~L-Gl  150 (796)
T PRK12906         78 GL-RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALTGK---GVHVVTVNEYLSSRDATEMGELYRWL-GL  150 (796)
T ss_pred             CC-CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcCC---CeEEEeccHHHHHhhHHHHHHHHHhc-CC
Confidence            44 78888887766665554  99999999999999999888877665   78999999999999999999999887 89


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHHH-HHHhcCC------CCCCCccEEEEcCcchhhcc------------
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL-ALARDKD------LSLKNVRHFILDECDKMLES------------  205 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~-~~~~~~~------~~~~~~~~vVvDE~h~~~~~------------  205 (423)
                      +++.+.++.+.......+ .  .+|+++|...|. ++++.+.      .....+.+.||||+|.++-+            
T Consensus       151 ~vg~i~~~~~~~~r~~~y-~--~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiLiDeartPLiisg~~  227 (796)
T PRK12906        151 TVGLNLNSMSPDEKRAAY-N--CDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSILIDEARTPLIISGQA  227 (796)
T ss_pred             eEEEeCCCCCHHHHHHHh-c--CCCeecCCccccccchhhccccchhhhhccCcceeeeccchheeeccCCCceecCCCC
Confidence            999998877665554444 2  499999998763 3444321      12356789999999987621            


Q ss_pred             ---CCcHHHHHHHHHhCCC--------------------Cc---------------------------------------
Q 014486          206 ---LDMRRDVQEIFKMTPH--------------------DK---------------------------------------  223 (423)
Q Consensus       206 ---~~~~~~~~~~~~~~~~--------------------~~---------------------------------------  223 (423)
                         ......+..+...+..                    ..                                       
T Consensus       228 ~~~~~~y~~~~~~v~~l~~~~~~~~~~~~~~~dy~id~~~k~v~lte~G~~~~e~~~~i~~l~~~~~~~~~~~i~~Al~A  307 (796)
T PRK12906        228 EKATDLYIRADRFVKTLIKDEAEDGDDDEDTGDYKIDEKTKTISLTEQGIRKAEKLFGLDNLYDSENTALAHHIDQALRA  307 (796)
T ss_pred             CcchHHHHHHHHHHHHHHhhhhccccccCCCCceEEEcccCceeecHHHHHHHHHHcCCccccCchhhhHHHHHHHHHHH
Confidence               0011111111111100                    00                                       


Q ss_pred             ---------------------------------------------------------------------eEEEEeccCCc
Q 014486          224 ---------------------------------------------------------------------QVMMFSATLSK  234 (423)
Q Consensus       224 ---------------------------------------------------------------------~~v~~SAT~~~  234 (423)
                                                                                           ++.+||+|...
T Consensus       308 ~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLHQaieaKe~v~i~~e~~t~a~It~qnfFr~Y~kl~GmTGTa~~  387 (796)
T PRK12906        308 NYIMLKDIDYVVQDGEVLIVDEFTGRVMEGRRYSDGLHQAIEAKEGVKIQEENQTLATITYQNFFRMYKKLSGMTGTAKT  387 (796)
T ss_pred             HHHHhcCCcEEEECCEEEEEeCCCCCcCCCCccChHHHHHHHHhcCCCcCCCceeeeeehHHHHHHhcchhhccCCCCHH
Confidence                                                                                 34556666554


Q ss_pred             cHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCC
Q 014486          235 EIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECN  312 (423)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~  312 (423)
                      +...+.+.+......  ++...+.. ..-....+......|...+.+.+...  .+.++||||+++..++.++..|.+.|
T Consensus       388 e~~Ef~~iY~l~vv~--IPtnkp~~-r~d~~d~i~~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~~~g  464 (796)
T PRK12906        388 EEEEFREIYNMEVIT--IPTNRPVI-RKDSPDLLYPTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLDEAG  464 (796)
T ss_pred             HHHHHHHHhCCCEEE--cCCCCCee-eeeCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHCC
Confidence            433333333322222  22211111 11112223345566777777777443  67899999999999999999999999


Q ss_pred             CCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCC---CCC-----EEEEccCCCCcchhhhcccccCCCCC
Q 014486          313 FPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIE---RVN-----IVINYDMPDSADTYLHRVGRAGRFGT  384 (423)
Q Consensus       313 ~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~---~~~-----~vi~~~~~~s~~~~~Q~~GR~~R~g~  384 (423)
                      +++..+|+++...++..+..+++.|.  |+|||++++||+|++   ++.     |||.++.|.|...+.|+.||+||.|.
T Consensus       465 i~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~  542 (796)
T PRK12906        465 IPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGD  542 (796)
T ss_pred             CCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCC
Confidence            99999999998777777777766665  999999999999995   788     99999999999999999999999999


Q ss_pred             ceEEEEEecCccc
Q 014486          385 KGLAITFVSSASD  397 (423)
Q Consensus       385 ~~~~~~~~~~~~~  397 (423)
                      +|.+..|++..++
T Consensus       543 ~G~s~~~~sleD~  555 (796)
T PRK12906        543 PGSSRFYLSLEDD  555 (796)
T ss_pred             CcceEEEEeccch
Confidence            9999999986543

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

Probab=99.97  E-value=3.1e-28  Score=239.28  Aligned_cols=322  Identities=21%  Similarity=0.212  Sum_probs=241.3

Q ss_pred             CCCCHHHHHHHHhC-CCCCCChhhhhcccccccC------CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           51 FLLKPELLRAIVDS-GFEHPSEVQHECIPQAILG------MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        51 ~~l~~~~~~~l~~~-~~~~~~~~Q~~~i~~~~~~------~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      |+.+...+..+.+. +| .-|+-|..||..+...      -|-+|||..|.|||.+++=++......++   ++.|+|||
T Consensus       577 f~~d~~~q~~F~~~FPy-eET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~GK---QVAvLVPT  652 (1139)
T COG1197         577 FPPDTEWQEEFEASFPY-EETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDGK---QVAVLVPT  652 (1139)
T ss_pred             CCCChHHHHHHHhcCCC-cCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcCCC---eEEEEccc
Confidence            44455555555553 56 6799999999988862      46899999999999998877777766553   89999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHH---HHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcc
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH---KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECD  200 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h  200 (423)
                      .-||+|.++.|++-...+ .+++..+.-=.+..++   .+.+.+|..||+|+|..-|     +....+.+++++||||=|
T Consensus       653 TlLA~QHy~tFkeRF~~f-PV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL-----~kdv~FkdLGLlIIDEEq  726 (1139)
T COG1197         653 TLLAQQHYETFKERFAGF-PVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLL-----SKDVKFKDLGLLIIDEEQ  726 (1139)
T ss_pred             HHhHHHHHHHHHHHhcCC-CeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhh-----CCCcEEecCCeEEEechh
Confidence            999999999998776666 4666666554444433   4566779999999997544     356788999999999999


Q ss_pred             hhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHH
Q 014486          201 KMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLN  280 (423)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  280 (423)
                      ++.-  .....+..+    ..+.-++-|||||-+....+.-.-..+...+...+....   . ++.++...+...  .-.
T Consensus       727 RFGV--k~KEkLK~L----r~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~---p-V~T~V~~~d~~~--ire  794 (1139)
T COG1197         727 RFGV--KHKEKLKEL----RANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRL---P-VKTFVSEYDDLL--IRE  794 (1139)
T ss_pred             hcCc--cHHHHHHHH----hccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCCc---c-eEEEEecCChHH--HHH
Confidence            8753  344444444    455569999999977666554444444444444433322   2 333333222221  111


Q ss_pred             HHHHh-hcCCcEEEEEcChhhHHHHHHHHHhC--CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCC
Q 014486          281 DLLDA-LDFNQVVIFVKSVSRAAELNKLLVEC--NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV  357 (423)
Q Consensus       281 ~ll~~-~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~  357 (423)
                      .++.. .+++++-..+|.++....+++.|+..  ..++.+.||.|+..+-+.++..|.+|+.+|||||.+++.|+|+|++
T Consensus       795 AI~REl~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnA  874 (1139)
T COG1197         795 AILRELLRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNA  874 (1139)
T ss_pred             HHHHHHhcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCC
Confidence            12222 36789999999999999999999986  5567789999999999999999999999999999999999999999


Q ss_pred             CEEEEccCC-CCcchhhhcccccCCCCCceEEEEEecC
Q 014486          358 NIVINYDMP-DSADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       358 ~~vi~~~~~-~s~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                      +.+|.-+.. ...+++.|-.||+||.++.+-+++++.+
T Consensus       875 NTiIIe~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~  912 (1139)
T COG1197         875 NTIIIERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPP  912 (1139)
T ss_pred             ceEEEeccccccHHHHHHhccccCCccceEEEEEeecC
Confidence            998865543 4688999999999999999999999985

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=2.1e-28  Score=237.19  Aligned_cols=149  Identities=17%  Similarity=0.290  Sum_probs=129.4

Q ss_pred             cCCCCCHHHHHHHH-----hCCCCCC---ChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEE
Q 014486           49 RDFLLKPELLRAIV-----DSGFEHP---SEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVL  120 (423)
Q Consensus        49 ~~~~l~~~~~~~l~-----~~~~~~~---~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil  120 (423)
                      +.|++.+.+.+.+.     .+||..|   +|+|.++++.++.+++++..++||+|||++|++|++..+..+.   .++||
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g~---~v~IV  141 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTGK---PVHLV  141 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhcC---CeEEE
Confidence            56788888888888     5688888   9999999999999999999999999999999999998775433   47899


Q ss_pred             ecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcCCCCCC-------Ccc
Q 014486          121 CHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDKDLSLK-------NVR  192 (423)
Q Consensus       121 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~~~~~~-------~~~  192 (423)
                      +|++.||.|.++.+..+.... ++++..+.||.+...+...+  . ++|+|+||++| +++++.+...++       .+.
T Consensus       142 TpTrELA~Qdae~m~~L~k~l-GLsV~~i~GG~~~~eq~~~y--~-~DIVygTPgRLgfDyLrd~~~~~~~~~~vqr~~~  217 (970)
T PRK12899        142 TVNDYLAQRDCEWVGSVLRWL-GLTTGVLVSGSPLEKRKEIY--Q-CDVVYGTASEFGFDYLRDNSIATRKEEQVGRGFY  217 (970)
T ss_pred             eCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHHHHc--C-CCEEEECCChhHHHHhhCCCCCcCHHHhhccccc
Confidence            999999999999999998876 79999999999988776555  2 69999999999 999987755554       568


Q ss_pred             EEEEcCcchhhc
Q 014486          193 HFILDECDKMLE  204 (423)
Q Consensus       193 ~vVvDE~h~~~~  204 (423)
                      ++|+||||.++.
T Consensus       218 ~~IIDEADsmLi  229 (970)
T PRK12899        218 FAIIDEVDSILI  229 (970)
T ss_pred             EEEEechhhhhh
Confidence            999999998873

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

Probab=99.97  E-value=1.3e-28  Score=250.74  Aligned_cols=317  Identities=18%  Similarity=0.190  Sum_probs=197.9

Q ss_pred             CCChhhhhccccccc-----CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           68 HPSEVQHECIPQAIL-----GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~-----~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      .+|+||.+++..+..     .+.++++++||||||.+++..+ ..+...+...++|+|+|+.+|+.|+.+.|..+.... 
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li-~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~-  490 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALM-YRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEG-  490 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHH-HHHHhcCccCeEEEEecHHHHHHHHHHHHHhccccc-
Confidence            589999999987763     3568999999999998865433 333333333489999999999999999988763211 


Q ss_pred             CceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC-----CCCCCCccEEEEcCcchhhc--------cC---
Q 014486          143 DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK-----DLSLKNVRHFILDECDKMLE--------SL---  206 (423)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~-----~~~~~~~~~vVvDE~h~~~~--------~~---  206 (423)
                      ...+..+.+.   ............+|+|+|.+++...+...     ...+..+++||+||||+...        ..   
T Consensus       491 ~~~~~~i~~i---~~L~~~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~~~~~~  567 (1123)
T PRK11448        491 DQTFASIYDI---KGLEDKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEGELQFR  567 (1123)
T ss_pred             ccchhhhhch---hhhhhhcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccchhccc
Confidence            1111111111   11111112223599999999998754321     13467889999999998531        00   


Q ss_pred             ---CcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHH--------------hcc---CCceeeeccc-ccccccc---
Q 014486          207 ---DMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKK--------------FMQ---DPMEIYVDDE-AKLTLHG---  262 (423)
Q Consensus       207 ---~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~--------------~~~---~~~~~~~~~~-~~~~~~~---  262 (423)
                         .+...++.++..+.  ...|++||||......+...              ++.   .|..+..... .......   
T Consensus       568 ~~~~~~~~yr~iL~yFd--A~~IGLTATP~r~t~~~FG~pv~~Ysl~eAI~DG~Lv~~~~p~~i~t~~~~~gi~~~~~e~  645 (1123)
T PRK11448        568 DQLDYVSKYRRVLDYFD--AVKIGLTATPALHTTEIFGEPVYTYSYREAVIDGYLIDHEPPIRIETRLSQEGIHFEKGEE  645 (1123)
T ss_pred             hhhhHHHHHHHHHhhcC--ccEEEEecCCccchhHHhCCeeEEeeHHHHHhcCCcccCcCCEEEEEEeccccccccccch
Confidence               12355666666553  46899999997654332211              111   0111110000 0000000   


Q ss_pred             ---ceE---EE--EEeCh--------HH-------HHHH----HHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC----
Q 014486          263 ---LVQ---HY--IKLSE--------LE-------KNRK----LNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC----  311 (423)
Q Consensus       263 ---~~~---~~--~~~~~--------~~-------~~~~----l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~----  311 (423)
                         ...   .+  ...++        ..       ....    +.+.+....++|+||||.+..+|..+.+.|.+.    
T Consensus       646 ~~~~~~~~~~i~~~~l~d~~~~~~~~~~~~vi~~~~~~~i~~~l~~~l~~~~~~KtiIF~~s~~HA~~i~~~L~~~f~~~  725 (1123)
T PRK11448        646 VEVINTQTGEIDLATLEDEVDFEVEDFNRRVITESFNRVVCEELAKYLDPTGEGKTLIFAATDAHADMVVRLLKEAFKKK  725 (1123)
T ss_pred             hhhcchhhhhhhhccCcHHHhhhHHHHHHHHhhHHHHHHHHHHHHHHHhccCCCcEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence               000   00  00000        00       0111    111222223479999999999999998887653    


Q ss_pred             --CC---CeEEEcCCCCHHHHHHHHHhhhcCCc-cEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCC-
Q 014486          312 --NF---PSICIHSGMSQEERLTRYKGFKEGNK-RILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGT-  384 (423)
Q Consensus       312 --~~---~~~~~~~~~~~~~r~~~~~~f~~~~~-~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~-  384 (423)
                        +.   .+..++|..+  ++..+++.|+++.. .|+|+++++.+|+|+|.+.+||++.++.|...|.|++||+.|.-. 
T Consensus       726 ~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v~~vVf~rpvkS~~lf~QmIGRgtR~~~~  803 (1123)
T PRK11448        726 YGQVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFLRRVRSRILYEQMLGRATRLCPE  803 (1123)
T ss_pred             cCCcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCcccccEEEEecCCCCHHHHHHHHhhhccCCcc
Confidence              12   3456888875  46778999999887 689999999999999999999999999999999999999999533 


Q ss_pred             -ceEEEEEec
Q 014486          385 -KGLAITFVS  393 (423)
Q Consensus       385 -~~~~~~~~~  393 (423)
                       ......+++
T Consensus       804 ~~K~~f~I~D  813 (1123)
T PRK11448        804 IGKTHFRIFD  813 (1123)
T ss_pred             CCCceEEEEe
Confidence             234444444

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

Probab=99.97  E-value=5.6e-29  Score=231.18  Aligned_cols=330  Identities=20%  Similarity=0.271  Sum_probs=223.7

Q ss_pred             CCChhhhhccccccc----CCceEEEccCCCcchhHHHHHHhhccCC-CCCCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           68 HPSEVQHECIPQAIL----GMDVICQAKSGMGKTAVFVLSTLQQTEP-NPGQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~~~~ii~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      .+++||.+.++++.+    |-++|++..+|.|||++.+. .+..+.. .+-...-||++|...|. +|..++++|.   |
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtIs-~l~yl~~~~~~~GPfLVi~P~StL~-NW~~Ef~rf~---P  241 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTIS-LLGYLKGRKGIPGPFLVIAPKSTLD-NWMNEFKRFT---P  241 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHHH-HHHHHHHhcCCCCCeEEEeeHhhHH-HHHHHHHHhC---C
Confidence            789999999998876    66799999999999987543 3332222 22122569999988774 4666677765   7


Q ss_pred             CceEEEEEcCcchHHH--HHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCC
Q 014486          143 DIKVAVFYGGVNIKIH--KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTP  220 (423)
Q Consensus       143 ~~~~~~~~~~~~~~~~--~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~  220 (423)
                      ++++.+++|+...+..  ...+..+.++|+|+|+++.++-  ...+.-..++++||||||++.+   ....+.++++.+.
T Consensus       242 ~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~d--k~~lk~~~W~ylvIDEaHRiKN---~~s~L~~~lr~f~  316 (971)
T KOG0385|consen  242 SLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKD--KSFLKKFNWRYLVIDEAHRIKN---EKSKLSKILREFK  316 (971)
T ss_pred             CcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhh--HHHHhcCCceEEEechhhhhcc---hhhHHHHHHHHhc
Confidence            8999999998754332  2334456789999999988752  2223335678999999999976   3444445666655


Q ss_pred             CCceEEEEeccCCcc-HHH---HH-------------------------------------H------------HhccCC
Q 014486          221 HDKQVMMFSATLSKE-IRP---VC-------------------------------------K------------KFMQDP  247 (423)
Q Consensus       221 ~~~~~v~~SAT~~~~-~~~---~~-------------------------------------~------------~~~~~~  247 (423)
                      ... .+++|+||-.. +..   ++                                     +            ..+...
T Consensus       317 ~~n-rLLlTGTPLQNNL~ELWaLLnFllPdiF~~~e~F~swF~~~~~~~~~e~v~~Lh~vL~pFlLRR~K~dVe~sLppK  395 (971)
T KOG0385|consen  317 TDN-RLLLTGTPLQNNLHELWALLNFLLPDIFNSAEDFDSWFDFTNCEGDQELVSRLHKVLRPFLLRRIKSDVEKSLPPK  395 (971)
T ss_pred             ccc-eeEeeCCcccccHHHHHHHHHhhchhhccCHHHHHHHHcccccccCHHHHHHHHhhhhHHHHHHHHHhHhhcCCCc
Confidence            433 68888996111 000   00                                     0            000000


Q ss_pred             cee--ee---------------------cccc----------------ccccccceEEE----------EEeChHHHHHH
Q 014486          248 MEI--YV---------------------DDEA----------------KLTLHGLVQHY----------IKLSELEKNRK  278 (423)
Q Consensus       248 ~~~--~~---------------------~~~~----------------~~~~~~~~~~~----------~~~~~~~~~~~  278 (423)
                      .++  ++                     ....                .+..+.+....          ..+....|...
T Consensus       396 kE~~iyvgms~mQkk~Y~~iL~kdl~~~n~~~~~~k~kL~NI~mQLRKccnHPYLF~g~ePg~pyttdehLv~nSGKm~v  475 (971)
T KOG0385|consen  396 KELIIYVGMSSMQKKWYKAILMKDLDALNGEGKGEKTKLQNIMMQLRKCCNHPYLFDGAEPGPPYTTDEHLVTNSGKMLV  475 (971)
T ss_pred             ceeeEeccchHHHHHHHHHHHHhcchhhcccccchhhHHHHHHHHHHHhcCCccccCCCCCCCCCCcchHHHhcCcceeh
Confidence            000  00                     0000                00000000000          01122335556


Q ss_pred             HHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCc---cEEEEcCccccCCC
Q 014486          279 LNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNK---RILVATDLVGRGID  353 (423)
Q Consensus       279 l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~---~ili~T~~~~~Gld  353 (423)
                      |..+|..+  .+++||||.+-....+.+.+++.-+++.+..+.|.++..+|...++.|.....   -.|++|.+++.|||
T Consensus       476 LDkLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGGLGIN  555 (971)
T KOG0385|consen  476 LDKLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGGLGIN  555 (971)
T ss_pred             HHHHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEeccccccccc
Confidence            66666554  56899999999999999999999999999999999999999999999987653   47789999999999


Q ss_pred             CCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEE--ecC-cccHHHHHHHHHHH
Q 014486          354 IERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITF--VSS-ASDSDILNQVSKFM  408 (423)
Q Consensus       354 ~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~--~~~-~~~~~~~~~~~~~~  408 (423)
                      +..+++||.||..|+|+.-.|+..||+|.||...|.+|  ++. .-+..++.....++
T Consensus       556 L~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLitentVEe~IveRA~~KL  613 (971)
T KOG0385|consen  556 LTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITENTVEEKIVERAAAKL  613 (971)
T ss_pred             cccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccchHHHHHHHHHHHHh
Confidence            99999999999999999999999999999998766654  443 33444444444444

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

Probab=99.97  E-value=1.2e-27  Score=203.14  Aligned_cols=313  Identities=16%  Similarity=0.220  Sum_probs=214.6

Q ss_pred             CCChhhhhccccccc----CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           68 HPSEVQHECIPQAIL----GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      ++++.|+.+-..+++    .++.+++|-||+|||..... .++.....+.  ++.+.+|+...+.+++.+++.-.   ++
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~-~i~~al~~G~--~vciASPRvDVclEl~~Rlk~aF---~~  170 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQ-GIEQALNQGG--RVCIASPRVDVCLELYPRLKQAF---SN  170 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHH-HHHHHHhcCC--eEEEecCcccchHHHHHHHHHhh---cc
Confidence            789999988776665    57899999999999986544 4444443333  88999999999999998888755   35


Q ss_pred             ceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCc
Q 014486          144 IKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK  223 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~  223 (423)
                      ..+..++|+......        ..++|+|...|+++.+       .|+++|+||+|.+-- ..-......+.+......
T Consensus       171 ~~I~~Lyg~S~~~fr--------~plvVaTtHQLlrFk~-------aFD~liIDEVDAFP~-~~d~~L~~Av~~ark~~g  234 (441)
T COG4098         171 CDIDLLYGDSDSYFR--------APLVVATTHQLLRFKQ-------AFDLLIIDEVDAFPF-SDDQSLQYAVKKARKKEG  234 (441)
T ss_pred             CCeeeEecCCchhcc--------ccEEEEehHHHHHHHh-------hccEEEEeccccccc-cCCHHHHHHHHHhhcccC
Confidence            688888887654322        3899999999987654       467899999997743 122222233334444466


Q ss_pred             eEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHH-------HHHHHHHHhh--cCCcEEEE
Q 014486          224 QVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKN-------RKLNDLLDAL--DFNQVVIF  294 (423)
Q Consensus       224 ~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~l~~ll~~~--~~~~~ivf  294 (423)
                      .+|++|||+++.+...+..--..  .+.+.... ...+.....++......|.       ..+...++..  .+.+++||
T Consensus       235 ~~IylTATp~k~l~r~~~~g~~~--~~klp~Rf-H~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF  311 (441)
T COG4098         235 ATIYLTATPTKKLERKILKGNLR--ILKLPARF-HGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIF  311 (441)
T ss_pred             ceEEEecCChHHHHHHhhhCCee--Eeecchhh-cCCCCCCCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEE
Confidence            79999999998766543321111  11111111 1111122233333333322       2556666544  34799999


Q ss_pred             EcChhhHHHHHHHHHhC-C-CCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCC--CCcc
Q 014486          295 VKSVSRAAELNKLLVEC-N-FPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMP--DSAD  370 (423)
Q Consensus       295 ~~~~~~~~~l~~~L~~~-~-~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~--~s~~  370 (423)
                      +++++..+.++..|+.. . ..+..+|+.  ...|.+..++|++|++++||+|.++++|+.+|++++.+.-..-  .+-+
T Consensus       312 ~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vlgaeh~vfTes  389 (441)
T COG4098         312 FPEIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTES  389 (441)
T ss_pred             ecchHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccccccceEEEecCCcccccHH
Confidence            99999999999999543 2 344567775  5578899999999999999999999999999999987765544  5677


Q ss_pred             hhhhcccccCCCC-CceEEEEEecCcccHHHHHHHHHH
Q 014486          371 TYLHRVGRAGRFG-TKGLAITFVSSASDSDILNQVSKF  407 (423)
Q Consensus       371 ~~~Q~~GR~~R~g-~~~~~~~~~~~~~~~~~~~~~~~~  407 (423)
                      .++|..||+||.- .+..-++|++......+.....+.
T Consensus       390 aLVQIaGRvGRs~~~PtGdv~FFH~G~skaM~~A~keI  427 (441)
T COG4098         390 ALVQIAGRVGRSLERPTGDVLFFHYGKSKAMKQARKEI  427 (441)
T ss_pred             HHHHHhhhccCCCcCCCCcEEEEeccchHHHHHHHHHH
Confidence            8999999999953 333334466666666666555543

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

Probab=99.96  E-value=4.5e-28  Score=237.97  Aligned_cols=319  Identities=18%  Similarity=0.224  Sum_probs=230.5

Q ss_pred             hCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           63 DSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        63 ~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      ..+| .|-++|++++..+-++.+++++||||+|||.+.-.++...+..+.   +++|.+|.++|..|.+..+....... 
T Consensus       115 ~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~q---rviYTsPIKALsNQKyrdl~~~fgdv-  189 (1041)
T COG4581         115 EYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDGQ---RVIYTSPIKALSNQKYRDLLAKFGDV-  189 (1041)
T ss_pred             hCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcCC---ceEeccchhhhhhhHHHHHHHHhhhh-
Confidence            3456 689999999999999999999999999999998887777766555   69999999999999988887654322 


Q ss_pred             CceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCC
Q 014486          143 DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHD  222 (423)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~  222 (423)
                      .-.++.++|+..++        +...++|.|.+.|.+++..+...+.++.+||+||+|.+.+ ..-...+..+...++..
T Consensus       190 ~~~vGL~TGDv~IN--------~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D-~eRG~VWEE~Ii~lP~~  260 (1041)
T COG4581         190 ADMVGLMTGDVSIN--------PDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGD-RERGVVWEEVIILLPDH  260 (1041)
T ss_pred             hhhccceecceeeC--------CCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccc-cccchhHHHHHHhcCCC
Confidence            22467888876654        3468999999999999988888889999999999999987 66777788899999999


Q ss_pred             ceEEEEeccCCccHH--HHHHHhccCCceeeeccccccccccceE---EEEE-eC-------------------------
Q 014486          223 KQVMMFSATLSKEIR--PVCKKFMQDPMEIYVDDEAKLTLHGLVQ---HYIK-LS-------------------------  271 (423)
Q Consensus       223 ~~~v~~SAT~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~-------------------------  271 (423)
                      .++|++|||+|+...  ..+......+..+......+.+......   ..+. +.                         
T Consensus       261 v~~v~LSATv~N~~EF~~Wi~~~~~~~~~vv~t~~RpvPL~~~~~~~~~l~~lvde~~~~~~~~~~~a~~~l~~~~~~~~  340 (1041)
T COG4581         261 VRFVFLSATVPNAEEFAEWIQRVHSQPIHVVSTEHRPVPLEHFVYVGKGLFDLVDEKKKFNAENFPSANRSLSCFSEKVR  340 (1041)
T ss_pred             CcEEEEeCCCCCHHHHHHHHHhccCCCeEEEeecCCCCCeEEEEecCCceeeeecccccchhhcchhhhhhhhccchhcc
Confidence            999999999987643  2222222333322221111111000000   0000 00                         


Q ss_pred             ----------------------hHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHh-------------------
Q 014486          272 ----------------------ELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVE-------------------  310 (423)
Q Consensus       272 ----------------------~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~-------------------  310 (423)
                                            ...+...+...+.....-++|+|+-++..|+..+..+..                   
T Consensus       341 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~iv~~l~~~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~  420 (1041)
T COG4581         341 ETDDGDVGRYARRTKALRGSAKGPAGRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDH  420 (1041)
T ss_pred             ccCccccccccccccccCCcccccccchHHHhhhhhhcCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHH
Confidence                                  000112234444444556899999999988887777652                   


Q ss_pred             ---------CCCC-------------eEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccC---
Q 014486          311 ---------CNFP-------------SICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDM---  365 (423)
Q Consensus       311 ---------~~~~-------------~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~---  365 (423)
                               ++++             ....|+++=+..+..+...|..|-++|+++|.+++.|+|.|.-++|+ ...   
T Consensus       421 ~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~-~~l~K~  499 (1041)
T COG4581         421 AIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPARTVVF-TSLSKF  499 (1041)
T ss_pred             HHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCcccceee-eeeEEe
Confidence                     1121             23568999999999999999999999999999999999999555444 332   


Q ss_pred             ------CCCcchhhhcccccCCCCCc--eEEEEEecCcc
Q 014486          366 ------PDSADTYLHRVGRAGRFGTK--GLAITFVSSAS  396 (423)
Q Consensus       366 ------~~s~~~~~Q~~GR~~R~g~~--~~~~~~~~~~~  396 (423)
                            .-++.+|.|+.|||||.|.+  |.++++..+..
T Consensus       500 dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~~~  538 (1041)
T COG4581         500 DGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPPFE  538 (1041)
T ss_pred             cCCceeecChhHHHHhhhhhccccccccceEEEecCCCC
Confidence                  23788999999999999965  77777644433

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

Probab=99.96  E-value=4.3e-28  Score=224.58  Aligned_cols=317  Identities=18%  Similarity=0.233  Sum_probs=228.8

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      ++-|+|..+|..+-++.++++.|.|.+|||.++-.++...+....   +++|.+|-++|..|-++++..-..     .++
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~kQ---RVIYTSPIKALSNQKYREl~~EF~-----DVG  200 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREKQ---RVIYTSPIKALSNQKYRELLEEFK-----DVG  200 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhcC---eEEeeChhhhhcchhHHHHHHHhc-----ccc
Confidence            678999999999999999999999999999999888888777654   899999999999999887765443     456


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEE
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM  227 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~  227 (423)
                      ..+|+..++        .....+|+|.+.|..++-++..-+..+.+||+||+|.+-+ ..-.-.+..-.-.+|++.+.++
T Consensus       201 LMTGDVTIn--------P~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRD-kERGVVWEETIIllP~~vr~VF  271 (1041)
T KOG0948|consen  201 LMTGDVTIN--------PDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRD-KERGVVWEETIILLPDNVRFVF  271 (1041)
T ss_pred             eeecceeeC--------CCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccc-cccceeeeeeEEeccccceEEE
Confidence            677766543        3358999999999998888887888999999999999976 3444445555667899999999


Q ss_pred             EeccCCccHHHHHHH---hccCCceeeeccccccccccce------EEEEEeChH-------------------------
Q 014486          228 FSATLSKEIRPVCKK---FMQDPMEIYVDDEAKLTLHGLV------QHYIKLSEL-------------------------  273 (423)
Q Consensus       228 ~SAT~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~-------------------------  273 (423)
                      +|||+|+... ++++   .-.+|..+...+-.+.+.....      -.+..+.+.                         
T Consensus       272 LSATiPNA~q-FAeWI~~ihkQPcHVVYTdyRPTPLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~~~~~~~~~  350 (1041)
T KOG0948|consen  272 LSATIPNARQ-FAEWICHIHKQPCHVVYTDYRPTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKAGESDGKK  350 (1041)
T ss_pred             EeccCCCHHH-HHHHHHHHhcCCceEEeecCCCCcceeeeecCCCCeeEEEEecccccchHHHHHHHHHhhccCCCcccc
Confidence            9999998743 3333   3334433332221111111000      001111000                         


Q ss_pred             ------------------HHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCC-----------------------
Q 014486          274 ------------------EKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECN-----------------------  312 (423)
Q Consensus       274 ------------------~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~-----------------------  312 (423)
                                        .....+...+-.....++|||+-++++|+.++-.+.+..                       
T Consensus       351 ~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~Lse  430 (1041)
T KOG0948|consen  351 KANKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQLSE  430 (1041)
T ss_pred             ccccccccCCcCCCCCCcccHHHHHHHHHhhcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHhcCh
Confidence                              011233344444456789999999999988877765521                       


Q ss_pred             ----------------CCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCC---------
Q 014486          313 ----------------FPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPD---------  367 (423)
Q Consensus       313 ----------------~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~---------  367 (423)
                                      -.+.+.||++-+--++-+.--|.+|-+++|+||...+.|+|-|.-++|+ ....+         
T Consensus       431 eDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvF-T~~rKfDG~~fRwi  509 (1041)
T KOG0948|consen  431 EDRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVF-TAVRKFDGKKFRWI  509 (1041)
T ss_pred             hhccchHHHHHHHHHHhccccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEE-eeccccCCcceeee
Confidence                            1244679999988888888899999999999999999999999655444 33221         


Q ss_pred             CcchhhhcccccCCCCCc--eEEEEEecCcccHHHHHH
Q 014486          368 SADTYLHRVGRAGRFGTK--GLAITFVSSASDSDILNQ  403 (423)
Q Consensus       368 s~~~~~Q~~GR~~R~g~~--~~~~~~~~~~~~~~~~~~  403 (423)
                      |-.+|+|+.|||||.|.+  |.|+++++...+......
T Consensus       510 ssGEYIQMSGRAGRRG~DdrGivIlmiDekm~~~~ak~  547 (1041)
T KOG0948|consen  510 SSGEYIQMSGRAGRRGIDDRGIVILMIDEKMEPQVAKD  547 (1041)
T ss_pred             cccceEEecccccccCCCCCceEEEEecCcCCHHHHHH
Confidence            566899999999999964  788888887666544333

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.96  E-value=3.8e-27  Score=228.16  Aligned_cols=316  Identities=17%  Similarity=0.213  Sum_probs=225.4

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .|++.|--+--.+  .+.-|..++||.|||+++.+|++.....+.   .+.|++|+..||.|.++++..+...+ ++++.
T Consensus        82 ~~ydVQliGgl~L--~~G~IaEm~TGEGKTL~a~lp~~l~al~g~---~VhIvT~ndyLA~RD~e~m~~l~~~l-Glsv~  155 (908)
T PRK13107         82 RHFDVQLLGGMVL--DSNRIAEMRTGEGKTLTATLPAYLNALTGK---GVHVITVNDYLARRDAENNRPLFEFL-GLTVG  155 (908)
T ss_pred             CcCchHHhcchHh--cCCccccccCCCCchHHHHHHHHHHHhcCC---CEEEEeCCHHHHHHHHHHHHHHHHhc-CCeEE
Confidence            6777777554444  455799999999999999999998776554   58999999999999999999998887 99999


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcC-CCCC-----CCccEEEEcCcchhhccC--------------
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDK-DLSL-----KNVRHFILDECDKMLESL--------------  206 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~-~~~~-----~~~~~vVvDE~h~~~~~~--------------  206 (423)
                      ++.++.+.......+  . ++|+++||..| +++++.+ ....     ..+.++||||+|.++.+.              
T Consensus       156 ~i~~~~~~~~r~~~Y--~-~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLiDEArtPLIISg~~~~~  232 (908)
T PRK13107        156 INVAGLGQQEKKAAY--N-ADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILIDEARTPLIISGAAEDS  232 (908)
T ss_pred             EecCCCCHHHHHhcC--C-CCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhccccCCCceeecCCCccc
Confidence            999987764332222  2 59999999999 8888766 2232     678899999999886320              


Q ss_pred             -CcHHHHHHHHHhCC-------------------CCc-------------------------------------------
Q 014486          207 -DMRRDVQEIFKMTP-------------------HDK-------------------------------------------  223 (423)
Q Consensus       207 -~~~~~~~~~~~~~~-------------------~~~-------------------------------------------  223 (423)
                       .....+..+...+.                   ...                                           
T Consensus       233 ~~~y~~~~~~v~~L~~~~~~~~~~~~~~~dy~idek~~~v~LTe~G~~~~e~~l~~~~~~~~~~~l~~~~~~~~~~~i~~  312 (908)
T PRK13107        233 SELYIKINTLIPNLIRQDKEDTEEYVGEGDYSIDEKAKQVHFTERGQEKVENLLIERGMLAEGDSLYSAANISLLHHVNA  312 (908)
T ss_pred             hHHHHHHHHHHHHHHhhhhccccccCCCCCEEEecCCCeeeechHHHHHHHHHHHhCCcccCcccccCchhhHHHHHHHH
Confidence             01111111110000                   000                                           


Q ss_pred             -------------------------------------------------------------------------eEEEEec
Q 014486          224 -------------------------------------------------------------------------QVMMFSA  230 (423)
Q Consensus       224 -------------------------------------------------------------------------~~v~~SA  230 (423)
                                                                                               ++.+||+
T Consensus       313 aL~A~~lf~~d~dYiV~dg~V~IVDe~TGRim~grrwsdGLHQaIEaKE~v~I~~e~~t~AsIT~QnfFr~Y~kL~GMTG  392 (908)
T PRK13107        313 ALRAHTLFEKDVDYIVQDNEVIIVDEHTGRTMPGRRWSEGLHQAVEAKEGVHIQNENQTLASITFQNYFRQYEKLAGMTG  392 (908)
T ss_pred             HHHHHHHHhcCCceEEECCEEEEEECCCCCCCCCCccchHHHHHHHHhcCCCCCCCceeeeeehHHHHHHhhhHhhcccC
Confidence                                                                                     2344555


Q ss_pred             cCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHH
Q 014486          231 TLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLL  308 (423)
Q Consensus       231 T~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L  308 (423)
                      |...+...+.+.+......+...  .+........ .+......|...+.+-+...  .+.++||||.+...++.++..|
T Consensus       393 Ta~te~~Ef~~iY~l~Vv~IPTn--kp~~R~d~~d-~iy~t~~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~ls~~L  469 (908)
T PRK13107        393 TADTEAFEFQHIYGLDTVVVPTN--RPMVRKDMAD-LVYLTADEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLARLM  469 (908)
T ss_pred             CChHHHHHHHHHhCCCEEECCCC--CCccceeCCC-cEEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHHHHHH
Confidence            54444333333333222222111  1111111111 23334455655555544322  5689999999999999999999


Q ss_pred             HhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCC---------------------------------
Q 014486          309 VECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIE---------------------------------  355 (423)
Q Consensus       309 ~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~---------------------------------  355 (423)
                      ...|+++..+|+.++..++..+...|+.|.  |+|||++++||+|+.                                 
T Consensus       470 ~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  547 (908)
T PRK13107        470 VKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDE  547 (908)
T ss_pred             HHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHH
Confidence            999999999999999999999999999988  999999999999986                                 


Q ss_pred             ----CCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          356 ----RVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       356 ----~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                          +--|||-...+.|-.--.|-.||+||.|.+|..-.|++-.++
T Consensus       548 V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSlED~  593 (908)
T PRK13107        548 VVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMEDS  593 (908)
T ss_pred             HHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEeCcH
Confidence                234688888888888889999999999999999999986444

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

Probab=99.95  E-value=2.5e-26  Score=214.64  Aligned_cols=313  Identities=19%  Similarity=0.197  Sum_probs=210.9

Q ss_pred             CCChhhhhccccccc----CCceEEEccCCCcchhHHHHHHhhccCCC-CCCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           68 HPSEVQHECIPQAIL----GMDVICQAKSGMGKTAVFVLSTLQQTEPN-PGQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~~~~ii~~~tGsGKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      .+.+||+.++.++..    +..+|+..++|.|||.+.+. .+..+..+ .-...+|||||. .+..||..++..|+   |
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiis-FLaaL~~S~k~~~paLIVCP~-Tii~qW~~E~~~w~---p  279 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIIS-FLAALHHSGKLTKPALIVCPA-TIIHQWMKEFQTWW---P  279 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHH-HHHHHhhcccccCceEEEccH-HHHHHHHHHHHHhC---c
Confidence            668999999998875    56699999999999976433 22222222 222378999996 68889988888776   5


Q ss_pred             CceEEEEEcCcch---------HHHHHHHh---cCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHH
Q 014486          143 DIKVAVFYGGVNI---------KIHKDLLK---NECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRR  210 (423)
Q Consensus       143 ~~~~~~~~~~~~~---------~~~~~~~~---~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~  210 (423)
                      .+++..+++..+.         ......+.   ..+..|+++|++.+.-  ....+.-..+.++|+||.|++.+ .  ..
T Consensus       280 ~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~--~~d~l~~~~W~y~ILDEGH~IrN-p--ns  354 (923)
T KOG0387|consen  280 PFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRI--QGDDLLGILWDYVILDEGHRIRN-P--NS  354 (923)
T ss_pred             ceEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhcc--cCcccccccccEEEecCcccccC-C--cc
Confidence            6789888886652         11111111   1234799999987753  22234446788999999999976 2  22


Q ss_pred             HHHHHHHhCCCCceEEEEeccCCcc-HHHH--------------------------------------------------
Q 014486          211 DVQEIFKMTPHDKQVMMFSATLSKE-IRPV--------------------------------------------------  239 (423)
Q Consensus       211 ~~~~~~~~~~~~~~~v~~SAT~~~~-~~~~--------------------------------------------------  239 (423)
                      .+...++.++ ..+.+.+|+||-.. +..+                                                  
T Consensus       355 ~islackki~-T~~RiILSGTPiQNnL~ELwsLfDFv~PG~Lgt~~~F~~~f~~pI~~GgyaNAs~~qv~~aykca~~Lr  433 (923)
T KOG0387|consen  355 KISLACKKIR-TVHRIILSGTPIQNNLTELWSLFDFVFPGKLGTLPVFQQNFEHPINRGGYANASPRQVQTAYKCAVALR  433 (923)
T ss_pred             HHHHHHHhcc-ccceEEeeCccccchHHHHHHHhhhccCCcccchHHHHhhhhhheeccccCCCCHHHHHHHHHHHHHHH
Confidence            3333334443 33456777775110 0000                                                  


Q ss_pred             --H------------HH-hccCCceee-------------------------ecccc-----------ccccccceEE--
Q 014486          240 --C------------KK-FMQDPMEIY-------------------------VDDEA-----------KLTLHGLVQH--  266 (423)
Q Consensus       240 --~------------~~-~~~~~~~~~-------------------------~~~~~-----------~~~~~~~~~~--  266 (423)
                        +            .. .+....+++                         +....           -+..+.+...  
T Consensus       434 ~lI~PylLRR~K~dv~~~~Lp~K~E~VlfC~LT~~QR~~Y~~fl~s~~v~~i~ng~~~~l~Gi~iLrkICnHPdll~~~~  513 (923)
T KOG0387|consen  434 DLISPYLLRRMKSDVKGLKLPKKEEIVLFCRLTKLQRRLYQRFLNSSEVNKILNGKRNCLSGIDILRKICNHPDLLDRRD  513 (923)
T ss_pred             HHhHHHHHHHHHHHhhhccCCCccceEEEEeccHHHHHHHHHHhhhHHHHHHHcCCccceechHHHHhhcCCcccccCcc
Confidence              0            00 000000000                         00000           0000000000  


Q ss_pred             --------E-EEeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHH-hCCCCeEEEcCCCCHHHHHHHHHhh
Q 014486          267 --------Y-IKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLV-ECNFPSICIHSGMSQEERLTRYKGF  334 (423)
Q Consensus       267 --------~-~~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~-~~~~~~~~~~~~~~~~~r~~~~~~f  334 (423)
                              + -......|...+..+++.+  .+.++|+|..++.-.+.+...|. ..++.++.+.|.++...|..+++.|
T Consensus       514 ~~~~~~~D~~g~~k~sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~F  593 (923)
T KOG0387|consen  514 EDEKQGPDYEGDPKRSGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRF  593 (923)
T ss_pred             cccccCCCcCCChhhcchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhh
Confidence                    0 1223345677777777665  45799999999999999999998 5799999999999999999999999


Q ss_pred             hcCCc--cEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEE
Q 014486          335 KEGNK--RILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITF  391 (423)
Q Consensus       335 ~~~~~--~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~  391 (423)
                      +++..  -+|++|.+.+-|+|+..++.||.|||.|+|+.-.|+.-|++|.||+..|+++
T Consensus       594 ne~~s~~VFLLTTrvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VY  652 (923)
T KOG0387|consen  594 NEDESIFVFLLTTRVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVY  652 (923)
T ss_pred             cCCCceEEEEEEecccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEE
Confidence            98775  3667999999999999999999999999999999999999999998777654

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

Probab=99.95  E-value=9.7e-27  Score=192.61  Aligned_cols=165  Identities=24%  Similarity=0.442  Sum_probs=138.4

Q ss_pred             ChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEE
Q 014486           70 SEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVF  149 (423)
Q Consensus        70 ~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~  149 (423)
                      ||+|.++++.+..++++++.+|||+|||++++++++..+... ...++++++|+++|+.|+.+.+..+... +++++..+
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~-~~~~~lii~P~~~l~~q~~~~~~~~~~~-~~~~~~~~   78 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG-KDARVLIIVPTRALAEQQFERLRKFFSN-TNVRVVLL   78 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT-SSSEEEEEESSHHHHHHHHHHHHHHTTT-TTSSEEEE
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC-CCceEEEEeecccccccccccccccccc-cccccccc
Confidence            689999999999999999999999999999999999887766 3349999999999999999999998876 47889999


Q ss_pred             EcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCC--CceEEE
Q 014486          150 YGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPH--DKQVMM  227 (423)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~--~~~~v~  227 (423)
                      +++............+.++|+|+||++|...+......+.++++||+||+|.+.. ..+...+..+...+..  ..++++
T Consensus        79 ~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~-~~~~~~~~~i~~~~~~~~~~~~i~  157 (169)
T PF00270_consen   79 HGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSD-ETFRAMLKSILRRLKRFKNIQIIL  157 (169)
T ss_dssp             STTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHH-TTHHHHHHHHHHHSHTTTTSEEEE
T ss_pred             cccccccccccccccccccccccCcchhhccccccccccccceeeccCccccccc-ccHHHHHHHHHHHhcCCCCCcEEE
Confidence            9988766343333344469999999999999988666777799999999999988 4777788888777633  588999


Q ss_pred             EeccCCccHH
Q 014486          228 FSATLSKEIR  237 (423)
Q Consensus       228 ~SAT~~~~~~  237 (423)
                      +|||+++.+.
T Consensus       158 ~SAT~~~~~~  167 (169)
T PF00270_consen  158 LSATLPSNVE  167 (169)
T ss_dssp             EESSSTHHHH
T ss_pred             EeeCCChhHh
Confidence            9999995543

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=5.1e-25  Score=211.51  Aligned_cols=289  Identities=20%  Similarity=0.285  Sum_probs=202.7

Q ss_pred             HHHHhC-CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           59 RAIVDS-GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        59 ~~l~~~-~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      +.+.+. |+ .|+..|+--...++.|+++-+.||||.|||.-.++..+-....+   .++++|+||..|+.|+++.++.+
T Consensus        73 ~fF~k~~G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~kg---kr~yii~PT~~Lv~Q~~~kl~~~  148 (1187)
T COG1110          73 EFFKKATGF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKKG---KRVYIIVPTTTLVRQVYERLKKF  148 (1187)
T ss_pred             HHHHHhhCC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHhcC---CeEEEEecCHHHHHHHHHHHHHH
Confidence            333343 55 89999999999999999999999999999975444333333322   29999999999999999999999


Q ss_pred             hccCCCceEEE-EEcCcchH---HHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc--------
Q 014486          138 STYLPDIKVAV-FYGGVNIK---IHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES--------  205 (423)
Q Consensus       138 ~~~~~~~~~~~-~~~~~~~~---~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~--------  205 (423)
                      .....+..+.. +|+.....   .-...+.++.++|+|+|.+.|...+..-  .--+|++|++|++|.++..        
T Consensus       149 ~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L--~~~kFdfifVDDVDA~LkaskNvDriL  226 (1187)
T COG1110         149 AEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEEL--SKLKFDFIFVDDVDAILKASKNVDRLL  226 (1187)
T ss_pred             HhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHh--cccCCCEEEEccHHHHHhccccHHHHH
Confidence            86653344444 55554433   3346677888999999998887655532  2247899999999987631        


Q ss_pred             --CCcHH-----------------------HHHHHHH--------hCCCCceEEEEeccCCccHH--HHHHHhccCCcee
Q 014486          206 --LDMRR-----------------------DVQEIFK--------MTPHDKQVMMFSATLSKEIR--PVCKKFMQDPMEI  250 (423)
Q Consensus       206 --~~~~~-----------------------~~~~~~~--------~~~~~~~~v~~SAT~~~~~~--~~~~~~~~~~~~~  250 (423)
                        .+|..                       .+.+..+        .-.+..+++..|||..+.-.  .+.+..+....  
T Consensus       227 ~LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~R~~LfReLlgFev--  304 (1187)
T COG1110         227 RLLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGSRLKLFRELLGFEV--  304 (1187)
T ss_pred             HHcCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCchHHHHHHHhCCcc--
Confidence              11111                       0111101        11234579999999865432  23333333211  


Q ss_pred             eeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcC---hhhHHHHHHHHHhCCCCeEEEcCCCCHHHH
Q 014486          251 YVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKS---VSRAAELNKLLVECNFPSICIHSGMSQEER  327 (423)
Q Consensus       251 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~---~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r  327 (423)
                         ........++...+...   .....+.++++.... -.|||++.   .+.++++++.|++.|+++..+|+.     .
T Consensus       305 ---G~~~~~LRNIvD~y~~~---~~~e~~~elvk~lG~-GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~  372 (1187)
T COG1110         305 ---GSGGEGLRNIVDIYVES---ESLEKVVELVKKLGD-GGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----K  372 (1187)
T ss_pred             ---CccchhhhheeeeeccC---ccHHHHHHHHHHhCC-CeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc-----c
Confidence               11223334444444443   444566677777764 58999999   999999999999999999999984     3


Q ss_pred             HHHHHhhhcCCccEEEEc----CccccCCCCCC-CCEEEEccCCC
Q 014486          328 LTRYKGFKEGNKRILVAT----DLVGRGIDIER-VNIVINYDMPD  367 (423)
Q Consensus       328 ~~~~~~f~~~~~~ili~T----~~~~~Gld~~~-~~~vi~~~~~~  367 (423)
                      .+.++.|..|++++||+.    ..+-+|+|+|. ++.+|+++.|+
T Consensus       373 ~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvPk  417 (1187)
T COG1110         373 EEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPK  417 (1187)
T ss_pred             hhhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCCc
Confidence            667999999999999965    57889999996 88999999883

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

Probab=99.94  E-value=1.5e-25  Score=218.91  Aligned_cols=307  Identities=17%  Similarity=0.183  Sum_probs=216.2

Q ss_pred             ChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEE
Q 014486           70 SEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVF  149 (423)
Q Consensus        70 ~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~  149 (423)
                      +....+.+..+..++.++|.||||||||......+++....  ...++.+.-|+|--|..+++++.+......+-.|++-
T Consensus        52 ~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~~--~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY~  129 (845)
T COG1643          52 TAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGLG--IAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYS  129 (845)
T ss_pred             HHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhcc--cCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeEE
Confidence            34444555566667789999999999999877766666552  2227888889998888888888776554434444433


Q ss_pred             EcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHH-HHHHHHhCCCCceEEEE
Q 014486          150 YGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRD-VQEIFKMTPHDKQVMMF  228 (423)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~-~~~~~~~~~~~~~~v~~  228 (423)
                      .-..+.       .+....|-++|.+.|++.+.... .++.+++||+||+|+-.-+.++.-. +..+....+.+.++|.|
T Consensus       130 iRfe~~-------~s~~Trik~mTdGiLlrei~~D~-~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIim  201 (845)
T COG1643         130 IRFESK-------VSPRTRIKVMTDGILLREIQNDP-LLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIM  201 (845)
T ss_pred             EEeecc-------CCCCceeEEeccHHHHHHHhhCc-ccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEE
Confidence            221111       12224899999999999777544 4789999999999976543444433 44556667767999999


Q ss_pred             eccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeC-hH----HHHHHHHHHHHhhcCCcEEEEEcChhhHHH
Q 014486          229 SATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS-EL----EKNRKLNDLLDALDFNQVVIFVKSVSRAAE  303 (423)
Q Consensus       229 SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~----~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~  303 (423)
                      |||+..+   .+..++.+...+.+....-   + +..+|.... ..    ...............+.+|||.+...+.+.
T Consensus       202 SATld~~---rfs~~f~~apvi~i~GR~f---P-Vei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~  274 (845)
T COG1643         202 SATLDAE---RFSAYFGNAPVIEIEGRTY---P-VEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIER  274 (845)
T ss_pred             ecccCHH---HHHHHcCCCCEEEecCCcc---c-eEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHH
Confidence            9999854   3344555444444333211   1 111221111 11    122222233333457899999999999999


Q ss_pred             HHHHHHh----CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCC------------
Q 014486          304 LNKLLVE----CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPD------------  367 (423)
Q Consensus       304 l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~------------  367 (423)
                      ..+.|.+    ....+.++||.++..++.++++--..|..+|+++|+++++++.++++++||+-+..+            
T Consensus       275 ~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VIDsG~ak~~~y~~~~g~~~  354 (845)
T COG1643         275 TAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTR  354 (845)
T ss_pred             HHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEecCCcccccccccccCcee
Confidence            9999998    346788899999999999998777777777999999999999999999999755433            


Q ss_pred             ------CcchhhhcccccCCCCCceEEEEEecC
Q 014486          368 ------SADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       368 ------s~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                            |-++..||.|||||.+ +|.|+-+|+.
T Consensus       355 L~~~~ISqAsA~QRaGRAGR~~-pGicyRLyse  386 (845)
T COG1643         355 LETEPISKASADQRAGRAGRTG-PGICYRLYSE  386 (845)
T ss_pred             eeEEEechhhhhhhccccccCC-CceEEEecCH
Confidence                  6667889999999984 6999999985

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.94  E-value=7e-26  Score=225.15  Aligned_cols=323  Identities=19%  Similarity=0.244  Sum_probs=208.6

Q ss_pred             CCChhhhhcccccccC---C-ceEEEccCCCcchhHHHHHHhhccCC-CCCCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           68 HPSEVQHECIPQAILG---M-DVICQAKSGMGKTAVFVLSTLQQTEP-NPGQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~---~-~~ii~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      ..++.|..++......   + .+++.||||+|||.+.+.++...... .....+++++.|+++++++++++++.+.... 
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~-  273 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLF-  273 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhccc-
Confidence            3488899888877763   4 68999999999999999988887776 3455599999999999999999999876543 


Q ss_pred             CceEEEEEcCcchHHHHHH-------------HhcCCCcEEEechHHHHHHHhc-CCCC---CCCccEEEEcCcchhhcc
Q 014486          143 DIKVAVFYGGVNIKIHKDL-------------LKNECPQIVVGTPGRILALARD-KDLS---LKNVRHFILDECDKMLES  205 (423)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~-------------~~~~~~~ilv~T~~~l~~~~~~-~~~~---~~~~~~vVvDE~h~~~~~  205 (423)
                      ++.....++..........             ....-..+.++|+......... ....   .-..+.+|+||+|.+...
T Consensus       274 ~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~  353 (733)
T COG1203         274 SVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADE  353 (733)
T ss_pred             ccccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhccc
Confidence            2222212333221111110             0011123444454444431111 1111   012357999999988763


Q ss_pred             CCcHHHHHHHHH-hCCCCceEEEEeccCCccHHHHHHHhccCCceeeecccccc--ccccceEE-EEEeChHHHHHHHHH
Q 014486          206 LDMRRDVQEIFK-MTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKL--TLHGLVQH-YIKLSELEKNRKLND  281 (423)
Q Consensus       206 ~~~~~~~~~~~~-~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~-~~~~~~~~~~~~l~~  281 (423)
                      . ....+..+.. ....+.++|++|||+|+.....+.........+........  ........ ...............
T Consensus       354 ~-~~~~l~~~i~~l~~~g~~ill~SATlP~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~  432 (733)
T COG1203         354 T-MLAALLALLEALAEAGVPVLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEELIEL  432 (733)
T ss_pred             c-hHHHHHHHHHHHHhCCCCEEEEecCCCHHHHHHHHHHHhcccceeccccccccccccccccccchhhhhhhhHhhhhc
Confidence            2 3333333333 33347789999999999999988887776555444322000  00000000 011111100011122


Q ss_pred             HHH-hhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhh----cCCccEEEEcCccccCCCCCC
Q 014486          282 LLD-ALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFK----EGNKRILVATDLVGRGIDIER  356 (423)
Q Consensus       282 ll~-~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~----~~~~~ili~T~~~~~Gld~~~  356 (423)
                      ... ...+++++|.||++..|..++..|+..+.++..+||.+...+|.+.++...    .+...|+|+|++++.|+|+. 
T Consensus       433 ~~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDid-  511 (733)
T COG1203         433 ISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDID-  511 (733)
T ss_pred             chhhhccCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEeccc-
Confidence            222 224579999999999999999999998878999999999999988877544    56778999999999999975 


Q ss_pred             CCEEEEccCCCCcchhhhcccccCCCC--CceEEEEEecCc
Q 014486          357 VNIVINYDMPDSADTYLHRVGRAGRFG--TKGLAITFVSSA  395 (423)
Q Consensus       357 ~~~vi~~~~~~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~  395 (423)
                      .+.+|  .-+..+...+||+||++|.|  ..|.++++....
T Consensus       512 fd~mI--Te~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~~  550 (733)
T COG1203         512 FDVLI--TELAPIDSLIQRAGRVNRHGKKENGKIYVYNDEE  550 (733)
T ss_pred             cCeee--ecCCCHHHHHHHHHHHhhcccccCCceeEeeccc
Confidence            44443  44566788999999999999  456666665543

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

Probab=99.94  E-value=1e-25  Score=215.17  Aligned_cols=343  Identities=18%  Similarity=0.220  Sum_probs=227.2

Q ss_pred             CCCHHHHHHHHhCCCCCCChhhhhcc--cccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHH
Q 014486           52 LLKPELLRAIVDSGFEHPSEVQHECI--PQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQ  129 (423)
Q Consensus        52 ~l~~~~~~~l~~~~~~~~~~~Q~~~i--~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  129 (423)
                      +++....-..+..|...++.+|.+++  +.++.+++.|...||+.|||+++-+.++.......+  .++.+.|..+.+..
T Consensus       207 ~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr--~~llilp~vsiv~E  284 (1008)
T KOG0950|consen  207 LPTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRR--NVLLILPYVSIVQE  284 (1008)
T ss_pred             CchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhh--ceeEecceeehhHH
Confidence            33333334444558889999999876  778889999999999999999999988887665544  78999999998888


Q ss_pred             HHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC--CCCCCCccEEEEcCcchhhccCC
Q 014486          130 ICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK--DLSLKNVRHFILDECDKMLESLD  207 (423)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~--~~~~~~~~~vVvDE~h~~~~~~~  207 (423)
                      -...+..+.... |+++-.+.|........+    . -.+.|||-++-..+++.-  .-.+..++.|||||.|.+.+ .+
T Consensus       285 k~~~l~~~~~~~-G~~ve~y~g~~~p~~~~k----~-~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d-~~  357 (1008)
T KOG0950|consen  285 KISALSPFSIDL-GFPVEEYAGRFPPEKRRK----R-ESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGD-KG  357 (1008)
T ss_pred             HHhhhhhhcccc-CCcchhhcccCCCCCccc----c-eeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeec-cc
Confidence            888888777666 778777776544322211    1 389999999765544321  12346678999999999876 34


Q ss_pred             cHHHHHHHH-----HhCCCCceEEEEeccCCccHHHHHHHhccCCceee-eccccccccccceEEEEEeChHHHHHHHHH
Q 014486          208 MRRDVQEIF-----KMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIY-VDDEAKLTLHGLVQHYIKLSELEKNRKLND  281 (423)
Q Consensus       208 ~~~~~~~~~-----~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  281 (423)
                      ....+..++     .......|+|+||||+++.  ..++.++..-.... ..+..-..+...-.......   +...+.+
T Consensus       358 rg~~lE~~l~k~~y~~~~~~~~iIGMSATi~N~--~lL~~~L~A~~y~t~fRPv~L~E~ik~G~~i~~~~---r~~~lr~  432 (1008)
T KOG0950|consen  358 RGAILELLLAKILYENLETSVQIIGMSATIPNN--SLLQDWLDAFVYTTRFRPVPLKEYIKPGSLIYESS---RNKVLRE  432 (1008)
T ss_pred             cchHHHHHHHHHHHhccccceeEeeeecccCCh--HHHHHHhhhhheecccCcccchhccCCCcccccch---hhHHHHH
Confidence            333333332     2333346899999999863  22333332111111 00000000000001111111   2222222


Q ss_pred             HH--------------------Hhhc-CCcEEEEEcChhhHHHHHHHHHh------------------------------
Q 014486          282 LL--------------------DALD-FNQVVIFVKSVSRAAELNKLLVE------------------------------  310 (423)
Q Consensus       282 ll--------------------~~~~-~~~~ivf~~~~~~~~~l~~~L~~------------------------------  310 (423)
                      +-                    +..+ +.++||||++++.++.++..+..                              
T Consensus       433 ia~l~~~~~g~~dpD~~v~L~tet~~e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~  512 (1008)
T KOG0950|consen  433 IANLYSSNLGDEDPDHLVGLCTETAPEGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGI  512 (1008)
T ss_pred             hhhhhhhhcccCCCcceeeehhhhhhcCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcc
Confidence            21                    1112 24599999999888777644432                              


Q ss_pred             --------CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE----ccCCCCcchhhhcccc
Q 014486          311 --------CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN----YDMPDSADTYLHRVGR  378 (423)
Q Consensus       311 --------~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~----~~~~~s~~~~~Q~~GR  378 (423)
                              ....+..+|++++..+|..+...|++|.+.|++||+.++.|+|+|..+++|-    .....+-.+|.|++||
T Consensus       513 ld~Vl~~ti~~GvAyHhaGLT~eER~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GR  592 (1008)
T KOG0950|consen  513 LDPVLAKTIPYGVAYHHAGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGR  592 (1008)
T ss_pred             cchHHheeccccceecccccccchHHHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhh
Confidence                    1234667899999999999999999999999999999999999998887763    2334567789999999


Q ss_pred             cCCCCC--ceEEEEEecCcccHHHHHHHHHHH
Q 014486          379 AGRFGT--KGLAITFVSSASDSDILNQVSKFM  408 (423)
Q Consensus       379 ~~R~g~--~~~~~~~~~~~~~~~~~~~~~~~~  408 (423)
                      |||+|-  .|.+++++.+.+....++.+..-+
T Consensus       593 AGR~gidT~GdsiLI~k~~e~~~~~~lv~~~~  624 (1008)
T KOG0950|consen  593 AGRTGIDTLGDSILIIKSSEKKRVRELVNSPL  624 (1008)
T ss_pred             hhhcccccCcceEEEeeccchhHHHHHHhccc
Confidence            999975  488999998776665555544433

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

Probab=99.93  E-value=1e-24  Score=212.26  Aligned_cols=318  Identities=19%  Similarity=0.223  Sum_probs=227.3

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      ..+..+...+..+..++.++|.|.||+|||.....-+++....+++..++++-.|+|--|..+++++..--....+-.++
T Consensus       173 Pa~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~~VG  252 (924)
T KOG0920|consen  173 PAYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLGEEVG  252 (924)
T ss_pred             ccHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHHHHhccccCCeee
Confidence            55778888888888899999999999999999888888877666666688888899988888888876543332343444


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEE
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM  227 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~  227 (423)
                      +-....+..     .. . ..+++||.+.|++.+.. ...+.++.+||+||+|.-....+|.-.+.+.+-..+++.++|+
T Consensus       253 Yqvrl~~~~-----s~-~-t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~~p~LkvIL  324 (924)
T KOG0920|consen  253 YQVRLESKR-----SR-E-TRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHERSINTDFLLILLKDLLPRNPDLKVIL  324 (924)
T ss_pred             EEEeeeccc-----CC-c-eeEEEecHHHHHHHhcc-CcccccCceeeeeeEEEccCCcccHHHHHHHHhhhCCCceEEE
Confidence            333322211     11 1 48999999999998876 5567899999999999887767888888777777788999999


Q ss_pred             EeccCCccHHHHHHHhccCCceeeeccccc---------------------cccccceEE-----EEEe-ChHHHHHHHH
Q 014486          228 FSATLSKEIRPVCKKFMQDPMEIYVDDEAK---------------------LTLHGLVQH-----YIKL-SELEKNRKLN  280 (423)
Q Consensus       228 ~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~~-----~~~~-~~~~~~~~l~  280 (423)
                      ||||+..+.   ...++.....+.+.....                     .........     .... ...-....+.
T Consensus       325 MSAT~dae~---fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~Li~  401 (924)
T KOG0920|consen  325 MSATLDAEL---FSDYFGGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEIDYDLIE  401 (924)
T ss_pred             eeeecchHH---HHHHhCCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhccccccHHHHH
Confidence            999987432   233333322222111000                     000000000     0000 0011223333


Q ss_pred             HHHHh----hcCCcEEEEEcChhhHHHHHHHHHhC-------CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccc
Q 014486          281 DLLDA----LDFNQVVIFVKSVSRAAELNKLLVEC-------NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVG  349 (423)
Q Consensus       281 ~ll~~----~~~~~~ivf~~~~~~~~~l~~~L~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~  349 (423)
                      .++..    ...+.+|||.+..++...+.+.|...       .+-+.++|+.++..+++.++...-.|..+|+++|++++
T Consensus       402 ~li~~I~~~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaTNIAE  481 (924)
T KOG0920|consen  402 DLIEYIDEREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILATNIAE  481 (924)
T ss_pred             HHHHhcccCCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhhhhhhhHh
Confidence            33332    24688999999999999999999652       24567799999999999999988899999999999999


Q ss_pred             cCCCCCCCCEEEEcc--------CCC----------CcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          350 RGIDIERVNIVINYD--------MPD----------SADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       350 ~Gld~~~~~~vi~~~--------~~~----------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      .+|.++++-+||+.+        +-.          |.....||.|||||. ++|.|+.+++....
T Consensus       482 TSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~~~  546 (924)
T KOG0920|consen  482 TSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRSRY  546 (924)
T ss_pred             hcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechhhh
Confidence            999999999999644        332          445668999999997 67999999986433

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

Probab=99.93  E-value=8.6e-25  Score=204.19  Aligned_cols=336  Identities=17%  Similarity=0.197  Sum_probs=220.1

Q ss_pred             CCChhhhhccccccc----CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           68 HPSEVQHECIPQAIL----GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      ++.+||.-.++++.-    +-++|++.++|.|||.+.+ +.+..+...+.....|||||+..| ..|..++.+|   +|.
T Consensus       399 ~LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQvI-aFlayLkq~g~~gpHLVVvPsSTl-eNWlrEf~kw---CPs  473 (941)
T KOG0389|consen  399 QLKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVI-AFLAYLKQIGNPGPHLVVVPSSTL-ENWLREFAKW---CPS  473 (941)
T ss_pred             cccchhhhhHHHHHHHHHccccceehhhccCcchhHHH-HHHHHHHHcCCCCCcEEEecchhH-HHHHHHHHHh---CCc
Confidence            578899998887653    4568999999999997643 333333332223367999999876 4455555555   488


Q ss_pred             ceEEEEEcCcchHHHHHHHhc---CCCcEEEechHHHHHHH-hcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhC
Q 014486          144 IKVAVFYGGVNIKIHKDLLKN---ECPQIVVGTPGRILALA-RDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMT  219 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~---~~~~ilv~T~~~l~~~~-~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~  219 (423)
                      +++-.++|....+...+....   ..++|+++|+.....-- .+..+.-.+|+++|+||+|.+.+  ....+++.+...-
T Consensus       474 l~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN--~~SeRy~~LM~I~  551 (941)
T KOG0389|consen  474 LKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKN--RTSERYKHLMSIN  551 (941)
T ss_pred             eEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhc--cchHHHHHhcccc
Confidence            899999998866555443322   36899999997653211 11112235678999999999987  3334444444432


Q ss_pred             CCCceEEEEeccCCcc-HHH---HHH------------------------------------------------------
Q 014486          220 PHDKQVMMFSATLSKE-IRP---VCK------------------------------------------------------  241 (423)
Q Consensus       220 ~~~~~~v~~SAT~~~~-~~~---~~~------------------------------------------------------  241 (423)
                        ..+.+++|+||-.. +.+   ++.                                                      
T Consensus       552 --An~RlLLTGTPLQNNL~ELiSLL~FvlP~vF~~~~~dl~~if~~k~~~d~d~e~~~l~qerIsrAK~im~PFILRR~K  629 (941)
T KOG0389|consen  552 --ANFRLLLTGTPLQNNLKELISLLAFVLPKVFDSSMEDLDVIFKAKKTSDGDIENALLSQERISRAKTIMKPFILRRLK  629 (941)
T ss_pred             --ccceEEeeCCcccccHHHHHHHHHHHhhHhhhccchHHHHHHhccCCccchhhHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence              44568899996100 000   000                                                      


Q ss_pred             -Hhcc-CCc---eee-------------------------ecccc-ccc------------cccceEEE-----------
Q 014486          242 -KFMQ-DPM---EIY-------------------------VDDEA-KLT------------LHGLVQHY-----------  267 (423)
Q Consensus       242 -~~~~-~~~---~~~-------------------------~~~~~-~~~------------~~~~~~~~-----------  267 (423)
                       ..+. -|.   .+.                         ..... ...            .+.+...+           
T Consensus       630 ~qVL~~LPpK~~~Ie~c~mse~Q~~~Y~~~~~~~~~~~~~~~~ns~~~~~~vlmqlRK~AnHPLL~R~~Y~de~L~~mak  709 (941)
T KOG0389|consen  630 SQVLKQLPPKIQRIEYCEMSEKQKQLYDELIELYDVKLNEVSKNSELKSGNVLMQLRKAANHPLLFRSIYTDEKLRKMAK  709 (941)
T ss_pred             HHHHHhcCCccceeEeeecchHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHhcChhHHHHhccHHHHHHHHH
Confidence             0000 000   000                         00000 000            00000000           


Q ss_pred             ---------------------------------------------EEeChHHHHHHHHHHHHhh--cCCcEEEEEcChhh
Q 014486          268 ---------------------------------------------IKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSR  300 (423)
Q Consensus       268 ---------------------------------------------~~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~  300 (423)
                                                                   ..+....|...|..+|...  .+.++|||.....-
T Consensus       710 ~il~e~ay~~~n~qyIfEDm~~msDfelHqLc~~f~~~~~f~L~d~~~mdSgK~r~L~~LLp~~k~~G~RVLiFSQFTqm  789 (941)
T KOG0389|consen  710 RILNEPAYKKANEQYIFEDMEVMSDFELHQLCCQFRHLSKFQLKDDLWMDSGKCRKLKELLPKIKKKGDRVLIFSQFTQM  789 (941)
T ss_pred             HHhCchhhhhcCHHHHHHHHHhhhHHHHHHHHHhcCCCcccccCCchhhhhhhHhHHHHHHHHHhhcCCEEEEeeHHHHH
Confidence                                                         0001223444555555443  35799999999999


Q ss_pred             HHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCc--cEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccc
Q 014486          301 AAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNK--RILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGR  378 (423)
Q Consensus       301 ~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~--~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR  378 (423)
                      .+.+...|.-.++....+.|.+.-..|+.+++.|..++.  -.|++|.+++.|||+..+++||.+|...+|..-.|+-.|
T Consensus       790 LDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GINLt~An~VIihD~dFNP~dD~QAEDR  869 (941)
T KOG0389|consen  790 LDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGINLTCANTVIIHDIDFNPYDDKQAEDR  869 (941)
T ss_pred             HHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCcceecccccceEEEeecCCCCcccchhHHH
Confidence            999999999999999999999999999999999997663  367799999999999999999999999999999999999


Q ss_pred             cCCCCCceEEEE--EecC-cccHHHHHHHHHHHhcch
Q 014486          379 AGRFGTKGLAIT--FVSS-ASDSDILNQVSKFMFLLI  412 (423)
Q Consensus       379 ~~R~g~~~~~~~--~~~~-~~~~~~~~~~~~~~~~~~  412 (423)
                      |+|.||...|.+  +++. .-+..++...++++.+..
T Consensus       870 cHRvGQtkpVtV~rLItk~TIEE~I~~lA~~KL~Le~  906 (941)
T KOG0389|consen  870 CHRVGQTKPVTVYRLITKSTIEEGILRLAKTKLALEA  906 (941)
T ss_pred             HHhhCCcceeEEEEEEecCcHHHHHHHHHHHhhhhhh
Confidence            999999865554  4554 445566666666665443

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=99.93  E-value=1.1e-24  Score=212.05  Aligned_cols=337  Identities=18%  Similarity=0.232  Sum_probs=225.5

Q ss_pred             CCCChhhhhccccccc----CCceEEEccCCCcchhHHH---HHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhc
Q 014486           67 EHPSEVQHECIPQAIL----GMDVICQAKSGMGKTAVFV---LSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFST  139 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~----~~~~ii~~~tGsGKT~~~~---~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  139 (423)
                      .++|.||-..+++++.    ++++|++.++|.|||...+   -.+.....-.+   ..||++|...+ ..|..++..|. 
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~~~~~g---pflvvvplst~-~~W~~ef~~w~-  443 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSLQIHG---PFLVVVPLSTI-TAWEREFETWT-  443 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHhhhccC---CeEEEeehhhh-HHHHHHHHHHh-
Confidence            5899999999998876    6889999999999997642   22222221111   46999998665 45677777775 


Q ss_pred             cCCCceEEEEEcCcchHHHHHH---HhcC-----CCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHH
Q 014486          140 YLPDIKVAVFYGGVNIKIHKDL---LKNE-----CPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRD  211 (423)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~---~~~~-----~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~  211 (423)
                         ++++.+++|...-+.....   +.+.     .++++++|++.++.  ....+.--.+.++++||||++.+.  -...
T Consensus       444 ---~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~Lk--Dk~~L~~i~w~~~~vDeahrLkN~--~~~l  516 (1373)
T KOG0384|consen  444 ---DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLK--DKAELSKIPWRYLLVDEAHRLKND--ESKL  516 (1373)
T ss_pred             ---hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhc--cHhhhccCCcceeeecHHhhcCch--HHHH
Confidence               6799999998765544332   2222     47999999999875  112233346778999999999762  2222


Q ss_pred             HHHHHHhCCCCceEEEEeccCCcc-HHHHHHHhc--cCCceeeec-------------------------------cccc
Q 014486          212 VQEIFKMTPHDKQVMMFSATLSKE-IRPVCKKFM--QDPMEIYVD-------------------------------DEAK  257 (423)
Q Consensus       212 ~~~~~~~~~~~~~~v~~SAT~~~~-~~~~~~~~~--~~~~~~~~~-------------------------------~~~~  257 (423)
                      +.. +..+.... .+++|+||-.. +..+. .++  ..|..+...                               ....
T Consensus       517 ~~~-l~~f~~~~-rllitgTPlQNsikEL~-sLl~Fl~P~kf~~~~~f~~~~~~~~e~~~~~L~~~L~P~~lRr~kkdve  593 (1373)
T KOG0384|consen  517 YES-LNQFKMNH-RLLITGTPLQNSLKELW-SLLHFLMPGKFDSWDEFLEEFDEETEEQVRKLQQILKPFLLRRLKKDVE  593 (1373)
T ss_pred             HHH-HHHhcccc-eeeecCCCccccHHHHH-HHhcccCCCCCCcHHHHHHhhcchhHHHHHHHHHHhhHHHHHHHHhhhc
Confidence            222 33333333 58888997432 22111 111  111111000                               0000


Q ss_pred             cccccceEEEEEe--------------------------------------------------ChHHH----------HH
Q 014486          258 LTLHGLVQHYIKL--------------------------------------------------SELEK----------NR  277 (423)
Q Consensus       258 ~~~~~~~~~~~~~--------------------------------------------------~~~~~----------~~  277 (423)
                      ...+.-...++.+                                                  ...++          ..
T Consensus       594 kslp~k~E~IlrVels~lQk~yYk~ILtkN~~~LtKG~~g~~~~lLNimmELkKccNHpyLi~gaee~~~~~~~~~~~d~  673 (1373)
T KOG0384|consen  594 KSLPPKEETILRVELSDLQKQYYKAILTKNFSALTKGAKGSTPSLLNIMMELKKCCNHPYLIKGAEEKILGDFRDKMRDE  673 (1373)
T ss_pred             cCCCCCcceEEEeehhHHHHHHHHHHHHhhHHHHhccCCCCCchHHHHHHHHHHhcCCccccCcHHHHHHHhhhhcchHH
Confidence            0000000011111                                                  00000          01


Q ss_pred             H-------------HHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCC---c
Q 014486          278 K-------------LNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN---K  339 (423)
Q Consensus       278 ~-------------l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~---~  339 (423)
                      .             |..||-.+  .+++||||.+-+.-.+.|.++|..++++.-.+.|.+....|+..++.|+...   .
T Consensus       674 ~L~~lI~sSGKlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddF  753 (1373)
T KOG0384|consen  674 ALQALIQSSGKLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDF  753 (1373)
T ss_pred             HHHHHHHhcCcEEeHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCce
Confidence            1             22222222  4579999999999999999999999999999999999999999999998644   4


Q ss_pred             cEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEE--EEec-CcccHHHHHHHHHHHhcchhhhh
Q 014486          340 RILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAI--TFVS-SASDSDILNQVSKFMFLLIGSFQ  416 (423)
Q Consensus       340 ~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~--~~~~-~~~~~~~~~~~~~~~~~~~~~~~  416 (423)
                      .+|+||.+++.|||+..++.||+||..|+|+.-.|+..||+|.||+..|-  -|++ ...+.++++...++|++.--=++
T Consensus       754 vFLLSTRAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~TvEeEilERAk~KmvLD~aVIQ  833 (1373)
T KOG0384|consen  754 VFLLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTVEEEILERAKLKMVLDHAVIQ  833 (1373)
T ss_pred             EEEEecccCcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCchHHHHHHHHHHHhhhHHHHHH
Confidence            68899999999999999999999999999999999999999999986554  4455 46678999999999987654444


Q ss_pred             hh
Q 014486          417 CL  418 (423)
Q Consensus       417 ~~  418 (423)
                      .+
T Consensus       834 ~m  835 (1373)
T KOG0384|consen  834 RM  835 (1373)
T ss_pred             hh
Confidence            43

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

Probab=99.93  E-value=2.3e-24  Score=199.23  Aligned_cols=308  Identities=16%  Similarity=0.180  Sum_probs=207.2

Q ss_pred             ChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEE
Q 014486           70 SEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVF  149 (423)
Q Consensus        70 ~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~  149 (423)
                      +.+-.+.+..+..++-++|.|+||||||.....-+.+.-....+  ++.+..|+|.-|..++.+...-..-.-+-.|++-
T Consensus        53 ~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~~~g--~I~~TQPRRVAavslA~RVAeE~~~~lG~~VGY~  130 (674)
T KOG0922|consen   53 YKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFASSG--KIACTQPRRVAAVSLAKRVAEEMGCQLGEEVGYT  130 (674)
T ss_pred             HHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhcccccCC--cEEeecCchHHHHHHHHHHHHHhCCCcCceeeeE
Confidence            34445666666677889999999999999866555554444333  5788889998888877777654322112233221


Q ss_pred             EcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHH-HHHHHHHhCCCCceEEEE
Q 014486          150 YGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRR-DVQEIFKMTPHDKQVMMF  228 (423)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~-~~~~~~~~~~~~~~~v~~  228 (423)
                      .-     .  ..-......|.+.|-++|++.+-.. -.++++++||+||||.-.-..+..- .++++.+ -++..++|.+
T Consensus       131 IR-----F--ed~ts~~TrikymTDG~LLRE~l~D-p~LskYsvIIlDEAHERsl~TDiLlGlLKki~~-~R~~LklIim  201 (674)
T KOG0922|consen  131 IR-----F--EDSTSKDTRIKYMTDGMLLREILKD-PLLSKYSVIILDEAHERSLHTDILLGLLKKILK-KRPDLKLIIM  201 (674)
T ss_pred             EE-----e--cccCCCceeEEEecchHHHHHHhcC-CccccccEEEEechhhhhhHHHHHHHHHHHHHh-cCCCceEEEE
Confidence            11     0  0111122589999999999855432 3468899999999996532222222 2233322 3446789999


Q ss_pred             eccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHH----HHHHHHHHHHhhcCCcEEEEEcChhhHHHH
Q 014486          229 SATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE----KNRKLNDLLDALDFNQVVIFVKSVSRAAEL  304 (423)
Q Consensus       229 SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l  304 (423)
                      |||+..+   .+..|+.....+.+....-.    +...+...+..+    ....+.++....+++-+|||.+.+++.+.+
T Consensus       202 SATlda~---kfS~yF~~a~i~~i~GR~fP----Vei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe~~  274 (674)
T KOG0922|consen  202 SATLDAE---KFSEYFNNAPILTIPGRTFP----VEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIEAA  274 (674)
T ss_pred             eeeecHH---HHHHHhcCCceEeecCCCCc----eeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHHHH
Confidence            9999843   44455555433443332111    111222222222    223445555556778999999999999999


Q ss_pred             HHHHHhC----C--C--CeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccC-----------
Q 014486          305 NKLLVEC----N--F--PSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDM-----------  365 (423)
Q Consensus       305 ~~~L~~~----~--~--~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~-----------  365 (423)
                      .+.|.+.    +  .  -+.++||.++..++.+++..-..|..+|+++|++++..+.++++..||+-+.           
T Consensus       275 ~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g  354 (674)
T KOG0922|consen  275 CELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTG  354 (674)
T ss_pred             HHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeeccccC
Confidence            9998775    1  1  2467999999999999988877899999999999999999999999996543           


Q ss_pred             -------CCCcchhhhcccccCCCCCceEEEEEecCcc
Q 014486          366 -------PDSADTYLHRVGRAGRFGTKGLAITFVSSAS  396 (423)
Q Consensus       366 -------~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  396 (423)
                             |-|..+..||.|||||.| +|.|+-+|+..+
T Consensus       355 ~~~L~v~~ISkasA~QRaGRAGRt~-pGkcyRLYte~~  391 (674)
T KOG0922|consen  355 LDSLIVVPISKASANQRAGRAGRTG-PGKCYRLYTESA  391 (674)
T ss_pred             ccceeEEechHHHHhhhcccCCCCC-CceEEEeeeHHH
Confidence                   337778899999999985 699999998543

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

Probab=99.93  E-value=3.6e-24  Score=206.27  Aligned_cols=313  Identities=20%  Similarity=0.241  Sum_probs=208.4

Q ss_pred             CCChhhhhcccccccC----CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           68 HPSEVQHECIPQAILG----MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~----~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      .+++-|+.++..+...    +..++.|.||||||.+|+-.+...+..++   .+|+++|-++|..|+.++++...    +
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~Gk---qvLvLVPEI~Ltpq~~~rf~~rF----g  270 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQGK---QVLVLVPEIALTPQLLARFKARF----G  270 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHcCC---EEEEEeccccchHHHHHHHHHHh----C
Confidence            5678899999888765    45999999999999999887777776554   89999999999999999998776    4


Q ss_pred             ceEEEEEcCcchHHHHHH---HhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc----CCcHHHHHHHH
Q 014486          144 IKVAVFYGGVNIKIHKDL---LKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES----LDMRRDVQEIF  216 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~---~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~----~~~~~~~~~~~  216 (423)
                      .++.+++++.+..+....   ..++..+|+|+|...++       ..+.++++||+||=|.-.-.    ..+...-..++
T Consensus       271 ~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF-------~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA~~  343 (730)
T COG1198         271 AKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEDGPRYHARDVAVL  343 (730)
T ss_pred             CChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhc-------CchhhccEEEEeccccccccCCcCCCcCHHHHHHH
Confidence            688899998876655444   45577899999998876       47889999999999965321    12223333334


Q ss_pred             HhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccc-cccccceEEEEEeChHHH----HHHHHHHH-Hhh-cCC
Q 014486          217 KMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAK-LTLHGLVQHYIKLSELEK----NRKLNDLL-DAL-DFN  289 (423)
Q Consensus       217 ~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~----~~~l~~ll-~~~-~~~  289 (423)
                      +....+.++|+-|||+.-+....+..  +....+.+..... ...+.+....+.......    ...+.+.+ +.+ .++
T Consensus       344 Ra~~~~~pvvLgSATPSLES~~~~~~--g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~ge  421 (730)
T COG1198         344 RAKKENAPVVLGSATPSLESYANAES--GKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERGE  421 (730)
T ss_pred             HHHHhCCCEEEecCCCCHHHHHhhhc--CceEEEEccccccccCCCcceEEeccccccccCccCCHHHHHHHHHHHhcCC
Confidence            44445778999999987554443322  1111122211111 111111111111111111    02222222 222 345


Q ss_pred             cEEEEEcChhh------------------------------------------------------------HHHHHHHHH
Q 014486          290 QVVIFVKSVSR------------------------------------------------------------AAELNKLLV  309 (423)
Q Consensus       290 ~~ivf~~~~~~------------------------------------------------------------~~~l~~~L~  309 (423)
                      ++|+|.|.+-.                                                            .+++.+.|+
T Consensus       422 Q~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~G~GterieeeL~  501 (730)
T COG1198         422 QVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEHLRAVGPGTERIEEELK  501 (730)
T ss_pred             eEEEEEccCCccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCeeEEecccHHHHHHHHH
Confidence            67777665332                                                            244445554


Q ss_pred             hC--CCCeEEEcCCCCHH--HHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCC------------Ccchhh
Q 014486          310 EC--NFPSICIHSGMSQE--ERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPD------------SADTYL  373 (423)
Q Consensus       310 ~~--~~~~~~~~~~~~~~--~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~------------s~~~~~  373 (423)
                      +.  +.++..+.++++..  .-...+..|.+|+.+|||.|++++.|.|+|+++.|...+...            ....+.
T Consensus       502 ~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~Er~fqll~  581 (730)
T COG1198         502 RLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLLM  581 (730)
T ss_pred             HHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchHHHHHHHHH
Confidence            43  45677777776543  346679999999999999999999999999999977655322            344578


Q ss_pred             hcccccCCCCCceEEEEEecCcc
Q 014486          374 HRVGRAGRFGTKGLAITFVSSAS  396 (423)
Q Consensus       374 Q~~GR~~R~g~~~~~~~~~~~~~  396 (423)
                      |..||+||.+.+|.+++-....+
T Consensus       582 QvaGRAgR~~~~G~VvIQT~~P~  604 (730)
T COG1198         582 QVAGRAGRAGKPGEVVIQTYNPD  604 (730)
T ss_pred             HHHhhhccCCCCCeEEEEeCCCC
Confidence            99999999999999987665433

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

Probab=99.93  E-value=1.9e-23  Score=200.16  Aligned_cols=316  Identities=16%  Similarity=0.142  Sum_probs=204.1

Q ss_pred             CCChhhhhccccccc---C-------CceEEEccCCCcchhHHHHHHhhccCCCCC----CeEEEEEecChHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAIL---G-------MDVICQAKSGMGKTAVFVLSTLQQTEPNPG----QVTALVLCHTRELAYQICHE  133 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~---~-------~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~----~~~~lil~P~~~L~~q~~~~  133 (423)
                      .++|||++++.-+..   |       ..+|++..+|+|||+..+..+...+...+.    -.++|||+|. .|+..|.++
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkkE  316 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKKE  316 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHhCcCccccccccEEEccH-HHHHHHHHH
Confidence            789999999976654   2       348999999999999765444444333332    1388999996 799999999


Q ss_pred             HHHHhccCCCceEEEEEcCcch--HHHHHHH----hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCC
Q 014486          134 FERFSTYLPDIKVAVFYGGVNI--KIHKDLL----KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLD  207 (423)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~----~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~  207 (423)
                      |.+|.... .+....+++..+.  -.....+    ..-..-|++.+++.+....+.  +....++++|+||.|+..+   
T Consensus       317 F~KWl~~~-~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~--il~~~~glLVcDEGHrlkN---  390 (776)
T KOG0390|consen  317 FGKWLGNH-RINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK--ILLIRPGLLVCDEGHRLKN---  390 (776)
T ss_pred             HHHhcccc-ccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH--HhcCCCCeEEECCCCCccc---
Confidence            99997643 6777777777653  1111111    111236888899988765543  4456789999999998865   


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeccCCc-c---------------------------------------------------
Q 014486          208 MRRDVQEIFKMTPHDKQVMMFSATLSK-E---------------------------------------------------  235 (423)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~v~~SAT~~~-~---------------------------------------------------  235 (423)
                      ....+...+..+. ..+.|++|+||-. +                                                   
T Consensus       391 ~~s~~~kaL~~l~-t~rRVLLSGTp~QNdl~EyFnlL~fvrP~~Lgs~~sf~k~~~~~i~~~~~~~~s~e~~~~~~rl~e  469 (776)
T KOG0390|consen  391 SDSLTLKALSSLK-TPRRVLLTGTPIQNDLKEYFNLLDFVRPGFLGSISSFKKKFEIPILRGRDADASEEDREREERLQE  469 (776)
T ss_pred             hhhHHHHHHHhcC-CCceEEeeCCcccccHHHHHHHHhhcChhhccchHHHHHHhhcccccccCCCcchhhhhhHHHHHH
Confidence            3333444444443 3457889999610 0                                                   


Q ss_pred             HHHHHHHhcc------------CCceeee--ccc------------c--c-----------------ccccc--------
Q 014486          236 IRPVCKKFMQ------------DPMEIYV--DDE------------A--K-----------------LTLHG--------  262 (423)
Q Consensus       236 ~~~~~~~~~~------------~~~~~~~--~~~------------~--~-----------------~~~~~--------  262 (423)
                      +..+...+..            ...++.+  ...            .  .                 ...+.        
T Consensus       470 L~~~t~~fi~rrt~~il~k~LP~k~e~vv~~n~t~~Q~~~~~~l~~~~~~~~~~~~~l~~~~~L~k~cnhP~L~~~~~~~  549 (776)
T KOG0390|consen  470 LRELTNKFILRRTGDILLKYLPGKYEYVVFCNPTPIQKELYKKLLDSMKMRTLKGYALELITKLKKLCNHPSLLLLCEKT  549 (776)
T ss_pred             HHHHHHhheeecccchhhhhCCCceeEEEEeCCcHHHHHHHHHHHHHHHhhhhhcchhhHHHHHHHHhcCHHhhcccccc
Confidence            1111111110            0000000  000            0  0                 00000        


Q ss_pred             -----------------ceEEEEEeChHHHHHHHHHHHHhh---cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCC
Q 014486          263 -----------------LVQHYIKLSELEKNRKLNDLLDAL---DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGM  322 (423)
Q Consensus       263 -----------------~~~~~~~~~~~~~~~~l~~ll~~~---~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~  322 (423)
                                       ............+...+..++...   ...++++..+.....+.+.+.++.+|+.++.++|.+
T Consensus       550 ~~e~~~~~~~~~~~~~~~~~~~~~~~ks~kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~  629 (776)
T KOG0390|consen  550 EKEKAFKNPALLLDPGKLKLDAGDGSKSGKLLVLVFLLEVIREKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKT  629 (776)
T ss_pred             cccccccChHhhhcccccccccccchhhhHHHHHHHHHHHHhhhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcCCC
Confidence                             000000111123344444444222   223455555666667777777777899999999999


Q ss_pred             CHHHHHHHHHhhhcCCc--c-EEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEE
Q 014486          323 SQEERLTRYKGFKEGNK--R-ILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITF  391 (423)
Q Consensus       323 ~~~~r~~~~~~f~~~~~--~-ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~  391 (423)
                      +..+|+.+++.|++...  . +|.+|.+.+.||++-+++.||.+|+.|+|+.-.|+++|+.|.||+..|+++
T Consensus       630 ~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iY  701 (776)
T KOG0390|consen  630 SIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIY  701 (776)
T ss_pred             chHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEE
Confidence            99999999999997543  3 555789999999999999999999999999999999999999999887764

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

Probab=99.92  E-value=7.7e-23  Score=201.46  Aligned_cols=299  Identities=16%  Similarity=0.175  Sum_probs=180.6

Q ss_pred             CCChhhhhccccccc----------CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAIL----------GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----------~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      -++++|..++..+..          .+.++++++||||||++++..+...+ .....+++|+|+|+.+|..|+.+.+..+
T Consensus       238 ~~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~-~~~~~~~vl~lvdR~~L~~Q~~~~f~~~  316 (667)
T TIGR00348       238 YQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKAL-ELLKNPKVFFVVDRRELDYQLMKEFQSL  316 (667)
T ss_pred             ehHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHH-hhcCCCeEEEEECcHHHHHHHHHHHHhh
Confidence            478899988877643          24699999999999998765544433 3334459999999999999999999887


Q ss_pred             hccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC--CCCCCCc-cEEEEcCcchhhccCCcHHHHHH
Q 014486          138 STYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK--DLSLKNV-RHFILDECDKMLESLDMRRDVQE  214 (423)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~--~~~~~~~-~~vVvDE~h~~~~~~~~~~~~~~  214 (423)
                      ....  .     .+..+.......+......|+|+|.++|...+...  ....... .+||+||||+.-.     ..+..
T Consensus       317 ~~~~--~-----~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~-----~~~~~  384 (667)
T TIGR00348       317 QKDC--A-----ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQY-----GELAK  384 (667)
T ss_pred             CCCC--C-----cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccc-----hHHHH
Confidence            5321  1     11122233334444444589999999998643321  1111112 2799999997533     22333


Q ss_pred             HH-HhCCCCceEEEEeccCCccHHH-HHHHhc---cCCceeeeccccccccccceEE-EEE------e------------
Q 014486          215 IF-KMTPHDKQVMMFSATLSKEIRP-VCKKFM---QDPMEIYVDDEAKLTLHGLVQH-YIK------L------------  270 (423)
Q Consensus       215 ~~-~~~~~~~~~v~~SAT~~~~~~~-~~~~~~---~~~~~~~~~~~~~~~~~~~~~~-~~~------~------------  270 (423)
                      .+ ..++ +...+++||||-..... ....+.   +.+...+. -............ +..      .            
T Consensus       385 ~l~~~~p-~a~~lGfTaTP~~~~d~~t~~~f~~~fg~~i~~Y~-~~~AI~dG~~~~i~Y~~~~~~~~~~~~~l~~~~~~~  462 (667)
T TIGR00348       385 NLKKALK-NASFFGFTGTPIFKKDRDTSLTFAYVFGRYLHRYF-ITDAIRDGLTVKIDYEDRLPEDHLDRKKLDAFFDEI  462 (667)
T ss_pred             HHHhhCC-CCcEEEEeCCCcccccccccccccCCCCCeEEEee-HHHHhhcCCeeeEEEEecchhhccChHHHHHHHHHH
Confidence            33 3444 56799999999542111 001111   11111100 0000000000000 000      0            


Q ss_pred             --------ChH-------------------HHHHHH-HHHHHhh------cCCcEEEEEcChhhHHHHHHHHHhC-----
Q 014486          271 --------SEL-------------------EKNRKL-NDLLDAL------DFNQVVIFVKSVSRAAELNKLLVEC-----  311 (423)
Q Consensus       271 --------~~~-------------------~~~~~l-~~ll~~~------~~~~~ivf~~~~~~~~~l~~~L~~~-----  311 (423)
                              .+.                   .....+ ..+++..      .+.+.+|||.++.+|..+++.|.+.     
T Consensus       463 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ia~~i~~h~~~~~~~~~~kamvv~~sr~~a~~~~~~l~~~~~~~~  542 (667)
T TIGR00348       463 FELLPERIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHYAKFKELFKFKAMVVAISRYACVEEKNALDEELNEKF  542 (667)
T ss_pred             HHhhhccccHHHHHHHHHHHHHHHhhhcChHHHHHHHHHHHHHHHHhhhcccCceeEEEecHHHHHHHHHHHHhhccccc
Confidence                    000                   000111 1111111      2479999999999999999988664     


Q ss_pred             CCCeEEEcCCCCHH---------------------HHHHHHHhhhc-CCccEEEEcCccccCCCCCCCCEEEEccCCCCc
Q 014486          312 NFPSICIHSGMSQE---------------------ERLTRYKGFKE-GNKRILVATDLVGRGIDIERVNIVINYDMPDSA  369 (423)
Q Consensus       312 ~~~~~~~~~~~~~~---------------------~r~~~~~~f~~-~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~  369 (423)
                      +...+.+++..+..                     ....++++|++ +..+|||+++++.+|+|.|.+++++...+..+.
T Consensus       543 ~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~ilIVvdmllTGFDaP~l~tLyldKplk~h  622 (667)
T TIGR00348       543 EASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPKLLIVVDMLLTGFDAPILNTLYLDKPLKYH  622 (667)
T ss_pred             CCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCceEEEEEcccccccCCCccceEEEecccccc
Confidence            23445565543322                     22467888876 678999999999999999999999998887764


Q ss_pred             chhhhcccccCCC
Q 014486          370 DTYLHRVGRAGRF  382 (423)
Q Consensus       370 ~~~~Q~~GR~~R~  382 (423)
                       .++|++||+.|.
T Consensus       623 -~LlQai~R~nR~  634 (667)
T TIGR00348       623 -GLLQAIARTNRI  634 (667)
T ss_pred             -HHHHHHHHhccc
Confidence             589999999993

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

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

Probab=99.92  E-value=5.8e-24  Score=201.17  Aligned_cols=310  Identities=18%  Similarity=0.220  Sum_probs=198.2

Q ss_pred             CCChhhhhccccccc----CC-ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           68 HPSEVQHECIPQAIL----GM-DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~~-~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      .+|+||..||..+..    |+ .+++.+.||+|||.+++. ++.++...+...++|+|+.+++|+.|.+..+..+.....
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAia-ii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~~  243 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIA-IIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFGT  243 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHHH-HHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCCcc
Confidence            789999999977654    43 399999999999998754 555554444444999999999999999988887764421


Q ss_pred             CceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC-----CCCCCCccEEEEcCcchhhccCCcHHHHHHHHH
Q 014486          143 DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK-----DLSLKNVRHFILDECDKMLESLDMRRDVQEIFK  217 (423)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~-----~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~  217 (423)
                        ....+.+. ...        +.++|.++|++++.......     .+....|++||+||||+     +.......++.
T Consensus       244 --~~n~i~~~-~~~--------~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHR-----gi~~~~~~I~d  307 (875)
T COG4096         244 --KMNKIEDK-KGD--------TSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHR-----GIYSEWSSILD  307 (875)
T ss_pred             --ceeeeecc-cCC--------cceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhh-----hHHhhhHHHHH
Confidence              22222221 111        12599999999999877654     23456699999999995     44455556666


Q ss_pred             hCCCCceEEEEeccCCccHHHHHHHhc-cCCceee--------------------ec--ccc----------ccccccc-
Q 014486          218 MTPHDKQVMMFSATLSKEIRPVCKKFM-QDPMEIY--------------------VD--DEA----------KLTLHGL-  263 (423)
Q Consensus       218 ~~~~~~~~v~~SAT~~~~~~~~~~~~~-~~~~~~~--------------------~~--~~~----------~~~~~~~-  263 (423)
                      .+..-.  +++||||........-.++ +.|...+                    +.  ..+          ......+ 
T Consensus       308 YFdA~~--~gLTATP~~~~d~~T~~~F~g~Pt~~YsleeAV~DGfLvpy~vi~i~~~~~~~G~~~~~~serek~~g~~i~  385 (875)
T COG4096         308 YFDAAT--QGLTATPKETIDRSTYGFFNGEPTYAYSLEEAVEDGFLVPYKVIRIDTDFDLDGWKPDAGSEREKLQGEAID  385 (875)
T ss_pred             HHHHHH--HhhccCcccccccccccccCCCcceeecHHHHhhccccCCCCceEEeeeccccCcCcCccchhhhhhccccC
Confidence            654333  4559998764332222222 2222221                    00  000          0000000 


Q ss_pred             -eEEEEEeCh-----------HHHHHHHHHHHHh--hc--CCcEEEEEcChhhHHHHHHHHHhCC-----CCeEEEcCCC
Q 014486          264 -VQHYIKLSE-----------LEKNRKLNDLLDA--LD--FNQVVIFVKSVSRAAELNKLLVECN-----FPSICIHSGM  322 (423)
Q Consensus       264 -~~~~~~~~~-----------~~~~~~l~~ll~~--~~--~~~~ivf~~~~~~~~~l~~~L~~~~-----~~~~~~~~~~  322 (423)
                       ........+           ..-...+.+.++.  ..  .+|+||||.+..||+.+...|....     --+..+.++.
T Consensus       386 ~dd~~~~~~d~dr~~v~~~~~~~V~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~  465 (875)
T COG4096         386 EDDQNFEARDFDRTLVIPFRTETVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDA  465 (875)
T ss_pred             cccccccccccchhccccchHHHHHHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccc
Confidence             000000000           0011233444444  11  4699999999999999999998752     2244566664


Q ss_pred             CHHHHHHHHHhhhcC--CccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCC-------CCceEEEEEec
Q 014486          323 SQEERLTRYKGFKEG--NKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRF-------GTKGLAITFVS  393 (423)
Q Consensus       323 ~~~~r~~~~~~f~~~--~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~-------g~~~~~~~~~~  393 (423)
                      ...  +..++.|...  -.+|.|+.+++.+|+|+|.|.+++++....|...|.|++||+-|.       +++..-+.+++
T Consensus       466 ~~~--q~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTRl~~~~~~~~~dK~~F~ifD  543 (875)
T COG4096         466 EQA--QALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRLCPDLGGPEQDKEFFTIFD  543 (875)
T ss_pred             hhh--HHHHHHHHhcCCCCceEEehhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCccccCccccCccccceeEEEEE
Confidence            443  3447777652  246888999999999999999999999999999999999999993       23345556665


Q ss_pred             CcccH
Q 014486          394 SASDS  398 (423)
Q Consensus       394 ~~~~~  398 (423)
                      .....
T Consensus       544 f~~~~  548 (875)
T COG4096         544 FVDNT  548 (875)
T ss_pred             hhhhh
Confidence            44443

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

Probab=99.92  E-value=5.8e-25  Score=195.57  Aligned_cols=301  Identities=19%  Similarity=0.190  Sum_probs=200.2

Q ss_pred             CCCCChhhhhcccccccC---CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           66 FEHPSEVQHECIPQAILG---MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        66 ~~~~~~~Q~~~i~~~~~~---~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      -..+||||.+++..+.-+   ++.+|..|+|+|||++.+-++.....      .||++|.+...++||..++..|.... 
T Consensus       300 st~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~tikK------~clvLcts~VSVeQWkqQfk~wsti~-  372 (776)
T KOG1123|consen  300 STQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACTIKK------SCLVLCTSAVSVEQWKQQFKQWSTIQ-  372 (776)
T ss_pred             ccccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeeeecc------cEEEEecCccCHHHHHHHHHhhcccC-
Confidence            348899999999998864   56999999999999876543333322      89999999999999999999987664 


Q ss_pred             CceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC--------CCCCCccEEEEcCcchhhccCCcHHHHHH
Q 014486          143 DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD--------LSLKNVRHFILDECDKMLESLDMRRDVQE  214 (423)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~--------~~~~~~~~vVvDE~h~~~~~~~~~~~~~~  214 (423)
                      +-.+..++.+...     ....+ ..|+|+|+.++..--++..        +.-..++++++||+|.+-. ..|++.+.-
T Consensus       373 d~~i~rFTsd~Ke-----~~~~~-~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA-~MFRRVlsi  445 (776)
T KOG1123|consen  373 DDQICRFTSDAKE-----RFPSG-AGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPA-KMFRRVLSI  445 (776)
T ss_pred             ccceEEeeccccc-----cCCCC-CcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchH-HHHHHHHHH
Confidence            4467777665321     12223 5899999988754221110        1235688999999998866 556666655


Q ss_pred             HHHhCCCCceEEEEeccCCccHHHHHHH-hccCCcee----------------eecc-------------ccccccccce
Q 014486          215 IFKMTPHDKQVMMFSATLSKEIRPVCKK-FMQDPMEI----------------YVDD-------------EAKLTLHGLV  264 (423)
Q Consensus       215 ~~~~~~~~~~~v~~SAT~~~~~~~~~~~-~~~~~~~~----------------~~~~-------------~~~~~~~~~~  264 (423)
                      +...+     .+++|||+-++-..+... |+..|..+                ....             ........  
T Consensus       446 v~aHc-----KLGLTATLvREDdKI~DLNFLIGPKlYEAnWmdL~~kGhIA~VqCaEVWCpMt~eFy~eYL~~~t~kr--  518 (776)
T KOG1123|consen  446 VQAHC-----KLGLTATLVREDDKITDLNFLIGPKLYEANWMDLQKKGHIAKVQCAEVWCPMTPEFYREYLRENTRKR--  518 (776)
T ss_pred             HHHHh-----hccceeEEeeccccccccceeecchhhhccHHHHHhCCceeEEeeeeeecCCCHHHHHHHHhhhhhhh--
Confidence            55544     489999985543221111 11111100                0000             00000111  


Q ss_pred             EEEEEeChHHHH---HHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhc-CCcc
Q 014486          265 QHYIKLSELEKN---RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKE-GNKR  340 (423)
Q Consensus       265 ~~~~~~~~~~~~---~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~-~~~~  340 (423)
                       ....+....|.   ..|.++.+. ++.|+|||..+.-....++-.|.+     -.++|.+++.+|..+++.|+- ..++
T Consensus       519 -~lLyvMNP~KFraCqfLI~~HE~-RgDKiIVFsDnvfALk~YAikl~K-----pfIYG~Tsq~ERm~ILqnFq~n~~vN  591 (776)
T KOG1123|consen  519 -MLLYVMNPNKFRACQFLIKFHER-RGDKIIVFSDNVFALKEYAIKLGK-----PFIYGPTSQNERMKILQNFQTNPKVN  591 (776)
T ss_pred             -heeeecCcchhHHHHHHHHHHHh-cCCeEEEEeccHHHHHHHHHHcCC-----ceEECCCchhHHHHHHHhcccCCccc
Confidence             11222233333   344444444 678999999998777776665543     357899999999999999984 5678


Q ss_pred             EEEEcCccccCCCCCCCCEEEEccCC-CCcchhhhcccccCCCC---CceEEEEEecC
Q 014486          341 ILVATDLVGRGIDIERVNIVINYDMP-DSADTYLHRVGRAGRFG---TKGLAITFVSS  394 (423)
Q Consensus       341 ili~T~~~~~Gld~~~~~~vi~~~~~-~s~~~~~Q~~GR~~R~g---~~~~~~~~~~~  394 (423)
                      .++.+.++...+|+|.++++|+...- .|-.+-.||+||.-|+.   ..+....||+-
T Consensus       592 TIFlSKVgDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAKk~~de~fnafFYSL  649 (776)
T KOG1123|consen  592 TIFLSKVGDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKRNDEEFNAFFYSL  649 (776)
T ss_pred             eEEEeeccCccccCCcccEEEEEcccccchHHHHHHHHHHHHHhhcCccccceeeeee
Confidence            99999999999999999999987654 35667889999998853   23444455543

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.92  E-value=1.7e-23  Score=203.81  Aligned_cols=128  Identities=22%  Similarity=0.301  Sum_probs=112.0

Q ss_pred             EEeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEc
Q 014486          268 IKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVAT  345 (423)
Q Consensus       268 ~~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T  345 (423)
                      +......|...+.+.+...  .+.++||||++++.++.+...|...|+++..+|+  .+.+|+..+..|..+...|+|||
T Consensus       576 vy~t~~eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIAT  653 (1025)
T PRK12900        576 VYKTRREKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIAT  653 (1025)
T ss_pred             EecCHHHHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEec
Confidence            3345566778888887554  6789999999999999999999999999999997  57899999999999999999999


Q ss_pred             CccccCCCCC---CCC-----EEEEccCCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          346 DLVGRGIDIE---RVN-----IVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       346 ~~~~~Gld~~---~~~-----~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      ++++||+|++   .+.     +||.+..|.|...+.|+.||+||.|.+|.+..|++..++
T Consensus       654 NMAGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~  713 (1025)
T PRK12900        654 NMAGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDE  713 (1025)
T ss_pred             cCcCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHH
Confidence            9999999998   443     458889999999999999999999999999999986443

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=99.91  E-value=5.5e-23  Score=182.78  Aligned_cols=327  Identities=14%  Similarity=0.188  Sum_probs=218.6

Q ss_pred             CCChhhhhccccccc-CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceE
Q 014486           68 HPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKV  146 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~-~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  146 (423)
                      .+-|+|++.+...+. |..++++.++|.|||++++. +........   ..||+||. .+-..|++.+.+|.....  .+
T Consensus       198 ~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAla-IA~yyraEw---plliVcPA-svrftWa~al~r~lps~~--pi  270 (689)
T KOG1000|consen  198 RLLPFQREGVIFALERGGRILLADEMGLGKTIQALA-IARYYRAEW---PLLIVCPA-SVRFTWAKALNRFLPSIH--PI  270 (689)
T ss_pred             hhCchhhhhHHHHHhcCCeEEEecccccchHHHHHH-HHHHHhhcC---cEEEEecH-HHhHHHHHHHHHhccccc--ce
Confidence            567999999987776 67799999999999998753 444444333   56999997 577889999999886642  24


Q ss_pred             EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEE
Q 014486          147 AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVM  226 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v  226 (423)
                      .++.++.+...   .+... ..|.|.+++.+..+-..  +.-..+++||+||+|.+.+  .-......+...+..-..+|
T Consensus       271 ~vv~~~~D~~~---~~~t~-~~v~ivSye~ls~l~~~--l~~~~~~vvI~DEsH~Lk~--sktkr~Ka~~dllk~akhvI  342 (689)
T KOG1000|consen  271 FVVDKSSDPLP---DVCTS-NTVAIVSYEQLSLLHDI--LKKEKYRVVIFDESHMLKD--SKTKRTKAATDLLKVAKHVI  342 (689)
T ss_pred             EEEecccCCcc---ccccC-CeEEEEEHHHHHHHHHH--HhcccceEEEEechhhhhc--cchhhhhhhhhHHHHhhheE
Confidence            44444432211   11112 37899999988664432  2224578999999999976  44444566666666667799


Q ss_pred             EEeccCC----cc---------------HHHHHHHhccC-Cceeeeccc--------------------------ccccc
Q 014486          227 MFSATLS----KE---------------IRPVCKKFMQD-PMEIYVDDE--------------------------AKLTL  260 (423)
Q Consensus       227 ~~SAT~~----~~---------------~~~~~~~~~~~-~~~~~~~~~--------------------------~~~~~  260 (423)
                      ++|+|+.    .+               ...+...++.. ...+..+..                          ...+ 
T Consensus       343 LLSGTPavSRP~elytqi~avd~tlfp~f~efa~rYCd~k~vr~~~Dykg~tnl~EL~~lL~k~lMIRRlK~dvL~qLP-  421 (689)
T KOG1000|consen  343 LLSGTPAVSRPSELYTQIRAVDHTLFPNFHEFAIRYCDGKQVRFCFDYKGCTNLEELAALLFKRLMIRRLKADVLKQLP-  421 (689)
T ss_pred             EecCCcccCCchhhhhhhhhhcccccccHHHHHHHhcCccccceeeecCCCCCHHHHHHHHHHHHHHHHHHHHHHhhCC-
Confidence            9999973    21               12222222221 111110000                          0001 


Q ss_pred             ccceEEEEEeCh---------------------H----------------HHHHHHHHHHHh------hcCCcEEEEEcC
Q 014486          261 HGLVQHYIKLSE---------------------L----------------EKNRKLNDLLDA------LDFNQVVIFVKS  297 (423)
Q Consensus       261 ~~~~~~~~~~~~---------------------~----------------~~~~~l~~ll~~------~~~~~~ivf~~~  297 (423)
                      ++...-.+....                     .                .|...+.+.+..      .++.|.+||+..
T Consensus       422 pKrr~Vv~~~~gr~da~~~~lv~~a~~~t~~~~~e~~~~~l~l~y~~tgiaK~~av~eyi~~~~~l~d~~~~KflVFaHH  501 (689)
T KOG1000|consen  422 PKRREVVYVSGGRIDARMDDLVKAAADYTKVNSMERKHESLLLFYSLTGIAKAAAVCEYILENYFLPDAPPRKFLVFAHH  501 (689)
T ss_pred             ccceEEEEEcCCccchHHHHHHHHhhhcchhhhhhhhhHHHHHHHHHhcccccHHHHHHHHhCcccccCCCceEEEEehh
Confidence            110111111100                     0                011122222222      145689999999


Q ss_pred             hhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcC-CccEE-EEcCccccCCCCCCCCEEEEccCCCCcchhhhc
Q 014486          298 VSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEG-NKRIL-VATDLVGRGIDIERVNIVINYDMPDSADTYLHR  375 (423)
Q Consensus       298 ~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~il-i~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~  375 (423)
                      ..-.+.+...+.++++..+.+.|.++...|....+.|..+ +..|- ++..+++.|+++...+.|++..++|+|.-++|+
T Consensus       502 ~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VVFaEL~wnPgvLlQA  581 (689)
T KOG1000|consen  502 QIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVVFAELHWNPGVLLQA  581 (689)
T ss_pred             HHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEEEEEecCCCceEEec
Confidence            9999999999999999999999999999999999999864 44544 466889999999999999999999999999999


Q ss_pred             ccccCCCCCceEEEE--EecC-cccHHHHHHHHHHHhc
Q 014486          376 VGRAGRFGTKGLAIT--FVSS-ASDSDILNQVSKFMFL  410 (423)
Q Consensus       376 ~GR~~R~g~~~~~~~--~~~~-~~~~~~~~~~~~~~~~  410 (423)
                      -.|++|.||+..|.+  |+.. ..++.++..+.+++..
T Consensus       582 EDRaHRiGQkssV~v~ylvAKgT~Ddy~Wp~l~~KL~v  619 (689)
T KOG1000|consen  582 EDRAHRIGQKSSVFVQYLVAKGTADDYMWPMLQQKLDV  619 (689)
T ss_pred             hhhhhhccccceeeEEEEEecCchHHHHHHHHHHHHHH
Confidence            999999999865544  4443 4456778888888764

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.91  E-value=2.8e-23  Score=194.16  Aligned_cols=310  Identities=20%  Similarity=0.193  Sum_probs=200.6

Q ss_pred             hhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC---CCeEEEEEecChHHHHHHHHHHHHHhccCC-CceEEEE
Q 014486           74 HECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP---GQVTALVLCHTRELAYQICHEFERFSTYLP-DIKVAVF  149 (423)
Q Consensus        74 ~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~---~~~~~lil~P~~~L~~q~~~~~~~~~~~~~-~~~~~~~  149 (423)
                      ++++.++..+.-+||||.||||||.+...-+.+.-....   .+..+=|.-|+|.-|..++++...-...++ .+....-
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            344455555666999999999999986655555432221   222667778999888877776654433321 1111111


Q ss_pred             EcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccC----CcHHHHHHHHHhCCC----
Q 014486          150 YGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESL----DMRRDVQEIFKMTPH----  221 (423)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~----~~~~~~~~~~~~~~~----  221 (423)
                      +.++         .+....|.++|-+.|++-+.+ .+.+..++.||+||||.-.-..    +...++..+.....+    
T Consensus       342 fd~t---------i~e~T~IkFMTDGVLLrEi~~-DflL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~ke~~~  411 (1172)
T KOG0926|consen  342 FDGT---------IGEDTSIKFMTDGVLLREIEN-DFLLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYYKEQCQ  411 (1172)
T ss_pred             eccc---------cCCCceeEEecchHHHHHHHH-hHhhhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHhhhhcc
Confidence            2221         122358999999999987764 5667889999999999654221    223333333333333    


Q ss_pred             --CceEEEEeccCCccHHHHHHHhcc-CCceeeeccccccccccceEEEEEeCh----HHHHHHHHHHHHhhcCCcEEEE
Q 014486          222 --DKQVMMFSATLSKEIRPVCKKFMQ-DPMEIYVDDEAKLTLHGLVQHYIKLSE----LEKNRKLNDLLDALDFNQVVIF  294 (423)
Q Consensus       222 --~~~~v~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~l~~ll~~~~~~~~ivf  294 (423)
                        ..++|.||||+.-.-..--+.++. .|..+.++.   ..++- ..++-.-..    .+.......+.+.++.+.+|||
T Consensus       412 ~kpLKLIIMSATLRVsDFtenk~LFpi~pPlikVdA---RQfPV-sIHF~krT~~DYi~eAfrKtc~IH~kLP~G~ILVF  487 (1172)
T KOG0926|consen  412 IKPLKLIIMSATLRVSDFTENKRLFPIPPPLIKVDA---RQFPV-SIHFNKRTPDDYIAEAFRKTCKIHKKLPPGGILVF  487 (1172)
T ss_pred             cCceeEEEEeeeEEecccccCceecCCCCceeeeec---ccCce-EEEeccCCCchHHHHHHHHHHHHhhcCCCCcEEEE
Confidence              567999999986332211112222 222222221   11111 112211111    1233456677788899999999


Q ss_pred             EcChhhHHHHHHHHHhC---------------------------------------------------------------
Q 014486          295 VKSVSRAAELNKLLVEC---------------------------------------------------------------  311 (423)
Q Consensus       295 ~~~~~~~~~l~~~L~~~---------------------------------------------------------------  311 (423)
                      +..+.+++.+.+.|+++                                                               
T Consensus       488 vTGQqEV~qL~~kLRK~~p~~f~~~k~~k~~k~~~e~k~~~s~~~~~~k~~dfe~Ed~~~~~ed~d~~~~~~~~~~~raa  567 (1172)
T KOG0926|consen  488 VTGQQEVDQLCEKLRKRFPESFGGVKMKKNVKAFKELKENPSDIGDSNKTDDFEEEDMYESDEDIDQELVDSGFASLRAA  567 (1172)
T ss_pred             EeChHHHHHHHHHHHhhCccccccchhhhhhhhccccccchhhhccCcccccchhcccccchhhhhhhhhcccchhhhhh
Confidence            99999999999999771                                                               


Q ss_pred             ------------------------------------CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCC
Q 014486          312 ------------------------------------NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIE  355 (423)
Q Consensus       312 ------------------------------------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~  355 (423)
                                                          ..-++++++-++...+.++++.--.|..-++|+|+++++.+.+|
T Consensus       568 ~~~~~De~~~~nge~e~d~~e~~~E~~~~~~~~~~~pLyvLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAETSLTIP  647 (1172)
T KOG0926|consen  568 FNALADENGSVNGEPEKDESEEGQEAEQGKGKFSPGPLYVLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAETSLTIP  647 (1172)
T ss_pred             hhccccccccccCCcccchhhhchhhhhccCCCCCCceEEeehhhhcCHHHhhhhccCCCCCceEEEEeccchhcccccC
Confidence                                                12255677777788888888877788888999999999999999


Q ss_pred             CCCEEEEccCCC------------------CcchhhhcccccCCCCCceEEEEEecCcccH
Q 014486          356 RVNIVINYDMPD------------------SADTYLHRVGRAGRFGTKGLAITFVSSASDS  398 (423)
Q Consensus       356 ~~~~vi~~~~~~------------------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  398 (423)
                      ++++||..+..+                  |-...-||+|||||.| +|.|+-+|++.-..
T Consensus       648 gIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtg-pGHcYRLYSSAVf~  707 (1172)
T KOG0926|consen  648 GIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTG-PGHCYRLYSSAVFS  707 (1172)
T ss_pred             CeeEEEeccchhhhccccccCceeEEEEeeeccccchhccccCCCC-CCceeehhhhHHhh
Confidence            999999766433                  4445579999999986 69999999864443

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

Probab=99.91  E-value=3.7e-23  Score=201.06  Aligned_cols=328  Identities=16%  Similarity=0.217  Sum_probs=214.5

Q ss_pred             CCChhhhhccccccc----CCceEEEccCCCcchhHHHHHHhh-ccCCC-----CCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAIL----GMDVICQAKSGMGKTAVFVLSTLQ-QTEPN-----PGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~~~~ii~~~tGsGKT~~~~~~~~~-~~~~~-----~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .+|.||++.+.++..    +-++|+|..+|.|||++.+-.+.. +....     -.....||+||+ .|+--|..++.+|
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            568999999998765    457999999999999986433332 22221     022237999996 7999999999888


Q ss_pred             hccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHH
Q 014486          138 STYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFK  217 (423)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~  217 (423)
                      ...   +++..+.|+...+...+.-.+. .+|+|++++.+.+-+..  +.-.++.++|+||-|.+.+   ....+.+..+
T Consensus      1054 ~pf---L~v~~yvg~p~~r~~lR~q~~~-~~iiVtSYDv~RnD~d~--l~~~~wNYcVLDEGHVikN---~ktkl~kavk 1124 (1549)
T KOG0392|consen 1054 FPF---LKVLQYVGPPAERRELRDQYKN-ANIIVTSYDVVRNDVDY--LIKIDWNYCVLDEGHVIKN---SKTKLTKAVK 1124 (1549)
T ss_pred             cch---hhhhhhcCChHHHHHHHhhccc-cceEEeeHHHHHHHHHH--HHhcccceEEecCcceecc---hHHHHHHHHH
Confidence            754   6888888876555444333333 49999999988642211  1124577999999999854   4566666666


Q ss_pred             hCCCCceEEEEeccCCcc-H------------------------------------------------------------
Q 014486          218 MTPHDKQVMMFSATLSKE-I------------------------------------------------------------  236 (423)
Q Consensus       218 ~~~~~~~~v~~SAT~~~~-~------------------------------------------------------------  236 (423)
                      .+.... .+.+|+||-.. +                                                            
T Consensus      1125 qL~a~h-RLILSGTPIQNnvleLWSLFdFLMPGfLGtEKqFqsrf~kpI~asRd~K~Sske~EaG~lAleaLHKqVLPF~ 1203 (1549)
T KOG0392|consen 1125 QLRANH-RLILSGTPIQNNVLELWSLFDFLMPGFLGTEKQFQSRFGKPILASRDPKSSSKEQEAGVLALEALHKQVLPFL 1203 (1549)
T ss_pred             HHhhcc-eEEeeCCCcccCHHHHHHHHHHhcccccCcHHHHHHHhcchhhhhcCcccchhHHHhhHHHHHHHHHHHHHHH
Confidence            666555 56788995100 0                                                            


Q ss_pred             ----------------------------HHHHHHhccCCc-eeee-ccccccccc--------------cceEE--EE--
Q 014486          237 ----------------------------RPVCKKFMQDPM-EIYV-DDEAKLTLH--------------GLVQH--YI--  268 (423)
Q Consensus       237 ----------------------------~~~~~~~~~~~~-~~~~-~~~~~~~~~--------------~~~~~--~~--  268 (423)
                                                  ..+.+.+..... .+.. .+.......              +...+  .+  
T Consensus      1204 LRRlKedVL~DLPpKIIQDyyCeLs~lQ~kLY~df~~~~k~~~~~~~d~~~~S~gt~~~HvFqaLqYlrKLcnHpaLvlt 1283 (1549)
T KOG0392|consen 1204 LRRLKEDVLKDLPPKIIQDYYCELSPLQKKLYRDFVKKAKQCVSSQIDGGEESLGTDKTHVFQALQYLRKLCNHPALVLT 1283 (1549)
T ss_pred             HHHHHHHHHhhCChhhhhheeeccCHHHHHHHHHHHHHhccccccccccchhccCcchHHHHHHHHHHHHhcCCcceeeC
Confidence                                        000000000000 0000 000000000              00000  00  


Q ss_pred             ---------------------EeChHHHHHHHHHHHHhh----------------cCCcEEEEEcChhhHHHHHHHHHhC
Q 014486          269 ---------------------KLSELEKNRKLNDLLDAL----------------DFNQVVIFVKSVSRAAELNKLLVEC  311 (423)
Q Consensus       269 ---------------------~~~~~~~~~~l~~ll~~~----------------~~~~~ivf~~~~~~~~~l~~~L~~~  311 (423)
                                           ......|...+.+++...                .+++++|||+-+..++.+.+.|.+.
T Consensus      1284 ~~hp~la~i~~~l~~~~~~LHdi~hspKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~ 1363 (1549)
T KOG0392|consen 1284 PVHPDLAAIVSHLAHFNSSLHDIQHSPKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKK 1363 (1549)
T ss_pred             CCcchHHHHHHHHHHhhhhHHHhhhchhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhh
Confidence                                 011223455666666443                2358999999999999998888665


Q ss_pred             CC---CeEEEcCCCCHHHHHHHHHhhhcC-CccEEE-EcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCce
Q 014486          312 NF---PSICIHSGMSQEERLTRYKGFKEG-NKRILV-ATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKG  386 (423)
Q Consensus       312 ~~---~~~~~~~~~~~~~r~~~~~~f~~~-~~~ili-~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~  386 (423)
                      -+   ....+.|..++.+|.++.++|+++ .+++|+ +|.+++.|+|+.+++.||+++-.|+|..-.|++.||+|.||+.
T Consensus      1364 ~mpsVtymRLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKr 1443 (1549)
T KOG0392|consen 1364 YMPSVTYMRLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKR 1443 (1549)
T ss_pred             hcCceeEEEecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCce
Confidence            33   344789999999999999999998 678776 7899999999999999999999999999999999999999986


Q ss_pred             EEEE--EecCcccHHHHHHHHH
Q 014486          387 LAIT--FVSSASDSDILNQVSK  406 (423)
Q Consensus       387 ~~~~--~~~~~~~~~~~~~~~~  406 (423)
                      .|-+  +++-.--.+.++.+++
T Consensus      1444 vVNVyRlItrGTLEEKVMgLQk 1465 (1549)
T KOG0392|consen 1444 VVNVYRLITRGTLEEKVMGLQK 1465 (1549)
T ss_pred             eeeeeeehhcccHHHHHhhHHH
Confidence            5443  4444333344444444

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

Probab=99.91  E-value=1e-21  Score=199.62  Aligned_cols=345  Identities=17%  Similarity=0.184  Sum_probs=211.5

Q ss_pred             HHHHHHHHhCCCCCCChhhhhccc----ccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           55 PELLRAIVDSGFEHPSEVQHECIP----QAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        55 ~~~~~~l~~~~~~~~~~~Q~~~i~----~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      +...+.+...||+ +|+.|.+.+.    .+..++++++.||||+|||++|++|++.... .+  .+++|.+||++|..|+
T Consensus       233 ~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~-~~--~~vvi~t~t~~Lq~Ql  308 (850)
T TIGR01407       233 SLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI-TE--KPVVISTNTKVLQSQL  308 (850)
T ss_pred             HHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc-CC--CeEEEEeCcHHHHHHH
Confidence            4666777777885 8999997555    5556788999999999999999999988766 22  2899999999999998


Q ss_pred             HH-HHHHHhccCC-CceEEEEEcCcchH---------------HH--------------------------------HHH
Q 014486          131 CH-EFERFSTYLP-DIKVAVFYGGVNIK---------------IH--------------------------------KDL  161 (423)
Q Consensus       131 ~~-~~~~~~~~~~-~~~~~~~~~~~~~~---------------~~--------------------------------~~~  161 (423)
                      .. .+..+....+ .+++..+.|+.+.-               ..                                ...
T Consensus       309 ~~~~~~~l~~~~~~~~~~~~~kG~~~ylcl~k~~~~l~~~~~~~~~~~~~~~~~~wl~~T~tGD~~el~~~~~~~~~~~~  388 (850)
T TIGR01407       309 LEKDIPLLNEILNFKINAALIKGKSNYLSLGKFSQILKDNTDNYEFNIFKMQVLVWLTETETGDLDELNLKGGNKMFFAQ  388 (850)
T ss_pred             HHHHHHHHHHHcCCCceEEEEEcchhhccHHHHHHHHhcCCCcHHHHHHHHHHHHHhccCCccCHhhccCCCcchhhHHH
Confidence            65 4555543331 36777777654220               00                                000


Q ss_pred             Hh-----------------------cCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc------CCc----
Q 014486          162 LK-----------------------NECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES------LDM----  208 (423)
Q Consensus       162 ~~-----------------------~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~------~~~----  208 (423)
                      +.                       ....+|+|+++..|+..+.....-+....++||||||++.+.      ..+    
T Consensus       389 i~~~~~l~~~c~~~~~Cf~~~ar~~a~~AdivItNHa~L~~~~~~~~~ilp~~~~lIiDEAH~L~d~a~~~~~~~ls~~~  468 (850)
T TIGR01407       389 VRHDGNLSKKDLFYEVDFYNRAQKNAEQAQILITNHAYLITRLVDNPELFPSFRDLIIDEAHHLPDIAENQLQEELDYAD  468 (850)
T ss_pred             hhcCCCCCCCCCCccccHHHHHHHHHhcCCEEEecHHHHHHHhhcccccCCCCCEEEEECcchHHHHHHHHhcceeCHHH
Confidence            00                       012579999999888765443333466689999999987521      000    


Q ss_pred             -HH----------------------------------------------------------------HHHHHHH------
Q 014486          209 -RR----------------------------------------------------------------DVQEIFK------  217 (423)
Q Consensus       209 -~~----------------------------------------------------------------~~~~~~~------  217 (423)
                       ..                                                                .+.....      
T Consensus       469 ~~~~l~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~  548 (850)
T TIGR01407       469 IKYQIDLIGKGENEQLLKRIQQLEKQEILEKLFDFETKDILKDLQAILDKLNKLLQIFSELSHKTVDQLRKFDLALKDDF  548 (850)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHH
Confidence             00                                                                0000000      


Q ss_pred             -----h----------C---------------------------CCCceEEEEeccCCcc-HHHHHHHhccCC-ce-eee
Q 014486          218 -----M----------T---------------------------PHDKQVMMFSATLSKE-IRPVCKKFMQDP-ME-IYV  252 (423)
Q Consensus       218 -----~----------~---------------------------~~~~~~v~~SAT~~~~-~~~~~~~~~~~~-~~-~~~  252 (423)
                           .          .                           +....+|++|||+... -.......++-. .. ...
T Consensus       549 ~~l~~~~~~~~~~wi~~~~~~~~~~~~l~~~pl~~~~~l~~~~~~~~~~~il~SATL~~~~~~~~~~~~lGl~~~~~~~~  628 (850)
T TIGR01407       549 KNIEQSLKEGHTSWISIENLQQKSTIRLYIKDYEVGDVLTKRLLPKFKSLIFTSATLKFSHSFESFPQLLGLTDVHFNTI  628 (850)
T ss_pred             HHHHHHhccCCeEEEEecCCCCCceEEEEeeeCcHHHHHHHHHhccCCeEEEEecccccCCChHHHHHhcCCCcccccee
Confidence                 0          0                           0112688999999742 123333333321 11 111


Q ss_pred             ccccccccccceEEEEE--eC------hHHHHH----HHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC----CCCeE
Q 014486          253 DDEAKLTLHGLVQHYIK--LS------ELEKNR----KLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC----NFPSI  316 (423)
Q Consensus       253 ~~~~~~~~~~~~~~~~~--~~------~~~~~~----~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~----~~~~~  316 (423)
                      . +....+......++.  .+      ...-..    .+.+++.. .++++|||+++.+..+.+++.|...    +++  
T Consensus       629 ~-~spf~~~~~~~l~v~~d~~~~~~~~~~~~~~~ia~~i~~l~~~-~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~--  704 (850)
T TIGR01407       629 E-PTPLNYAENQRVLIPTDAPAIQNKSLEEYAQEIASYIIEITAI-TSPKILVLFTSYEMLHMVYDMLNELPEFEGYE--  704 (850)
T ss_pred             c-CCCCCHHHcCEEEecCCCCCCCCCChHHHHHHHHHHHHHHHHh-cCCCEEEEeCCHHHHHHHHHHHhhhccccCce--
Confidence            1 111111111111111  11      111112    22233333 4578999999999999999999752    333  


Q ss_pred             EEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCC--EEEEccCCCC--------------------------
Q 014486          317 CIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVN--IVINYDMPDS--------------------------  368 (423)
Q Consensus       317 ~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~--~vi~~~~~~s--------------------------  368 (423)
                      .+..+.. ..|..+++.|++++..||++|+.+.+|+|+++..  +||...+|..                          
T Consensus       705 ~l~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~  783 (850)
T TIGR01407       705 VLAQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVIPRLPFANPKHPLTKKYWQKLEQEGKNPFYDYV  783 (850)
T ss_pred             EEecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEEeCCCCCCCCCHHHHHHHHHHHHhcCCchHHhh
Confidence            2333333 5788899999999999999999999999999855  5777776642                          


Q ss_pred             ----cchhhhcccccCCCCCceEEEEEecCccc-HHHHHHHHHHH
Q 014486          369 ----ADTYLHRVGRAGRFGTKGLAITFVSSASD-SDILNQVSKFM  408 (423)
Q Consensus       369 ----~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~-~~~~~~~~~~~  408 (423)
                          ...+.|.+||+.|..++..++++.+.... ..+.+.+-+.+
T Consensus       784 lP~A~~~l~Qa~GRlIRs~~D~G~v~ilD~R~~~~~Yg~~~~~sL  828 (850)
T TIGR01407       784 LPMAIIRLRQALGRLIRRENDRGSIVILDRRLVGKRYGKRFEKSL  828 (850)
T ss_pred             HHHHHHHHHHhhccccccCCceEEEEEEccccccchHHHHHHHhC
Confidence                12357999999999888778888876533 23334444443

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.

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.91  E-value=5.1e-23  Score=188.93  Aligned_cols=312  Identities=17%  Similarity=0.183  Sum_probs=210.2

Q ss_pred             CCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceE
Q 014486           67 EHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKV  146 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  146 (423)
                      ...+++-.+.+.++..++-+||.|.||||||.+...-+.+.-...++ .++-+..|+|.-|..++.+..+-.    +.+.
T Consensus       264 LPVy~ykdell~av~e~QVLiI~GeTGSGKTTQiPQyL~EaGytk~g-k~IgcTQPRRVAAmSVAaRVA~EM----gvkL  338 (902)
T KOG0923|consen  264 LPVYPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQYLYEAGYTKGG-KKIGCTQPRRVAAMSVAARVAEEM----GVKL  338 (902)
T ss_pred             CCchhhHHHHHHHHHhCcEEEEEcCCCCCccccccHHHHhcccccCC-ceEeecCcchHHHHHHHHHHHHHh----Cccc
Confidence            35566667777777778889999999999999865545554443333 357788899999999887776543    2222


Q ss_pred             EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEE
Q 014486          147 AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVM  226 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v  226 (423)
                      +.-.| .+++.+..  .+...-+=++|-++|++-+.. ...+..+++|||||||.-.-..+..-.+.+-...+++..+++
T Consensus       339 G~eVG-YsIRFEdc--TSekTvlKYMTDGmLlREfL~-epdLasYSViiiDEAHERTL~TDILfgLvKDIar~RpdLKll  414 (902)
T KOG0923|consen  339 GHEVG-YSIRFEDC--TSEKTVLKYMTDGMLLREFLS-EPDLASYSVIIVDEAHERTLHTDILFGLVKDIARFRPDLKLL  414 (902)
T ss_pred             ccccc-eEEEeccc--cCcceeeeeecchhHHHHHhc-cccccceeEEEeehhhhhhhhhhHHHHHHHHHHhhCCcceEE
Confidence            22111 11111111  011236778999999885443 345788999999999965432333323333334456788999


Q ss_pred             EEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHH----HHHHhhcCCcEEEEEcChhhHH
Q 014486          227 MFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLN----DLLDALDFNQVVIFVKSVSRAA  302 (423)
Q Consensus       227 ~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~ll~~~~~~~~ivf~~~~~~~~  302 (423)
                      ..|||+..+   ....|+.+...+.+... ..   .+..+|-..++.+-.....    .+....+.+-+|||....++..
T Consensus       415 IsSAT~DAe---kFS~fFDdapIF~iPGR-Ry---PVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIE  487 (902)
T KOG0923|consen  415 ISSATMDAE---KFSAFFDDAPIFRIPGR-RY---PVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIE  487 (902)
T ss_pred             eeccccCHH---HHHHhccCCcEEeccCc-cc---ceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHHHH
Confidence            999999854   34456655544444322 11   1122333344444333222    2223336688999999999888


Q ss_pred             HHHHHHHhC---------CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccC--------
Q 014486          303 ELNKLLVEC---------NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDM--------  365 (423)
Q Consensus       303 ~l~~~L~~~---------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~--------  365 (423)
                      ...+.|.++         .+-++++|++++...+..+++---+|..+|++||+++++.+.++++.+||+-+.        
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            777776553         345778999999999999988888888999999999999999999999996443        


Q ss_pred             ----------CCCcchhhhcccccCCCCCceEEEEEecCc
Q 014486          366 ----------PDSADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       366 ----------~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                                |-|.+...||.|||||.| +|.|+-+|+..
T Consensus       568 rtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt~~  606 (902)
T KOG0923|consen  568 RTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYTAW  606 (902)
T ss_pred             CcCceeEEEeeechhhhhhhccccCCCC-CCceEEeechh
Confidence                      336677889999999986 69999999853

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.91  E-value=4e-22  Score=189.14  Aligned_cols=316  Identities=19%  Similarity=0.185  Sum_probs=218.9

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      |+ .|++.|--+.-.+++|  -+..+.||.|||+++.+|++.....+.   .+.+++|+.-||.|-++++..+...+ ++
T Consensus        76 g~-r~ydvQlig~l~Ll~G--~VaEM~TGEGKTLvA~l~a~l~AL~G~---~VhvvT~NdyLA~RDae~m~~ly~~L-GL  148 (764)
T PRK12326         76 GL-RPFDVQLLGALRLLAG--DVIEMATGEGKTLAGAIAAAGYALQGR---RVHVITVNDYLARRDAEWMGPLYEAL-GL  148 (764)
T ss_pred             CC-CcchHHHHHHHHHhCC--CcccccCCCCHHHHHHHHHHHHHHcCC---CeEEEcCCHHHHHHHHHHHHHHHHhc-CC
Confidence            44 7899999888777765  578999999999999999888776554   78999999999999999999998887 89


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHHH-HHHhcCC------CCCCCccEEEEcCcchhhcc------------
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL-ALARDKD------LSLKNVRHFILDECDKMLES------------  205 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~-~~~~~~~------~~~~~~~~vVvDE~h~~~~~------------  205 (423)
                      ++..+.++.+.......+ .  .+|+++|...|- ++++.+.      .....+.++||||+|.++-+            
T Consensus       149 svg~i~~~~~~~err~aY-~--~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiLIDeArtPLiISg~~  225 (764)
T PRK12326        149 TVGWITEESTPEERRAAY-A--CDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVLVDEALVPLVLAGST  225 (764)
T ss_pred             EEEEECCCCCHHHHHHHH-c--CCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhheeccccCceeeeCCC
Confidence            999998887755444444 3  499999997652 2333222      22356889999999987621            


Q ss_pred             --CCcHHHHHHHHHhCCCC--------c----------------------------------------------------
Q 014486          206 --LDMRRDVQEIFKMTPHD--------K----------------------------------------------------  223 (423)
Q Consensus       206 --~~~~~~~~~~~~~~~~~--------~----------------------------------------------------  223 (423)
                        ......+..+...+...        .                                                    
T Consensus       226 ~~~~~y~~~~~~v~~L~~~~dy~ide~~k~v~LTe~G~~~~e~~l~~~~ly~~~~~~~~~~~i~~AL~A~~l~~~d~dYi  305 (764)
T PRK12326        226 PGEAPRGEIAELVRRLREGKDYEIDDDGRNVHLTDKGARKVEKALGGIDLYSEEHVGTTLTQVNVALHAHALLQRDVHYI  305 (764)
T ss_pred             cchhHHHHHHHHHHhcCcCCcEEEEcCCCeeEecHHHHHHHHHHcCCccccCcchhHHHHHHHHHHHHHHHHHhcCCcEE
Confidence              00111111111111110        0                                                    


Q ss_pred             ----------------------------------------------------------eEEEEeccCCccHHHHHHHhcc
Q 014486          224 ----------------------------------------------------------QVMMFSATLSKEIRPVCKKFMQ  245 (423)
Q Consensus       224 ----------------------------------------------------------~~v~~SAT~~~~~~~~~~~~~~  245 (423)
                                                                                ++.+||+|.......+.+.+..
T Consensus       306 V~dgeV~iVDe~TGRvm~grrwsdGLHQaIEaKE~v~i~~e~~t~AsIT~QnfFr~Y~kLsGMTGTa~t~~~Ef~~iY~l  385 (764)
T PRK12326        306 VRDGKVHLINASRGRIAQLQRWPDGLQAAVEAKEGLETTETGEVLDTITVQALIGRYPTVCGMTGTAVAAGEQLRQFYDL  385 (764)
T ss_pred             EECCEEEEEECCCCCcCCCCccChHHHHHHHHHcCCCCCCCceeeehhhHHHHHHhcchheeecCCChhHHHHHHHHhCC
Confidence                                                                      4566777766555544444433


Q ss_pred             CCceeeeccccccccccceEEEEEeChHHHHHHHHHHH-Hh-hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCC
Q 014486          246 DPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLL-DA-LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMS  323 (423)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll-~~-~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~  323 (423)
                      ...  .++...+........ .+......|...+.+-+ +. ..+.|+||.|.+++.++.++..|.+.|++..+++..-.
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 GVS--VIPPNKPNIREDEAD-RVYATAAEKNDAIVEHIAEVHETGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKND  462 (764)
T ss_pred             cEE--ECCCCCCceeecCCC-ceEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCch
Confidence            322  222222222222222 23334455555554444 33 25689999999999999999999999999999998754


Q ss_pred             HHHHHHHHHhhhcCC-ccEEEEcCccccCCCCC---------------CCCEEEEccCCCCcchhhhcccccCCCCCceE
Q 014486          324 QEERLTRYKGFKEGN-KRILVATDLVGRGIDIE---------------RVNIVINYDMPDSADTYLHRVGRAGRFGTKGL  387 (423)
Q Consensus       324 ~~~r~~~~~~f~~~~-~~ili~T~~~~~Gld~~---------------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~  387 (423)
                      ..+ ..++..  .|+ ..|.|||++++||.|+.               +--|||....+.|-.--.|-.||+||.|.+|.
T Consensus       463 ~~E-A~IIa~--AG~~gaVTIATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGs  539 (764)
T PRK12326        463 AEE-ARIIAE--AGKYGAVTVSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGS  539 (764)
T ss_pred             HhH-HHHHHh--cCCCCcEEEEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCc
Confidence            333 333332  343 45999999999999986               33479999999999999999999999999999


Q ss_pred             EEEEecCcc
Q 014486          388 AITFVSSAS  396 (423)
Q Consensus       388 ~~~~~~~~~  396 (423)
                      .-.|++-.+
T Consensus       540 s~f~lSleD  548 (764)
T PRK12326        540 SVFFVSLED  548 (764)
T ss_pred             eeEEEEcch
Confidence            999998543

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.89  E-value=3e-21  Score=187.96  Aligned_cols=130  Identities=20%  Similarity=0.320  Sum_probs=111.2

Q ss_pred             HHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCC
Q 014486          276 NRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGID  353 (423)
Q Consensus       276 ~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld  353 (423)
                      ...+...+...  .+.++||||++...++.+.+.|.+.|+++..+|++++..+|.++++.|+.|+++|||||+.+++|+|
T Consensus       428 i~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGfD  507 (655)
T TIGR00631       428 VDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLD  507 (655)
T ss_pred             HHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCee
Confidence            33444444332  4578999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCEEEEcc-----CCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHH
Q 014486          354 IERVNIVINYD-----MPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF  407 (423)
Q Consensus       354 ~~~~~~vi~~~-----~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~  407 (423)
                      +|++++||+++     .|.+...|+||+||+||. ..|.++++++. ....+...|.+.
T Consensus       508 iP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~-~~~~~~~ai~~~  564 (655)
T TIGR00631       508 LPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADK-ITDSMQKAIEET  564 (655)
T ss_pred             eCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcC-CCHHHHHHHHHH
Confidence            99999999988     799999999999999998 57899888874 444444544443

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

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.88  E-value=1.2e-21  Score=180.42  Aligned_cols=309  Identities=16%  Similarity=0.171  Sum_probs=198.8

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .....+.+.+.-+..++-++|.++||||||.+...-+++.-....+  .+-+..|.|.-|..++.+..+-....-+-.++
T Consensus       356 Pvf~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~edGY~~~G--mIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VG  433 (1042)
T KOG0924|consen  356 PVFACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYEDGYADNG--MIGCTQPRRVAAISVAKRVAEEMGVTLGDTVG  433 (1042)
T ss_pred             chHHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHhcccccCC--eeeecCchHHHHHHHHHHHHHHhCCccccccc
Confidence            3445555555556667779999999999999865555554443332  55666799999999888876544221121221


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEE
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM  227 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~  227 (423)
                      +     .++  .......+..|=+.|-+.|++-.-. ...+..+++||+||||.-.-+.+..-.+.+....-+.+.++|.
T Consensus       434 Y-----sIR--FEdvT~~~T~IkymTDGiLLrEsL~-d~~L~kYSviImDEAHERslNtDilfGllk~~larRrdlKliV  505 (1042)
T KOG0924|consen  434 Y-----SIR--FEDVTSEDTKIKYMTDGILLRESLK-DRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLARRRDLKLIV  505 (1042)
T ss_pred             e-----EEE--eeecCCCceeEEEeccchHHHHHhh-hhhhhheeEEEechhhhcccchHHHHHHHHHHHHhhccceEEE
Confidence            1     111  1111122247888899888762221 2346788999999999765433433333333333455788999


Q ss_pred             EeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHH-HHHH---HHHhhcCCcEEEEEcChhhHHH
Q 014486          228 FSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNR-KLND---LLDALDFNQVVIFVKSVSRAAE  303 (423)
Q Consensus       228 ~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~l~~---ll~~~~~~~~ivf~~~~~~~~~  303 (423)
                      +|||+...   .+..|+++...+.+....-   + +...+...+..+-.. .+..   +....+.+-+|||.+..+..+.
T Consensus       506 tSATm~a~---kf~nfFgn~p~f~IpGRTy---P-V~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~  578 (1042)
T KOG0924|consen  506 TSATMDAQ---KFSNFFGNCPQFTIPGRTY---P-VEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIEC  578 (1042)
T ss_pred             eeccccHH---HHHHHhCCCceeeecCCcc---c-eEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhH
Confidence            99999843   3445555444444433221   1 111122222222111 1111   1122355789999998887655


Q ss_pred             HHHHHHh----C------CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccC--------
Q 014486          304 LNKLLVE----C------NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDM--------  365 (423)
Q Consensus       304 l~~~L~~----~------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~--------  365 (423)
                      ....++.    .      ++.++.+++.++..-+.++++.-..|..+++|||+++++.+.++++.+||..+.        
T Consensus       579 t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kvyn~  658 (1042)
T KOG0924|consen  579 TCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNP  658 (1042)
T ss_pred             HHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCceeeeeccc
Confidence            5444433    1      577889999999999999988777888999999999999999999999997654        


Q ss_pred             ----------CCCcchhhhcccccCCCCCceEEEEEecC
Q 014486          366 ----------PDSADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       366 ----------~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                                |-|-...-||.|||||.| +|.|+-+|+.
T Consensus       659 ~~G~D~L~~~pIS~AnA~QRaGRAGRt~-pG~cYRlYTe  696 (1042)
T KOG0924|consen  659 RIGMDALQIVPISQANADQRAGRAGRTG-PGTCYRLYTE  696 (1042)
T ss_pred             ccccceeEEEechhccchhhccccCCCC-Ccceeeehhh
Confidence                      336667789999999986 6899999885

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.88  E-value=5.4e-21  Score=185.93  Aligned_cols=315  Identities=17%  Similarity=0.173  Sum_probs=213.4

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .|++.|--+--.+  .+.-|..+.||+|||+++.+|++.....+.   .+.+++|+.-||.|-++++..+...+ ++++.
T Consensus        82 ~~ydVQliGg~~L--h~G~iaEM~TGEGKTLvA~l~a~l~al~G~---~VhvvT~ndyLA~RD~e~m~~l~~~l-Gl~v~  155 (913)
T PRK13103         82 RHFDVQLIGGMTL--HEGKIAEMRTGEGKTLVGTLAVYLNALSGK---GVHVVTVNDYLARRDANWMRPLYEFL-GLSVG  155 (913)
T ss_pred             CcchhHHHhhhHh--ccCccccccCCCCChHHHHHHHHHHHHcCC---CEEEEeCCHHHHHHHHHHHHHHhccc-CCEEE
Confidence            6777777654433  456899999999999999999987766554   78999999999999999999999887 89999


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcCC------CCCCCccEEEEcCcchhhcc---------------
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDKD------LSLKNVRHFILDECDKMLES---------------  205 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~~------~~~~~~~~vVvDE~h~~~~~---------------  205 (423)
                      ++.++.+.......+.   .+|+++|..-| +++++...      .-...+.++||||+|.++-+               
T Consensus       156 ~i~~~~~~~err~~Y~---~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiLIDEArtPLIISg~~~~~  232 (913)
T PRK13103        156 IVTPFQPPEEKRAAYA---ADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSILIDEARTPLIISGQAEDS  232 (913)
T ss_pred             EECCCCCHHHHHHHhc---CCEEEEcccccccchhhccceechhhhcccccceeEechhhheeccccCCceeecCCCccc
Confidence            9988776655554444   49999999876 33343321      12377899999999987621               


Q ss_pred             CCcHHHHHHHHHhCCC--------------------Cc------------------------------------------
Q 014486          206 LDMRRDVQEIFKMTPH--------------------DK------------------------------------------  223 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~--------------------~~------------------------------------------  223 (423)
                      ......+..+...+..                    ..                                          
T Consensus       233 ~~~y~~~~~~v~~L~~~~~~~~~~~~~~~~y~idek~~~v~LTe~G~~~~e~~~~~~~i~~~~~~ly~~~~~~~~~~i~~  312 (913)
T PRK13103        233 SKLYIEINRLIPRLKQHIEEVEGQVTQEGHFTIDEKTRQVELNEAGHQFIEEMLTQAGLLAEGESLYSAHNLGLLTHVYA  312 (913)
T ss_pred             hHHHHHHHHHHHHHHhhhhccccccCCCCCeEEEcCCCeeeechHHHHHHHHHhhhCCCcccchhccChhhhHHHHHHHH
Confidence            0001111111111100                    00                                          


Q ss_pred             -------------------------------------------------------------------------eEEEEec
Q 014486          224 -------------------------------------------------------------------------QVMMFSA  230 (423)
Q Consensus       224 -------------------------------------------------------------------------~~v~~SA  230 (423)
                                                                                               ++.+||+
T Consensus       313 AL~A~~lf~~d~dYiV~dg~V~IVDe~TGR~m~grrwsdGLHQaIEaKE~v~I~~e~~t~AsIT~QnfFr~Y~kLsGMTG  392 (913)
T PRK13103        313 GLRAHKLFHRNVEYIVQDGQVLLIDEHTGRTMPGRRLSEGLHQAIEAKENLNIQAESQTLASTTFQNYFRLYNKLSGMTG  392 (913)
T ss_pred             HHHHHHHHhcCCcEEEECCEEEEEECCCCCcCCCCccchHHHHHHHHHcCCCcCCCceeEEeehHHHHHHhcchhccCCC
Confidence                                                                                     3444555


Q ss_pred             cCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHH
Q 014486          231 TLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLL  308 (423)
Q Consensus       231 T~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L  308 (423)
                      |...+...+.+.+......+..  ..+........ .+......|...+.+-+...  .+.|+||-+.+++.++.+++.|
T Consensus       393 Ta~te~~Ef~~iY~l~Vv~IPT--nkP~~R~D~~d-~vy~t~~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~ls~~L  469 (913)
T PRK13103        393 TADTEAFEFRQIYGLDVVVIPP--NKPLARKDFND-LVYLTAEEKYAAIITDIKECMALGRPVLVGTATIETSEHMSNLL  469 (913)
T ss_pred             CCHHHHHHHHHHhCCCEEECCC--CCCcccccCCC-eEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHH
Confidence            5544444443333333222222  11112222222 23344556665555544432  5689999999999999999999


Q ss_pred             HhCCCCeEEEcCCCCHHHHHHHHHhhhcCC-ccEEEEcCccccCCCCC--------------------------------
Q 014486          309 VECNFPSICIHSGMSQEERLTRYKGFKEGN-KRILVATDLVGRGIDIE--------------------------------  355 (423)
Q Consensus       309 ~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~ili~T~~~~~Gld~~--------------------------------  355 (423)
                      +..|++.-+++......+- .++.  ..|. ..|.|||++++||.|+.                                
T Consensus       470 ~~~gi~h~VLNAk~~~~EA-~IIa--~AG~~GaVTIATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e  546 (913)
T PRK13103        470 KKEGIEHKVLNAKYHEKEA-EIIA--QAGRPGALTIATNMAGRGTDILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQ  546 (913)
T ss_pred             HHcCCcHHHhccccchhHH-HHHH--cCCCCCcEEEeccCCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHH
Confidence            9999998888887553332 3333  3443 46999999999999984                                


Q ss_pred             -----CCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          356 -----RVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       356 -----~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                           +--|||-...+.|-.--.|-.||+||.|.+|..-.|++-.++
T Consensus       547 ~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSlED~  593 (913)
T PRK13103        547 QVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDS  593 (913)
T ss_pred             HHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcH
Confidence                 334788888999998899999999999999999999986433

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.87  E-value=1.4e-20  Score=160.16  Aligned_cols=185  Identities=35%  Similarity=0.513  Sum_probs=147.9

Q ss_pred             CCCCCCChhhhhcccccccC-CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           64 SGFEHPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        64 ~~~~~~~~~Q~~~i~~~~~~-~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      .++.+|+++|.++++.+... +.+++.+|||+|||.++..+++......... +++|++|+..++.|+.+.+..+.... 
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~-~~l~~~p~~~~~~~~~~~~~~~~~~~-   81 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGK-RVLVLVPTRELAEQWAEELKKLGPSL-   81 (201)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccCCC-cEEEEeCCHHHHHHHHHHHHHHhccC-
Confidence            45678999999999999998 9999999999999999888888877765433 89999999999999999998876543 


Q ss_pred             CceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCC
Q 014486          143 DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHD  222 (423)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~  222 (423)
                      ........++.........+.++..+++++|++.+.............++++|+||+|.+.. ..+...+..+...+++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~-~~~~~~~~~~~~~~~~~  160 (201)
T smart00487       82 GLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLD-GGFGDQLEKLLKLLPKN  160 (201)
T ss_pred             CeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhc-CCcHHHHHHHHHhCCcc
Confidence            22333444444434444555555459999999999998887776778899999999999976 36778888888888788


Q ss_pred             ceEEEEeccCCccHHHHHHHhccCCceee
Q 014486          223 KQVMMFSATLSKEIRPVCKKFMQDPMEIY  251 (423)
Q Consensus       223 ~~~v~~SAT~~~~~~~~~~~~~~~~~~~~  251 (423)
                      .+++++|||++.........+......+.
T Consensus       161 ~~~v~~saT~~~~~~~~~~~~~~~~~~~~  189 (201)
T smart00487      161 VQLLLLSATPPEEIENLLELFLNDPVFID  189 (201)
T ss_pred             ceEEEEecCCchhHHHHHHHhcCCCEEEe
Confidence            99999999999888887777776554443

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.87  E-value=8.7e-20  Score=179.29  Aligned_cols=134  Identities=20%  Similarity=0.287  Sum_probs=113.3

Q ss_pred             HHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCC
Q 014486          277 RKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDI  354 (423)
Q Consensus       277 ~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~  354 (423)
                      ..+...+...  .+.++||||++...++.+.+.|.+.|+++..+|+++++.+|..++..|+.|++.|+|||+.+++|+|+
T Consensus       433 ~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGfdl  512 (652)
T PRK05298        433 DDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDI  512 (652)
T ss_pred             HHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCccc
Confidence            3444444333  45789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCEEEEccC-----CCCcchhhhcccccCCCCCceEEEEEecCc--------ccHHHHHHHHHHHhcc
Q 014486          355 ERVNIVINYDM-----PDSADTYLHRVGRAGRFGTKGLAITFVSSA--------SDSDILNQVSKFMFLL  411 (423)
Q Consensus       355 ~~~~~vi~~~~-----~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~  411 (423)
                      |++++||+++.     |.+...|+||+||+||. ..|.+++|++..        .+......++..++..
T Consensus       513 p~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~  581 (652)
T PRK05298        513 PEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKITDSMQKAIDETERRREIQIAYNEE  581 (652)
T ss_pred             cCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecCCCHHHHHHHHHHHHHHHHHHHhhhc
Confidence            99999998874     78999999999999996 689999998742        3445555555555543

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.86  E-value=6.4e-20  Score=176.71  Aligned_cols=316  Identities=18%  Similarity=0.225  Sum_probs=213.0

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      |+ +|++.|--+--.+..|  -|..+.||-|||+++.+|+......+.   .+-|++...-||..=++++..+...+ |+
T Consensus        76 G~-r~ydVQliGglvLh~G--~IAEMkTGEGKTLvAtLpayLnAL~Gk---gVhVVTvNdYLA~RDae~mg~vy~fL-GL  148 (925)
T PRK12903         76 GK-RPYDVQIIGGIILDLG--SVAEMKTGEGKTITSIAPVYLNALTGK---GVIVSTVNEYLAERDAEEMGKVFNFL-GL  148 (925)
T ss_pred             CC-CcCchHHHHHHHHhcC--CeeeecCCCCccHHHHHHHHHHHhcCC---ceEEEecchhhhhhhHHHHHHHHHHh-CC
Confidence            44 7888887776555544  589999999999999998877666554   57788888999999999999888887 99


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcCC------CCCCCccEEEEcCcchhhcc------------
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDKD------LSLKNVRHFILDECDKMLES------------  205 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~~------~~~~~~~~vVvDE~h~~~~~------------  205 (423)
                      ++++...+.........+.   .+|+++|...| +++++.+.      .-...+.+.||||+|.++-+            
T Consensus       149 svG~i~~~~~~~~rr~aY~---~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSILIDEArTPLIISg~~  225 (925)
T PRK12903        149 SVGINKANMDPNLKREAYA---CDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSILIDEAKTPLIISGGQ  225 (925)
T ss_pred             ceeeeCCCCChHHHHHhcc---CCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchheeecccCCcccccCCC
Confidence            9999887766555444442   49999999876 33554332      12466889999999987621            


Q ss_pred             ---CCcHHHHHHHHHhCCC-------Cc----------------------------------------------------
Q 014486          206 ---LDMRRDVQEIFKMTPH-------DK----------------------------------------------------  223 (423)
Q Consensus       206 ---~~~~~~~~~~~~~~~~-------~~----------------------------------------------------  223 (423)
                         .........+...+..       ..                                                    
T Consensus       226 ~~~~~~Y~~~~~~v~~L~~~dy~iDek~k~v~LTe~G~~~~E~~l~i~nLy~~~n~~l~h~i~~AL~A~~lf~rd~dYiV  305 (925)
T PRK12903        226 SNDSNLYLAADQFVRTLKEDDYKIDEETKAISLTEKGIKKANKFFKLKNLYDIENSELVHRIQNALRAHKVMKEDVEYIV  305 (925)
T ss_pred             ccchHHHHHHHHHHHhccccceEEecccceEEECHhHHHHHHHHcCCCcccChhhHHHHHHHHHHHHHHHHHhcCCceEE
Confidence               0011111122211111       00                                                    


Q ss_pred             ---------------------------------------------------------eEEEEeccCCccHHHHHHHhccC
Q 014486          224 ---------------------------------------------------------QVMMFSATLSKEIRPVCKKFMQD  246 (423)
Q Consensus       224 ---------------------------------------------------------~~v~~SAT~~~~~~~~~~~~~~~  246 (423)
                                                                               ++.+||+|...+...+.+.+...
T Consensus       306 ~dg~V~IVDefTGR~m~gRrwsdGLHQaIEAKEgv~I~~e~~TlAsIT~QnfFr~Y~kLsGMTGTA~te~~Ef~~iY~l~  385 (925)
T PRK12903        306 RDGKIELVDQFTGRIMEGRSYSEGLQQAIQAKEMVEIEPETKTLATITYQNFFRLFKKLSGMTGTAKTEEQEFIDIYNMR  385 (925)
T ss_pred             ECCEEEEEECCCCCCCCCCccchHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhhccCCCCHHHHHHHHHHhCCC
Confidence                                                                     34556666555444444433333


Q ss_pred             CceeeeccccccccccceEEEEEeChHHHHHHHHHHHHh-h-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCH
Q 014486          247 PMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDA-L-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQ  324 (423)
Q Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~-~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~  324 (423)
                      ...+...  .+........ .+......|...+.+-+.. + .+.|+||.|.+++.++.++..|.+.|++..+++.....
T Consensus       386 Vv~IPTn--kP~~R~D~~d-~iy~t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~e  462 (925)
T PRK12903        386 VNVVPTN--KPVIRKDEPD-SIFGTKHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAKQNA  462 (925)
T ss_pred             EEECCCC--CCeeeeeCCC-cEEEcHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeecccchh
Confidence            3222221  1111111111 2334455566555554432 2 56799999999999999999999999999999987443


Q ss_pred             HHHHHHHHhhhcCC-ccEEEEcCccccCCCCCCC--------CEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCc
Q 014486          325 EERLTRYKGFKEGN-KRILVATDLVGRGIDIERV--------NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       325 ~~r~~~~~~f~~~~-~~ili~T~~~~~Gld~~~~--------~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      .+ ..++.  ..|. ..|.|||++++||.|+.--        -|||....+.|-.--.|..||+||.|.+|..-.|++-.
T Consensus       463 ~E-A~IIa--~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLe  539 (925)
T PRK12903        463 RE-AEIIA--KAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLD  539 (925)
T ss_pred             hH-HHHHH--hCCCCCeEEEecccccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEEecc
Confidence            32 22332  3453 4699999999999999632        28999999998888899999999999999999998854


Q ss_pred             c
Q 014486          396 S  396 (423)
Q Consensus       396 ~  396 (423)
                      +
T Consensus       540 D  540 (925)
T PRK12903        540 D  540 (925)
T ss_pred             h
Confidence            3

>COG4889 Predicted helicase [General function prediction only]

Probab=99.86  E-value=3.1e-22  Score=188.92  Aligned_cols=327  Identities=16%  Similarity=0.171  Sum_probs=192.3

Q ss_pred             CCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccC----CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           47 GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG----MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        47 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~----~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      .|+.+.. ..+..+|.-..-..|||||+.|+.+.+.+    ...=+.+.+|+|||++.+- +.+.+..    .++|+++|
T Consensus       141 DW~~f~p-~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLk-isEala~----~~iL~LvP  214 (1518)
T COG4889         141 DWDIFDP-TELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLK-ISEALAA----ARILFLVP  214 (1518)
T ss_pred             ChhhcCc-cccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHH-HHHHHhh----hheEeecc
Confidence            3554443 34445555555668999999999988874    2244555699999998754 4444443    38999999


Q ss_pred             ChHHHHHHHHHHHHHhccCCCceEEEEEcCcchH-----------------------HHHHHH-hcCCCcEEEechHHHH
Q 014486          123 TRELAYQICHEFERFSTYLPDIKVAVFYGGVNIK-----------------------IHKDLL-KNECPQIVVGTPGRIL  178 (423)
Q Consensus       123 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------~~~~~~-~~~~~~ilv~T~~~l~  178 (423)
                      +.+|..|..+++..-.. . .+....++++....                       ...... ....--|+++|++++.
T Consensus       215 SIsLLsQTlrew~~~~~-l-~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~  292 (1518)
T COG4889         215 SISLLSQTLREWTAQKE-L-DFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLP  292 (1518)
T ss_pred             hHHHHHHHHHHHhhccC-c-cceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchH
Confidence            99999997666543211 1 34444444433221                       111111 1122469999999998


Q ss_pred             HHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCC-----CCceEEEEeccCCccHHH---HH----------
Q 014486          179 ALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTP-----HDKQVMMFSATLSKEIRP---VC----------  240 (423)
Q Consensus       179 ~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~-----~~~~~v~~SAT~~~~~~~---~~----------  240 (423)
                      ..-+.....+..|++||+||||+..+- .....-...+....     +..+.+.|||||.--...   .+          
T Consensus       293 ~i~eAQe~G~~~fDliicDEAHRTtGa-~~a~dd~saFt~vHs~~niKa~kRlYmTATPkiy~eS~K~kAkd~s~~l~SM  371 (1518)
T COG4889         293 RIKEAQEAGLDEFDLIICDEAHRTTGA-TLAGDDKSAFTRVHSDQNIKAAKRLYMTATPKIYSESSKAKAKDHSAELSSM  371 (1518)
T ss_pred             HHHHHHHcCCCCccEEEecchhccccc-eecccCcccceeecCcchhHHHHhhhcccCchhhchhhhhhhhhccceeecc
Confidence            877777778889999999999987652 22211111111111     123567899997321111   00          


Q ss_pred             --------------------HHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHH-------Hhh-------
Q 014486          241 --------------------KKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLL-------DAL-------  286 (423)
Q Consensus       241 --------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll-------~~~-------  286 (423)
                                          +..+.+...+.+.....................-.......++       ++.       
T Consensus       372 DDe~~fGeef~rl~FgeAv~rdlLTDYKVmvlaVd~~~i~~~~~~~~~~~~~~L~~dd~~kIvG~wnGlakr~g~~n~~~  451 (1518)
T COG4889         372 DDELTFGEEFHRLGFGEAVERDLLTDYKVMVLAVDKEVIAGVLQSVLSGPSKGLALDDVSKIVGCWNGLAKRNGEDNDLK  451 (1518)
T ss_pred             chhhhhchhhhcccHHHHHHhhhhccceEEEEEechhhhhhhhhhhccCcccccchhhhhhhhhhhhhhhhhcccccccc
Confidence                                0111111111110000000000000000000000111111111       111       


Q ss_pred             -------cCCcEEEEEcChhhHHHHHHHHHh-------------CCC--CeEEEcCCCCHHHHHHHHH---hhhcCCccE
Q 014486          287 -------DFNQVVIFVKSVSRAAELNKLLVE-------------CNF--PSICIHSGMSQEERLTRYK---GFKEGNKRI  341 (423)
Q Consensus       287 -------~~~~~ivf~~~~~~~~~l~~~L~~-------------~~~--~~~~~~~~~~~~~r~~~~~---~f~~~~~~i  341 (423)
                             +..+.|-||.++++.+.+++.+..             .++  .+..+.|.|+..+|...+.   .|...+++|
T Consensus       452 ~~~~d~ap~~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckI  531 (1518)
T COG4889         452 NIKADTAPMQRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKI  531 (1518)
T ss_pred             CCcCCchHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCCcchhee
Confidence                   113578999999888777665533             133  3445678999999855543   345677889


Q ss_pred             EEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCC
Q 014486          342 LVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRF  382 (423)
Q Consensus       342 li~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~  382 (423)
                      |--..++++|+|+|.++.||++++..++.+.+|.+||++|-
T Consensus       532 lSNaRcLSEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRK  572 (1518)
T COG4889         532 LSNARCLSEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRK  572 (1518)
T ss_pred             eccchhhhcCCCccccceEEEecCchhHHHHHHHHHHHHHh
Confidence            98899999999999999999999999999999999999994

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.86  E-value=1.7e-20  Score=166.79  Aligned_cols=318  Identities=15%  Similarity=0.183  Sum_probs=208.4

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ...|...+.++...+.|++..-...+.++.+.+..+..++-+++.|+||||||.....+.+........  .+....|.+
T Consensus        24 ~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~~--~v~CTQprr  101 (699)
T KOG0925|consen   24 INPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHLT--GVACTQPRR  101 (699)
T ss_pred             cCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhcc--ceeecCchH
Confidence            456889999999999998875556666666777777778889999999999999887777766554442  566777999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC--------CCCCCccEEEE
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD--------LSLKNVRHFIL  196 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~--------~~~~~~~~vVv  196 (423)
                      .-|.+++.+...-.    +++.+.-.|- +++.           --.++|..++++...+.        -.+..+++||+
T Consensus       102 vaamsva~RVadEM----Dv~lG~EVGy-sIrf-----------EdC~~~~T~Lky~tDgmLlrEams~p~l~~y~viiL  165 (699)
T KOG0925|consen  102 VAAMSVAQRVADEM----DVTLGEEVGY-SIRF-----------EDCTSPNTLLKYCTDGMLLREAMSDPLLGRYGVIIL  165 (699)
T ss_pred             HHHHHHHHHHHHHh----ccccchhccc-cccc-----------cccCChhHHHHHhcchHHHHHHhhCcccccccEEEe
Confidence            98888887665543    3443333331 1111           11234444444333221        23678999999


Q ss_pred             cCcchhhccCCc-HHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHH
Q 014486          197 DECDKMLESLDM-RRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEK  275 (423)
Q Consensus       197 DE~h~~~~~~~~-~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  275 (423)
                      ||||.-.-..+. ...+..+...- ++.++|.+|||+..   ..++.++.++..+.+....  +   ....|...++.+.
T Consensus       166 DeahERtlATDiLmGllk~v~~~r-pdLk~vvmSatl~a---~Kfq~yf~n~Pll~vpg~~--P---vEi~Yt~e~erDy  236 (699)
T KOG0925|consen  166 DEAHERTLATDILMGLLKEVVRNR-PDLKLVVMSATLDA---EKFQRYFGNAPLLAVPGTH--P---VEIFYTPEPERDY  236 (699)
T ss_pred             chhhhhhHHHHHHHHHHHHHHhhC-CCceEEEeecccch---HHHHHHhCCCCeeecCCCC--c---eEEEecCCCChhH
Confidence            999965321222 22334444443 58899999999864   3556666666555554311  1   1112222233333


Q ss_pred             HH----HHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC---------CCCeEEEcCCCCHHHHHHHHHhhh---cC--
Q 014486          276 NR----KLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC---------NFPSICIHSGMSQEERLTRYKGFK---EG--  337 (423)
Q Consensus       276 ~~----~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~---------~~~~~~~~~~~~~~~r~~~~~~f~---~~--  337 (423)
                      .+    .+.++.....++-++||....++.+...+.+...         ...++++|    +.+..++++--.   +|  
T Consensus       237 lEaairtV~qih~~ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~  312 (699)
T KOG0925|consen  237 LEAAIRTVLQIHMCEEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAY  312 (699)
T ss_pred             HHHHHHHHHHHHhccCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC----chhhccccCCCCcccCCCc
Confidence            33    3344444446788999999999988888877643         24566777    344444433222   12  


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEccC------------------CCCcchhhhcccccCCCCCceEEEEEecC
Q 014486          338 NKRILVATDLVGRGIDIERVNIVINYDM------------------PDSADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       338 ~~~ili~T~~~~~Gld~~~~~~vi~~~~------------------~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                      ..+|+|+|++++..+.++++.+||.-+.                  |-|..+..||.||+||. .+|+|+.+|+.
T Consensus       313 ~RkvVvstniaetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt-~pGkcfrLYte  386 (699)
T KOG0925|consen  313 GRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTE  386 (699)
T ss_pred             cceEEEEecchheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecH
Confidence            2479999999999999999999996442                  45777889999999996 67999999984

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=99.86  E-value=4.4e-19  Score=159.94  Aligned_cols=174  Identities=18%  Similarity=0.268  Sum_probs=124.0

Q ss_pred             CceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhh-cCCcEEEEEcChhh
Q 014486          222 DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDAL-DFNQVVIFVKSVSR  300 (423)
Q Consensus       222 ~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~-~~~~~ivf~~~~~~  300 (423)
                      ..|+|++||||.+.-.....   ....+-.+.+.+-..+. +   .+......-...+.++-... .+.+++|-+-+++-
T Consensus       386 ~~q~i~VSATPg~~E~e~s~---~~vveQiIRPTGLlDP~-i---evRp~~~QvdDL~~EI~~r~~~~eRvLVTtLTKkm  458 (663)
T COG0556         386 IPQTIYVSATPGDYELEQSG---GNVVEQIIRPTGLLDPE-I---EVRPTKGQVDDLLSEIRKRVAKNERVLVTTLTKKM  458 (663)
T ss_pred             cCCEEEEECCCChHHHHhcc---CceeEEeecCCCCCCCc-e---eeecCCCcHHHHHHHHHHHHhcCCeEEEEeehHHH
Confidence            35899999999865433211   12222223332221111 1   11111112222333333222 35799999999999


Q ss_pred             HHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccC-----CCCcchhhhc
Q 014486          301 AAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDM-----PDSADTYLHR  375 (423)
Q Consensus       301 ~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~-----~~s~~~~~Q~  375 (423)
                      |+.+.++|.+.|+++..+|+++..-+|.++++..+.|..+|||+-+.+-+|+|+|-|..|..+|.     .+|-.+++|-
T Consensus       459 AEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQt  538 (663)
T COG0556         459 AEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQT  538 (663)
T ss_pred             HHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeecCccccccccchHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999988774     5688999999


Q ss_pred             ccccCCCCCceEEEEEecCcccHHHHHHH
Q 014486          376 VGRAGRFGTKGLAITFVSSASDSDILNQV  404 (423)
Q Consensus       376 ~GR~~R~g~~~~~~~~~~~~~~~~~~~~~  404 (423)
                      +|||.|. -.|.|+++.+ .....+..+|
T Consensus       539 IGRAARN-~~GkvIlYAD-~iT~sM~~Ai  565 (663)
T COG0556         539 IGRAARN-VNGKVILYAD-KITDSMQKAI  565 (663)
T ss_pred             HHHHhhc-cCCeEEEEch-hhhHHHHHHH
Confidence            9999995 4577876654 4444444444

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

Probab=99.85  E-value=2.4e-19  Score=173.63  Aligned_cols=116  Identities=21%  Similarity=0.263  Sum_probs=101.4

Q ss_pred             HHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCc--cEEEEcCcccc
Q 014486          275 KNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNK--RILVATDLVGR  350 (423)
Q Consensus       275 ~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~--~ili~T~~~~~  350 (423)
                      |...|.-||..+  .++++|||+.-..-.+.+...|..+|+-++.+.|.+.-++|+..+++|+.+..  ..+++|...+.
T Consensus      1261 KLQtLAiLLqQLk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSggv 1340 (1958)
T KOG0391|consen 1261 KLQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGGV 1340 (1958)
T ss_pred             hHHHHHHHHHHHHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCcc
Confidence            334444444433  45789999999999999999999999999999999999999999999998763  57779999999


Q ss_pred             CCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEE
Q 014486          351 GIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAIT  390 (423)
Q Consensus       351 Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~  390 (423)
                      |||+.+++.||+||..|++.=-.|+..||+|.|+...+.+
T Consensus      1341 GiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqtRDVHI 1380 (1958)
T KOG0391|consen 1341 GINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVHI 1380 (1958)
T ss_pred             ccccccCceEEEecCCCCchhhhHHHHHHHhhcCccceEE
Confidence            9999999999999999999999999999999999876654

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=99.85  E-value=5.6e-21  Score=183.15  Aligned_cols=316  Identities=17%  Similarity=0.186  Sum_probs=207.5

Q ss_pred             CCChhhhhccccccc----CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           68 HPSEVQHECIPQAIL----GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      .+++||...+.++..    +-+.|++.+||.|||.+.+-.+...+........-||+||+..|.. |..++..   +.|.
T Consensus       394 ~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP~LvivPlstL~N-W~~Ef~k---WaPS  469 (1157)
T KOG0386|consen  394 ELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEHKQMQGPFLIIVPLSTLVN-WSSEFPK---WAPS  469 (1157)
T ss_pred             CCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHHcccCCCeEEeccccccCC-chhhccc---cccc
Confidence            889999999988775    3459999999999998766555544444333335699999998866 4444544   4477


Q ss_pred             ceEEEEEcCcchHHH-HHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCC
Q 014486          144 IKVAVFYGGVNIKIH-KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHD  222 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~-~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~  222 (423)
                      +....+.|....+.. ...+..+.++|+++|++.+..  ....+.--++.++||||.|++.+.   ...+...+.-....
T Consensus       470 v~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik--dk~lLsKI~W~yMIIDEGHRmKNa---~~KLt~~L~t~y~~  544 (1157)
T KOG0386|consen  470 VQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK--DKALLSKISWKYMIIDEGHRMKNA---ICKLTDTLNTHYRA  544 (1157)
T ss_pred             eeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC--CHHHHhccCCcceeecccccccch---hhHHHHHhhccccc
Confidence            788888876544322 234445778999999998765  222223356778999999999752   22222222212223


Q ss_pred             ceEEEEeccCCcc----HHHHHHH--------------------------------------------------------
Q 014486          223 KQVMMFSATLSKE----IRPVCKK--------------------------------------------------------  242 (423)
Q Consensus       223 ~~~v~~SAT~~~~----~~~~~~~--------------------------------------------------------  242 (423)
                      ...+++|+|+-..    +..++..                                                        
T Consensus       545 q~RLLLTGTPLQN~LpELWaLLNFlLP~IFnS~~~FeqWFN~PFantGek~eLteEEtlLIIrRLHkVLRPFlLRRlKke  624 (1157)
T KOG0386|consen  545 QRRLLLTGTPLQNNLPELWALLNFLLPNIFNSCKAFEQWFNQPFANTGEKVELTEEETLLIIRRLHKVLRPFLLRRLKKE  624 (1157)
T ss_pred             hhhhhhcCChhhhccHHHHHHHHHhccchhhhHhHHHHHhhhhhhhcCCcccccchHHHHHHHHHHHhhhHHHHHhhhHH
Confidence            3345566664100    0000000                                                        


Q ss_pred             ---hccCCcee-----------------------eecc-ccc----------------cccccce----EEE-------E
Q 014486          243 ---FMQDPMEI-----------------------YVDD-EAK----------------LTLHGLV----QHY-------I  268 (423)
Q Consensus       243 ---~~~~~~~~-----------------------~~~~-~~~----------------~~~~~~~----~~~-------~  268 (423)
                         .+......                       .++. ...                +..+.+.    ..+       .
T Consensus       625 VE~~LPdKve~viKC~mSalQq~lY~~m~~~g~l~~d~~~g~~g~k~L~N~imqLRKiCNHP~lf~~ve~~~~~~~~~~d  704 (1157)
T KOG0386|consen  625 VEQELPDKVEDVIKCDMSALQQSLYKQMQNKGQLLKDTAKGKKGYKPLFNTIMQLRKLCNHPYLFANVENSYTLHYDIKD  704 (1157)
T ss_pred             HhhhCchhhhHhhheehhhhhHhhhHHHHhCCCCCcCchhccccchhhhhHhHHHHHhcCCchhhhhhccccccccChhH
Confidence               00000000                       0000 000                0000000    000       0


Q ss_pred             EeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCc---cEEE
Q 014486          269 KLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNK---RILV  343 (423)
Q Consensus       269 ~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~---~ili  343 (423)
                      .+....|...+..++-.+  .+++++.||.-......+..+|.-.++....+.|.+...+|...++.|+....   .+|.
T Consensus       705 L~R~sGKfELLDRiLPKLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~Fll  784 (1157)
T KOG0386|consen  705 LVRVSGKFELLDRILPKLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLL  784 (1157)
T ss_pred             HHHhccHHHHHHhhhHHHHhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeeee
Confidence            011123444455554333  35899999999999999999999999999999999999999999999997654   4677


Q ss_pred             EcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEe
Q 014486          344 ATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFV  392 (423)
Q Consensus       344 ~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~  392 (423)
                      +|.+.+.|+|+..++.||.||..|+|....|+..|++|.|+...|-++.
T Consensus       785 stragglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~r  833 (1157)
T KOG0386|consen  785 STRAGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLR  833 (1157)
T ss_pred             eecccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeee
Confidence            9999999999999999999999999999999999999999987666654

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

Probab=99.85  E-value=1.2e-18  Score=174.90  Aligned_cols=332  Identities=17%  Similarity=0.185  Sum_probs=199.5

Q ss_pred             CCCCCCChhhhhcccc----cccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHH-HHHHHHHh
Q 014486           64 SGFEHPSEVQHECIPQ----AILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI-CHEFERFS  138 (423)
Q Consensus        64 ~~~~~~~~~Q~~~i~~----~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~-~~~~~~~~  138 (423)
                      .|| .+|+-|.+-...    +..++.+++.|+||+|||++|++|++....    +.+++|++||++|+.|+ .+.+..+.
T Consensus       242 ~~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~~----~~~vvI~t~T~~Lq~Ql~~~~i~~l~  316 (820)
T PRK07246        242 LGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQSD----QRQIIVSVPTKILQDQIMAEEVKAIQ  316 (820)
T ss_pred             CCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhcC----CCcEEEEeCcHHHHHHHHHHHHHHHH
Confidence            355 689999874333    333677999999999999999999887642    23899999999999999 46676665


Q ss_pred             ccCCCceEEEEEcCcchHHH-----------------------------------------------HHHHh--------
Q 014486          139 TYLPDIKVAVFYGGVNIKIH-----------------------------------------------KDLLK--------  163 (423)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~~-----------------------------------------------~~~~~--------  163 (423)
                      ... ++++..+.|+.+.-..                                               +..+.        
T Consensus       317 ~~~-~~~~~~~kg~~~ylcl~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~~El~~~~~~~~~w~~i~~~~~~~~~  395 (820)
T PRK07246        317 EVF-HIDCHSLKGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIKQKQRYAAYFDQLKHDGNLSQS  395 (820)
T ss_pred             Hhc-CCcEEEEECCcccccHHHHHHHhhccCcchHHHHHHHHHHHHHhcCCCCCHhhccCCccccHHHHHhhccCCCCCC
Confidence            554 5677766665431100                                               00000        


Q ss_pred             ---------------cCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc------CCc-----HH-------
Q 014486          164 ---------------NECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES------LDM-----RR-------  210 (423)
Q Consensus       164 ---------------~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~------~~~-----~~-------  210 (423)
                                     ....+|+|++...|+..+.... .+...+++||||||++.+-      ..+     ..       
T Consensus       396 cp~~~~cf~~~ar~~a~~AdivItNHall~~~~~~~~-~~p~~~~lIiDEAH~l~~~~~~~~~~~~~~~~~~~~l~~~~~  474 (820)
T PRK07246        396 SLFYDYDFWKRSYEKAKTARLLITNHAYFLTRVQDDK-DFARNKVLVFDEAQKLMLQLEQLSRHQLNITSFLQTIQKALS  474 (820)
T ss_pred             CCcchhhHHHHHHHHHHhCCEEEEchHHHHHHHhhcc-CCCCCCEEEEECcchhHHHHHHHhcceecHHHHHHHHHHHHH
Confidence                           0125799999998887654332 3577899999999987531      000     00       


Q ss_pred             -------------------------------------------HH-----------HHHHHh------------------
Q 014486          211 -------------------------------------------DV-----------QEIFKM------------------  218 (423)
Q Consensus       211 -------------------------------------------~~-----------~~~~~~------------------  218 (423)
                                                                 .+           ..++..                  
T Consensus       475 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~l~~~~~~~~~~~~~~~~~~~W~e~~~~~~~~~~  554 (820)
T PRK07246        475 GPLPLLQKRLLESISFELLQLSEQFYQGKERQLIHDSLSRLHQYFSELEVAGFQELQAFFATAEGDYWLESEKQSEKRVT  554 (820)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEecCCCCccee
Confidence                                                       00           000000                  


Q ss_pred             ---------------CCCCceEEEEeccCC--ccHHHHHHHhccCCceeeeccccccccccceEEEE--EeC------hH
Q 014486          219 ---------------TPHDKQVMMFSATLS--KEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYI--KLS------EL  273 (423)
Q Consensus       219 ---------------~~~~~~~v~~SAT~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~------~~  273 (423)
                                     ++....+|++|||++  +.. .+...+....... ...+  ..+......+.  ..+      ..
T Consensus       555 ~l~~~pl~v~~~~~~~~~~~~~i~tSATL~v~~~f-~~~~~lGl~~~~~-~~~~--~~~~~~~~~~i~~~~p~~~~~~~~  630 (820)
T PRK07246        555 YLNSASKAFTHFSQLLPETCKTYFVSATLQISPRV-SLADLLGFEEYLF-HKIE--KDKKQDQLVVVDQDMPLVTETSDE  630 (820)
T ss_pred             EEEeeeCcHHHHHHHHhcCCeEEEEecccccCCCC-cHHHHcCCCccce-ecCC--CChHHccEEEeCCCCCCCCCCChH
Confidence                           011126789999996  222 2332222211111 0000  01111111111  011      11


Q ss_pred             HHHHHHHHHHHh--hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccC
Q 014486          274 EKNRKLNDLLDA--LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRG  351 (423)
Q Consensus       274 ~~~~~l~~ll~~--~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~G  351 (423)
                      .-...+.+.+..  ..+++++|+++|.+..+.+++.|.....+. ...|...  .+..++++|++++..||++|..+.+|
T Consensus       631 ~~~~~~~~~i~~~~~~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLlG~~sFwEG  707 (820)
T PRK07246        631 VYAEEIAKRLEELKQLQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILLGLGSFWEG  707 (820)
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEEecchhhCC
Confidence            111222222211  246899999999999999999997665444 3333222  24567999999888899999999999


Q ss_pred             CCCCC--CCEEEEccCCCC------------------------------cchhhhcccccCCCCCceEEEEEecCccc-H
Q 014486          352 IDIER--VNIVINYDMPDS------------------------------ADTYLHRVGRAGRFGTKGLAITFVSSASD-S  398 (423)
Q Consensus       352 ld~~~--~~~vi~~~~~~s------------------------------~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~-~  398 (423)
                      +|+|+  ...||...+|..                              .-.+.|.+||.-|...+..+++++++.-. .
T Consensus       708 VD~p~~~~~~viI~kLPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~ilD~R~~~k  787 (820)
T PRK07246        708 VDFVQADRMIEVITRLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLILDRRILTK  787 (820)
T ss_pred             CCCCCCCeEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEEECCccccc
Confidence            99974  556777776641                              22457999999999887777888876532 3


Q ss_pred             HHHHHHHHHHh
Q 014486          399 DILNQVSKFMF  409 (423)
Q Consensus       399 ~~~~~~~~~~~  409 (423)
                      .+.+.+-+-+.
T Consensus       788 ~Yg~~~l~sLP  798 (820)
T PRK07246        788 SYGKQILASLA  798 (820)
T ss_pred             HHHHHHHHhCC
Confidence            33444444443

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

Probab=99.84  E-value=1.4e-19  Score=173.00  Aligned_cols=157  Identities=14%  Similarity=0.143  Sum_probs=107.8

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc-eE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI-KV  146 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~-~~  146 (423)
                      -|-.+|++.+..+=.+.+++|.|||.+|||++...++=..+.....+ .++++.|+.+|+.|+...+....... .+ ..
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLResD~~-VVIyvaPtKaLVnQvsa~VyaRF~~~-t~~rg  588 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRESDSD-VVIYVAPTKALVNQVSANVYARFDTK-TFLRG  588 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhcCCC-EEEEecchHHHhhhhhHHHHHhhccC-ccccc
Confidence            57788999999888899999999999999998766555555554444 89999999999999887776543111 11 11


Q ss_pred             EEEEcCcchHHHHHHHhcC--CCcEEEechHHHHHHHhc---CCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCC
Q 014486          147 AVFYGGVNIKIHKDLLKNE--CPQIVVGTPGRILALARD---KDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPH  221 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~--~~~ilv~T~~~l~~~~~~---~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~  221 (423)
                      ..+.|...     +.+.-.  ..+|+|+-|+.+-.++..   ..-....+++||+||+|.+.+ ..-...+..+....  
T Consensus       589 ~sl~g~lt-----qEYsinp~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~-~ed~l~~Eqll~li--  660 (1330)
T KOG0949|consen  589 VSLLGDLT-----QEYSINPWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGN-EEDGLLWEQLLLLI--  660 (1330)
T ss_pred             hhhHhhhh-----HHhcCCchhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccc-cccchHHHHHHHhc--
Confidence            11122111     111111  249999999999887766   334457899999999999876 33333333333333  


Q ss_pred             CceEEEEeccCCc
Q 014486          222 DKQVMMFSATLSK  234 (423)
Q Consensus       222 ~~~~v~~SAT~~~  234 (423)
                      .++++.+|||..+
T Consensus       661 ~CP~L~LSATigN  673 (1330)
T KOG0949|consen  661 PCPFLVLSATIGN  673 (1330)
T ss_pred             CCCeeEEecccCC
Confidence            3568999999754

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.83  E-value=1.2e-18  Score=168.92  Aligned_cols=276  Identities=20%  Similarity=0.202  Sum_probs=178.7

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      |+ +|++.|--+.-.  -.+.-|+.+.||.|||+++.+|+......+.   .+.|++++..||.+-++++..+...+ ++
T Consensus        74 G~-r~ydvQlig~l~--L~~G~IaEm~TGEGKTL~a~l~ayl~aL~G~---~VhVvT~NdyLA~RD~e~m~pvy~~L-GL  146 (870)
T CHL00122         74 GL-RHFDVQLIGGLV--LNDGKIAEMKTGEGKTLVATLPAYLNALTGK---GVHIVTVNDYLAKRDQEWMGQIYRFL-GL  146 (870)
T ss_pred             CC-CCCchHhhhhHh--hcCCccccccCCCCchHHHHHHHHHHHhcCC---ceEEEeCCHHHHHHHHHHHHHHHHHc-CC
Confidence            44 578888766543  3566899999999999999999876555433   78999999999999999999998888 89


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHHH-HHHhcCC------CCCCCccEEEEcCcchhhccC-----------
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL-ALARDKD------LSLKNVRHFILDECDKMLESL-----------  206 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~-~~~~~~~------~~~~~~~~vVvDE~h~~~~~~-----------  206 (423)
                      +++++.++.+.......+.   .+|+++|...|- ++++.+.      .....+.++||||+|.++-+.           
T Consensus       147 svg~i~~~~~~~err~aY~---~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiLIDeArTPLiISg~~  223 (870)
T CHL00122        147 TVGLIQEGMSSEERKKNYL---KDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSILIDEARTPLIISGQS  223 (870)
T ss_pred             ceeeeCCCCChHHHHHhcC---CCCEecCCccccccchhhccCcChHHhhccccceeeeecchhheeccCCCceeccCCC
Confidence            9999988777665544443   399999997552 3443322      124568899999999876110           


Q ss_pred             ----CcHHHHHHHHHhCCC-------------------------------------------------------C-----
Q 014486          207 ----DMRRDVQEIFKMTPH-------------------------------------------------------D-----  222 (423)
Q Consensus       207 ----~~~~~~~~~~~~~~~-------------------------------------------------------~-----  222 (423)
                          ........+.+.+..                                                       +     
T Consensus       224 ~~~~~~y~~~~~~v~~L~~~~dy~vdek~k~v~LTe~G~~~~e~~l~i~~ly~~~~~~~~~i~~AL~A~~lf~~d~dYiV  303 (870)
T CHL00122        224 KTNIDKYIVADELAKYLEKNVHYEVDEKNKNVILTEQGILFIEKILKIEDLYSANDPWIPYILNALKAKELFFKNVHYIV  303 (870)
T ss_pred             ccchHHHHHHHHHHHhcCcCCCeEEEcCCCceEecHHHHHHHHHHcCCccccccccHHHHHHHHHHHHHHHHhcCCcEEE
Confidence                000001111111100                                                       0     


Q ss_pred             --------------------------------------------------------ceEEEEeccCCccHHHHHHHhccC
Q 014486          223 --------------------------------------------------------KQVMMFSATLSKEIRPVCKKFMQD  246 (423)
Q Consensus       223 --------------------------------------------------------~~~v~~SAT~~~~~~~~~~~~~~~  246 (423)
                                                                              .++.+||+|...+...+.+.+...
T Consensus       304 ~dgeV~iVDe~TGR~m~grrws~GLHQaiEaKEgv~It~e~~tlAsIT~QnfFr~Y~kL~GMTGTa~te~~Ef~~iY~l~  383 (870)
T CHL00122        304 RNNEIIIVDEFTGRIMPGRRWSDGLHQAIEAKENLPIRQETETLASITYQNFFLLYPKLSGMTGTAKTEELEFEKIYNLE  383 (870)
T ss_pred             ECCEEEEEECCCCcCCCCCccchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHHhCchhcccCCCCHHHHHHHHHHhCCC
Confidence                                                                    046677777765544444433333


Q ss_pred             CceeeeccccccccccceEEEEEeChHHHHHHHHHH-HHhh-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCH
Q 014486          247 PMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDL-LDAL-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQ  324 (423)
Q Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l-l~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~  324 (423)
                      ...  ++...+....... ..+......|...+.+- ...+ .+.|+||-|.+++..+.+++.|...|++..+++.....
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 VVC--IPTHRPMLRKDLP-DLIYKDELSKWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAKPEN  460 (870)
T ss_pred             EEE--CCCCCCccceeCC-CeEEeCHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCCCcc
Confidence            322  2222222222222 22333444555544443 3332 56899999999999999999999999999999987432


Q ss_pred             -HHHHHHHHhhhcCC-ccEEEEcCccccCCCCC
Q 014486          325 -EERLTRYKGFKEGN-KRILVATDLVGRGIDIE  355 (423)
Q Consensus       325 -~~r~~~~~~f~~~~-~~ili~T~~~~~Gld~~  355 (423)
                       ..-..++..  .|. ..|.|||++++||.|+.
T Consensus       461 ~~~EA~IIA~--AG~~G~VTIATNMAGRGTDI~  491 (870)
T CHL00122        461 VRRESEIVAQ--AGRKGSITIATNMAGRGTDII  491 (870)
T ss_pred             chhHHHHHHh--cCCCCcEEEeccccCCCcCee
Confidence             333344433  344 46999999999999973

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=99.83  E-value=8.5e-20  Score=169.00  Aligned_cols=116  Identities=19%  Similarity=0.276  Sum_probs=101.6

Q ss_pred             HHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCc-cEEEEcCccccC
Q 014486          275 KNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNK-RILVATDLVGRG  351 (423)
Q Consensus       275 ~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~-~ili~T~~~~~G  351 (423)
                      |...+..+|..+  .++++|+|++-.+-.+.+.++|..+++....+.|.....+|..+++.|....+ -+|++|.+.+.|
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            344455555444  45789999999999999999999999999999999999999999999998665 466799999999


Q ss_pred             CCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEE
Q 014486          352 IDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAIT  390 (423)
Q Consensus       352 ld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~  390 (423)
                      ||+..++.||+|+..|+|.--.|++.||+|.||...|.+
T Consensus      1109 INLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtv 1147 (1185)
T KOG0388|consen 1109 INLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTV 1147 (1185)
T ss_pred             ccccccceEEEecCCCCcchhhHHHHHHHhccCccceee
Confidence            999999999999999999999999999999999876554

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

Probab=99.82  E-value=2.7e-17  Score=157.91  Aligned_cols=125  Identities=14%  Similarity=0.109  Sum_probs=89.1

Q ss_pred             HHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcC----CccEEEEcCccccCCCC
Q 014486          279 LNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEG----NKRILVATDLVGRGIDI  354 (423)
Q Consensus       279 l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~----~~~ili~T~~~~~Gld~  354 (423)
                      +..++.. ..+.++|.+.+...++.+++.|...---.+.+.|..+  .+...++.|++.    ...||++|..+.+|+|+
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            3444433 4578999999999999999999764223344455432  345678888864    67899999999999999


Q ss_pred             --------C--CCCEEEEccCCCCc-------------------------chhhhcccccCCCCCc--eEEEEEecCccc
Q 014486          355 --------E--RVNIVINYDMPDSA-------------------------DTYLHRVGRAGRFGTK--GLAITFVSSASD  397 (423)
Q Consensus       355 --------~--~~~~vi~~~~~~s~-------------------------~~~~Q~~GR~~R~g~~--~~~~~~~~~~~~  397 (423)
                              |  .+++||+..+|..+                         -.+.|.+||.-|...+  ..++.+.++...
T Consensus       539 ~~~~~~p~~G~~Ls~ViI~kLPF~~~dp~a~~~~~~~~g~~~f~~~p~a~i~lkQg~GRLIR~~~D~~~G~i~ilD~R~~  618 (636)
T TIGR03117       539 THKPVSPDKDNLLTDLIITCAPFGLNRSLSMLKRIRKTSVRPWEIINESLMMLRQGLGRLVRHPDMPQNRRIHMLDGRIH  618 (636)
T ss_pred             CCccCCCCCCCcccEEEEEeCCCCcCChHHHHHHHHhcCCChHhhhHHHHHHHHHhcCceeecCCCcCceEEEEEeCCCC
Confidence                    3  38899988887422                         2457999999998887  778888887644


Q ss_pred             HHHHHHHHH
Q 014486          398 SDILNQVSK  406 (423)
Q Consensus       398 ~~~~~~~~~  406 (423)
                      ..+...+.+
T Consensus       619 ~~yg~~~~~  627 (636)
T TIGR03117       619 WPYMESWQE  627 (636)
T ss_pred             chhHHHHHH
Confidence            444444433

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.

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=99.82  E-value=9.7e-19  Score=155.99  Aligned_cols=120  Identities=18%  Similarity=0.163  Sum_probs=98.4

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCC-cc-EEEEcCccccCCCCCCCCEEEEcc
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN-KR-ILVATDLVGRGIDIERVNIVINYD  364 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~-ili~T~~~~~Gld~~~~~~vi~~~  364 (423)
                      ..-|.|||.+...-.+-+.-.|.+.|+.++.+.|+|++..|...++.|.++- +. +|++-.+.+.-+|+..+.+|+..|
T Consensus       637 ~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteASqVFmmD  716 (791)
T KOG1002|consen  637 RTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEASQVFMMD  716 (791)
T ss_pred             cchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechhceeEeec
Confidence            3457899999999999999999999999999999999999999999999754 44 455669999999999999999999


Q ss_pred             CCCCcchhhhcccccCCCCCc--eEEEEEecCcccHHHHHHHHH
Q 014486          365 MPDSADTYLHRVGRAGRFGTK--GLAITFVSSASDSDILNQVSK  406 (423)
Q Consensus       365 ~~~s~~~~~Q~~GR~~R~g~~--~~~~~~~~~~~~~~~~~~~~~  406 (423)
                      |-|++.--.|...|.+|.||.  -.++-|+-...-...+-.+++
T Consensus       717 PWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEnsiE~kIieLQe  760 (791)
T KOG1002|consen  717 PWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIENSIEEKIIELQE  760 (791)
T ss_pred             ccccHHHHhhhhhhHHhhcCccceeEEEeehhccHHHHHHHHHH
Confidence            999999999999999999975  455555544333333333333

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

Probab=99.82  E-value=4.7e-19  Score=139.88  Aligned_cols=118  Identities=45%  Similarity=0.634  Sum_probs=109.5

Q ss_pred             HHHHHHHHHHHhhc--CCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccC
Q 014486          274 EKNRKLNDLLDALD--FNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRG  351 (423)
Q Consensus       274 ~~~~~l~~ll~~~~--~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~G  351 (423)
                      .+...+..++....  .+++||||++...++.+.+.|.+.+.++..+|++++..+|..+++.|.++...+|++|+++++|
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            67777777777663  7899999999999999999999988999999999999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEE
Q 014486          352 IDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITF  391 (423)
Q Consensus       352 ld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~  391 (423)
                      +|+|.+++||++++|++...+.|++||++|.|+.|.++++
T Consensus        92 ~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079          92 IDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             cChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEeC
Confidence            9999999999999999999999999999999998887653

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

Probab=99.81  E-value=1.5e-18  Score=160.89  Aligned_cols=116  Identities=19%  Similarity=0.209  Sum_probs=98.3

Q ss_pred             HHHHHHHHHHhh---cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhc--CCccE-EEEcCcc
Q 014486          275 KNRKLNDLLDAL---DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKE--GNKRI-LVATDLV  348 (423)
Q Consensus       275 ~~~~l~~ll~~~---~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~--~~~~i-li~T~~~  348 (423)
                      |...+.+.++..   ...+++|.....+....+...+++.|.....++|.....+|+.+++.|+.  |..+| |++-.+.
T Consensus       730 Ki~~~l~~le~i~~~skeK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLtAG  809 (901)
T KOG4439|consen  730 KIAMVLEILETILTSSKEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLTAG  809 (901)
T ss_pred             HHHHHHHHHHHHhhcccceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEccC
Confidence            444444444443   45788999888888899999999999999999999999999999999975  33344 4566889


Q ss_pred             ccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEE
Q 014486          349 GRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAIT  390 (423)
Q Consensus       349 ~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~  390 (423)
                      +.|+|+-+.+|+|.+|+-|+|+--.|++.|..|.||+..|++
T Consensus       810 GVGLNL~GaNHlilvDlHWNPaLEqQAcDRIYR~GQkK~V~I  851 (901)
T KOG4439|consen  810 GVGLNLIGANHLILVDLHWNPALEQQACDRIYRMGQKKDVFI  851 (901)
T ss_pred             cceeeecccceEEEEecccCHHHHHHHHHHHHHhcccCceEE
Confidence            999999999999999999999999999999999999988775

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.80  E-value=2.9e-17  Score=167.92  Aligned_cols=123  Identities=16%  Similarity=0.135  Sum_probs=91.4

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhCCC--CeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCC--CCEEEE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVECNF--PSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIER--VNIVIN  362 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~~~--~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~--~~~vi~  362 (423)
                      .+++++|++++.+..+.+++.|.....  ....+..+++...|..+++.|++++..||++|..+.+|+|+|+  +++||.
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            457899999999999999999976432  1233344444456788999999888889999999999999997  578998


Q ss_pred             ccCCCC-c-----------------------------chhhhcccccCCCCCceEEEEEecCccc-HHHHHHHHHHHh
Q 014486          363 YDMPDS-A-----------------------------DTYLHRVGRAGRFGTKGLAITFVSSASD-SDILNQVSKFMF  409 (423)
Q Consensus       363 ~~~~~s-~-----------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~~~~-~~~~~~~~~~~~  409 (423)
                      ..+|.. |                             -.+.|.+||+-|..++..++++.++.-. ..+.+.+-+.+.
T Consensus       831 ~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v~ilD~R~~~k~Yg~~~l~sLP  908 (928)
T PRK08074        831 VRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTVFVLDRRLTTTSYGKYFLESLP  908 (928)
T ss_pred             ecCCCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEEEEecCccccchHHHHHHHhCC
Confidence            887751 1                             2346999999999888778888876533 334444444443

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=99.80  E-value=1.4e-18  Score=157.24  Aligned_cols=281  Identities=18%  Similarity=0.224  Sum_probs=183.2

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL  162 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (423)
                      .+-++-+|||.||||.-    +++++...+   ..++.-|.+-||.++++++++.     ++.+..++|.........  
T Consensus       191 RkIi~H~GPTNSGKTy~----ALqrl~~ak---sGvycGPLrLLA~EV~~r~na~-----gipCdL~TGeE~~~~~~~--  256 (700)
T KOG0953|consen  191 RKIIMHVGPTNSGKTYR----ALQRLKSAK---SGVYCGPLRLLAHEVYDRLNAL-----GIPCDLLTGEERRFVLDN--  256 (700)
T ss_pred             heEEEEeCCCCCchhHH----HHHHHhhhc---cceecchHHHHHHHHHHHhhhc-----CCCccccccceeeecCCC--
Confidence            34578889999999975    455655554   5699999999999999998876     788888888543222111  


Q ss_pred             hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHH
Q 014486          163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKK  242 (423)
Q Consensus       163 ~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~  242 (423)
                       ...++.+-||.++..        --..+.+.|+||.+.+.+...=.+..+.++........++   +-  +.+.++.+.
T Consensus       257 -~~~a~hvScTVEM~s--------v~~~yeVAViDEIQmm~Dp~RGwAWTrALLGl~AdEiHLC---Ge--psvldlV~~  322 (700)
T KOG0953|consen  257 -GNPAQHVSCTVEMVS--------VNTPYEVAVIDEIQMMRDPSRGWAWTRALLGLAADEIHLC---GE--PSVLDLVRK  322 (700)
T ss_pred             -CCcccceEEEEEEee--------cCCceEEEEehhHHhhcCcccchHHHHHHHhhhhhhhhcc---CC--chHHHHHHH
Confidence             123577788877653        1245679999999998764322233334444333332222   11  223344443


Q ss_pred             hccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCC-eEEEcCC
Q 014486          243 FMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFP-SICIHSG  321 (423)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~  321 (423)
                      .+...-.-           ..+..|....+..-...+..-++++.++-+|| |-+++....+...+.+.+.. +.+++|.
T Consensus       323 i~k~TGd~-----------vev~~YeRl~pL~v~~~~~~sl~nlk~GDCvV-~FSkk~I~~~k~kIE~~g~~k~aVIYGs  390 (700)
T KOG0953|consen  323 ILKMTGDD-----------VEVREYERLSPLVVEETALGSLSNLKPGDCVV-AFSKKDIFTVKKKIEKAGNHKCAVIYGS  390 (700)
T ss_pred             HHhhcCCe-----------eEEEeecccCcceehhhhhhhhccCCCCCeEE-EeehhhHHHHHHHHHHhcCcceEEEecC
Confidence            33211100           00112222221111123334445556566555 44567788888888877655 9999999


Q ss_pred             CCHHHHHHHHHhhhc--CCccEEEEcCccccCCCCCCCCEEEEccCC---------CCcchhhhcccccCCCCC---ceE
Q 014486          322 MSQEERLTRYKGFKE--GNKRILVATDLVGRGIDIERVNIVINYDMP---------DSADTYLHRVGRAGRFGT---KGL  387 (423)
Q Consensus       322 ~~~~~r~~~~~~f~~--~~~~ili~T~~~~~Gld~~~~~~vi~~~~~---------~s~~~~~Q~~GR~~R~g~---~~~  387 (423)
                      +++..|.+.-..|++  ++.+|||||+++++|+|+ +++.||++++.         .+..+..|.+|||||.|.   .|.
T Consensus       391 LPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~  469 (700)
T KOG0953|consen  391 LPPETRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGE  469 (700)
T ss_pred             CCCchhHHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEeecccCCcccceeccHHHHHHHhhcccccccCCcCce
Confidence            999999999999987  889999999999999999 58889998865         367788999999999874   366


Q ss_pred             EEEEecCcccHHHHHHHHHHHh
Q 014486          388 AITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       388 ~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                      +..+..     +.+..+.+.|+
T Consensus       470 vTtl~~-----eDL~~L~~~l~  486 (700)
T KOG0953|consen  470 VTTLHS-----EDLKLLKRILK  486 (700)
T ss_pred             EEEeeH-----hhHHHHHHHHh
Confidence            666654     23455555554

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

Probab=99.79  E-value=5.4e-19  Score=160.17  Aligned_cols=338  Identities=15%  Similarity=0.064  Sum_probs=217.8

Q ss_pred             HHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHh
Q 014486           59 RAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFS  138 (423)
Q Consensus        59 ~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~  138 (423)
                      +.+.++.-+....+|.+++..+.+|.+.++.-.|.+||++++.............. ..+++.|+.++++....-+.-..
T Consensus       277 ~~~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~~s-~~~~~~~~~~~~~~~~~~~~V~~  355 (1034)
T KOG4150|consen  277 SLLNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCHAT-NSLLPSEMVEHLRNGSKGQVVHV  355 (1034)
T ss_pred             HHHhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCccc-ceecchhHHHHhhccCCceEEEE
Confidence            44445555677899999999999999999999999999999887777655544433 67999999998877544332222


Q ss_pred             ccCCCceEEEEE-cCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC----CCCCCccEEEEcCcchhhccCC--cHHH
Q 014486          139 TYLPDIKVAVFY-GGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD----LSLKNVRHFILDECDKMLESLD--MRRD  211 (423)
Q Consensus       139 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~----~~~~~~~~vVvDE~h~~~~~~~--~~~~  211 (423)
                      ...|..+.+++. .+...+.....+.....+++++.|+......-.+.    ..+-...++++||+|..+...+  ....
T Consensus       356 ~~I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~  435 (1034)
T KOG4150|consen  356 EVIKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQDQ  435 (1034)
T ss_pred             EehhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHHHHH
Confidence            222223322221 11222223333433336999999987765322111    2234556799999998765211  1112


Q ss_pred             HHHHHHhC-----CCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEE---eChHHH---HHHHH
Q 014486          212 VQEIFKMT-----PHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIK---LSELEK---NRKLN  280 (423)
Q Consensus       212 ~~~~~~~~-----~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~---~~~l~  280 (423)
                      ++++...+     +.+.|++-.+||+...+...-..+..+.......+..+......+.+--.   ....++   .....
T Consensus       436 ~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~DGSPs~~K~~V~WNP~~~P~~~~~~~~~i~E~s  515 (1034)
T KOG4150|consen  436 LRALSDLIKGFEASINMGVYDGDTPYKDRTRLRSELANLSELELVTIDGSPSSEKLFVLWNPSAPPTSKSEKSSKVVEVS  515 (1034)
T ss_pred             HHHHHHHHHHHHhhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEEecCCCCccceEEEeCCCCCCcchhhhhhHHHHHH
Confidence            22222221     33678999999998777655555544444333322221111111111000   011112   22222


Q ss_pred             HHHHhh--cCCcEEEEEcChhhHHHHHHHHHhC----CC----CeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCcccc
Q 014486          281 DLLDAL--DFNQVVIFVKSVSRAAELNKLLVEC----NF----PSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGR  350 (423)
Q Consensus       281 ~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~----~~----~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~  350 (423)
                      .++...  .+-++|.||+++..++-+....+..    +.    .+..|.|+....+|..+....-.|+..-+|+|++++.
T Consensus       516 ~~~~~~i~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALEL  595 (1034)
T KOG4150|consen  516 HLFAEMVQHGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALEL  595 (1034)
T ss_pred             HHHHHHHHcCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhh
Confidence            222211  3468999999999988776654432    21    2345789999999999999999999999999999999


Q ss_pred             CCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          351 GIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       351 Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      |+|+..++.|++.+.|.|++.+.|..|||||.+++..++++.....-
T Consensus       596 GIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~PV  642 (1034)
T KOG4150|consen  596 GIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGPV  642 (1034)
T ss_pred             ccccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEeccch
Confidence            99999999999999999999999999999999999887776654333

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.78  E-value=6.3e-17  Score=156.91  Aligned_cols=274  Identities=18%  Similarity=0.181  Sum_probs=176.5

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .|++.|--+--.+  ++.-|..+.||-|||+++.+|+......+.   .+-|++++.-||..-++++..+...+ +++++
T Consensus        85 r~ydVQliGgl~L--h~G~IAEM~TGEGKTL~atlpaylnAL~Gk---gVhVVTvNdYLA~RDae~m~~vy~~L-GLtvg  158 (939)
T PRK12902         85 RHFDVQLIGGMVL--HEGQIAEMKTGEGKTLVATLPSYLNALTGK---GVHVVTVNDYLARRDAEWMGQVHRFL-GLSVG  158 (939)
T ss_pred             CcchhHHHhhhhh--cCCceeeecCCCChhHHHHHHHHHHhhcCC---CeEEEeCCHHHHHhHHHHHHHHHHHh-CCeEE
Confidence            6777776664444  456899999999999999999988777655   68999999999999999999988887 99999


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcC------CCCCCCccEEEEcCcchhhcc---------------
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDK------DLSLKNVRHFILDECDKMLES---------------  205 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~------~~~~~~~~~vVvDE~h~~~~~---------------  205 (423)
                      ++.++.+.......+ .  .+|+++|+..| +++++.+      ......+.++||||+|.++-+               
T Consensus       159 ~i~~~~~~~err~aY-~--~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSILIDEArTPLIISg~~~~~  235 (939)
T PRK12902        159 LIQQDMSPEERKKNY-A--CDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSILIDEARTPLIISGQVERP  235 (939)
T ss_pred             EECCCCChHHHHHhc-C--CCeEEecCCcccccchhhhhcccccccccCccceEEEecccceeeccCCCcccccCCCccc
Confidence            988776655444333 2  49999999876 2233221      123467889999999987621               


Q ss_pred             CCcHHHHHHHHHhCCC--------------Cc------------------------------------------------
Q 014486          206 LDMRRDVQEIFKMTPH--------------DK------------------------------------------------  223 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~--------------~~------------------------------------------------  223 (423)
                      .........+.+.+..              ..                                                
T Consensus       236 ~~~y~~~~~~~~~L~~~~~~~~~~dy~idek~~~v~LTe~G~~~~e~~~~i~nLy~~~~~~~~~i~~AL~A~~lf~~d~d  315 (939)
T PRK12902        236 QEKYQKAAEVAAALQRKDGIDPEGDYEVDEKQRNVLLTDEGFAKAEQLLGVSDLFDPQDPWAHYIFNALKAKELFIKDVN  315 (939)
T ss_pred             hHHHHHHHHHHHHhhhhcccCCCCCeEEecCCCeeeEcHHHHHHHHHHhCchhhcCcccHHHHHHHHHHHHHHHHhcCCe
Confidence            0011111111111110              00                                                


Q ss_pred             ------------------------------------------------------------eEEEEeccCCccHHHHHHHh
Q 014486          224 ------------------------------------------------------------QVMMFSATLSKEIRPVCKKF  243 (423)
Q Consensus       224 ------------------------------------------------------------~~v~~SAT~~~~~~~~~~~~  243 (423)
                                                                                  ++.+||+|...+...+.+.+
T Consensus       316 YiV~dg~V~IVDe~TGR~m~grrws~GLHQaIEaKE~v~it~e~~tlAsIT~QnfFr~Y~kLsGMTGTa~te~~Ef~~iY  395 (939)
T PRK12902        316 YIVRNGEVVIVDEFTGRVMPGRRWSDGLHQAIEAKEGVEIQPETQTLASITYQNFFLLYPKLAGMTGTAKTEEVEFEKTY  395 (939)
T ss_pred             EEEECCEEEEEECCCCCCCCCCccchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCCHHHHHHHHHHh
Confidence                                                                        34556666554444443333


Q ss_pred             ccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHH-Hhh-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCC
Q 014486          244 MQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLL-DAL-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSG  321 (423)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll-~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~  321 (423)
                      ......+..  ..+........ .+......|...+.+-+ ..+ .+.|+||-|.+++.++.++..|.+.|++..+++..
T Consensus       396 ~l~Vv~IPT--nkP~~R~d~~d-~vy~t~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk  472 (939)
T PRK12902        396 KLEVTVIPT--NRPRRRQDWPD-QVYKTEIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAK  472 (939)
T ss_pred             CCcEEEcCC--CCCeeeecCCC-eEEcCHHHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCC
Confidence            333222222  11111222222 23334455655555443 332 56899999999999999999999999999999986


Q ss_pred             -CCHHHHHHHHHhhhcCC-ccEEEEcCccccCCCCC
Q 014486          322 -MSQEERLTRYKGFKEGN-KRILVATDLVGRGIDIE  355 (423)
Q Consensus       322 -~~~~~r~~~~~~f~~~~-~~ili~T~~~~~Gld~~  355 (423)
                       .....-..++..  .|+ ..|.|||++++||.|+.
T Consensus       473 ~~~~~~EA~IIa~--AG~~GaVTIATNMAGRGTDIk  506 (939)
T PRK12902        473 PENVEREAEIVAQ--AGRKGAVTIATNMAGRGTDII  506 (939)
T ss_pred             CcchHhHHHHHHh--cCCCCcEEEeccCCCCCcCEe
Confidence             333333444432  444 45999999999999974

>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=99.78  E-value=4.9e-19  Score=125.55  Aligned_cols=78  Identities=45%  Similarity=0.729  Sum_probs=75.5

Q ss_pred             HHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCC
Q 014486          306 KLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFG  383 (423)
Q Consensus       306 ~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g  383 (423)
                      +.|+..++++..+||+++..+|..+++.|++++..|||+|+++++|+|+|.+++||++++|+++..|.|++||++|.|
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 ....

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.76  E-value=3.7e-17  Score=130.92  Aligned_cols=144  Identities=38%  Similarity=0.503  Sum_probs=107.8

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHh
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLK  163 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (423)
                      +++++.+|||+|||.+++..+......... .+++|++|+..++.|+.+.+..+...  ...+..+.+............
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~~-~~~lv~~p~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~   77 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLKG-GQVLVLAPTRELANQVAERLKELFGE--GIKVGYLIGGTSIKQQEKLLS   77 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcccC-CCEEEEcCcHHHHHHHHHHHHHHhhC--CcEEEEEecCcchhHHHHHhc
Confidence            468999999999999988888777665333 38999999999999999988887643  467777777655554443333


Q ss_pred             cCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccC
Q 014486          164 NECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATL  232 (423)
Q Consensus       164 ~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~  232 (423)
                      . ..+|+++|++.+.............++++|+||+|.+.. ..................+++++||||
T Consensus        78 ~-~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~-~~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          78 G-KTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLN-QGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             C-CCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhh-cchHHHHHHHHhhCCccceEEEEeccC
Confidence            3 369999999999887776655567788999999999976 333333223344456678899999996

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

>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=99.74  E-value=2.6e-17  Score=138.07  Aligned_cols=155  Identities=19%  Similarity=0.187  Sum_probs=103.3

Q ss_pred             CCChhhhhccccccc-------CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhcc
Q 014486           68 HPSEVQHECIPQAIL-------GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTY  140 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~-------~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~  140 (423)
                      .|+++|.+++..+..       .+.+++.+|||+|||.+++..+.....      ++++++|+..|+.|+.+.+..+...
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~------~~l~~~p~~~l~~Q~~~~~~~~~~~   76 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR------KVLIVAPNISLLEQWYDEFDDFGSE   76 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC------EEEEEESSHHHHHHHHHHHHHHSTT
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc------ceeEecCHHHHHHHHHHHHHHhhhh
Confidence            589999999999884       578999999999999998765655555      8899999999999999999766543


Q ss_pred             CCCceE---------EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC-----------CCCCCccEEEEcCcc
Q 014486          141 LPDIKV---------AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD-----------LSLKNVRHFILDECD  200 (423)
Q Consensus       141 ~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~-----------~~~~~~~~vVvDE~h  200 (423)
                      ......         .....................+++++|.+.+........           .....+++||+||||
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH  156 (184)
T PF04851_consen   77 KYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAH  156 (184)
T ss_dssp             SEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGG
T ss_pred             hhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhh
Confidence            211100         001111111122233334446999999999987654321           223567899999999


Q ss_pred             hhhccCCcHHHHHHHHHhCCCCceEEEEeccCCc
Q 014486          201 KMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSK  234 (423)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~  234 (423)
                      ++.....    +..+..  .+...+++|||||++
T Consensus       157 ~~~~~~~----~~~i~~--~~~~~~l~lTATp~r  184 (184)
T PF04851_consen  157 HYPSDSS----YREIIE--FKAAFILGLTATPFR  184 (184)
T ss_dssp             CTHHHHH----HHHHHH--SSCCEEEEEESS-S-
T ss_pred             hcCCHHH----HHHHHc--CCCCeEEEEEeCccC
Confidence            8765211    444444  556779999999864

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 ....

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

Probab=99.74  E-value=3.8e-16  Score=156.19  Aligned_cols=130  Identities=16%  Similarity=0.158  Sum_probs=95.0

Q ss_pred             HHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCC-eEEEcCCCCHHHHHHHHHhhhcCCc-cEEEEcCccccCCCC
Q 014486          277 RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFP-SICIHSGMSQEERLTRYKGFKEGNK-RILVATDLVGRGIDI  354 (423)
Q Consensus       277 ~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~~~~r~~~~~~f~~~~~-~ili~T~~~~~Gld~  354 (423)
                      ..+..++...+ ++++||+++...++.+.+.+...... .+..++..+..   ..++.|..+.- .++|+|..+++|+|+
T Consensus       469 ~~i~~~~~~~~-~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~~~---~~l~~f~~~~~~~~lv~~gsf~EGVD~  544 (654)
T COG1199         469 AYLREILKASP-GGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDERE---ELLEKFKASGEGLILVGGGSFWEGVDF  544 (654)
T ss_pred             HHHHHHHhhcC-CCEEEEeccHHHHHHHHHHHhhcCccceeeecCCCcHH---HHHHHHHHhcCCeEEEeeccccCcccC
Confidence            34444444444 58999999999999999999987653 34455544433   67777876554 899999999999999


Q ss_pred             CC--CCEEEEccCCC------------------------------CcchhhhcccccCCCCCceEEEEEecCcccHH-HH
Q 014486          355 ER--VNIVINYDMPD------------------------------SADTYLHRVGRAGRFGTKGLAITFVSSASDSD-IL  401 (423)
Q Consensus       355 ~~--~~~vi~~~~~~------------------------------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~-~~  401 (423)
                      ++  +++||..+.|.                              .+..+.|.+||+.|..++..++++++...... +.
T Consensus       545 ~g~~l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD~R~~~~~y~  624 (654)
T COG1199         545 PGDALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDKRYATKRYG  624 (654)
T ss_pred             CCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEecccchhhhHH
Confidence            87  57899888776                              22345799999999888888888888755443 55


Q ss_pred             HHHHHHHhc
Q 014486          402 NQVSKFMFL  410 (423)
Q Consensus       402 ~~~~~~~~~  410 (423)
                      ..+.+.+..
T Consensus       625 ~~l~~~l~~  633 (654)
T COG1199         625 KLLLDSLPP  633 (654)
T ss_pred             HHHHHhCCC
Confidence            555555543

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=99.71  E-value=7.2e-16  Score=151.21  Aligned_cols=125  Identities=24%  Similarity=0.309  Sum_probs=97.4

Q ss_pred             eChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCC-ccEEEEcC
Q 014486          270 LSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN-KRILVATD  346 (423)
Q Consensus       270 ~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~ili~T~  346 (423)
                      .....|...+.+-+...  .+.|+||-+.+++..+.++..|...|++.-+++......+..-+ .  ..|. ..|.|||+
T Consensus       608 ~t~~eK~~Aii~ei~~~~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIV-A--~AG~~GaVTIATN  684 (1112)
T PRK12901        608 KTKREKYNAVIEEITELSEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIV-A--EAGQPGTVTIATN  684 (1112)
T ss_pred             cCHHHHHHHHHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHH-H--hcCCCCcEEEecc
Confidence            34445555554444333  56899999999999999999999999998888887553333322 2  2343 45999999


Q ss_pred             ccccCCCCC--------CCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          347 LVGRGIDIE--------RVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       347 ~~~~Gld~~--------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      +++||.|+.        +--+||-...+.|..--.|-.||+||.|.+|..-.|++-.++
T Consensus       685 MAGRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLEDd  743 (1112)
T PRK12901        685 MAGRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLEDN  743 (1112)
T ss_pred             CcCCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEcccH
Confidence            999999996        456799999999999999999999999999999999986443

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

Probab=99.70  E-value=2.4e-15  Score=147.91  Aligned_cols=329  Identities=16%  Similarity=0.208  Sum_probs=213.8

Q ss_pred             CCChhhhhcccccccC-CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceE
Q 014486           68 HPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKV  146 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~-~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  146 (423)
                      ...|+|.++++.+... .++++.+|+|||||.++-++++.   +.. ..+++++.|..+.+..++..+.+-.....|..+
T Consensus      1143 ~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~---~~~-~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~ 1218 (1674)
T KOG0951|consen 1143 DFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR---PDT-IGRAVYIAPLEEIADEQYRDWEKKFSKLLGLRI 1218 (1674)
T ss_pred             ccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC---Ccc-ceEEEEecchHHHHHHHHHHHHHhhccccCceE
Confidence            4489999999998875 55999999999999998877776   222 238999999999888776666543333357888


Q ss_pred             EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCC-----cHHHHHHHHHhCCC
Q 014486          147 AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLD-----MRRDVQEIFKMTPH  221 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~-----~~~~~~~~~~~~~~  221 (423)
                      ..++|..+...  +.+..+  +|+|+||+++..+ +    ....+++.|+||+|.+.+..+     .-. ++.+...+.+
T Consensus      1219 ~~l~ge~s~~l--kl~~~~--~vii~tpe~~d~l-q----~iQ~v~l~i~d~lh~igg~~g~v~evi~S-~r~ia~q~~k 1288 (1674)
T KOG0951|consen 1219 VKLTGETSLDL--KLLQKG--QVIISTPEQWDLL-Q----SIQQVDLFIVDELHLIGGVYGAVYEVICS-MRYIASQLEK 1288 (1674)
T ss_pred             EecCCccccch--HHhhhc--ceEEechhHHHHH-h----hhhhcceEeeehhhhhcccCCceEEEEee-HHHHHHHHHh
Confidence            88888765543  233333  9999999998766 2    567789999999998864211     112 6677777778


Q ss_pred             CceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChH-HHH-----HHHHHHH-HhhcCCcEEEE
Q 014486          222 DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEL-EKN-----RKLNDLL-DALDFNQVVIF  294 (423)
Q Consensus       222 ~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~-----~~l~~ll-~~~~~~~~ivf  294 (423)
                      ..+++++|..+.+.- ++  ......-.+...+.....+-.+..+.+..... ...     ..+..+. ....+++.+||
T Consensus      1289 ~ir~v~ls~~lana~-d~--ig~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~a~~~k~~~vf 1365 (1674)
T KOG0951|consen 1289 KIRVVALSSSLANAR-DL--IGASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRHAGNRKPAIVF 1365 (1674)
T ss_pred             heeEEEeehhhccch-hh--ccccccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHHhcCCCCeEEE
Confidence            889999998887642 22  11111112222222222222222222222211 111     1111111 12256889999


Q ss_pred             EcChhhHHHHHHHHHhC----------------------CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCC
Q 014486          295 VKSVSRAAELNKLLVEC----------------------NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGI  352 (423)
Q Consensus       295 ~~~~~~~~~l~~~L~~~----------------------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gl  352 (423)
                      +++++++..++..|-..                      ..+..+=|.+++..+..-+..-|..|.+.|+|...- ..|+
T Consensus      1366 ~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v~s~~-~~~~ 1444 (1674)
T KOG0951|consen 1366 LPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCVMSRD-CYGT 1444 (1674)
T ss_pred             eccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEEEEcc-cccc
Confidence            99999988776554321                      112222277888888888888899999999998766 7777


Q ss_pred             CCCCCCEEEEcc-----------CCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhhhhhh
Q 014486          353 DIERVNIVINYD-----------MPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSFQCL  418 (423)
Q Consensus       353 d~~~~~~vi~~~-----------~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  418 (423)
                      -... +.||..+           .+.+...+.|++|++.|+   |.|+++.+.....-+.+-+.+.+.+.-..-+|+
T Consensus      1445 ~~~~-~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~~---~k~vi~~~~~~k~yykkfl~e~lPves~lq~~l 1517 (1674)
T KOG0951|consen 1445 KLKA-HLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASGA---GKCVIMCHTPKKEYYKKFLYEPLPVESHLQHCL 1517 (1674)
T ss_pred             cccc-eEEEEecceeecccccccccCchhHHHHHhhhhcCC---ccEEEEecCchHHHHHHhccCcCchHHHHHHHH
Confidence            6643 3344222           245678899999999995   568888887666655566666666655555554

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.69  E-value=1.4e-14  Score=145.08  Aligned_cols=110  Identities=19%  Similarity=0.240  Sum_probs=82.2

Q ss_pred             CCcEEEEEcChhhHHHHHHHHHhCCC-------CeEEEcCCCCHHHHHHHHHhhhc----CCccEEEEc--CccccCCCC
Q 014486          288 FNQVVIFVKSVSRAAELNKLLVECNF-------PSICIHSGMSQEERLTRYKGFKE----GNKRILVAT--DLVGRGIDI  354 (423)
Q Consensus       288 ~~~~ivf~~~~~~~~~l~~~L~~~~~-------~~~~~~~~~~~~~r~~~~~~f~~----~~~~ili~T--~~~~~Gld~  354 (423)
                      ++.+|||+++....+.+.+.+...+.       ..+.+-+ -...++..+++.|+.    ++..||+++  ..+++|+|+
T Consensus       522 pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~-~~~~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEGIDf  600 (705)
T TIGR00604       522 PDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVET-KDAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEGIDF  600 (705)
T ss_pred             CCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeC-CCcchHHHHHHHHHHHHhcCCceEEEEecCCcccCcccc
Confidence            47899999999999999888876432       1222222 222577888999964    455699998  889999999


Q ss_pred             CC--CCEEEEccCCC-Cc------------------------------chhhhcccccCCCCCceEEEEEecCcccH
Q 014486          355 ER--VNIVINYDMPD-SA------------------------------DTYLHRVGRAGRFGTKGLAITFVSSASDS  398 (423)
Q Consensus       355 ~~--~~~vi~~~~~~-s~------------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  398 (423)
                      ++  +++||.+++|. ++                              ....|.+||+-|..++-.++++++.....
T Consensus       601 ~~~~~r~ViivGlPf~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~a~~~v~QaiGR~IR~~~D~G~iillD~R~~~  677 (705)
T TIGR00604       601 CDDLGRAVIMVGIPYEYTESRILLARLEFLRDQYPIRENQDFYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDKRYAR  677 (705)
T ss_pred             CCCCCcEEEEEccCCCCCCCHHHHHHHHHHHhhcCCCccHHHHHHHHHHHHHHHhCccccCcCceEEEEEEehhcCC
Confidence            87  78999999886 21                              12369999999998888888888765443

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).

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.68  E-value=2.9e-14  Score=141.58  Aligned_cols=106  Identities=17%  Similarity=0.240  Sum_probs=80.2

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhC-CCCeEEEcCCCCHHHHHHHHHhhh----cCCccEEEEcCccccCCCCCC--CCE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVEC-NFPSICIHSGMSQEERLTRYKGFK----EGNKRILVATDLVGRGIDIER--VNI  359 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~----~~~~~ili~T~~~~~Gld~~~--~~~  359 (423)
                      ..+.++|++++....+.+++.|... +.+ +...+.   ..+..+++.|+    .++..||++|..+.+|+|+|+  +++
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            3456899999999999999998753 333 334453   24666776666    467779999999999999987  788


Q ss_pred             EEEccCCCC-c-----------------------------chhhhcccccCCCCCceEEEEEecCcc
Q 014486          360 VINYDMPDS-A-----------------------------DTYLHRVGRAGRFGTKGLAITFVSSAS  396 (423)
Q Consensus       360 vi~~~~~~s-~-----------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~~~  396 (423)
                      ||...+|.. |                             ..+.|.+||.-|..++..++++.++..
T Consensus       609 vII~kLPF~~p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~D~G~i~ilD~R~  675 (697)
T PRK11747        609 VIITKIPFAVPDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTILDRRL  675 (697)
T ss_pred             EEEEcCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCCceEEEEEEcccc
Confidence            999887752 1                             134699999999988877888888753

>PRK14873 primosome assembly protein PriA; Provisional

Probab=99.67  E-value=2.5e-15  Score=146.46  Aligned_cols=140  Identities=12%  Similarity=0.099  Sum_probs=99.8

Q ss_pred             EEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHH---Hh
Q 014486           87 ICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDL---LK  163 (423)
Q Consensus        87 ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~  163 (423)
                      +..+.+|||||.+|+-.+.+.+..++   .+||++|...|+.|+.+.+++...   +..+..++++.+..+..+.   ..
T Consensus       164 i~~~~~GSGKTevyl~~i~~~l~~Gk---~vLvLvPEi~lt~q~~~rl~~~f~---~~~v~~lhS~l~~~~R~~~w~~~~  237 (665)
T PRK14873        164 VWQALPGEDWARRLAAAAAATLRAGR---GALVVVPDQRDVDRLEAALRALLG---AGDVAVLSAGLGPADRYRRWLAVL  237 (665)
T ss_pred             HhhcCCCCcHHHHHHHHHHHHHHcCC---eEEEEecchhhHHHHHHHHHHHcC---CCcEEEECCCCCHHHHHHHHHHHh
Confidence            34444699999999876666655443   799999999999999999987653   2468889998876655443   45


Q ss_pred             cCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc----CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHH
Q 014486          164 NECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES----LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV  239 (423)
Q Consensus       164 ~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~----~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~  239 (423)
                      ++..+|+|+|...++       ..+.++++|||||=|.-.-.    ..+...-..+++....+.++|+.|||+.-+....
T Consensus       238 ~G~~~IViGtRSAvF-------aP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTPSles~~~  310 (665)
T PRK14873        238 RGQARVVVGTRSAVF-------APVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAEAQAL  310 (665)
T ss_pred             CCCCcEEEEcceeEE-------eccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHHcCCcEEEECCCCCHHHHHH
Confidence            677899999988775       47789999999999954321    1122222223333345778999999988665443

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.66  E-value=4e-16  Score=112.03  Aligned_cols=81  Identities=46%  Similarity=0.762  Sum_probs=77.0

Q ss_pred             HHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCC
Q 014486          303 ELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRF  382 (423)
Q Consensus       303 ~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~  382 (423)
                      .+.+.|...++++..+||.++..+|..+++.|+++...+||+|+++++|+|++.+++||++++|+++..|.|++||++|.
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            46677888899999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 014486          383 G  383 (423)
Q Consensus       383 g  383 (423)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            6

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=99.66  E-value=2.2e-15  Score=156.78  Aligned_cols=333  Identities=18%  Similarity=0.213  Sum_probs=209.3

Q ss_pred             CCCChhhhhccccccc-----CCceEEEccCCCcchhHHHHHHhhccCCCCC-CeEEEEEecChHHHHHHHHHHHHHhcc
Q 014486           67 EHPSEVQHECIPQAIL-----GMDVICQAKSGMGKTAVFVLSTLQQTEPNPG-QVTALVLCHTRELAYQICHEFERFSTY  140 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~-----~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~-~~~~lil~P~~~L~~q~~~~~~~~~~~  140 (423)
                      ..+++||...+.++..     +.+.+++.++|.|||+..+..+......... .+.+++++|+ +++.+|.+++.++.. 
T Consensus       337 ~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~-s~~~nw~~e~~k~~~-  414 (866)
T COG0553         337 AELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPA-SLLSNWKREFEKFAP-  414 (866)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecH-HHHHHHHHHHhhhCc-
Confidence            4688999999987662     5678999999999998876655542222221 2378999997 677888888877764 


Q ss_pred             CCCce-EEEEEcCcch----HHHHHHHhcC----CCcEEEechHHHHHHH-hcCCCCCCCccEEEEcCcchhhccCCcHH
Q 014486          141 LPDIK-VAVFYGGVNI----KIHKDLLKNE----CPQIVVGTPGRILALA-RDKDLSLKNVRHFILDECDKMLESLDMRR  210 (423)
Q Consensus       141 ~~~~~-~~~~~~~~~~----~~~~~~~~~~----~~~ilv~T~~~l~~~~-~~~~~~~~~~~~vVvDE~h~~~~~~~~~~  210 (423)
                        .++ +..++|....    ......+...    .++++++|++.+.... ....+.-..+..+|+||+|.+.+.  ...
T Consensus       415 --~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~ikn~--~s~  490 (866)
T COG0553         415 --DLRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKND--QSS  490 (866)
T ss_pred             --cccceeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHHhhceeeeeehhhHHHHhhh--hhH
Confidence              445 7777776642    2333333322    2589999999887732 222344466788999999997652  111


Q ss_pred             HHHHHHHhCCCCceEEEEeccCC-ccHH--------------------------------------------------HH
Q 014486          211 DVQEIFKMTPHDKQVMMFSATLS-KEIR--------------------------------------------------PV  239 (423)
Q Consensus       211 ~~~~~~~~~~~~~~~v~~SAT~~-~~~~--------------------------------------------------~~  239 (423)
                      ....+. .+.... .+.+|+||- +.+.                                                  ..
T Consensus       491 ~~~~l~-~~~~~~-~~~LtgTPlen~l~eL~sl~~~f~~p~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  568 (866)
T COG0553         491 EGKALQ-FLKALN-RLDLTGTPLENRLGELWSLLQEFLNPGLLGTSFAIFTRLFEKPIQAEEDIGPLEARELGIELLRKL  568 (866)
T ss_pred             HHHHHH-HHhhcc-eeeCCCChHhhhHHHHHHHHHHHhCCccccchHHHHHHHHhhhhhhcccccchhhHHHHHHHHHHH
Confidence            111111 111111 244555540 0000                                                  00


Q ss_pred             HHHhc-cCC-ce--ee--------------------------ec----------c---cc---------cc-------cc
Q 014486          240 CKKFM-QDP-ME--IY--------------------------VD----------D---EA---------KL-------TL  260 (423)
Q Consensus       240 ~~~~~-~~~-~~--~~--------------------------~~----------~---~~---------~~-------~~  260 (423)
                      +..+. ... ..  +.                          ..          .   ..         ..       ..
T Consensus       569 i~~f~lrr~k~~~~v~~~Lp~k~e~~~~~~l~~~q~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l  648 (866)
T COG0553         569 LSPFILRRTKEDVEVLKELPPKIEKVLECELSEEQRELYEALLEGAEKNQQLLEDLEKADSDENRIGDSELNILALLTRL  648 (866)
T ss_pred             HHHHhhcccccchhHHHhCChhhhhhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccchhhHHHHHHHHH
Confidence            00000 000 00  00                          00          0   00         00       00


Q ss_pred             ccceEEEEEeC-----------------------------hH-HHHHHHHHHH-Hh--hcCC--cEEEEEcChhhHHHHH
Q 014486          261 HGLVQHYIKLS-----------------------------EL-EKNRKLNDLL-DA--LDFN--QVVIFVKSVSRAAELN  305 (423)
Q Consensus       261 ~~~~~~~~~~~-----------------------------~~-~~~~~l~~ll-~~--~~~~--~~ivf~~~~~~~~~l~  305 (423)
                      ..+..+.....                             .. .|...+.+++ ..  ..+.  ++++|++.....+.+.
T Consensus       649 r~~~~~p~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~k~~~l~~ll~~~~~~~~~~~kvlifsq~t~~l~il~  728 (866)
T COG0553         649 RQICNHPALVDEGLEATFDRIVLLLREDKDFDYLKKPLIQLSKGKLQALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLE  728 (866)
T ss_pred             HHhccCccccccccccccchhhhhhhcccccccccchhhhccchHHHHHHHHHHHHHHhhcccccEEEEeCcHHHHHHHH
Confidence            00000000000                             00 4556666666 22  2344  8999999999999999


Q ss_pred             HHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcC--CccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCC
Q 014486          306 KLLVECNFPSICIHSGMSQEERLTRYKGFKEG--NKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFG  383 (423)
Q Consensus       306 ~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~--~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g  383 (423)
                      ..|...++....++|.++...|...++.|.++  ...+++++.+++.|+|+..+++||++|+.|++....|+..|++|.|
T Consensus       729 ~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~kagg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~Rig  808 (866)
T COG0553         729 DYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIG  808 (866)
T ss_pred             HHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEecccccceeecccceEEEeccccChHHHHHHHHHHHHhc
Confidence            99999998899999999999999999999986  3456668899999999999999999999999999999999999999


Q ss_pred             CceEEEEE--ecCcc-cHHHHHHHHHH
Q 014486          384 TKGLAITF--VSSAS-DSDILNQVSKF  407 (423)
Q Consensus       384 ~~~~~~~~--~~~~~-~~~~~~~~~~~  407 (423)
                      |+..+.++  +.... +..++....++
T Consensus       809 Q~~~v~v~r~i~~~tiEe~i~~~~~~K  835 (866)
T COG0553         809 QKRPVKVYRLITRGTIEEKILELQEKK  835 (866)
T ss_pred             CcceeEEEEeecCCcHHHHHHHHHHHH
Confidence            98665543  43333 34444444443

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=99.65  E-value=1.5e-14  Score=142.78  Aligned_cols=320  Identities=18%  Similarity=0.162  Sum_probs=178.9

Q ss_pred             HHHHHhCCCCCCChhhhhccccccc----C--Cc--eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHH
Q 014486           58 LRAIVDSGFEHPSEVQHECIPQAIL----G--MD--VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQ  129 (423)
Q Consensus        58 ~~~l~~~~~~~~~~~Q~~~i~~~~~----~--~~--~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  129 (423)
                      .+.+.+..-..-+.+|-+|+..+..    .  +.  ++-.|.||+|||++=. -|+..+.....+.+..|..-.|.|..|
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            3444433333456788888877664    1  12  6778999999998753 344444444455577777778888888


Q ss_pred             HHHHHHHHhccCCCceEEEEEcCcchHHHHH-------------------------------------------HHhc--
Q 014486          130 ICHEFERFSTYLPDIKVAVFYGGVNIKIHKD-------------------------------------------LLKN--  164 (423)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------------------------~~~~--  164 (423)
                      .-+.+++-.... +-..+++.|+....+...                                           .+.+  
T Consensus       477 TGda~r~rL~L~-~ddLAVlIGs~Av~~L~e~~~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~  555 (1110)
T TIGR02562       477 TGHALKTRLNLS-DDDLAVLIGGTAVQTLFDLSKEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDD  555 (1110)
T ss_pred             chHHHHHhcCCC-ccceEEEECHHHHHHHHHHHhhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccCh
Confidence            877776644332 334444444432211110                                           0000  


Q ss_pred             -----CCCcEEEechHHHHHHHhcC---CCCC----CCccEEEEcCcchhhccCCcHHHHHHHHHhC-CCCceEEEEecc
Q 014486          165 -----ECPQIVVGTPGRILALARDK---DLSL----KNVRHFILDECDKMLESLDMRRDVQEIFKMT-PHDKQVMMFSAT  231 (423)
Q Consensus       165 -----~~~~ilv~T~~~l~~~~~~~---~~~~----~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-~~~~~~v~~SAT  231 (423)
                           -...++|||++.++......   ...+    -.-+.||+||+|.+..  .....+.+++..+ ....++++||||
T Consensus       556 k~~rll~apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaYD~--~~~~~L~rlL~w~~~lG~~VlLmSAT  633 (1110)
T TIGR02562       556 KEKTLLAAPVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDYEP--EDLPALLRLVQLAGLLGSRVLLSSAT  633 (1110)
T ss_pred             hhhhhhcCCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccCCH--HHHHHHHHHHHHHHHcCCCEEEEeCC
Confidence                 01469999999998765221   1111    1134699999997754  2233344444422 225779999999


Q ss_pred             CCccHHHHHHHhc-----------cCC---ceee--eccccccc----------------------------cccceEEE
Q 014486          232 LSKEIRPVCKKFM-----------QDP---MEIY--VDDEAKLT----------------------------LHGLVQHY  267 (423)
Q Consensus       232 ~~~~~~~~~~~~~-----------~~~---~~~~--~~~~~~~~----------------------------~~~~~~~~  267 (423)
                      +|+.+...+...+           +.+   ..+-  ..++....                            ...-.-..
T Consensus       634 LP~~l~~~L~~Ay~~G~~~~q~~~g~~~~~~~i~CaW~DE~~~~~~~~~~~~~F~~~H~~Fv~~R~~~L~~~p~~R~a~i  713 (1110)
T TIGR02562       634 LPPALVKTLFRAYEAGRQMYQALYGQPKKPLNICCAWVDEPQVWQADCNQKSEFIQRHQDFLRDRAVQLAKKPVRRLAEL  713 (1110)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhcCCCCCCcceeEEeecccCchhhhhcCHHHHHHHHHHHHHHHHHHHhcCcccceEEE
Confidence            9988765432221           211   1111  00000000                            00000011


Q ss_pred             EEeChH-----HHHHHHHH--------HHHhh----c-CCc----EEEEEcChhhHHHHHHHHHhC----C--CCeEEEc
Q 014486          268 IKLSEL-----EKNRKLND--------LLDAL----D-FNQ----VVIFVKSVSRAAELNKLLVEC----N--FPSICIH  319 (423)
Q Consensus       268 ~~~~~~-----~~~~~l~~--------ll~~~----~-~~~----~ivf~~~~~~~~~l~~~L~~~----~--~~~~~~~  319 (423)
                      ..++..     .....+..        +...+    + .++    .+|-.++++.+-.+++.|...    +  +.+.+||
T Consensus       714 ~~~~~~~~~~~~~~~~~a~~i~~~~~~LH~~h~~~~~~sgk~VSfGliR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yH  793 (1110)
T TIGR02562       714 LSLSSLPRENESTYLALAQSLLEGALRLHQAHAQTDPKSEKKVSVGLIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYH  793 (1110)
T ss_pred             eecCCcccchhHHHHHHHHHHHHHHHHHHHHhCccCCCCCeEEEEEEEEEcCchHHHHHHHHHHhhccccCCceeEEEec
Confidence            111111     11111111        11111    1 122    478888888888887777654    2  3477799


Q ss_pred             CCCCHHHHHHHHHhh---------------------h-c----CCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhh
Q 014486          320 SGMSQEERLTRYKGF---------------------K-E----GNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYL  373 (423)
Q Consensus       320 ~~~~~~~r~~~~~~f---------------------~-~----~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~  373 (423)
                      +..+...|..+.+..                     . +    +...|+|+|++.+.|+|+. .+  ..+..|.++...+
T Consensus       794 Sr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~~~i~v~Tqv~E~g~D~d-fd--~~~~~~~~~~sli  870 (1110)
T TIGR02562       794 AQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNHLFIVLATPVEEVGRDHD-YD--WAIADPSSMRSII  870 (1110)
T ss_pred             ccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCCCeEEEEeeeEEEEeccc-CC--eeeeccCcHHHHH
Confidence            998777776654332                     1 1    3567999999999999973 34  3344577788999


Q ss_pred             hcccccCCCCC
Q 014486          374 HRVGRAGRFGT  384 (423)
Q Consensus       374 Q~~GR~~R~g~  384 (423)
                      |++||+.|.|.
T Consensus       871 Q~aGR~~R~~~  881 (1110)
T TIGR02562       871 QLAGRVNRHRL  881 (1110)
T ss_pred             HHhhccccccc
Confidence            99999999764

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.

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=99.65  E-value=7.6e-15  Score=140.49  Aligned_cols=117  Identities=17%  Similarity=0.187  Sum_probs=99.0

Q ss_pred             HHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHh----------------------CCCCeEEEcCCCCHHHHHHH
Q 014486          275 KNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVE----------------------CNFPSICIHSGMSQEERLTR  330 (423)
Q Consensus       275 ~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~----------------------~~~~~~~~~~~~~~~~r~~~  330 (423)
                      |.-.|.++|...  -+.+.|||.++....+-+..+|..                      .|.....+.|..+...|...
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            344566666544  368999999999998888888754                      24567788999999999999


Q ss_pred             HHhhhcCC----ccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEE
Q 014486          331 YKGFKEGN----KRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITF  391 (423)
Q Consensus       331 ~~~f~~~~----~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~  391 (423)
                      .+.|++..    .-.||+|.+.+.|+|+-.++.||+||-.|+|+.-.|.+=|+.|.||..-|+++
T Consensus      1207 ~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyiY 1271 (1567)
T KOG1015|consen 1207 AEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYIY 1271 (1567)
T ss_pred             HHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceeeh
Confidence            99998643    23899999999999999999999999999999999999999999998888764

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

Probab=99.56  E-value=3.9e-13  Score=129.63  Aligned_cols=288  Identities=13%  Similarity=0.182  Sum_probs=179.3

Q ss_pred             ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhc
Q 014486           85 DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN  164 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (423)
                      -.+|.+|+|+|||.+..-++-..+.. +. .++|+++.+++|+.+....++...-  ++..  .+.....     ..+..
T Consensus        51 V~vVRSpMGTGKTtaLi~wLk~~l~~-~~-~~VLvVShRrSL~~sL~~rf~~~~l--~gFv--~Y~d~~~-----~~i~~  119 (824)
T PF02399_consen   51 VLVVRSPMGTGKTTALIRWLKDALKN-PD-KSVLVVSHRRSLTKSLAERFKKAGL--SGFV--NYLDSDD-----YIIDG  119 (824)
T ss_pred             eEEEECCCCCCcHHHHHHHHHHhccC-CC-CeEEEEEhHHHHHHHHHHHHhhcCC--Ccce--eeecccc-----ccccc
Confidence            37999999999998765555444432 22 2899999999999999988875421  1221  1111111     01111


Q ss_pred             CCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHH-------HHHHHHhCCCCceEEEEeccCCccHH
Q 014486          165 ECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRD-------VQEIFKMTPHDKQVMMFSATLSKEIR  237 (423)
Q Consensus       165 ~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~-------~~~~~~~~~~~~~~v~~SAT~~~~~~  237 (423)
                      ..++-+++..++|.++.   ...+.++++||+||+-..+.. -+.+.       +..+...+.....+|++-|++.....
T Consensus       120 ~~~~rLivqIdSL~R~~---~~~l~~yDvVIIDEv~svL~q-L~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tv  195 (824)
T PF02399_consen  120 RPYDRLIVQIDSLHRLD---GSLLDRYDVVIIDEVMSVLNQ-LFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTV  195 (824)
T ss_pred             cccCeEEEEehhhhhcc---cccccccCEEEEehHHHHHHH-HhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHH
Confidence            12467777888886543   224567899999999988762 23222       33344556667889999999999999


Q ss_pred             HHHHHhccCCceeeecccccc-ccccceEEEE----------------------------------EeChHHHHHHHHHH
Q 014486          238 PVCKKFMQDPMEIYVDDEAKL-TLHGLVQHYI----------------------------------KLSELEKNRKLNDL  282 (423)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~----------------------------------~~~~~~~~~~l~~l  282 (423)
                      ++++.+........+..+... ....-.-.+.                                  .....+.......+
T Consensus       196 dFl~~~Rp~~~i~vI~n~y~~~~fs~R~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tF~~~L  275 (824)
T PF02399_consen  196 DFLASCRPDENIHVIVNTYASPGFSNRRCTFLRSLGTDTLAAALNPEDENADTSPTPKHSPDPTATAAISNDETTFFSEL  275 (824)
T ss_pred             HHHHHhCCCCcEEEEEeeeecCCcccceEEEecccCcHHHHHHhCCcccccccCCCcCCCCccccccccccchhhHHHHH
Confidence            998887654332221111000 0000000000                                  00001122344445


Q ss_pred             HHhh-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCC--CE
Q 014486          283 LDAL-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV--NI  359 (423)
Q Consensus       283 l~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~--~~  359 (423)
                      +..+ .++++.||+.+...++.+++..+..+..+..+++.-+..+.    +.  -++.+|++-|+++..|+++...  +-
T Consensus       276 ~~~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~dv----~~--W~~~~VviYT~~itvG~Sf~~~HF~~  349 (824)
T PF02399_consen  276 LARLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLEDV----ES--WKKYDVVIYTPVITVGLSFEEKHFDS  349 (824)
T ss_pred             HHHHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCcccc----cc--ccceeEEEEeceEEEEeccchhhceE
Confidence            5554 35678889999999999999999888888889887665532    22  3578999999999999998654  33


Q ss_pred             EEEccCC----CCcchhhhcccccCCCCCceEEEEEecC
Q 014486          360 VINYDMP----DSADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       360 vi~~~~~----~s~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                      |+.|--|    .++.+..|++||+..... ...+++++.
T Consensus       350 ~f~yvk~~~~gpd~~s~~Q~lgRvR~l~~-~ei~v~~d~  387 (824)
T PF02399_consen  350 MFAYVKPMSYGPDMVSVYQMLGRVRSLLD-NEIYVYIDA  387 (824)
T ss_pred             EEEEecCCCCCCcHHHHHHHHHHHHhhcc-CeEEEEEec
Confidence            4444323    234467999999976543 455555553

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

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=99.52  E-value=4.5e-12  Score=119.52  Aligned_cols=115  Identities=16%  Similarity=0.237  Sum_probs=93.0

Q ss_pred             CcEEEEEcChhhHHHHHHHHHhCC------------------CCeEEEcCCCCHHHHHHHHHhhhcCC---ccEEEEcCc
Q 014486          289 NQVVIFVKSVSRAAELNKLLVECN------------------FPSICIHSGMSQEERLTRYKGFKEGN---KRILVATDL  347 (423)
Q Consensus       289 ~~~ivf~~~~~~~~~l~~~L~~~~------------------~~~~~~~~~~~~~~r~~~~~~f~~~~---~~ili~T~~  347 (423)
                      .++|||..+....+.+.+.|..+.                  ...+.+.|..+..+|++.+.+|++..   .-++++|.+
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            468999999999999988887752                  24556788899999999999998643   247889999


Q ss_pred             cccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEE---ecCcccHHHHHH
Q 014486          348 VGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITF---VSSASDSDILNQ  403 (423)
Q Consensus       348 ~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~---~~~~~~~~~~~~  403 (423)
                      ...|+|+-..+.+|.++..|++..-.|++.|+.|.||+..|+++   ++..-+..+++.
T Consensus       800 g~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYRlVmD~~lEkkIydR  858 (1387)
T KOG1016|consen  800 GSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYRLVMDNSLEKKIYDR  858 (1387)
T ss_pred             ccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEeehhhhhhHHHHHHH
Confidence            99999999999999999999999999999999999998877754   333344444443

>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=2.9e-11  Score=111.03  Aligned_cols=238  Identities=18%  Similarity=0.219  Sum_probs=163.2

Q ss_pred             CcEEEechHHHHHHHhcC------CCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCC--------------------
Q 014486          167 PQIVVGTPGRILALARDK------DLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTP--------------------  220 (423)
Q Consensus       167 ~~ilv~T~~~l~~~~~~~------~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~--------------------  220 (423)
                      .||||++|=-|...+...      ...++.+.++|+|.+|.+.- .+ ...+..+++.++                    
T Consensus       132 SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~M-QN-W~Hv~~v~~~lN~~P~~~~~~DfsRVR~w~Ld  209 (442)
T PF06862_consen  132 SDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLM-QN-WEHVLHVFEHLNLQPKKSHDTDFSRVRPWYLD  209 (442)
T ss_pred             CCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHH-hh-HHHHHHHHHHhccCCCCCCCCCHHHHHHHHHc
Confidence            589999999888777642      23378899999999998763 12 222222222222                    


Q ss_pred             ----CCceEEEEeccCCccHHHHHHHhccCCce-eee--ccc----cccccccceEEEEEeCh-------HHHHH-----
Q 014486          221 ----HDKQVMMFSATLSKEIRPVCKKFMQDPME-IYV--DDE----AKLTLHGLVQHYIKLSE-------LEKNR-----  277 (423)
Q Consensus       221 ----~~~~~v~~SAT~~~~~~~~~~~~~~~~~~-~~~--~~~----~~~~~~~~~~~~~~~~~-------~~~~~-----  277 (423)
                          .-+|.|++|+...+++..+....+.+..- +.+  ...    -......+.+.+...+.       ..+..     
T Consensus       210 g~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~~s~~~~~d~Rf~yF~~~  289 (442)
T PF06862_consen  210 GQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDCSSPADDPDARFKYFTKK  289 (442)
T ss_pred             CcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecCCCcchhhhHHHHHHHHH
Confidence                23499999999999998888775544321 111  111    01222333344433221       11221     


Q ss_pred             HHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccc--cCCCCC
Q 014486          278 KLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVG--RGIDIE  355 (423)
Q Consensus       278 ~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~--~Gld~~  355 (423)
                      .+-.+......+.+|||+++.-+--.+.++|+..++....++.-++..+-.++-..|..|+.+||+.|.-+-  +=..+.
T Consensus       290 iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfrRy~ir  369 (442)
T PF06862_consen  290 ILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFRRYRIR  369 (442)
T ss_pred             HHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhhhceec
Confidence            122222133457899999999999999999999999999999999999999999999999999999997654  457788


Q ss_pred             CCCEEEEccCCCCcchhhhcccccCCCCC------ceEEEEEecCcccHHHHHHHHHHHhc
Q 014486          356 RVNIVINYDMPDSADTYLHRVGRAGRFGT------KGLAITFVSSASDSDILNQVSKFMFL  410 (423)
Q Consensus       356 ~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~------~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (423)
                      ++++||+|++|..+.-|...+.-.+....      ...|.++++.- +.   ..|++..|.
T Consensus       370 Gi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~-D~---~~LErIVGt  426 (442)
T PF06862_consen  370 GIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKY-DA---LRLERIVGT  426 (442)
T ss_pred             CCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHh-HH---HHHHHHhCH
Confidence            89999999999999988877765555433      57888888743 32   345555553

; GO: 0005634 nucleus

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

Probab=99.49  E-value=3.4e-13  Score=102.85  Aligned_cols=136  Identities=19%  Similarity=0.183  Sum_probs=80.3

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL  162 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (423)
                      |+-.++..++|+|||.-.+.-++.+....+.  ++|||.|||.++..+.+.++.       ..+..-..... .   .. 
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~~~~--rvLvL~PTRvva~em~~aL~~-------~~~~~~t~~~~-~---~~-   69 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAIKRRL--RVLVLAPTRVVAEEMYEALKG-------LPVRFHTNARM-R---TH-   69 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHHHTT----EEEEESSHHHHHHHHHHTTT-------SSEEEESTTSS--------
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHHHccC--eEEEecccHHHHHHHHHHHhc-------CCcccCceeee-c---cc-
Confidence            4447899999999999877666665444333  899999999999988876643       23322222111 1   11 


Q ss_pred             hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccC-CcHHHHHHHHHhCCCCceEEEEeccCCccH
Q 014486          163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESL-DMRRDVQEIFKMTPHDKQVMMFSATLSKEI  236 (423)
Q Consensus       163 ~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~-~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~  236 (423)
                       .+..-|-++|+..+.+++.+ .....++++||+||||...... .++..+... ... ....+|++|||+|...
T Consensus        70 -~g~~~i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~Dp~sIA~rg~l~~~-~~~-g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen   70 -FGSSIIDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFTDPTSIAARGYLREL-AES-GEAKVIFMTATPPGSE  140 (148)
T ss_dssp             --SSSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--SHHHHHHHHHHHHH-HHT-TS-EEEEEESS-TT--
T ss_pred             -cCCCcccccccHHHHHHhcC-cccccCccEEEEeccccCCHHHHhhheeHHHh-hhc-cCeeEEEEeCCCCCCC
Confidence             12247889999998887655 5567899999999999653210 112222222 222 2357999999999654

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 ....

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

Probab=99.47  E-value=9.8e-12  Score=126.97  Aligned_cols=139  Identities=17%  Similarity=0.136  Sum_probs=93.9

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHh
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLK  163 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (423)
                      +.++|+.-+|||||++.+. +...+......+++++||.++.|-.|..+.+..+........     ...+.....+.+.
T Consensus       274 ~~G~IWHtqGSGKTlTm~~-~A~~l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~-----~~~s~~~Lk~~l~  347 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFK-LARLLLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP-----KAESTSELKELLE  347 (962)
T ss_pred             CceEEEeecCCchHHHHHH-HHHHHHhccCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc-----cccCHHHHHHHHh
Confidence            4599999999999998544 333333336677999999999999999999999875432111     3445555556666


Q ss_pred             cCCCcEEEechHHHHHHHhcC-C-CCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCC
Q 014486          164 NECPQIVVGTPGRILALARDK-D-LSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLS  233 (423)
Q Consensus       164 ~~~~~ilv~T~~~l~~~~~~~-~-~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~  233 (423)
                      .+.-.|+|||-++|-...... . ..-.+--+||+||||+--    +...-..+...++ ....+++|+||-
T Consensus       348 ~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRSQ----~G~~~~~~~~~~~-~a~~~gFTGTPi  414 (962)
T COG0610         348 DGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRSQ----YGELAKLLKKALK-KAIFIGFTGTPI  414 (962)
T ss_pred             cCCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhcc----ccHHHHHHHHHhc-cceEEEeeCCcc
Confidence            554599999999998876553 1 112233468999999642    2222222233333 366999999984

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=99.47  E-value=2.6e-12  Score=124.81  Aligned_cols=312  Identities=20%  Similarity=0.245  Sum_probs=194.0

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .|+..|.-+  .+.-+..-+..+-||-|||+++.+|+.-....++   .+.+++..--||..-++++..+..+. +++++
T Consensus        80 ~~~dVQliG--~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~gk---gVhvVTvNdYLA~RDae~m~~l~~~L-GlsvG  153 (822)
T COG0653          80 RHFDVQLLG--GIVLHLGDIAEMRTGEGKTLVATLPAYLNALAGK---GVHVVTVNDYLARRDAEWMGPLYEFL-GLSVG  153 (822)
T ss_pred             ChhhHHHhh--hhhhcCCceeeeecCCchHHHHHHHHHHHhcCCC---CcEEeeehHHhhhhCHHHHHHHHHHc-CCcee
Confidence            455555544  4555566889999999999999999887776655   56888888899999999999988887 99999


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcCC------CCCCCccEEEEcCcchhhcc---------------
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDKD------LSLKNVRHFILDECDKMLES---------------  205 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~~------~~~~~~~~vVvDE~h~~~~~---------------  205 (423)
                      +...+....+....+.   .+|.++|...| +++++.+.      .....+.+.|+||++.++-+               
T Consensus       154 ~~~~~m~~~ek~~aY~---~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSILIDEARtPLiISG~~~~~  230 (822)
T COG0653         154 VILAGMSPEEKRAAYA---CDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSILIDEARTPLIISGPAEDS  230 (822)
T ss_pred             eccCCCChHHHHHHHh---cCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhheeeeccccceeeecccccC
Confidence            9988886665555544   49999998765 22222211      12346889999999987621               


Q ss_pred             CCcHHHHHHHHHhCCCC--------c------------------------------------------------------
Q 014486          206 LDMRRDVQEIFKMTPHD--------K------------------------------------------------------  223 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~~--------~------------------------------------------------------  223 (423)
                      ...+..+..+...+...        .                                                      
T Consensus       231 ~~~Y~~~~~~v~~l~~~~d~~iDek~k~v~lte~G~~kae~~f~~~~Ly~~en~~~~h~~~~alrA~~l~~~D~dYIVrd  310 (822)
T COG0653         231 SELYKKVDDLVRLLSEDEDFTIDEKSKNVSLTESGLEKAEELLGIENLYDLENVNLVHHLNQALRAHILFFRDVDYIVRD  310 (822)
T ss_pred             chHHHHHHHHHHHhccccceeecchhcccccchhhHHHHHHHhCcccccchhhHHHHhhHHHHHHHHHHhhcCCeeEEec
Confidence            11222333333222211        0                                                      


Q ss_pred             -------------------------------------------------------eEEEEeccCCccHHHHHHHhccCCc
Q 014486          224 -------------------------------------------------------QVMMFSATLSKEIRPVCKKFMQDPM  248 (423)
Q Consensus       224 -------------------------------------------------------~~v~~SAT~~~~~~~~~~~~~~~~~  248 (423)
                                                                             ++.+||+|...+...+...+.....
T Consensus       311 ~ev~IvD~ftGR~m~gRr~s~GLhQAiEAKEgv~i~~e~~tlatITfQn~fR~y~kl~gmTGTa~te~~EF~~iY~l~vv  390 (822)
T COG0653         311 GEVVIVDEFTGRMMEGRRWSDGLHQAIEAKEGVEIQEENQTLATITFQNLFRLYPKLAGMTGTADTEEEEFDVIYGLDVV  390 (822)
T ss_pred             CeEEEEecccCCcccCcCCCchhHHHHHHhcCCcccccceeehhhhHHHHHhhhhhhcCCCCcchhhhhhhhhccCCcee
Confidence                                                                   1112222222222222222222221


Q ss_pred             eeeeccccccccccceEEEEEeChHHHHHHHHHHHHh-h-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHH
Q 014486          249 EIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDA-L-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEE  326 (423)
Q Consensus       249 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~-~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~  326 (423)
                      .+....+  ...... ...+......|...+..-+.. + .+.|+||-+.+++.++.+.+.|.+.|++..++.......+
T Consensus       391 ~iPTnrp--~~R~D~-~D~vy~t~~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLNAk~h~~E  467 (822)
T COG0653         391 VIPTNRP--IIRLDE-PDLVYKTEEEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRKAGIPHNVLNAKNHARE  467 (822)
T ss_pred             eccCCCc--ccCCCC-ccccccchHHHHHHHHHHHHHHHhcCCCEEEcCcceecchhHHHHHHhcCCCceeeccccHHHH
Confidence            1111111  111111 111222344455444444432 2 5689999999999999999999999999989988876444


Q ss_pred             HHHHHHhhhcCCc-cEEEEcCccccCCCCCCCC-----------EEEEccCCCCcchhhhcccccCCCCCceEEEEEecC
Q 014486          327 RLTRYKGFKEGNK-RILVATDLVGRGIDIERVN-----------IVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       327 r~~~~~~f~~~~~-~ili~T~~~~~Gld~~~~~-----------~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                      -..+  .+ .|.. -|-|||+++++|-|+.--.           +||-...-.|-.--.|-.||+||.|-+|..-.+++-
T Consensus       468 A~Ii--a~-AG~~gaVTiATNMAGRGTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S~F~lSl  544 (822)
T COG0653         468 AEII--AQ-AGQPGAVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLSL  544 (822)
T ss_pred             HHHH--hh-cCCCCccccccccccCCcccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchhhhhhhh
Confidence            4433  22 3333 4889999999999985322           344444444444456999999999988888877764

>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=99.43  E-value=6.6e-13  Score=120.46  Aligned_cols=146  Identities=15%  Similarity=0.186  Sum_probs=84.3

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccC--CCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTE--PNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKD  160 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~--~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (423)
                      .+.++++.++|+|||.+.+..+.....  ...+...+||++|. .+..||..++.++.... .+++..+.+.........
T Consensus        25 ~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~-~~~v~~~~~~~~~~~~~~  102 (299)
T PF00176_consen   25 PRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPD-SLRVIIYDGDSERRRLSK  102 (299)
T ss_dssp             T-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT--TS-EEEESSSCHHHHTTS
T ss_pred             CCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeecc-chhhhhhhhhccccccc-cccccccccccccccccc
Confidence            356999999999999887665542221  22221258999999 78899999999987542 567777776651111111


Q ss_pred             HHhcCCCcEEEechHHHHHHHh---cCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCcc
Q 014486          161 LLKNECPQIVVGTPGRILALAR---DKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKE  235 (423)
Q Consensus       161 ~~~~~~~~ilv~T~~~l~~~~~---~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~  235 (423)
                      .. ...++++++|++.+.....   ...+...++++||+||+|.+.+  ........+ ..+. ...++++||||-..
T Consensus       103 ~~-~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k~--~~s~~~~~l-~~l~-~~~~~lLSgTP~~n  175 (299)
T PF00176_consen  103 NQ-LPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLKN--KDSKRYKAL-RKLR-ARYRWLLSGTPIQN  175 (299)
T ss_dssp             SS-CCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGTT--TTSHHHHHH-HCCC-ECEEEEE-SS-SSS
T ss_pred             cc-cccceeeeccccccccccccccccccccccceeEEEeccccccc--ccccccccc-cccc-cceEEeeccccccc
Confidence            11 2336999999999981000   0011123488999999999954  222223333 3344 56688999998543

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.

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.26  E-value=1.2e-10  Score=105.71  Aligned_cols=329  Identities=16%  Similarity=0.198  Sum_probs=197.9

Q ss_pred             CCCCChhhhhcccccccCCceEE-EccCCCcc--hhHHHHHHhhccCC----------------------------CCCC
Q 014486           66 FEHPSEVQHECIPQAILGMDVIC-QAKSGMGK--TAVFVLSTLQQTEP----------------------------NPGQ  114 (423)
Q Consensus        66 ~~~~~~~Q~~~i~~~~~~~~~ii-~~~tGsGK--T~~~~~~~~~~~~~----------------------------~~~~  114 (423)
                      -.++++.|.+.+..+..-++++. ....+.|+  +.+|.+-++.++..                            +-..
T Consensus       214 s~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tR  293 (698)
T KOG2340|consen  214 SEPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTR  293 (698)
T ss_pred             cCcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCC
Confidence            45889999999988888888553 33345566  34555655543211                            1134


Q ss_pred             eEEEEEecChHHHHHHHHHHHHHhccCCCceEEE------------------------------EEcCcc--------hH
Q 014486          115 VTALVLCHTRELAYQICHEFERFSTYLPDIKVAV------------------------------FYGGVN--------IK  156 (423)
Q Consensus       115 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~------------------------------~~~~~~--------~~  156 (423)
                      |++||+||+++-|-.+...+..++.....-+..+                              +.|+++        +.
T Consensus       294 pkVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~ft  373 (698)
T KOG2340|consen  294 PKVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAFT  373 (698)
T ss_pred             ceEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHHH
Confidence            7999999999999999998887743221101110                              111111        11


Q ss_pred             HHHHHHhc--CCCcEEEechHHHHHHHhcCCC------CCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCC------
Q 014486          157 IHKDLLKN--ECPQIVVGTPGRILALARDKDL------SLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHD------  222 (423)
Q Consensus       157 ~~~~~~~~--~~~~ilv~T~~~l~~~~~~~~~------~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~------  222 (423)
                      ...-.+..  ...+|+||+|=-|..++.+...      .++.+.++|||-+|.++- .++. .+..++..+...      
T Consensus       374 kKtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~-QNwE-hl~~ifdHLn~~P~k~h~  451 (698)
T KOG2340|consen  374 KKTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLM-QNWE-HLLHIFDHLNLQPSKQHD  451 (698)
T ss_pred             HHHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHH-hhHH-HHHHHHHHhhcCcccccC
Confidence            11111111  1259999999988887773322      257788999999998875 3333 333333333221      


Q ss_pred             ------------------ceEEEEeccCCccHHHHHHHhccCCceee----eccc-----cccccccceEE-----EEEe
Q 014486          223 ------------------KQVMMFSATLSKEIRPVCKKFMQDPMEIY----VDDE-----AKLTLHGLVQH-----YIKL  270 (423)
Q Consensus       223 ------------------~~~v~~SAT~~~~~~~~~~~~~~~~~~~~----~~~~-----~~~~~~~~~~~-----~~~~  270 (423)
                                        +|.+++|+--.+....+...++.+..--.    +...     ...+...+.+.     ....
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                              26666666655555555544443321110    0000     00011111111     1122


Q ss_pred             ChHHHHHHHHHHHHhh---cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc
Q 014486          271 SELEKNRKLNDLLDAL---DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL  347 (423)
Q Consensus       271 ~~~~~~~~l~~ll~~~---~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~  347 (423)
                      ++..-...+..++-..   ....+|||.++.-.--++.++++..++....++.-.+...-.++-.-|-.|...+|+.|.-
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            2222222333333222   2346899999999999999999998888777777777776666777799999999999976


Q ss_pred             cc--cCCCCCCCCEEEEccCCCCcchhh---hcccccCCCC----CceEEEEEecCcc
Q 014486          348 VG--RGIDIERVNIVINYDMPDSADTYL---HRVGRAGRFG----TKGLAITFVSSAS  396 (423)
Q Consensus       348 ~~--~Gld~~~~~~vi~~~~~~s~~~~~---Q~~GR~~R~g----~~~~~~~~~~~~~  396 (423)
                      +-  +-.++.+++.||+|.+|..|.-|.   -+.+|+.-.|    ..-.|.++++.-+
T Consensus       612 ~hffrR~~ikGVk~vVfYqpP~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD  669 (698)
T KOG2340|consen  612 AHFFRRYHIKGVKNVVFYQPPNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYD  669 (698)
T ss_pred             hhhhhhheecceeeEEEecCCCCcHHHHHHHhhhhhhhccCCccccceEEEEEeechh
Confidence            54  568899999999999999998775   4445544333    2357778887543

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=99.13  E-value=1.4e-10  Score=111.36  Aligned_cols=307  Identities=19%  Similarity=0.225  Sum_probs=179.1

Q ss_pred             cccccccCCceEEEccCCCcchhHHHHHHhhccCCCC--CCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCc
Q 014486           76 CIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP--GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGV  153 (423)
Q Consensus        76 ~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~--~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~  153 (423)
                      .+..+..+..++|.+.||+|||..+..-+++.....+  ....+.+..|++..+..+++++.+.-....+-.+     +.
T Consensus       386 i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tv-----gy  460 (1282)
T KOG0921|consen  386 ILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETC-----GY  460 (1282)
T ss_pred             HHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhcccc-----cc
Confidence            3333344556899999999999998888888766544  2235677789998888888777543211111111     11


Q ss_pred             chHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCC
Q 014486          154 NIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLS  233 (423)
Q Consensus       154 ~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~  233 (423)
                      +.+... ......--|..||.+-+++......   ..+.++|+||.|...-..+|...+.+=..-..+...++++|||+.
T Consensus       461 ~vRf~S-a~prpyg~i~fctvgvllr~~e~gl---rg~sh~i~deiherdv~~dfll~~lr~m~~ty~dl~v~lmsatId  536 (1282)
T KOG0921|consen  461 NVRFDS-ATPRPYGSIMFCTVGVLLRMMENGL---RGISHVIIDEIHERDVDTDFVLIVLREMISTYRDLRVVLMSATID  536 (1282)
T ss_pred             cccccc-cccccccceeeeccchhhhhhhhcc---cccccccchhhhhhccchHHHHHHHHhhhccchhhhhhhhhcccc
Confidence            111111 1111112689999999988776543   456789999999876544554444333333334444555555543


Q ss_pred             ccH--------------------HHHHHHhccCCceeeeccccccccccceEEEEE-------------e----------
Q 014486          234 KEI--------------------RPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIK-------------L----------  270 (423)
Q Consensus       234 ~~~--------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~----------  270 (423)
                      .+.                    ..+.......+....-..+....... ......             .          
T Consensus       537 Td~f~~~f~~~p~~~~~grt~pvq~F~led~~~~~~~vp~~~~~~k~k~-~~~~~~~~~ddK~~n~n~~~dd~~~~~~~~  615 (1282)
T KOG0921|consen  537 TDLFTNFFSSIPDVTVHGRTFPVQSFFLEDIIQMTQFVPSEPSQKKRKK-DDDEEDEEVDDKGRNMNILCDPSYNESTRT  615 (1282)
T ss_pred             hhhhhhhhccccceeeccccccHHHHHHHHhhhhhhccCCCcCccchhh-cccccCchhhhcccccccccChhhcchhhh
Confidence            332                    11111111111111100000000000 000000             0          


Q ss_pred             -----ChHHHH-HHHHHHHHh----hcCCcEEEEEcChhhHHHHHHHHHhC-------CCCeEEEcCCCCHHHHHHHHHh
Q 014486          271 -----SELEKN-RKLNDLLDA----LDFNQVVIFVKSVSRAAELNKLLVEC-------NFPSICIHSGMSQEERLTRYKG  333 (423)
Q Consensus       271 -----~~~~~~-~~l~~ll~~----~~~~~~ivf~~~~~~~~~l~~~L~~~-------~~~~~~~~~~~~~~~r~~~~~~  333 (423)
                           .+.... ..+..++..    .-.+.+++|.+.....-.+...|...       .++.+.+|+.....+..++.+.
T Consensus       616 am~~~se~d~~f~l~Eal~~~i~s~~i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~  695 (1282)
T KOG0921|consen  616 AMSRLSEKDIPFGLIEALLNDIASRNIDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEP  695 (1282)
T ss_pred             hhhcchhhcchhHHHHHHHhhhcccCCccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCc
Confidence                 000000 111111111    12467899999988888887777553       4678889999998888888888


Q ss_pred             hhcCCccEEEEcCccccCCCCCCCCEEEEccCC------------------CCcchhhhcccccCCCCCceEEEEEec
Q 014486          334 FKEGNKRILVATDLVGRGIDIERVNIVINYDMP------------------DSADTYLHRVGRAGRFGTKGLAITFVS  393 (423)
Q Consensus       334 f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~------------------~s~~~~~Q~~GR~~R~g~~~~~~~~~~  393 (423)
                      ...|..++++.|.++...+.+.++..||+.+..                  .+.....||.||+||. .+|.+..+++
T Consensus       696 ~p~gv~kii~stniaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grv-R~G~~f~lcs  772 (1282)
T KOG0921|consen  696 VPEGVTKIILSTNIAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRV-RPGFCFHLCS  772 (1282)
T ss_pred             ccccccccccccceeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHhhcccCcee-cccccccccH
Confidence            888999999999999999999887777743321                  2566779999999996 4566666554

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.10  E-value=7.7e-10  Score=98.50  Aligned_cols=72  Identities=21%  Similarity=0.229  Sum_probs=55.6

Q ss_pred             CCCCCChhhhhcc----cccccCCceEEEccCCCcchhHHHHHHhhccCCCCC---CeEEEEEecChHHHHHHHHHHHHH
Q 014486           65 GFEHPSEVQHECI----PQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPG---QVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        65 ~~~~~~~~Q~~~i----~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~---~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .| .|+|.|.+.+    ..+..++++++.+|||+|||++++.|++..+...+.   ..+++|.++|..+..|....+++.
T Consensus         6 Py-~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488        6 PY-EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            44 4699999844    445558889999999999999999999865443222   237899999999988887777654

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.10  E-value=7.7e-10  Score=98.50  Aligned_cols=72  Identities=21%  Similarity=0.229  Sum_probs=55.6

Q ss_pred             CCCCCChhhhhcc----cccccCCceEEEccCCCcchhHHHHHHhhccCCCCC---CeEEEEEecChHHHHHHHHHHHHH
Q 014486           65 GFEHPSEVQHECI----PQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPG---QVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        65 ~~~~~~~~Q~~~i----~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~---~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .| .|+|.|.+.+    ..+..++++++.+|||+|||++++.|++..+...+.   ..+++|.++|..+..|....+++.
T Consensus         6 Py-~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489        6 PY-EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            44 4699999844    445558889999999999999999999865443222   237899999999988887777654

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=99.07  E-value=7.5e-10  Score=107.87  Aligned_cols=120  Identities=17%  Similarity=0.131  Sum_probs=99.4

Q ss_pred             cEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCc-c-EEEEcCccccCCCCCCCCEEEEccCCC
Q 014486          290 QVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNK-R-ILVATDLVGRGIDIERVNIVINYDMPD  367 (423)
Q Consensus       290 ~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~-~-ili~T~~~~~Gld~~~~~~vi~~~~~~  367 (423)
                      +++||+....-+..+.-.|...++....+.|.++...|.+.+..|..+.. . .+++..+.+.|+|+..+.+|+..++-|
T Consensus       541 kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slkag~~glnlt~a~~v~~~d~~w  620 (674)
T KOG1001|consen  541 KIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAGKVGLNLTAASHVLLMDPWW  620 (674)
T ss_pred             ceeeehhHHHHHHHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHHHhhhhhchhhhhHHHhhchhc
Confidence            89999999999999988888889999999999999999999999986543 3 445789999999999999999999999


Q ss_pred             CcchhhhcccccCCCCCceEEEE---EecCcccHHHHHHHHHHHh
Q 014486          368 SADTYLHRVGRAGRFGTKGLAIT---FVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       368 s~~~~~Q~~GR~~R~g~~~~~~~---~~~~~~~~~~~~~~~~~~~  409 (423)
                      +|....|++-|++|-||...+.+   ++-...+..+++.=+++..
T Consensus       621 np~~eeQaidR~hrigq~k~v~v~r~~i~dtveer~l~iq~~K~~  665 (674)
T KOG1001|consen  621 NPAVEEQAIDRAHRIGQTKPVKVSRFIIKDTVEERILKIQEKKRE  665 (674)
T ss_pred             ChHHHHHHHHHHHHhcccceeeeeeehhhhccHHHHHHHHHHHHH
Confidence            99999999999999998876665   2333445555555444443

>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=99.04  E-value=3.8e-09  Score=91.38  Aligned_cols=130  Identities=22%  Similarity=0.278  Sum_probs=96.6

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      |+ .|++.|.-++-.+..|  -|+...||-|||++..+++......+.   .+-|++.+..||..=++++..+...+ ++
T Consensus        75 g~-~p~~vQll~~l~L~~G--~laEm~TGEGKTli~~l~a~~~AL~G~---~V~vvT~NdyLA~RD~~~~~~~y~~L-Gl  147 (266)
T PF07517_consen   75 GL-RPYDVQLLGALALHKG--RLAEMKTGEGKTLIAALPAALNALQGK---GVHVVTSNDYLAKRDAEEMRPFYEFL-GL  147 (266)
T ss_dssp             S-----HHHHHHHHHHHTT--SEEEESTTSHHHHHHHHHHHHHHTTSS----EEEEESSHHHHHHHHHHHHHHHHHT-T-
T ss_pred             CC-cccHHHHhhhhhcccc--eeEEecCCCCcHHHHHHHHHHHHHhcC---CcEEEeccHHHhhccHHHHHHHHHHh-hh
Confidence            44 7899999888766554  499999999999999888877766554   78899999999999999999999888 99


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHH-HHhcCCC------CCCCccEEEEcCcchhhc
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA-LARDKDL------SLKNVRHFILDECDKMLE  204 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~-~~~~~~~------~~~~~~~vVvDE~h~~~~  204 (423)
                      ++....++.+.......+.   .+|+++|...+.- +++....      ....+.++||||+|.++-
T Consensus       148 sv~~~~~~~~~~~r~~~Y~---~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~Li  211 (266)
T PF07517_consen  148 SVGIITSDMSSEERREAYA---ADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSILI  211 (266)
T ss_dssp             -EEEEETTTEHHHHHHHHH---SSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHTT
T ss_pred             ccccCccccCHHHHHHHHh---CcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEEE
Confidence            9999999887655444443   3899999987753 4443211      146788999999998864

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 ....

>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A

Probab=98.77  E-value=2.2e-08  Score=81.73  Aligned_cols=115  Identities=23%  Similarity=0.239  Sum_probs=80.1

Q ss_pred             HHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCC--CeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcC--ccccCCCCCC
Q 014486          281 DLLDALDFNQVVIFVKSVSRAAELNKLLVECNF--PSICIHSGMSQEERLTRYKGFKEGNKRILVATD--LVGRGIDIER  356 (423)
Q Consensus       281 ~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~--~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~--~~~~Gld~~~  356 (423)
                      ++++..+ +.++||+++.+..+.+.+.++....  ....+..  +..++..+++.|+.++..||+++.  .+.+|+|+++
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            4444444 8899999999999999999887632  1122232  255778889999999999999998  9999999996


Q ss_pred             --CCEEEEccCCCC-c-----------------------------chhhhcccccCCCCCceEEEEEecCcccH
Q 014486          357 --VNIVINYDMPDS-A-----------------------------DTYLHRVGRAGRFGTKGLAITFVSSASDS  398 (423)
Q Consensus       357 --~~~vi~~~~~~s-~-----------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  398 (423)
                        +++||..++|.. +                             ....|.+||+-|..++..+++++++....
T Consensus        80 ~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~R~~~  153 (167)
T PF13307_consen   80 DLLRAVIIVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDSRFLS  153 (167)
T ss_dssp             ESEEEEEEES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESGGGGG
T ss_pred             chhheeeecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcCcccc
Confidence              778999998852 1                             12359999999998888888888865444

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=98.76  E-value=7.3e-08  Score=96.54  Aligned_cols=72  Identities=18%  Similarity=0.282  Sum_probs=55.7

Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCC-----CC----ceEEEEEecCcccHHHHHHHHHHH
Q 014486          338 NKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRF-----GT----KGLAITFVSSASDSDILNQVSKFM  408 (423)
Q Consensus       338 ~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~-----g~----~~~~~~~~~~~~~~~~~~~~~~~~  408 (423)
                      ..+.+++.+++.+|.|.|++-.+..+....|...-.|.+||.-|.     |.    ......++.+..+.+..+.|.+..
T Consensus       501 ~~~fifs~~al~egwd~~~~~~~~~l~~~~s~~~~~q~~gr~lr~~vnq~G~R~~~~~~~LTvianesy~dFa~~LQ~EI  580 (986)
T PRK15483        501 TRRFLFSKWTLREGWDNPNVFQIAKLRSSGSETSKLQEVGRGLRLPVDENGHRVSQEEFRLNYLIDYDEKDFASKLVGEI  580 (986)
T ss_pred             CeEEEEEhHHhhhcCCCCCeEEEEEeccCCchHHHHHHhccceeccccccCccccCccEEEEEEeCccHHHHHHHHHHHH
Confidence            578999999999999999999888899888998999999999993     21    112344555666666666666665


Q ss_pred             h
Q 014486          409 F  409 (423)
Q Consensus       409 ~  409 (423)
                      +
T Consensus       581 ~  581 (986)
T PRK15483        581 N  581 (986)
T ss_pred             H
Confidence            4

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=98.71  E-value=1.7e-06  Score=83.90  Aligned_cols=73  Identities=21%  Similarity=0.252  Sum_probs=57.1

Q ss_pred             CCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCC--CCceEE----------EEEecCcccHHHHHHH
Q 014486          337 GNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRF--GTKGLA----------ITFVSSASDSDILNQV  404 (423)
Q Consensus       337 ~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~--g~~~~~----------~~~~~~~~~~~~~~~~  404 (423)
                      ...+.+++..++-+|+|-|++=.+.-+....|..+=.|.+||.-|.  ++.|.=          ..++.+..+...+..|
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            3578999999999999999999999999999999999999999993  333321          2244456777777777


Q ss_pred             HHHHh
Q 014486          405 SKFMF  409 (423)
Q Consensus       405 ~~~~~  409 (423)
                      .+.+.
T Consensus       562 qkEI~  566 (985)
T COG3587         562 QKEIN  566 (985)
T ss_pred             HHHHH
Confidence            76655

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

Probab=98.66  E-value=3.4e-08  Score=97.19  Aligned_cols=131  Identities=21%  Similarity=0.310  Sum_probs=101.0

Q ss_pred             CCChhhhhccccccc-CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceE
Q 014486           68 HPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKV  146 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~-~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  146 (423)
                      ...|.|.+.+..+.. ..++++-+|||+|||.++-+++...+...+.. +++++.|..+|+..-.+....-... +++++
T Consensus       927 ~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p~~-kvvyIap~kalvker~~Dw~~r~~~-~g~k~ 1004 (1230)
T KOG0952|consen  927 YFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYPGS-KVVYIAPDKALVKERSDDWSKRDEL-PGIKV 1004 (1230)
T ss_pred             ccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCCCc-cEEEEcCCchhhcccccchhhhccc-CCcee
Confidence            556788888766665 46699999999999999999888877766654 9999999999988876666544332 47888


Q ss_pred             EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHh--cCCCCCCCccEEEEcCcchhhc
Q 014486          147 AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALAR--DKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~--~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      .-..|.....  ......  ++++|+||+++..+.+  .....+.+++.+|+||.|.+.+
T Consensus      1005 ie~tgd~~pd--~~~v~~--~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~ 1060 (1230)
T KOG0952|consen 1005 IELTGDVTPD--VKAVRE--ADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGE 1060 (1230)
T ss_pred             EeccCccCCC--hhheec--CceEEcccccccCccccccchhhhccccceeecccccccC
Confidence            8888866543  222222  5999999999988877  3445678999999999998876

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=98.65  E-value=8.1e-07  Score=89.02  Aligned_cols=65  Identities=9%  Similarity=0.092  Sum_probs=55.2

Q ss_pred             cEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCC
Q 014486          168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLS  233 (423)
Q Consensus       168 ~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~  233 (423)
                      .|+++||..+..=+-.+.+.+.++..|||||||++.+ .....-+.++++..++..-+.++|++|.
T Consensus         9 gi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~-~~~eaFI~rlyr~~n~~gfIkafSdsP~   73 (814)
T TIGR00596         9 GIFSITSRILVVDLLTGIIPPELITGILVLRADRIIE-SSQEAFILRLYRQKNKTGFIKAFSDNPE   73 (814)
T ss_pred             CEEEEechhhHhHHhcCCCCHHHccEEEEeecccccc-cccHHHHHHHHHHhCCCcceEEecCCCc
Confidence            8999999999886667788999999999999999987 5666677788877777888999999963

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

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=98.61  E-value=3e-07  Score=80.11  Aligned_cols=69  Identities=20%  Similarity=0.223  Sum_probs=49.2

Q ss_pred             CCChhhhhcccccccCCc-eEEEccCCCcchhHHHHHHhhcc-----CCCCCCeEEEEEecChHHHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAILGMD-VICQAKSGMGKTAVFVLSTLQQT-----EPNPGQVTALVLCHTRELAYQICHEFER  136 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~-~ii~~~tGsGKT~~~~~~~~~~~-----~~~~~~~~~lil~P~~~L~~q~~~~~~~  136 (423)
                      ++++.|.+|+..++.... .+|.||+|+|||.+....+....     .....+.++|+++|+..-+.++.+.+.+
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            367899999999999888 99999999999965443333331     1122333899999999999999888877

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=98.51  E-value=4.7e-07  Score=78.70  Aligned_cols=161  Identities=19%  Similarity=0.184  Sum_probs=99.7

Q ss_pred             CCChhhhhccccccc----------CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAIL----------GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----------~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .+...|-+++-...+          +..+++-..||.||-.+..-.|++....+..  ++|+++.+..|-....+.++.+
T Consensus        37 ~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr~--r~vwvS~s~dL~~Da~RDl~DI  114 (303)
T PF13872_consen   37 LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRGRK--RAVWVSVSNDLKYDAERDLRDI  114 (303)
T ss_pred             cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcCCC--ceEEEECChhhhhHHHHHHHHh
Confidence            356777766644331          3458999999999998766666666555443  7899999999999888888877


Q ss_pred             hccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC---CCC--------CC-ccEEEEcCcchhhcc
Q 014486          138 STYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD---LSL--------KN-VRHFILDECDKMLES  205 (423)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~---~~~--------~~-~~~vVvDE~h~~~~~  205 (423)
                      ...  .+.+..+..   .... .. ..-...|+++|+..|........   ..+        .+ =.+||+||||...+.
T Consensus       115 G~~--~i~v~~l~~---~~~~-~~-~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~  187 (303)
T PF13872_consen  115 GAD--NIPVHPLNK---FKYG-DI-IRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNL  187 (303)
T ss_pred             CCC--cccceechh---hccC-cC-CCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCC
Confidence            543  222222211   0000 00 11123799999999877543211   110        11 237999999998763


Q ss_pred             CC-------cHHHHHHHHHhCCCCceEEEEeccCCccHHH
Q 014486          206 LD-------MRRDVQEIFKMTPHDKQVMMFSATLSKEIRP  238 (423)
Q Consensus       206 ~~-------~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~  238 (423)
                      ..       .......+...+| ..++|.+|||...+...
T Consensus       188 ~~~~~~~sk~g~avl~LQ~~LP-~ARvvY~SATgasep~N  226 (303)
T PF13872_consen  188 SSGSKKPSKTGIAVLELQNRLP-NARVVYASATGASEPRN  226 (303)
T ss_pred             CccCccccHHHHHHHHHHHhCC-CCcEEEecccccCCCce
Confidence            22       1234455666665 45599999998766443

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=98.49  E-value=4.7e-07  Score=76.03  Aligned_cols=123  Identities=17%  Similarity=0.222  Sum_probs=71.6

Q ss_pred             CCChhhhhcccccccCC--ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCce
Q 014486           68 HPSEVQHECIPQAILGM--DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIK  145 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~--~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  145 (423)
                      ++++-|++++..++.+.  -.++.|+.|+|||.+. ..+...+...+  .++++++||...+..+.+..        ++.
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~~g--~~v~~~apT~~Aa~~L~~~~--------~~~   69 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEAAG--KRVIGLAPTNKAAKELREKT--------GIE   69 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHHTT----EEEEESSHHHHHHHHHHH--------TS-
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHhCC--CeEEEECCcHHHHHHHHHhh--------Ccc
Confidence            46889999999997654  3788999999999753 33443333332  38999999998877765542        111


Q ss_pred             EEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC----CCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCC
Q 014486          146 VAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD----LSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPH  221 (423)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~----~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~  221 (423)
                                               ..|-..++.......    ..+...++|||||+-.+.     ...+..++.....
T Consensus        70 -------------------------a~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~-----~~~~~~ll~~~~~  119 (196)
T PF13604_consen   70 -------------------------AQTIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVD-----SRQLARLLRLAKK  119 (196)
T ss_dssp             -------------------------EEEHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-B-----HHHHHHHHHHS-T
T ss_pred             -------------------------hhhHHHHHhcCCcccccccccCCcccEEEEecccccC-----HHHHHHHHHHHHh
Confidence                                     122222222111110    114566799999998654     3456666676666


Q ss_pred             -CceEEEEecc
Q 014486          222 -DKQVMMFSAT  231 (423)
Q Consensus       222 -~~~~v~~SAT  231 (423)
                       ..++|++.-+
T Consensus       120 ~~~klilvGD~  130 (196)
T PF13604_consen  120 SGAKLILVGDP  130 (196)
T ss_dssp             -T-EEEEEE-T
T ss_pred             cCCEEEEECCc
Confidence             5666766544

>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=98.48  E-value=4.9e-07  Score=75.17  Aligned_cols=142  Identities=15%  Similarity=0.213  Sum_probs=72.5

Q ss_pred             CCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc--
Q 014486           67 EHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI--  144 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~--  144 (423)
                      ...++.|..++..++..+-+++.||.|+|||+.++..+++.+..+. ..+++++-|..+..+.    +    ...|+-  
T Consensus         3 ~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~-~~kiii~Rp~v~~~~~----l----GflpG~~~   73 (205)
T PF02562_consen    3 KPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEGE-YDKIIITRPPVEAGED----L----GFLPGDLE   73 (205)
T ss_dssp             ---SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS--SEEEEEE-S--TT------------SS-----
T ss_pred             cCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhCC-CcEEEEEecCCCCccc----c----ccCCCCHH
Confidence            3568899999999997777999999999999999888888776643 3388888887653111    1    111110  


Q ss_pred             -eEEEEEc-------Cc-chHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHH
Q 014486          145 -KVAVFYG-------GV-NIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEI  215 (423)
Q Consensus       145 -~~~~~~~-------~~-~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~  215 (423)
                       +...+..       .. ........+.++  .|-+.....+.      ...+. -.+||+|||+.+.     ...+..+
T Consensus        74 eK~~p~~~p~~d~l~~~~~~~~~~~~~~~~--~Ie~~~~~~iR------Grt~~-~~~iIvDEaQN~t-----~~~~k~i  139 (205)
T PF02562_consen   74 EKMEPYLRPIYDALEELFGKEKLEELIQNG--KIEIEPLAFIR------GRTFD-NAFIIVDEAQNLT-----PEELKMI  139 (205)
T ss_dssp             ----TTTHHHHHHHTTTS-TTCHHHHHHTT--SEEEEEGGGGT------T--B--SEEEEE-SGGG-------HHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhChHhHHHHhhcC--eEEEEehhhhc------Ccccc-ceEEEEecccCCC-----HHHHHHH
Confidence             0000000       00 000011111122  45554443332      12222 2789999999553     5678888


Q ss_pred             HHhCCCCceEEEEecc
Q 014486          216 FKMTPHDKQVMMFSAT  231 (423)
Q Consensus       216 ~~~~~~~~~~v~~SAT  231 (423)
                      +.++..+.+++++.-.
T Consensus       140 lTR~g~~skii~~GD~  155 (205)
T PF02562_consen  140 LTRIGEGSKIIITGDP  155 (205)
T ss_dssp             HTTB-TT-EEEEEE--
T ss_pred             HcccCCCcEEEEecCc
Confidence            8889888888877544

; GO: 0005524 ATP binding; PDB: 3B85_A.

>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]

Probab=98.47  E-value=4e-07  Score=85.64  Aligned_cols=86  Identities=15%  Similarity=0.187  Sum_probs=66.9

Q ss_pred             HHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHh
Q 014486           59 RAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFS  138 (423)
Q Consensus        59 ~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~  138 (423)
                      +.+-..++..++..|..|+.++++..-.+|+||+|+|||.+..-.+++.......  .+|+++|+..-+.|+++.+.+. 
T Consensus       401 ~~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~~~~--~VLvcApSNiAVDqLaeKIh~t-  477 (935)
T KOG1802|consen  401 RRFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQHAG--PVLVCAPSNIAVDQLAEKIHKT-  477 (935)
T ss_pred             hhhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHhcCC--ceEEEcccchhHHHHHHHHHhc-
Confidence            4444556778999999999999999999999999999998765544444443322  7899999999999999888764 


Q ss_pred             ccCCCceEEEEEc
Q 014486          139 TYLPDIKVAVFYG  151 (423)
Q Consensus       139 ~~~~~~~~~~~~~  151 (423)
                          ++++..+..
T Consensus       478 ----gLKVvRl~a  486 (935)
T KOG1802|consen  478 ----GLKVVRLCA  486 (935)
T ss_pred             ----CceEeeeeh
Confidence                566665543

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=98.35  E-value=1.7e-06  Score=82.99  Aligned_cols=79  Identities=20%  Similarity=0.326  Sum_probs=60.4

Q ss_pred             HHhhhcCCccEEEEcCccccCCCCCCCC--------EEEEccCCCCcchhhhcccccCCCCCc---eEEEEEecCcccHH
Q 014486          331 YKGFKEGNKRILVATDLVGRGIDIERVN--------IVINYDMPDSADTYLHRVGRAGRFGTK---GLAITFVSSASDSD  399 (423)
Q Consensus       331 ~~~f~~~~~~ili~T~~~~~Gld~~~~~--------~vi~~~~~~s~~~~~Q~~GR~~R~g~~---~~~~~~~~~~~~~~  399 (423)
                      -++|..|+-.|-|-+.+++-||.++.-+        +-|-+.+|||....+|..||++|.+|-   --++++..-..+..
T Consensus       850 KqrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQVsaPEYvFlIseLAGErR  929 (1300)
T KOG1513|consen  850 KQRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQVSAPEYVFLISELAGERR  929 (1300)
T ss_pred             HhhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccccCCCeEEEEehhhccchH
Confidence            3578899999999999999999986543        345689999999999999999998863   34555555566666


Q ss_pred             HHHHHHHHHh
Q 014486          400 ILNQVSKFMF  409 (423)
Q Consensus       400 ~~~~~~~~~~  409 (423)
                      .-..+.|.|+
T Consensus       930 FAS~VAKRLE  939 (1300)
T KOG1513|consen  930 FASIVAKRLE  939 (1300)
T ss_pred             HHHHHHHHHH
Confidence            6665555554

>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=98.29  E-value=2.6e-06  Score=71.42  Aligned_cols=151  Identities=21%  Similarity=0.196  Sum_probs=89.9

Q ss_pred             CcCCCCCHHHHHHHHhCCCCCCChhhhhccccccc---CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           48 FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL---GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        48 ~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~---~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      |+....+.+++=.+.. ++ .+|+.|.+....+..   +++.+...-||.|||.+ ++|++.....++.. -+.+++|. 
T Consensus         5 w~p~~~P~wLl~E~e~-~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsV-I~Pmla~~LAdg~~-LvrviVpk-   79 (229)
T PF12340_consen    5 WDPMEYPDWLLFEIES-NI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSV-IVPMLALALADGSR-LVRVIVPK-   79 (229)
T ss_pred             CCchhChHHHHHHHHc-Cc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccch-HHHHHHHHHcCCCc-EEEEEcCH-
Confidence            4444444444333322 23 689999999988886   57899999999999987 46777766655544 77788884 


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEE--EEcCcchHH----HHH----HHhcCCCcEEEechHHHHHHHhc-------CCC-
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAV--FYGGVNIKI----HKD----LLKNECPQIVVGTPGRILALARD-------KDL-  186 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~--~~~~~~~~~----~~~----~~~~~~~~ilv~T~~~l~~~~~~-------~~~-  186 (423)
                      +|..|..+.+..-....-+-.+..  +.-......    ...    ..... -.|+++||+.++.+.-.       ... 
T Consensus        80 ~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~-~gill~~PEhilSf~L~~le~l~~~~~~  158 (229)
T PF12340_consen   80 ALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRS-GGILLATPEHILSFKLKGLERLQDGKPE  158 (229)
T ss_pred             HHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHc-CCEEEeChHHHHHHHHHHHHHHHhcCHH
Confidence            799999888876543322222222  222222111    111    11112 38999999987653211       110 


Q ss_pred             ----------CCCCccEEEEcCcchhhc
Q 014486          187 ----------SLKNVRHFILDECDKMLE  204 (423)
Q Consensus       187 ----------~~~~~~~vVvDE~h~~~~  204 (423)
                                -+.....-|+||+|.++.
T Consensus       159 ~~~~l~~~q~~l~~~~rdilDEsDe~L~  186 (229)
T PF12340_consen  159 EARELLKIQKWLDEHSRDILDESDEILS  186 (229)
T ss_pred             HHHHHHHHHHHHHhcCCeEeECchhccC
Confidence                      022344578999997654

There are two conserved sequence motifs: LLE and NMG.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=98.23  E-value=7.9e-06  Score=75.55  Aligned_cols=109  Identities=16%  Similarity=0.232  Sum_probs=65.7

Q ss_pred             ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhc
Q 014486           85 DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN  164 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (423)
                      -++|.|.+|||||++++- ++..+.....+.+++++++...|...+.+.+.....  +.                     
T Consensus         3 v~~I~G~aGTGKTvla~~-l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~--~~---------------------   58 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALN-LAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKKYN--PK---------------------   58 (352)
T ss_pred             EEEEEecCCcCHHHHHHH-HHHHhhccccCCceEEEEecchHHHHHHHHHhhhcc--cc---------------------
Confidence            378999999999987654 333332222233789999999998887776654320  00                     


Q ss_pred             CCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccC------CcHHHHHHHHHh
Q 014486          165 ECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESL------DMRRDVQEIFKM  218 (423)
Q Consensus       165 ~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~------~~~~~~~~~~~~  218 (423)
                       .....+..+..+.............+++|||||||++....      .....+..+.+.
T Consensus        59 -~~~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   59 -LKKSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             -hhhhhhhhhHHHHhhcccccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence             01233334444433222223455778999999999997621      123445555554

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK10536 hypothetical protein; Provisional

Probab=98.15  E-value=4.6e-05  Score=65.38  Aligned_cols=147  Identities=12%  Similarity=0.120  Sum_probs=78.5

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHH-------HHHHHHHHH
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAY-------QICHEFERF  137 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~-------q~~~~~~~~  137 (423)
                      ++...+..|...+..+..+..+++.||+|+|||+.++...++.+.... ..++++.-|.....+       ...+.+..|
T Consensus        56 ~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~-~~kIiI~RP~v~~ge~LGfLPG~~~eK~~p~  134 (262)
T PRK10536         56 PILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKD-VDRIIVTRPVLQADEDLGFLPGDIAEKFAPY  134 (262)
T ss_pred             cccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCC-eeEEEEeCCCCCchhhhCcCCCCHHHHHHHH
Confidence            455678889999888888778999999999999988776776554432 325555556543211       011111111


Q ss_pred             hccC-CCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHH
Q 014486          138 STYL-PDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIF  216 (423)
Q Consensus       138 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~  216 (423)
                      .... ..+..  +.+.   ......+......|-+.....+    +..  .+ +-.+||+|||+.+.     ...+..++
T Consensus       135 ~~pi~D~L~~--~~~~---~~~~~~~~~~~~~Iei~~l~ym----RGr--tl-~~~~vIvDEaqn~~-----~~~~k~~l  197 (262)
T PRK10536        135 FRPVYDVLVR--RLGA---SFMQYCLRPEIGKVEIAPFAYM----RGR--TF-ENAVVILDEAQNVT-----AAQMKMFL  197 (262)
T ss_pred             HHHHHHHHHH--HhCh---HHHHHHHHhccCcEEEecHHHh----cCC--cc-cCCEEEEechhcCC-----HHHHHHHH
Confidence            1000 00000  0010   0001111111113444443322    222  22 22789999999663     36777788


Q ss_pred             HhCCCCceEEEEe
Q 014486          217 KMTPHDKQVMMFS  229 (423)
Q Consensus       217 ~~~~~~~~~v~~S  229 (423)
                      ..++.+.++|++.
T Consensus       198 tR~g~~sk~v~~G  210 (262)
T PRK10536        198 TRLGENVTVIVNG  210 (262)
T ss_pred             hhcCCCCEEEEeC
Confidence            8888888766654

>PF13245 AAA_19: Part of AAA domain

Probab=98.14  E-value=5.7e-06  Score=57.24  Aligned_cols=50  Identities=24%  Similarity=0.303  Sum_probs=37.0

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccC--CCCCCeEEEEEecChHHHHHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTE--PNPGQVTALVLCHTRELAYQICHEF  134 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~--~~~~~~~~lil~P~~~L~~q~~~~~  134 (423)
                      +-++|.||+|+|||.+.+-.+.....  ..+ +.++++++|++..+.++.+.+
T Consensus        11 ~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~-~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   11 PLFVVQGPPGTGKTTTLAARIAELLAARADP-GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHHhcCC-CCeEEEECCCHHHHHHHHHHH
Confidence            33666999999999766555555442  222 448999999999999888777

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=98.09  E-value=2.5e-05  Score=61.39  Aligned_cols=78  Identities=22%  Similarity=0.215  Sum_probs=57.6

Q ss_pred             EEcCCCCHHHHHHHHHhhhcCC-ccEEEEcCccccCCCCCC--CCEEEEccCCCC-------------------------
Q 014486          317 CIHSGMSQEERLTRYKGFKEGN-KRILVATDLVGRGIDIER--VNIVINYDMPDS-------------------------  368 (423)
Q Consensus       317 ~~~~~~~~~~r~~~~~~f~~~~-~~ili~T~~~~~Gld~~~--~~~vi~~~~~~s-------------------------  368 (423)
                      .+..+....+...+++.|++.. ..||+++..+++|+|+++  +++||..+.|..                         
T Consensus        26 i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~  105 (141)
T smart00492       26 LLVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPFPYPDSPILKARLELLRDKGQIRPFDF  105 (141)
T ss_pred             EEEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhCCCCchhH
Confidence            3344445556788899998654 369999988999999997  678998887741                         


Q ss_pred             ------cchhhhcccccCCCCCceEEEEEecC
Q 014486          369 ------ADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       369 ------~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                            ...+.|.+||+-|..++-.+++++++
T Consensus       106 ~~~~~a~~~l~Qa~GR~iR~~~D~g~i~l~D~  137 (141)
T smart00492      106 VSLPDAMRTLAQCVGRLIRGANDYGVVVIADK  137 (141)
T ss_pred             HHHHHHHHHHHHHhCccccCcCceEEEEEEec
Confidence                  12346999999998877777777764

>KOG1803 consensus DNA helicase [Replication, recombination and repair]

Probab=98.07  E-value=1.3e-05  Score=75.35  Aligned_cols=64  Identities=22%  Similarity=0.230  Sum_probs=51.9

Q ss_pred             CCChhhhhcccccccCCc-eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAILGMD-VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEF  134 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~-~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~  134 (423)
                      .+.+.|+.|+......++ .++.||+|+|||.+....+.+....++   ++|++.||..-+..+.+++
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~~k---~VLVcaPSn~AVdNiverl  249 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQKK---RVLVCAPSNVAVDNIVERL  249 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHcCC---eEEEEcCchHHHHHHHHHh
Confidence            567889999988888766 799999999999987665555554443   8999999999999988864

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=98.03  E-value=2.4e-05  Score=61.60  Aligned_cols=70  Identities=20%  Similarity=0.245  Sum_probs=53.0

Q ss_pred             HHHHHHHHhhhcCCc---cEEEEcCc--cccCCCCCC--CCEEEEccCCCC-----------------------------
Q 014486          325 EERLTRYKGFKEGNK---RILVATDL--VGRGIDIER--VNIVINYDMPDS-----------------------------  368 (423)
Q Consensus       325 ~~r~~~~~~f~~~~~---~ili~T~~--~~~Gld~~~--~~~vi~~~~~~s-----------------------------  368 (423)
                      .+...+++.|++...   .||+++.-  +++|+|+++  +++||..+.|..                             
T Consensus        31 ~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~  110 (142)
T smart00491       31 GETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPFPNPDSPILRARLEYLDEKGGIRPFDEVYLF  110 (142)
T ss_pred             chHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCcHHHHHHH
Confidence            344677888886443   58888876  999999987  678998887751                             


Q ss_pred             --cchhhhcccccCCCCCceEEEEEecC
Q 014486          369 --ADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       369 --~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                        .....|.+||+-|..++-.+++++++
T Consensus       111 ~a~~~~~Qa~GR~iR~~~D~g~i~l~D~  138 (142)
T smart00491      111 DAMRALAQAIGRAIRHKNDYGVVVLLDK  138 (142)
T ss_pred             HHHHHHHHHhCccccCccceEEEEEEec
Confidence              11236999999999888777877765

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.03  E-value=3.9e-05  Score=75.02  Aligned_cols=140  Identities=16%  Similarity=0.224  Sum_probs=84.5

Q ss_pred             hhhhhcccccccCCceEEEccCCCcchhHHH--HHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEE
Q 014486           71 EVQHECIPQAILGMDVICQAKSGMGKTAVFV--LSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAV  148 (423)
Q Consensus        71 ~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~--~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~  148 (423)
                      +.|+.++...+.++-.+|.|++|+|||.+..  +..+..........++++.+||..-+..+.+.+.......   ... 
T Consensus       148 ~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~~~~l---~~~-  223 (586)
T TIGR01447       148 NWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKNL---AAA-  223 (586)
T ss_pred             HHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhhhccc---ccc-
Confidence            6899999999998889999999999998642  2223222222223478999999988887776665432211   100 


Q ss_pred             EEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhc------CCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCC
Q 014486          149 FYGGVNIKIHKDLLKNECPQIVVGTPGRILALARD------KDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHD  222 (423)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~------~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~  222 (423)
                             .    ..... ..+-..|-.+++.....      ...+...+++|||||+-.+.     ...+..++..++..
T Consensus       224 -------~----~~~~~-~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMvd-----~~l~~~ll~al~~~  286 (586)
T TIGR01447       224 -------E----ALIAA-LPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMVD-----LPLMAKLLKALPPN  286 (586)
T ss_pred             -------h----hhhhc-cccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccCC-----HHHHHHHHHhcCCC
Confidence                   0    00000 01223444444432211      11123357899999998553     34566777888888


Q ss_pred             ceEEEEecc
Q 014486          223 KQVMMFSAT  231 (423)
Q Consensus       223 ~~~v~~SAT  231 (423)
                      .++|++.-.
T Consensus       287 ~rlIlvGD~  295 (586)
T TIGR01447       287 TKLILLGDK  295 (586)
T ss_pred             CEEEEECCh
Confidence            888876544

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=98.03  E-value=4.7e-05  Score=76.65  Aligned_cols=126  Identities=20%  Similarity=0.200  Sum_probs=77.2

Q ss_pred             CCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceE
Q 014486           67 EHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKV  146 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  146 (423)
                      ..+++-|++++..+..++-+++.|++|+|||.+. -.++..+...+....++++.||..-|..+.+..        +...
T Consensus       322 ~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~--------g~~a  392 (720)
T TIGR01448       322 KGLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGGLLPVGLAAPTGRAAKRLGEVT--------GLTA  392 (720)
T ss_pred             CCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCCCceEEEEeCchHHHHHHHHhc--------CCcc
Confidence            3789999999999988888999999999999754 223333322221237888899987766543321        1110


Q ss_pred             EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhc-----CCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCC
Q 014486          147 AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARD-----KDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPH  221 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~-----~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~  221 (423)
                                               .|-.+++.....     ........++||+||++.+..     ..+..++..++.
T Consensus       393 -------------------------~Tih~lL~~~~~~~~~~~~~~~~~~~llIvDEaSMvd~-----~~~~~Ll~~~~~  442 (720)
T TIGR01448       393 -------------------------STIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMDT-----WLALSLLAALPD  442 (720)
T ss_pred             -------------------------ccHHHHhhccCCccchhhhhccccCCEEEEeccccCCH-----HHHHHHHHhCCC
Confidence                                     111111111000     001123567999999997643     345666667777


Q ss_pred             CceEEEEecc
Q 014486          222 DKQVMMFSAT  231 (423)
Q Consensus       222 ~~~~v~~SAT  231 (423)
                      ..++|++.-+
T Consensus       443 ~~rlilvGD~  452 (720)
T TIGR01448       443 HARLLLVGDT  452 (720)
T ss_pred             CCEEEEECcc
Confidence            8888876544

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.97  E-value=7.5e-05  Score=73.23  Aligned_cols=140  Identities=14%  Similarity=0.113  Sum_probs=84.2

Q ss_pred             ChhhhhcccccccCCceEEEccCCCcchhHHHH--HHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           70 SEVQHECIPQAILGMDVICQAKSGMGKTAVFVL--STLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        70 ~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~--~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .+.|+.|+...+.++-.+|.|++|+|||.+...  ..+..... .....++++.||..-|..+.+.+.......   .. 
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~-~~~~~i~l~APTgkAA~rL~e~~~~~~~~~---~~-  228 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLAD-GERCRIRLAAPTGKAAARLTESLGKALRQL---PL-  228 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC-CCCcEEEEECCcHHHHHHHHHHHHhhhhcc---cc-
Confidence            478999998888888899999999999986422  22222211 122378889999988888877665433221   10 


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHh------cCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCC
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALAR------DKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPH  221 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~------~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~  221 (423)
                            .  ...   ... ...-..|-.+++....      ....+.-.+++|||||+-.+.     ...+..++..+++
T Consensus       229 ------~--~~~---~~~-~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd-----~~lm~~ll~al~~  291 (615)
T PRK10875        229 ------T--DEQ---KKR-IPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMVD-----LPMMARLIDALPP  291 (615)
T ss_pred             ------c--hhh---hhc-CCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhccc-----HHHHHHHHHhccc
Confidence                  0  000   000 0112234344433211      111122346899999998553     4566677778888


Q ss_pred             CceEEEEecc
Q 014486          222 DKQVMMFSAT  231 (423)
Q Consensus       222 ~~~~v~~SAT  231 (423)
                      ..++|++.-.
T Consensus       292 ~~rlIlvGD~  301 (615)
T PRK10875        292 HARVIFLGDR  301 (615)
T ss_pred             CCEEEEecch
Confidence            8888887654

>KOG0383 consensus Predicted helicase [General function prediction only]

Probab=97.94  E-value=5.8e-07  Score=87.06  Aligned_cols=74  Identities=22%  Similarity=0.219  Sum_probs=60.2

Q ss_pred             HHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhc---CCccEEEEcCccccC
Q 014486          277 RKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKE---GNKRILVATDLVGRG  351 (423)
Q Consensus       277 ~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~---~~~~ili~T~~~~~G  351 (423)
                      ..|..+++..  .+++++||..-++-.+-+.+.+...+ ....+.|..+..+|+.+++.|+.   .....|++|.+.+.|
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            3344444333  46799999999999999999998888 88899999999999999999984   345688999988766

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=97.84  E-value=4e-05  Score=67.87  Aligned_cols=147  Identities=14%  Similarity=0.169  Sum_probs=87.2

Q ss_pred             CCCCCCChhhhhcccccccCCc--eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccC
Q 014486           64 SGFEHPSEVQHECIPQAILGMD--VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYL  141 (423)
Q Consensus        64 ~~~~~~~~~Q~~~i~~~~~~~~--~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~  141 (423)
                      .|+......|.-|+..++...-  +.+.|+.|+|||+.++.+.+++....+...++++.=|+..+.+.+        .+.
T Consensus       224 wGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dI--------GfL  295 (436)
T COG1875         224 WGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDI--------GFL  295 (436)
T ss_pred             hccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCccccc--------CcC
Confidence            3677777889999998887533  788999999999999998888877666665878877876553221        111


Q ss_pred             CCc---eEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCC----------ccEEEEcCcchhhccCCc
Q 014486          142 PDI---KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKN----------VRHFILDECDKMLESLDM  208 (423)
Q Consensus       142 ~~~---~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~----------~~~vVvDE~h~~~~~~~~  208 (423)
                      |+.   +-..|.+..  ......+.+.    -=++.+.+...+....+.+..          =.+||+|||+.+.     
T Consensus       296 PG~eEeKm~PWmq~i--~DnLE~L~~~----~~~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLT-----  364 (436)
T COG1875         296 PGTEEEKMGPWMQAI--FDNLEVLFSP----NEPGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLT-----  364 (436)
T ss_pred             CCchhhhccchHHHH--HhHHHHHhcc----cccchHHHHHHHhccceeeeeeeeecccccccceEEEehhhccC-----
Confidence            211   000000000  0001111110    011233344444333332211          2479999999653     


Q ss_pred             HHHHHHHHHhCCCCceEEEEe
Q 014486          209 RRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       209 ~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ...+..+..+.....++|++.
T Consensus       365 pheikTiltR~G~GsKIVl~g  385 (436)
T COG1875         365 PHELKTILTRAGEGSKIVLTG  385 (436)
T ss_pred             HHHHHHHHHhccCCCEEEEcC
Confidence            567888999999888777654

>PF13871 Helicase_C_4: Helicase_C-like

Probab=97.83  E-value=6.4e-05  Score=65.38  Aligned_cols=81  Identities=20%  Similarity=0.351  Sum_probs=62.2

Q ss_pred             HHHHhhhcCCccEEEEcCccccCCCCC--------CCCEEEEccCCCCcchhhhcccccCCCCCce---EEEEEecCccc
Q 014486          329 TRYKGFKEGNKRILVATDLVGRGIDIE--------RVNIVINYDMPDSADTYLHRVGRAGRFGTKG---LAITFVSSASD  397 (423)
Q Consensus       329 ~~~~~f~~~~~~ili~T~~~~~Gld~~--------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~---~~~~~~~~~~~  397 (423)
                      ...+.|.+|+.+|+|.+.+++.|+.+.        +-++-|.+.+|||....+|..||++|.||..   ..++...-..|
T Consensus        52 ~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~~~gE  131 (278)
T PF13871_consen   52 AEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTDLPGE  131 (278)
T ss_pred             HHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecCCHHH
Confidence            346789999999999999999999875        3455778999999999999999999999853   22223333456


Q ss_pred             HHHHHHHHHHHh
Q 014486          398 SDILNQVSKFMF  409 (423)
Q Consensus       398 ~~~~~~~~~~~~  409 (423)
                      ......+.+.|.
T Consensus       132 ~Rfas~va~rL~  143 (278)
T PF13871_consen  132 RRFASTVARRLE  143 (278)
T ss_pred             HHHHHHHHHHHh
Confidence            666677766664

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=97.76  E-value=6.7e-05  Score=73.55  Aligned_cols=108  Identities=17%  Similarity=0.181  Sum_probs=66.4

Q ss_pred             CcEEEEEcChhhHHHHHHHHHhC-------CCCeEEEcCCCCHHHHHHHHHhhhc--------CCccEEEEcCccccCCC
Q 014486          289 NQVVIFVKSVSRAAELNKLLVEC-------NFPSICIHSGMSQEERLTRYKGFKE--------GNKRILVATDLVGRGID  353 (423)
Q Consensus       289 ~~~ivf~~~~~~~~~l~~~L~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~--------~~~~ili~T~~~~~Gld  353 (423)
                      ..+|+|+++....+.+....+..       +...+.+... +..+-.+++..|.+        |..-.-||--..++|+|
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            34899999987777765544432       2222222222 33444444555542        22234456688999999


Q ss_pred             CCC--CCEEEEccCCCC--------------------------------------cchhhhcccccCCCCCceEEEEEec
Q 014486          354 IER--VNIVINYDMPDS--------------------------------------ADTYLHRVGRAGRFGTKGLAITFVS  393 (423)
Q Consensus       354 ~~~--~~~vi~~~~~~s--------------------------------------~~~~~Q~~GR~~R~g~~~~~~~~~~  393 (423)
                      +.+  .+.||..++|.-                                      ..-.-|++||+-|.-++=.++++++
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            975  678999888751                                      1123599999999877756666777


Q ss_pred             Cccc
Q 014486          394 SASD  397 (423)
Q Consensus       394 ~~~~  397 (423)
                      ...+
T Consensus       721 ~Rfe  724 (945)
T KOG1132|consen  721 DRFE  724 (945)
T ss_pred             chhh
Confidence            5444

>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=97.76  E-value=4.1e-05  Score=69.87  Aligned_cols=122  Identities=18%  Similarity=0.126  Sum_probs=74.0

Q ss_pred             CChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC-CCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           69 PSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN-PGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        69 ~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~-~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      +++-|.+++..  ..++++|.|+.|||||.+.+--++..+... ..+.++|++++|+..+..+.+++...........  
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            46889999987  677899999999999998766655554443 2344899999999999999999988654321000  


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHH-HHhcCCCCC-CCccEEEEcCcc
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILA-LARDKDLSL-KNVRHFILDECD  200 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~-~~~~~~~~~-~~~~~vVvDE~h  200 (423)
                           ............. ..+.|+|.+.+.. +++...... -.-.+-++|+..
T Consensus        77 -----~~~~~~~~~~~~~-~~~~i~T~hsf~~~ll~~~~~~~~~~~~~~i~~~~~  125 (315)
T PF00580_consen   77 -----SDNERLRRQLSNI-DRIYISTFHSFCYRLLREYGYEIGIDPNFEILDEEE  125 (315)
T ss_dssp             -----TT-HHHHHHHHHC-TTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHH
T ss_pred             -----ccccccccccccc-chheeehhhhhhhhhhhhhhhhhhccccceeecchh
Confidence                 0000111111122 3788999988766 333211111 122346666665

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 ....

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.73  E-value=0.00031  Score=72.30  Aligned_cols=123  Identities=14%  Similarity=0.085  Sum_probs=74.1

Q ss_pred             CCChhhhhcccccccCCc-eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceE
Q 014486           68 HPSEVQHECIPQAILGMD-VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKV  146 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~-~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  146 (423)
                      .+++-|+.++..++.+++ ++|.|+.|+|||++ +-.+...+...  +.+++.+.||-.-+..+.+.        .++. 
T Consensus       346 ~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~~--G~~V~~~ApTGkAA~~L~e~--------tGi~-  413 (988)
T PRK13889        346 VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEAA--GYEVRGAALSGIAAENLEGG--------SGIA-  413 (988)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHHc--CCeEEEecCcHHHHHHHhhc--------cCcc-
Confidence            699999999999998655 78999999999975 33333333222  23788999997655443320        0111 


Q ss_pred             EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhC-CCCceE
Q 014486          147 AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMT-PHDKQV  225 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-~~~~~~  225 (423)
                                              -.|-.+|+.-.......+...++|||||+-.+..     ..+..++... ....++
T Consensus       414 ------------------------a~TI~sll~~~~~~~~~l~~~~vlIVDEASMv~~-----~~m~~LL~~a~~~garv  464 (988)
T PRK13889        414 ------------------------SRTIASLEHGWGQGRDLLTSRDVLVIDEAGMVGT-----RQLERVLSHAADAGAKV  464 (988)
T ss_pred             ------------------------hhhHHHHHhhhcccccccccCcEEEEECcccCCH-----HHHHHHHHhhhhCCCEE
Confidence                                    1122223221112223355678999999996643     2344455433 446677


Q ss_pred             EEEecc
Q 014486          226 MMFSAT  231 (423)
Q Consensus       226 v~~SAT  231 (423)
                      |++.=+
T Consensus       465 VLVGD~  470 (988)
T PRK13889        465 VLVGDP  470 (988)
T ss_pred             EEECCH
Confidence            776554

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=97.70  E-value=0.00014  Score=63.03  Aligned_cols=47  Identities=21%  Similarity=0.398  Sum_probs=37.4

Q ss_pred             CCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCc
Q 014486          186 LSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSK  234 (423)
Q Consensus       186 ~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~  234 (423)
                      .....++.+|+||||.+..  +....+++.....+...++++++-.+.+
T Consensus       125 ~~~~~fKiiIlDEcdsmts--daq~aLrr~mE~~s~~trFiLIcnylsr  171 (346)
T KOG0989|consen  125 YPCPPFKIIILDECDSMTS--DAQAALRRTMEDFSRTTRFILICNYLSR  171 (346)
T ss_pred             CCCCcceEEEEechhhhhH--HHHHHHHHHHhccccceEEEEEcCChhh
Confidence            3456779999999999975  6777788888888888888888776543

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.66  E-value=0.00074  Score=68.48  Aligned_cols=61  Identities=15%  Similarity=0.112  Sum_probs=44.0

Q ss_pred             CCChhhhhcccccccC-CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHH
Q 014486           68 HPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQIC  131 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~-~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  131 (423)
                      .+++-|+.++..++.+ +-++|.|++|+|||...- .+...+...  +.++++++||..-+..+.
T Consensus       352 ~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll~-~i~~~~~~~--g~~V~~~ApTg~Aa~~L~  413 (744)
T TIGR02768       352 RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLK-AAREAWEAA--GYRVIGAALSGKAAEGLQ  413 (744)
T ss_pred             CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHHH-HHHHHHHhC--CCeEEEEeCcHHHHHHHH
Confidence            6899999999998874 558999999999997532 233333222  237889999976655543

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.

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=97.60  E-value=0.0002  Score=73.01  Aligned_cols=146  Identities=17%  Similarity=0.137  Sum_probs=91.5

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCC-----------C----CCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPN-----------P----GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~-----------~----~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      |+.++++..+|+|||..-+...+......           +    ....+|||+|. ++..||.+++......  ++++.
T Consensus       374 g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~-aIl~QW~~EI~kH~~~--~lKv~  450 (1394)
T KOG0298|consen  374 GKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPN-AILMQWFEEIHKHISS--LLKVL  450 (1394)
T ss_pred             CcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcH-HHHHHHHHHHHHhccc--cceEE
Confidence            56789999999999988766555432110           0    11267999996 7889999999887754  46888


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCC------------------CC--CccEEEEcCcchhhccCC
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLS------------------LK--NVRHFILDECDKMLESLD  207 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~------------------~~--~~~~vVvDE~h~~~~~~~  207 (423)
                      .+.|-.+......... ..+||+++|++.|..-+.+....                  +-  .|=.|++|||+.+-.   
T Consensus       451 ~Y~Girk~~~~~~~el-~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEaQMves---  526 (1394)
T KOG0298|consen  451 LYFGIRKTFWLSPFEL-LQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEAQMVES---  526 (1394)
T ss_pred             EEechhhhcccCchhh-hccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHHHhhcc---
Confidence            8877543322111111 22799999999997644332110                  11  111399999997743   


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeccCCccH
Q 014486          208 MRRDVQEIFKMTPHDKQVMMFSATLSKEI  236 (423)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~v~~SAT~~~~~  236 (423)
                      ......+....++... .=++|+||-..+
T Consensus       527 ssS~~a~M~~rL~~in-~W~VTGTPiq~I  554 (1394)
T KOG0298|consen  527 SSSAAAEMVRRLHAIN-RWCVTGTPIQKI  554 (1394)
T ss_pred             hHHHHHHHHHHhhhhc-eeeecCCchhhh
Confidence            4444555555554333 567899975443

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.60  E-value=0.0009  Score=69.48  Aligned_cols=138  Identities=15%  Similarity=0.105  Sum_probs=80.5

Q ss_pred             CCCHHHHHHHHhCCCCCCChhhhhccccccc-CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           52 LLKPELLRAIVDSGFEHPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        52 ~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~-~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      .+++..++.....++ .+++-|+.++..+.. ++-.+|.|+.|+|||.+. -.+...+...+  .+++.+.||-.-+..+
T Consensus       366 ~v~~~~l~a~~~~~~-~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l-~~~~~~~e~~G--~~V~g~ApTgkAA~~L  441 (1102)
T PRK13826        366 GVREAVLAATFARHA-RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMM-KAAREAWEAAG--YRVVGGALAGKAAEGL  441 (1102)
T ss_pred             CCCHHHHHHHHhcCC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHH-HHHHHHHHHcC--CeEEEEcCcHHHHHHH
Confidence            445555555444443 799999999998865 344899999999999753 23333332222  2788899997765554


Q ss_pred             HHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHH
Q 014486          131 CHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRR  210 (423)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~  210 (423)
                      .+..        ++..                         .|-.+|+.........+..-++|||||+..+.     ..
T Consensus       442 ~e~~--------Gi~a-------------------------~TIas~ll~~~~~~~~l~~~~vlVIDEAsMv~-----~~  483 (1102)
T PRK13826        442 EKEA--------GIQS-------------------------RTLSSWELRWNQGRDQLDNKTVFVLDEAGMVA-----SR  483 (1102)
T ss_pred             HHhh--------CCCe-------------------------eeHHHHHhhhccCccCCCCCcEEEEECcccCC-----HH
Confidence            3211        2221                         12222211111122345556799999999653     33


Q ss_pred             HHHHHHHhCC-CCceEEEEecc
Q 014486          211 DVQEIFKMTP-HDKQVMMFSAT  231 (423)
Q Consensus       211 ~~~~~~~~~~-~~~~~v~~SAT  231 (423)
                      .+..++.... ...++|++.-+
T Consensus       484 ~m~~Ll~~~~~~garvVLVGD~  505 (1102)
T PRK13826        484 QMALFVEAVTRAGAKLVLVGDP  505 (1102)
T ss_pred             HHHHHHHHHHhcCCEEEEECCH
Confidence            4444555443 46677776554

>PRK04296 thymidine kinase; Provisional

Probab=97.56  E-value=0.00015  Score=60.53  Aligned_cols=36  Identities=14%  Similarity=0.099  Sum_probs=24.0

Q ss_pred             ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           85 DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      -.++.||+|+|||...+-.+...... +  .+++++-|.
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~-g--~~v~i~k~~   39 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEER-G--MKVLVFKPA   39 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHc-C--CeEEEEecc
Confidence            46889999999997665544433333 2  277777663

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=97.51  E-value=0.00058  Score=67.91  Aligned_cols=137  Identities=18%  Similarity=0.151  Sum_probs=83.0

Q ss_pred             CCCCHHHHHHHHhCCCCCCChhhhhcccccccCCc-eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHH
Q 014486           51 FLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMD-VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQ  129 (423)
Q Consensus        51 ~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~-~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  129 (423)
                      ..+.|...+.    -+..++.-|++|+..++..++ .+|.|=+|+|||.+....+--....++   ++|+.+=|..-+..
T Consensus       656 ~~~~p~~~~~----~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~LIkiL~~~gk---kVLLtsyThsAVDN  728 (1100)
T KOG1805|consen  656 KVLIPKIKKI----ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVALGK---KVLLTSYTHSAVDN  728 (1100)
T ss_pred             cccCchhhHH----HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHHHHHHHHcCC---eEEEEehhhHHHHH
Confidence            3455555553    233788999999999998776 889999999999865433322222222   78888888777777


Q ss_pred             HHHHHHHHhccCCCceEEEEEcCcchHHHHHH-----------------HhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          130 ICHEFERFSTYLPDIKVAVFYGGVNIKIHKDL-----------------LKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      +.-.++.+     ++.+..+..+.....+.+.                 +.+. +.|+.||--.+-+    ..+....|+
T Consensus       729 ILiKL~~~-----~i~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~-~~IVa~TClgi~~----plf~~R~FD  798 (1100)
T KOG1805|consen  729 ILIKLKGF-----GIYILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQ-TSIVACTCLGINH----PLFVNRQFD  798 (1100)
T ss_pred             HHHHHhcc-----CcceeecCCccccchHHHHHhcccccchhhHHHHHHHhCC-CcEEEEEccCCCc----hhhhccccC
Confidence            66555544     3333333333322222222                 2222 4677777433322    122345689


Q ss_pred             EEEEcCcchhhc
Q 014486          193 HFILDECDKMLE  204 (423)
Q Consensus       193 ~vVvDE~h~~~~  204 (423)
                      ++|+|||-.+..
T Consensus       799 ~cIiDEASQI~l  810 (1100)
T KOG1805|consen  799 YCIIDEASQILL  810 (1100)
T ss_pred             EEEEcccccccc
Confidence            999999998764

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.47  E-value=0.00034  Score=54.61  Aligned_cols=20  Identities=20%  Similarity=0.248  Sum_probs=13.4

Q ss_pred             CCceEEEccCCCcchhHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~  102 (423)
                      ++.++|.||+|+|||...-.
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~   23 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKR   23 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHH
Confidence            45589999999999976433

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=97.47  E-value=0.0043  Score=56.69  Aligned_cols=135  Identities=13%  Similarity=0.218  Sum_probs=76.1

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL  162 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (423)
                      ++.+.+.||||-|||.+..-.+.......+....+||-+.+--.+.  .++++.++... ++.                 
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA--~EQLk~Ya~im-~vp-----------------  262 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGA--VEQLKTYADIM-GVP-----------------  262 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhH--HHHHHHHHHHh-CCc-----------------
Confidence            5668999999999998754333333323333336677666543322  23344444333 333                 


Q ss_pred             hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCc-cHHHHHH
Q 014486          163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSK-EIRPVCK  241 (423)
Q Consensus       163 ~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~-~~~~~~~  241 (423)
                           =.++-+|.-|...+.    .+.++++|.||=+-+--.+......+..+........-.+.+|||... ++...+.
T Consensus       263 -----~~vv~~~~el~~ai~----~l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~  333 (407)
T COG1419         263 -----LEVVYSPKELAEAIE----ALRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIK  333 (407)
T ss_pred             -----eEEecCHHHHHHHHH----HhhcCCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHH
Confidence                 344555555554333    345557888887764322233344555555555455567889999864 4455555


Q ss_pred             HhccC
Q 014486          242 KFMQD  246 (423)
Q Consensus       242 ~~~~~  246 (423)
                      .|..-
T Consensus       334 ~f~~~  338 (407)
T COG1419         334 QFSLF  338 (407)
T ss_pred             HhccC
Confidence            55443

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]

Probab=97.42  E-value=0.00028  Score=65.29  Aligned_cols=73  Identities=15%  Similarity=0.111  Sum_probs=45.2

Q ss_pred             CCCCCChhhhhcccccc----cCCceEEEccCCCcchhHHHHHHhhccCCCC-CCeEEEEEecChHHHHHHHHHHHHH
Q 014486           65 GFEHPSEVQHECIPQAI----LGMDVICQAKSGMGKTAVFVLSTLQQTEPNP-GQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~----~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .|...+|.|.+=...+.    .+.+.++.+|+|+|||.+.+-.++....+.+ ...+.++.+-|..-.+....+++.+
T Consensus        13 PY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~l   90 (755)
T KOG1131|consen   13 PYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKRL   90 (755)
T ss_pred             CCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHHH
Confidence            34566777765443333    3677999999999999876655555433333 2236677766665555555555544

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=97.39  E-value=0.003  Score=60.80  Aligned_cols=118  Identities=18%  Similarity=0.243  Sum_probs=82.0

Q ss_pred             HHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCC-------CeEEEcCCCCHHHHHHHHHhhh----cCCccEEEEc-
Q 014486          278 KLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNF-------PSICIHSGMSQEERLTRYKGFK----EGNKRILVAT-  345 (423)
Q Consensus       278 ~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~-------~~~~~~~~~~~~~r~~~~~~f~----~~~~~ili~T-  345 (423)
                      .+.++....+ +-+++|+++.+....+.+.....|+       +.+.+...-+   -..+++.|.    .|...+|++. 
T Consensus       620 ~~~nL~~~VP-gGvV~FfPSy~yL~~v~k~w~~~gil~ri~~kK~vF~E~k~~---~~dvl~~Ya~a~~~g~GaiLlaVV  695 (821)
T KOG1133|consen  620 SISNLSNAVP-GGVVCFFPSYAYLGQVRKRWEQNGILARIVGKKKVFYEPKDT---VEDVLEGYAEAAERGRGAILLAVV  695 (821)
T ss_pred             HHHHHHhhCC-CcEEEEeccHHHHHHHHHHHHhcchHHHhhccchhhccCccc---HHHHHHHHHHHhhcCCCeEEEEEe
Confidence            3444444445 7799999999999999988876543       2333333333   344555554    3555577654 


Q ss_pred             -CccccCCCCCC--CCEEEEccCCCC--------------------------------cchhhhcccccCCCCCceEEEE
Q 014486          346 -DLVGRGIDIER--VNIVINYDMPDS--------------------------------ADTYLHRVGRAGRFGTKGLAIT  390 (423)
Q Consensus       346 -~~~~~Gld~~~--~~~vi~~~~~~s--------------------------------~~~~~Q~~GR~~R~g~~~~~~~  390 (423)
                       ..+++|||+.+  +++|+.+++|..                                +...-|.+|||-|.-++-.+++
T Consensus       696 GGKlSEGINF~D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~~~~gagke~yEnlCMkAVNQsIGRAIRH~~DYA~i~  775 (821)
T KOG1133|consen  696 GGKLSEGINFSDDLGRAVVVVGLPYPNIQSVELQERMKHLDGKLPTPGAGKELYENLCMKAVNQSIGRAIRHRKDYASIY  775 (821)
T ss_pred             ccccccccccccccccEEEEeecCCCCCCCHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHhhhccceeEE
Confidence             78999999987  889999998862                                1123599999999888888888


Q ss_pred             EecCcccHH
Q 014486          391 FVSSASDSD  399 (423)
Q Consensus       391 ~~~~~~~~~  399 (423)
                      +++..+...
T Consensus       776 LlD~RY~~p  784 (821)
T KOG1133|consen  776 LLDKRYARP  784 (821)
T ss_pred             EehhhhcCc
Confidence            888766533

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.37  E-value=0.0016  Score=60.24  Aligned_cols=122  Identities=13%  Similarity=0.128  Sum_probs=64.0

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCC--CCCCeEEEEEecC-hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEP--NPGQVTALVLCHT-RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKD  160 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~--~~~~~~~lil~P~-~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (423)
                      +.+++.||||+|||.+..-.+......  ..+...+++-+.+ +.-+..+   ++.++... ++.+..            
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQ---L~~~a~~l-gvpv~~------------  238 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQ---IQTYGDIM-GIPVKA------------  238 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHH---HHHHhhcC-CcceEe------------
Confidence            458899999999998764333222211  1222233343433 3333322   34444332 333221            


Q ss_pred             HHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCC-ceEEEEeccCCcc
Q 014486          161 LLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHD-KQVMMFSATLSKE  235 (423)
Q Consensus       161 ~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~-~~~v~~SAT~~~~  235 (423)
                                +-+++.+...+..    +.+.++|++|++.+...+......+..++...... ..++.+|||....
T Consensus       239 ----------~~~~~~l~~~L~~----~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~  300 (388)
T PRK12723        239 ----------IESFKDLKEEITQ----SKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTS  300 (388)
T ss_pred             ----------eCcHHHHHHHHHH----hCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHH
Confidence                      1133444443332    25678999999998753222234555555554433 4578899998743

>PRK06526 transposase; Provisional

Probab=97.30  E-value=0.00065  Score=59.35  Aligned_cols=23  Identities=22%  Similarity=0.209  Sum_probs=18.5

Q ss_pred             cccCCceEEEccCCCcchhHHHH
Q 014486           80 AILGMDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        80 ~~~~~~~ii~~~tGsGKT~~~~~  102 (423)
                      +..+.++++.||+|+|||..+..
T Consensus        95 i~~~~nlll~Gp~GtGKThLa~a  117 (254)
T PRK06526         95 VTGKENVVFLGPPGTGKTHLAIG  117 (254)
T ss_pred             hhcCceEEEEeCCCCchHHHHHH
Confidence            34567899999999999976544

>PRK14974 cell division protein FtsY; Provisional

Probab=97.30  E-value=0.003  Score=57.31  Aligned_cols=55  Identities=13%  Similarity=0.285  Sum_probs=41.2

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhc
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFM  244 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~  244 (423)
                      +.++|++|.+.++..+......+..+.+...+...++.++||...+....++.+.
T Consensus       222 ~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~~~a~~f~  276 (336)
T PRK14974        222 GIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQAREFN  276 (336)
T ss_pred             CCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccchhHHHHHHHHH
Confidence            4579999999988654556677777777777777788899998776666555544

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

Probab=97.28  E-value=0.00097  Score=57.40  Aligned_cols=87  Identities=30%  Similarity=0.442  Sum_probs=66.9

Q ss_pred             CCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcC-cchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCC
Q 014486          112 PGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGG-VNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKN  190 (423)
Q Consensus       112 ~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~  190 (423)
                      .+.|.+|||+.+---|..+...++.+...  +..++-+..- ....++...+.+...+|.||||+++..+++.+.+.+.+
T Consensus       124 ~gsP~~lvvs~SalRa~dl~R~l~~~~~k--~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~  201 (252)
T PF14617_consen  124 KGSPHVLVVSSSALRAADLIRALRSFKGK--DCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSN  201 (252)
T ss_pred             CCCCEEEEEcchHHHHHHHHHHHHhhccC--CchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCccc
Confidence            45678999999877777777777766321  2234333333 36677778888777899999999999999999999999


Q ss_pred             ccEEEEcCcc
Q 014486          191 VRHFILDECD  200 (423)
Q Consensus       191 ~~~vVvDE~h  200 (423)
                      +.+||+|--|
T Consensus       202 l~~ivlD~s~  211 (252)
T PF14617_consen  202 LKRIVLDWSY  211 (252)
T ss_pred             CeEEEEcCCc
Confidence            9999999876

>TIGR00376 DNA helicase, putative

Probab=97.25  E-value=0.0005  Score=68.31  Aligned_cols=66  Identities=18%  Similarity=0.167  Sum_probs=51.6

Q ss_pred             CCChhhhhcccccccC-CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER  136 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~-~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  136 (423)
                      .+++.|..++..++.. ...+|.||+|+|||.+..-.+.+....+   .++|+++||..-+.++.+.+..
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            5688999999998876 5689999999999976554443333322   2899999999999998888765

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=97.24  E-value=0.00096  Score=57.79  Aligned_cols=45  Identities=16%  Similarity=0.234  Sum_probs=27.2

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCc
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSK  234 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~  234 (423)
                      +.+++|+|++|.+.....+...+-.++..+......+++|++.++
T Consensus        97 ~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p  141 (234)
T PRK05642         97 QYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSP  141 (234)
T ss_pred             hCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCH
Confidence            446899999998765334455566666554443334566666443

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.21  E-value=0.0017  Score=56.37  Aligned_cols=18  Identities=11%  Similarity=0.253  Sum_probs=15.1

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      ..+++.||+|+|||....
T Consensus        46 ~~l~l~Gp~G~GKThLl~   63 (235)
T PRK08084         46 GYIYLWSREGAGRSHLLH   63 (235)
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            568999999999997543

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.19  E-value=0.0017  Score=51.17  Aligned_cols=40  Identities=15%  Similarity=0.135  Sum_probs=25.0

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      +..+++.||+|+|||..... ++..+....  ..++++.+...
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~-l~~~~~~~~--~~~~~~~~~~~   41 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARA-LARELGPPG--GGVIYIDGEDI   41 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHH-HHhccCCCC--CCEEEECCEEc
Confidence            45689999999999986543 333333222  14566666543

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.

>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=97.18  E-value=0.0019  Score=54.02  Aligned_cols=55  Identities=15%  Similarity=0.259  Sum_probs=37.1

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHh
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKF  243 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~  243 (423)
                      .++++|++|-+-+...+......+..+.....+..-.+.+|||...+....+..+
T Consensus        82 ~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~~~  136 (196)
T PF00448_consen   82 KGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQALAF  136 (196)
T ss_dssp             TTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHHHH
T ss_pred             cCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHHHH
Confidence            3457899999876543334556677777777777778899999887655544443

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 ....

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.17  E-value=0.0044  Score=56.93  Aligned_cols=132  Identities=14%  Similarity=0.157  Sum_probs=63.7

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL  162 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (423)
                      +..+++.||||+|||.+....+.......+.. ++.+++ +...-.--.+.++.|.... ++.+..              
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~-~V~lit-~D~~R~ga~EqL~~~a~~~-gv~~~~--------------  199 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGAS-KVALLT-TDSYRIGGHEQLRIFGKIL-GVPVHA--------------  199 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCC-eEEEEe-cccccccHHHHHHHHHHHc-CCceEe--------------
Confidence            56689999999999987654333322222212 333333 2221111123344444333 333322              


Q ss_pred             hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHH-HHHH
Q 014486          163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIR-PVCK  241 (423)
Q Consensus       163 ~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~-~~~~  241 (423)
                              +.++..+...+.    .+.+.++|+||.+-+.-.+......+..+.........++.+|||...... ..+.
T Consensus       200 --------~~~~~~l~~~l~----~l~~~DlVLIDTaG~~~~d~~l~e~La~L~~~~~~~~~lLVLsAts~~~~l~evi~  267 (374)
T PRK14722        200 --------VKDGGDLQLALA----ELRNKHMVLIDTIGMSQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGDTLNEVVQ  267 (374)
T ss_pred             --------cCCcccHHHHHH----HhcCCCEEEEcCCCCCcccHHHHHHHHHHhccCCCCeEEEEecCccChHHHHHHHH
Confidence                    223333333222    234557899999975422112223333332323334457889999865543 3444


Q ss_pred             Hh
Q 014486          242 KF  243 (423)
Q Consensus       242 ~~  243 (423)
                      .|
T Consensus       268 ~f  269 (374)
T PRK14722        268 AY  269 (374)
T ss_pred             HH
Confidence            44

>PRK11054 helD DNA helicase IV; Provisional

Probab=97.17  E-value=0.0021  Score=64.32  Aligned_cols=83  Identities=18%  Similarity=0.143  Sum_probs=57.7

Q ss_pred             CCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC-CCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           66 FEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP-GQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        66 ~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      -..+++-|++++..-  ..+++|.|..|||||.+.+--+...+.... .+.++|+++.++..|..+.+++...... .++
T Consensus       194 ~~~L~~~Q~~av~~~--~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~lg~-~~v  270 (684)
T PRK11054        194 SSPLNPSQARAVVNG--EDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERLGT-EDI  270 (684)
T ss_pred             CCCCCHHHHHHHhCC--CCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhcCC-CCc
Confidence            347999999998643  356899999999999886554443332221 2338999999999999999988776531 244


Q ss_pred             eEEEEEc
Q 014486          145 KVAVFYG  151 (423)
Q Consensus       145 ~~~~~~~  151 (423)
                      .+..+|+
T Consensus       271 ~v~TFHS  277 (684)
T PRK11054        271 TARTFHA  277 (684)
T ss_pred             EEEeHHH
Confidence            4444444

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.15  E-value=0.0073  Score=55.43  Aligned_cols=131  Identities=14%  Similarity=0.190  Sum_probs=67.8

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEe-cCh-HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLC-HTR-ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDL  161 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~-P~~-~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (423)
                      +.+.+.||+|+|||......+.... ..+ ...+++-+ |.+ ..+.|+.    .+.... ++.                
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~-~~G-kkVglI~aDt~RiaAvEQLk----~yae~l-gip----------------  298 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFH-GKK-KTVGFITTDHSRIGTVQQLQ----DYVKTI-GFE----------------  298 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHH-HcC-CcEEEEecCCcchHHHHHHH----HHhhhc-CCc----------------
Confidence            4578999999999987554433332 222 21334444 333 2334433    332221 222                


Q ss_pred             HhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCc-cHHHHH
Q 014486          162 LKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSK-EIRPVC  240 (423)
Q Consensus       162 ~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~-~~~~~~  240 (423)
                            -+.+.++..+...+..... ..++++|++|-+=+...+......+..+.....+..-++.+|||... ++...+
T Consensus       299 ------v~v~~d~~~L~~aL~~lk~-~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~  371 (436)
T PRK11889        299 ------VIAVRDEAAMTRALTYFKE-EARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEII  371 (436)
T ss_pred             ------EEecCCHHHHHHHHHHHHh-ccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHH
Confidence                  2223455555554432110 12468999999876543223344455555544444446668887654 445555


Q ss_pred             HHhc
Q 014486          241 KKFM  244 (423)
Q Consensus       241 ~~~~  244 (423)
                      +.|.
T Consensus       372 ~~F~  375 (436)
T PRK11889        372 TNFK  375 (436)
T ss_pred             HHhc
Confidence            5544

>PRK08181 transposase; Validated

Probab=97.14  E-value=0.0019  Score=56.73  Aligned_cols=46  Identities=22%  Similarity=0.250  Sum_probs=26.9

Q ss_pred             ccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           81 ILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      -.++++++.||+|+|||..+.....+... .+.  ++++ ++...|..+.
T Consensus       104 ~~~~nlll~Gp~GtGKTHLa~Aia~~a~~-~g~--~v~f-~~~~~L~~~l  149 (269)
T PRK08181        104 AKGANLLLFGPPGGGKSHLAAAIGLALIE-NGW--RVLF-TRTTDLVQKL  149 (269)
T ss_pred             hcCceEEEEecCCCcHHHHHHHHHHHHHH-cCC--ceee-eeHHHHHHHH
Confidence            35678999999999999755433322222 221  4444 4445555544

>PRK06893 DNA replication initiation factor; Validated

Probab=97.11  E-value=0.0016  Score=56.33  Aligned_cols=47  Identities=15%  Similarity=0.270  Sum_probs=28.4

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCC-CCceEEEEeccCCcc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTP-HDKQVMMFSATLSKE  235 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~-~~~~~v~~SAT~~~~  235 (423)
                      .+.+++++||+|.+.....+...+..++.... ...+++++|++.++.
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~  137 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPH  137 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChH
Confidence            35578999999988653334444444444333 244566777776543

>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=97.06  E-value=0.0053  Score=48.64  Aligned_cols=18  Identities=22%  Similarity=0.359  Sum_probs=15.4

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      ++.+++.||+|+|||...
T Consensus        19 ~~~v~i~G~~G~GKT~l~   36 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLA   36 (151)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            567999999999999653

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.

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=97.04  E-value=0.00085  Score=67.47  Aligned_cols=70  Identities=13%  Similarity=0.046  Sum_probs=54.3

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC-CCCCeEEEEEecChHHHHHHHHHHHHHhc
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP-NPGQVTALVLCHTRELAYQICHEFERFST  139 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~  139 (423)
                      .+++-|++++.+.  ...++|.|++|||||.+.+.-+...+.. +-.+.++|+++.|+..|.++.+++.....
T Consensus         2 ~Ln~~Q~~av~~~--~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919          2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            4789999998753  4678899999999999876666655543 22234899999999999999999987653

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.02  E-value=0.054  Score=60.99  Aligned_cols=236  Identities=12%  Similarity=0.138  Sum_probs=119.9

Q ss_pred             CCChhhhhcccccccCC--ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCce
Q 014486           68 HPSEVQHECIPQAILGM--DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIK  145 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~--~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  145 (423)
                      .+++-|+.++..++...  -.+|.|+.|+|||.+. -.+...+...+  .++++++|+..-+.++.+......       
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l-~~l~~~~~~~G--~~V~~lAPTgrAA~~L~e~~g~~A-------  498 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIA-QLLLHLASEQG--YEIQIITAGSLSAQELRQKIPRLA-------  498 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHH-HHHHHHHHhcC--CeEEEEeCCHHHHHHHHHHhcchh-------
Confidence            68899999999988864  4899999999999753 23333333222  388999999877666654332110       


Q ss_pred             EEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhC-CCCce
Q 014486          146 VAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMT-PHDKQ  224 (423)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-~~~~~  224 (423)
                             ..+..+...+..   ..-..|...|+    .....+..-++|||||+-.+.     ...+..++... ....+
T Consensus       499 -------~Ti~~~l~~l~~---~~~~~tv~~fl----~~~~~l~~~~vlIVDEAsMl~-----~~~~~~Ll~~a~~~gar  559 (1960)
T TIGR02760       499 -------STFITWVKNLFN---DDQDHTVQGLL----DKSSPFSNKDIFVVDEANKLS-----NNELLKLIDKAEQHNSK  559 (1960)
T ss_pred             -------hhHHHHHHhhcc---cccchhHHHhh----cccCCCCCCCEEEEECCCCCC-----HHHHHHHHHHHhhcCCE
Confidence                   001111111111   11122333333    223344567899999999653     34455555544 45788


Q ss_pred             EEEEeccC--C----ccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHH-HHHHHhh-cCCcEEEEEc
Q 014486          225 VMMFSATL--S----KEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKL-NDLLDAL-DFNQVVIFVK  296 (423)
Q Consensus       225 ~v~~SAT~--~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~ll~~~-~~~~~ivf~~  296 (423)
                      +|++.-+-  +    ......+....  ...+.+.... .....+  .+.......+...+ ..++... ...+++|+..
T Consensus       560 vVlvGD~~QL~sV~aG~~f~~L~~~g--v~t~~l~~i~-rq~~~v--~i~~~~~~~r~~~ia~~y~~L~~~r~~tliv~~  634 (1960)
T TIGR02760       560 LILLNDSAQRQGMSAGSAIDLLKEGG--VTTYAWVDTK-QQKASV--EISEAVDKLRVDYIASAWLDLTPDRQNSQVLAT  634 (1960)
T ss_pred             EEEEcChhhcCccccchHHHHHHHCC--CcEEEeeccc-ccCcce--eeeccCchHHHHHHHHHHHhcccccCceEEEcC
Confidence            88876652  1    12223333321  1111111111 110111  11122222222222 2333322 3345899999


Q ss_pred             ChhhHHHHHHHHHh----CCC------CeEEEc-CCCCHHHHHHHHHhhhcCC
Q 014486          297 SVSRAAELNKLLVE----CNF------PSICIH-SGMSQEERLTRYKGFKEGN  338 (423)
Q Consensus       297 ~~~~~~~l~~~L~~----~~~------~~~~~~-~~~~~~~r~~~~~~f~~~~  338 (423)
                      +....+.+....+.    .|.      ....+. ..++..++... ..|+.|.
T Consensus       635 t~~dr~~Ln~~iR~~L~~~G~L~~~~~~~~~L~p~~lt~~e~r~~-~~Yr~Gd  686 (1960)
T TIGR02760       635 THREQQDLTQIIRNALKQEGQLSRQEVTVPTLKPVNLTGIQRRNA-AHYKQGM  686 (1960)
T ss_pred             CcHHHHHHHHHHHHHHHHcCCcCCCceEEEEeccCCCCHHHHhhH-hhcCCCC
Confidence            88887777666543    332      222232 35666666633 5565544

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.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.98  E-value=0.015  Score=55.04  Aligned_cols=129  Identities=17%  Similarity=0.270  Sum_probs=65.1

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhcc-CCCCCCeEEEEE-ecC-hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQT-EPNPGQVTALVL-CHT-RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK  159 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~-~~~~~~~~~lil-~P~-~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (423)
                      ++.+++.||||+|||.+....+.... ...+ . ++.++ +.+ +.-+   .+.++.+.... ++.+             
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g-~-~V~li~~D~~r~~a---~eqL~~~a~~~-~vp~-------------  281 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGK-K-KVALITLDTYRIGA---VEQLKTYAKIM-GIPV-------------  281 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCC-C-eEEEEECCccHHHH---HHHHHHHHHHh-CCce-------------
Confidence            45688999999999987654333332 2222 2 34443 332 3212   12333333222 2222             


Q ss_pred             HHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhC-CCCceEEEEeccCCcc-HH
Q 014486          160 DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMT-PHDKQVMMFSATLSKE-IR  237 (423)
Q Consensus       160 ~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-~~~~~~v~~SAT~~~~-~~  237 (423)
                               ..+.++..+...+..    +.+.++|+||-+-+...+......+..+.... .+....+.+|||.... +.
T Consensus       282 ---------~~~~~~~~l~~~l~~----~~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~  348 (424)
T PRK05703        282 ---------EVVYDPKELAKALEQ----LRDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLK  348 (424)
T ss_pred             ---------EccCCHHhHHHHHHH----hCCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHH
Confidence                     222344444444432    23578999999975433222334455555522 2334578899988753 33


Q ss_pred             HHHHHh
Q 014486          238 PVCKKF  243 (423)
Q Consensus       238 ~~~~~~  243 (423)
                      .....+
T Consensus       349 ~~~~~f  354 (424)
T PRK05703        349 DIYKHF  354 (424)
T ss_pred             HHHHHh
Confidence            443433

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.96  E-value=0.0021  Score=59.74  Aligned_cols=59  Identities=19%  Similarity=0.249  Sum_probs=41.0

Q ss_pred             CChhhhhccccc------ccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           69 PSEVQHECIPQA------ILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        69 ~~~~Q~~~i~~~------~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      +++-|+.++..+      ..+..+++.|+-|+|||+.+- .+...+...  +..+++++||..-|..+
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~-~i~~~~~~~--~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIK-AIIDYLRSR--GKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHH-HHHHHhccc--cceEEEecchHHHHHhc
Confidence            567888888777      567789999999999997542 233333322  23788899987654443

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>TIGR01075 uvrD DNA helicase II

Probab=96.96  E-value=0.0024  Score=65.07  Aligned_cols=83  Identities=16%  Similarity=0.193  Sum_probs=60.7

Q ss_pred             CCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC-CCeEEEEEecChHHHHHHHHHHHHHhccC-CCc
Q 014486           67 EHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP-GQVTALVLCHTRELAYQICHEFERFSTYL-PDI  144 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~L~~q~~~~~~~~~~~~-~~~  144 (423)
                      ..+++-|++++.+.  ...++|.|..|||||.+..--+...+...+ .+.++|+++-|+..|..+.+++.++.... .++
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~~~~~~~~   80 (715)
T TIGR01075         3 DGLNDKQREAVAAP--PGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALLGTSARGM   80 (715)
T ss_pred             cccCHHHHHHHcCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHhcccccCc
Confidence            35889999998753  467999999999999987666655543322 33489999999999999999998876431 234


Q ss_pred             eEEEEEc
Q 014486          145 KVAVFYG  151 (423)
Q Consensus       145 ~~~~~~~  151 (423)
                      .+..+|+
T Consensus        81 ~i~TfHs   87 (715)
T TIGR01075        81 WIGTFHG   87 (715)
T ss_pred             EEEcHHH
Confidence            5555544

Designed to identify uvrD members of the uvrD/rep subfamily.

>PRK08727 hypothetical protein; Validated

Probab=96.93  E-value=0.0023  Score=55.43  Aligned_cols=47  Identities=4%  Similarity=0.070  Sum_probs=25.9

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhC-CCCceEEEEeccCCccH
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMT-PHDKQVMMFSATLSKEI  236 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-~~~~~~v~~SAT~~~~~  236 (423)
                      +..+||+||+|.+..+......+-.+.... ....++|+.|-.+|...
T Consensus        93 ~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l  140 (233)
T PRK08727         93 GRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGL  140 (233)
T ss_pred             cCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhh
Confidence            346899999998865333333333343332 22345565555555544

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.91  E-value=0.00087  Score=63.27  Aligned_cols=144  Identities=19%  Similarity=0.195  Sum_probs=73.5

Q ss_pred             EccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhcc-CCCceEEEEEcCcchHHHHHH---Hhc
Q 014486           89 QAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTY-LPDIKVAVFYGGVNIKIHKDL---LKN  164 (423)
Q Consensus        89 ~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~---~~~  164 (423)
                      .+.||||||++..-.|++....+-.  .-|+.|......+-....+..-.+. + -..-....++..++.....   -.+
T Consensus         3 ~matgsgkt~~ma~lil~~y~kgyr--~flffvnq~nilekt~~nftd~~s~ky-lf~e~i~~~d~~i~ikkvn~fsehn   79 (812)
T COG3421           3 EMATGSGKTLVMAGLILECYKKGYR--NFLFFVNQANILEKTKLNFTDSVSSKY-LFSENININDENIEIKKVNNFSEHN   79 (812)
T ss_pred             ccccCCChhhHHHHHHHHHHHhchh--hEEEEecchhHHHHHHhhcccchhhhH-hhhhhhhcCCceeeeeeecccCccC
Confidence            4679999999876666665554332  5677777766655544333211000 0 0000011111111111000   023


Q ss_pred             CCCcEEEechHHHHHHHhcCCC------CCCCccE-EEEcCcchhhcc--------CCcHHHHHHH---HHhCCCCceEE
Q 014486          165 ECPQIVVGTPGRILALARDKDL------SLKNVRH-FILDECDKMLES--------LDMRRDVQEI---FKMTPHDKQVM  226 (423)
Q Consensus       165 ~~~~ilv~T~~~l~~~~~~~~~------~~~~~~~-vVvDE~h~~~~~--------~~~~~~~~~~---~~~~~~~~~~v  226 (423)
                      ....|.++|.+.|...+.+...      ++.+.++ .+-||+|++...        ......+...   ....+++.-++
T Consensus        80 d~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~nkd~~~l  159 (812)
T COG3421          80 DAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQNKDNLLL  159 (812)
T ss_pred             CceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhcCCCceee
Confidence            3368999999999875543322      2444554 567999998642        1111112211   22234455678


Q ss_pred             EEeccCCcc
Q 014486          227 MFSATLSKE  235 (423)
Q Consensus       227 ~~SAT~~~~  235 (423)
                      .+|||.|.+
T Consensus       160 ef~at~~k~  168 (812)
T COG3421         160 EFSATIPKE  168 (812)
T ss_pred             hhhhcCCcc
Confidence            899999854

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=96.89  E-value=0.0028  Score=64.56  Aligned_cols=82  Identities=21%  Similarity=0.246  Sum_probs=60.3

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC-CCCCeEEEEEecChHHHHHHHHHHHHHhcc-CCCce
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP-NPGQVTALVLCHTRELAYQICHEFERFSTY-LPDIK  145 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~~-~~~~~  145 (423)
                      .+++-|++++.+.  ...++|.|..|||||.+.+--+...+.. +-.+.++|+++-|+..|.++.+++.++... ..++.
T Consensus         9 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~~~~~~~~   86 (721)
T PRK11773          9 SLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLGTSQGGMW   86 (721)
T ss_pred             hcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhccCCCCCE
Confidence            5899999998753  4678999999999998876655554432 223348999999999999999999887643 12345


Q ss_pred             EEEEEc
Q 014486          146 VAVFYG  151 (423)
Q Consensus       146 ~~~~~~  151 (423)
                      +..+|+
T Consensus        87 i~TfHs   92 (721)
T PRK11773         87 VGTFHG   92 (721)
T ss_pred             EEcHHH
Confidence            555555

>PHA02533 17 large terminase protein; Provisional

Probab=96.87  E-value=0.0087  Score=58.11  Aligned_cols=123  Identities=16%  Similarity=0.165  Sum_probs=74.9

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc-eE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI-KV  146 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~-~~  146 (423)
                      .|.|+|+..+..+..++-.++..+=..|||.+....++......+ +..+++++|+..-|..+.+.++.+....|.+ ..
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~~-~~~v~i~A~~~~QA~~vF~~ik~~ie~~P~l~~~  137 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFNK-DKNVGILAHKASMAAEVLDRTKQAIELLPDFLQP  137 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhCC-CCEEEEEeCCHHHHHHHHHHHHHHHHhCHHHhhc
Confidence            688999999887755556788888999999876654443333222 2389999999999999988888776554432 11


Q ss_pred             EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          147 AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                      .....+    .....+.++ ..|.+.|.+.       ....-.+..++++||+|.+.
T Consensus       138 ~i~~~~----~~~I~l~NG-S~I~~lss~~-------~t~rG~~~~~liiDE~a~~~  182 (534)
T PHA02533        138 GIVEWN----KGSIELENG-SKIGAYASSP-------DAVRGNSFAMIYIDECAFIP  182 (534)
T ss_pred             ceeecC----ccEEEeCCC-CEEEEEeCCC-------CccCCCCCceEEEeccccCC
Confidence            110000    000111233 3554444321       11122345689999999663

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=96.70  E-value=0.0068  Score=51.89  Aligned_cols=48  Identities=15%  Similarity=0.286  Sum_probs=30.6

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhC-CCCceEEEEeccCCccH
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMT-PHDKQVMMFSATLSKEI  236 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-~~~~~~v~~SAT~~~~~  236 (423)
                      ...+++++|++|.+.+.......+..++..+ ....++|+.|...|..+
T Consensus        96 ~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l  144 (219)
T PF00308_consen   96 RSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSEL  144 (219)
T ss_dssp             CTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTT
T ss_pred             hcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccc
Confidence            3567899999999876333344454444443 34567777777777654

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.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.67  E-value=0.007  Score=52.26  Aligned_cols=20  Identities=20%  Similarity=0.140  Sum_probs=16.4

Q ss_pred             cCCceEEEccCCCcchhHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~  101 (423)
                      .+..+++.||+|+|||..+.
T Consensus        37 ~~~~lll~G~~G~GKT~la~   56 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQ   56 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            35679999999999997653

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.

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=96.66  E-value=0.0087  Score=58.67  Aligned_cols=127  Identities=14%  Similarity=0.148  Sum_probs=79.3

Q ss_pred             CCChhhhhcccccccC--CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHH-HHHHHHhccCCCc
Q 014486           68 HPSEVQHECIPQAILG--MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQIC-HEFERFSTYLPDI  144 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~--~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~-~~~~~~~~~~~~~  144 (423)
                      ..+|||.+.++.+-..  +.+++..++-+|||.+.+..+...+...+.  .+|++.||..+|..+. +++..+....|.+
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 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQDPG--PMLYVQPTDDAAKDFSKERLDPMIRASPVL   93 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeCCC--CEEEEEEcHHHHHHHHHHHHHHHHHhCHHH
Confidence            5678999888877664  468999999999999766666666665554  6899999999999976 6666666555544


Q ss_pred             eEEEEE---cCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          145 KVAVFY---GGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       145 ~~~~~~---~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      +-.+-.   .........+.+. +. .+.+....+-      ..+.-..++++++||++.+..
T Consensus        94 ~~~~~~~~~~~~~~t~~~k~f~-gg-~l~~~ga~S~------~~l~s~~~r~~~~DEvD~~p~  148 (557)
T PF05876_consen   94 RRKLSPSKSRDSGNTILYKRFP-GG-FLYLVGANSP------SNLRSRPARYLLLDEVDRYPD  148 (557)
T ss_pred             HHHhCchhhcccCCchhheecC-CC-EEEEEeCCCC------cccccCCcCEEEEechhhccc
Confidence            322111   1111111222222 21 3443332211      123335678999999998843

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 [].

>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=96.65  E-value=0.0027  Score=51.66  Aligned_cols=123  Identities=19%  Similarity=0.165  Sum_probs=51.5

Q ss_pred             EEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcch-HHHHHHHhcC
Q 014486           87 ICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNI-KIHKDLLKNE  165 (423)
Q Consensus        87 ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  165 (423)
                      ++.|+-|-|||.+.-+.+........  .+++|.+|+.+-++...+.+..-.... +.+.     .... ..........
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~~--~~I~vtAP~~~~~~~lf~~~~~~l~~~-~~~~-----~~~~~~~~~~~~~~~   72 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKGK--IRILVTAPSPENVQTLFEFAEKGLKAL-GYKE-----EKKKRIGQIIKLRFN   72 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-------EEEE-SS--S-HHHHHCC--------------------------------
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhcC--ceEEEecCCHHHHHHHHHHHHhhcccc-cccc-----ccccccccccccccc
Confidence            57899999999775554443333322  378999999988777766554332211 1111     0000 0000011111


Q ss_pred             CCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCC
Q 014486          166 CPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLS  233 (423)
Q Consensus       166 ~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~  233 (423)
                      ...|-+..|+.+....       ...+++|||||=.+     -.+.+..+....   . .+++|.|.-
T Consensus        73 ~~~i~f~~Pd~l~~~~-------~~~DlliVDEAAaI-----p~p~L~~ll~~~---~-~vv~stTi~  124 (177)
T PF05127_consen   73 KQRIEFVAPDELLAEK-------PQADLLIVDEAAAI-----PLPLLKQLLRRF---P-RVVFSTTIH  124 (177)
T ss_dssp             CCC--B--HHHHCCT-----------SCEEECTGGGS------HHHHHHHHCCS---S-EEEEEEEBS
T ss_pred             cceEEEECCHHHHhCc-------CCCCEEEEechhcC-----CHHHHHHHHhhC---C-EEEEEeecc
Confidence            2477777777765321       23478999999754     234444444332   3 566677763

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.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.61  E-value=0.0032  Score=63.79  Aligned_cols=69  Identities=14%  Similarity=0.079  Sum_probs=53.8

Q ss_pred             CChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC-CCCCeEEEEEecChHHHHHHHHHHHHHhc
Q 014486           69 PSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP-NPGQVTALVLCHTRELAYQICHEFERFST  139 (423)
Q Consensus        69 ~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~  139 (423)
                      +++-|++++.+  ...+++|.|..|||||.+.+--+...+.. ...+.++|+++.|+..+.++.+++.+...
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l~   71 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTLG   71 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhC
Confidence            67899999865  35679999999999999877666665543 22334789999999999999998877653

Designed to identify rep members of the uvrD/rep subfamily.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.60  E-value=0.016  Score=52.80  Aligned_cols=40  Identities=15%  Similarity=0.015  Sum_probs=29.0

Q ss_pred             CCChhhhhcccccccC----CceEEEccCCCcchhHHHHHHhhc
Q 014486           68 HPSEVQHECIPQAILG----MDVICQAKSGMGKTAVFVLSTLQQ  107 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~----~~~ii~~~tGsGKT~~~~~~~~~~  107 (423)
                      .++|+|...+..+...    +..++.||.|.|||..+...+...
T Consensus         3 ~~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~~l   46 (328)
T PRK05707          3 EIYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAERLAAAL   46 (328)
T ss_pred             cCCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHHHHHHH
Confidence            3578888888887764    348899999999997665433333

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=96.59  E-value=0.0071  Score=49.32  Aligned_cols=89  Identities=15%  Similarity=0.097  Sum_probs=51.5

Q ss_pred             ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhc
Q 014486           85 DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN  164 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (423)
                      =.++.+|+.||||.-.+-.+......+.   ++++..|...-         ++     +.....-+.|.+.         
T Consensus         6 l~~i~gpM~SGKT~eLl~r~~~~~~~g~---~v~vfkp~iD~---------R~-----~~~~V~Sr~G~~~---------   59 (201)
T COG1435           6 LEFIYGPMFSGKTEELLRRARRYKEAGM---KVLVFKPAIDT---------RY-----GVGKVSSRIGLSS---------   59 (201)
T ss_pred             EEEEEccCcCcchHHHHHHHHHHHHcCC---eEEEEeccccc---------cc-----ccceeeeccCCcc---------
Confidence            3689999999999864443333333222   78888886431         11     1111111222211         


Q ss_pred             CCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchh
Q 014486          165 ECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM  202 (423)
Q Consensus       165 ~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~  202 (423)
                        ..++|-.+..+...+........ +++|.+|||+=+
T Consensus        60 --~A~~i~~~~~i~~~i~~~~~~~~-~~~v~IDEaQF~   94 (201)
T COG1435          60 --EAVVIPSDTDIFDEIAALHEKPP-VDCVLIDEAQFF   94 (201)
T ss_pred             --cceecCChHHHHHHHHhcccCCC-cCEEEEehhHhC
Confidence              35666677777776665433322 789999999944

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.58  E-value=0.012  Score=63.52  Aligned_cols=62  Identities=18%  Similarity=0.172  Sum_probs=44.4

Q ss_pred             CCChhhhhcccccccC--CceEEEccCCCcchhHH--HHHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           68 HPSEVQHECIPQAILG--MDVICQAKSGMGKTAVF--VLSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~--~~~ii~~~tGsGKT~~~--~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      .+++-|+.++..++.+  +-++|.|..|+|||.+.  ++.++..+... .+..++.+.||..-+..+
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e~-~g~~V~glAPTgkAa~~L  900 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPES-ERPRVVGLGPTHRAVGEM  900 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhhc-cCceEEEEechHHHHHHH
Confidence            6899999999999975  55899999999999863  22233332222 223788899998766554

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=96.57  E-value=0.0083  Score=57.99  Aligned_cols=135  Identities=13%  Similarity=0.134  Sum_probs=74.8

Q ss_pred             CceEEEccCCCcchhHHHHHHhhcc-CCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQT-EPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL  162 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~-~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (423)
                      +.+++..|=|-|||......++..+ .....+..++++++++.-|..+.+.+..+....|.+....-         .+.+
T Consensus        23 ~~~~l~v~RkNGKS~l~a~i~ly~l~~~g~~~~~i~~~A~~~~QA~~~f~~~~~~i~~~~~l~~~~~---------~~~~   93 (477)
T PF03354_consen   23 REVYLEVPRKNGKSTLAAAIALYMLFLDGEPGAEIYCAANTRDQAKIVFDEAKKMIEASPELRKRKK---------PKII   93 (477)
T ss_pred             EEEEEEEcCccCccHHHHHHHHHHHhcCCccCceEEEEeCCHHHHHHHHHHHHHHHHhChhhccchh---------hhhh
Confidence            3488888999999976544444333 33334458999999999999999999988776544332110         0000


Q ss_pred             hcCCCcEEEechHHHHHHHhc--CCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          163 KNECPQIVVGTPGRILALARD--KDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       163 ~~~~~~ilv~T~~~l~~~~~~--~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ....-.|.....+.++..+..  ....-.+..++|+||+|...+ ......+..-... .++++++.+|
T Consensus        94 ~~~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~i~DE~h~~~~-~~~~~~l~~g~~~-r~~pl~~~IS  160 (477)
T PF03354_consen   94 KSNKKEIEFPKTGSFFKALSSDADSLDGLNPSLAIFDELHAHKD-DELYDALESGMGA-RPNPLIIIIS  160 (477)
T ss_pred             hhhceEEEEcCCCcEEEEEecCCCCccCCCCceEEEeCCCCCCC-HHHHHHHHhhhcc-CCCceEEEEe
Confidence            010013332222222221111  122234568999999998765 2233333333333 3355555554

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]

Probab=96.52  E-value=0.0024  Score=68.04  Aligned_cols=94  Identities=23%  Similarity=0.365  Sum_probs=76.2

Q ss_pred             cEEEEEcChhhHHHHHHHHHhCC-CCeEEEcCCCC-----------HHHHHHHHHhhhcCCccEEEEcCccccCCCCCCC
Q 014486          290 QVVIFVKSVSRAAELNKLLVECN-FPSICIHSGMS-----------QEERLTRYKGFKEGNKRILVATDLVGRGIDIERV  357 (423)
Q Consensus       290 ~~ivf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~-----------~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~  357 (423)
                      ..++|++....+....+.++... ..+..+.|.+.           ...+.+++..|.....++|++|+++.+|+|++.+
T Consensus       294 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~~  373 (1606)
T KOG0701|consen  294 SGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPKC  373 (1606)
T ss_pred             hheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhhh
Confidence            46999999999988888887652 22222433322           3335778899999999999999999999999999


Q ss_pred             CEEEEccCCCCcchhhhcccccCCCC
Q 014486          358 NIVINYDMPDSADTYLHRVGRAGRFG  383 (423)
Q Consensus       358 ~~vi~~~~~~s~~~~~Q~~GR~~R~g  383 (423)
                      +.++.++.|.....|+|..||+.+..
T Consensus       374 ~~~~~~~~~~~~~~~vq~~~r~~~~~  399 (1606)
T KOG0701|consen  374 NLVVLFDAPTYYRSYVQKKGRARAAD  399 (1606)
T ss_pred             hhheeccCcchHHHHHHhhcccccch
Confidence            99999999999999999999997754

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=96.52  E-value=0.02  Score=52.74  Aligned_cols=40  Identities=13%  Similarity=0.345  Sum_probs=26.0

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEec
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSA  230 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SA  230 (423)
                      ...++||+||+|.+..  .....+..++...+...++|+.+.
T Consensus       124 ~~~~vlilDe~~~l~~--~~~~~L~~~le~~~~~~~~Il~~~  163 (337)
T PRK12402        124 ADYKTILLDNAEALRE--DAQQALRRIMEQYSRTCRFIIATR  163 (337)
T ss_pred             CCCcEEEEeCcccCCH--HHHHHHHHHHHhccCCCeEEEEeC
Confidence            4567999999998754  334455566665555666665543

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.51  E-value=0.0098  Score=56.31  Aligned_cols=23  Identities=22%  Similarity=0.265  Sum_probs=17.4

Q ss_pred             CceEEEccCCCcchhHHHHHHhh
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQ  106 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~  106 (423)
                      +..++.||.|+|||.++.+.+-.
T Consensus        41 ha~Lf~GP~GtGKTTlAriLAk~   63 (484)
T PRK14956         41 HAYIFFGPRGVGKTTIARILAKR   63 (484)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            34799999999999876554333

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.49  E-value=0.02  Score=62.82  Aligned_cols=62  Identities=18%  Similarity=0.181  Sum_probs=43.9

Q ss_pred             CCChhhhhcccccccCC--ceEEEccCCCcchhHH--HHHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           68 HPSEVQHECIPQAILGM--DVICQAKSGMGKTAVF--VLSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~--~~ii~~~tGsGKT~~~--~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      .+++-|+.++..++.+.  -++|.|..|+|||...  ++.++..+... .+..++.++||..-+..+
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l~~v~~~~~~l~~~-~~~~V~glAPTgrAAk~L 1032 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQFRAVMSAVNTLPES-ERPRVVGLGPTHRAVGEM 1032 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhhcc-cCceEEEECCcHHHHHHH
Confidence            68999999999999864  4899999999999763  22222222222 233788899998766554

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.46  E-value=0.018  Score=55.00  Aligned_cols=39  Identities=8%  Similarity=0.217  Sum_probs=25.1

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ...+++|+||+|.+..  .....+.+.++.-++...+|+.+
T Consensus       115 ~~~KVvIIDEah~Ls~--~A~NaLLK~LEePp~~v~fIlat  153 (491)
T PRK14964        115 SKFKVYIIDEVHMLSN--SAFNALLKTLEEPAPHVKFILAT  153 (491)
T ss_pred             CCceEEEEeChHhCCH--HHHHHHHHHHhCCCCCeEEEEEe
Confidence            5788999999998864  22334455555555555555554

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.46  E-value=0.008  Score=57.35  Aligned_cols=47  Identities=21%  Similarity=0.255  Sum_probs=27.1

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICH  132 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~  132 (423)
                      +.+++.|++|+|||... .++...+.....+.+++++.+ ..+...+..
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~  188 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIESNFSDLKVSYMSG-DEFARKAVD  188 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHHHH
Confidence            45899999999999643 334443332222336666555 455544443

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.45  E-value=0.015  Score=55.79  Aligned_cols=44  Identities=9%  Similarity=0.092  Sum_probs=24.7

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQ  129 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  129 (423)
                      +.+++.||+|+|||...-. +...+.....+.+++++.. ..+..+
T Consensus       149 ~~l~l~G~~G~GKThL~~a-i~~~~~~~~~~~~v~yi~~-~~~~~~  192 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHA-IGNYILEKNPNAKVVYVTS-EKFTND  192 (450)
T ss_pred             CeEEEECCCCCCHHHHHHH-HHHHHHHhCCCCeEEEEEH-HHHHHH
Confidence            4589999999999975433 3333332222225555543 444433

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=96.41  E-value=0.019  Score=58.63  Aligned_cols=39  Identities=15%  Similarity=0.270  Sum_probs=28.8

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ..++++||||+|.|..  .-...+.++++..+....+|+++
T Consensus       119 ~~~KV~IIDEad~lt~--~a~NaLLK~LEEpP~~~~fIl~t  157 (824)
T PRK07764        119 SRYKIFIIDEAHMVTP--QGFNALLKIVEEPPEHLKFIFAT  157 (824)
T ss_pred             CCceEEEEechhhcCH--HHHHHHHHHHhCCCCCeEEEEEe
Confidence            5678999999999875  44455667777777777677665

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=96.40  E-value=0.0058  Score=51.07  Aligned_cols=39  Identities=15%  Similarity=0.281  Sum_probs=28.3

Q ss_pred             CCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEE
Q 014486          188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMF  228 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~  228 (423)
                      ....+.||+||||.+..  +....+++......+..++.+.
T Consensus       111 ~grhKIiILDEADSMT~--gAQQAlRRtMEiyS~ttRFala  149 (333)
T KOG0991|consen  111 PGRHKIIILDEADSMTA--GAQQALRRTMEIYSNTTRFALA  149 (333)
T ss_pred             CCceeEEEeeccchhhh--HHHHHHHHHHHHHcccchhhhh
Confidence            36678999999999975  6666777777766665554443

>PRK08116 hypothetical protein; Validated

Probab=96.39  E-value=0.023  Score=50.24  Aligned_cols=43  Identities=14%  Similarity=0.166  Sum_probs=25.3

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      ..+++.|++|+|||..+. ++...+...+.  .++ .++...+...+
T Consensus       115 ~gl~l~G~~GtGKThLa~-aia~~l~~~~~--~v~-~~~~~~ll~~i  157 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAA-CIANELIEKGV--PVI-FVNFPQLLNRI  157 (268)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHHcCC--eEE-EEEHHHHHHHH
Confidence            359999999999997654 34444433321  344 44444554433

>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=96.38  E-value=0.037  Score=46.06  Aligned_cols=48  Identities=15%  Similarity=0.146  Sum_probs=31.9

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      ++|.||+|+|||...+-.+...+..+.   +++|++. .+...++.+.+..+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~---~v~~~s~-e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGE---PGLYVTL-EESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCC---cEEEEEC-CCCHHHHHHHHHHc
Confidence            689999999999876554554443322   6777765 35566666666655

A related protein is found in archaea.

>PF13173 AAA_14: AAA domain

Probab=96.38  E-value=0.046  Score=42.35  Aligned_cols=37  Identities=8%  Similarity=0.228  Sum_probs=24.4

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      .-.+|++||+|.+   .++...+..+.... ++.+++ +|++
T Consensus        61 ~~~~i~iDEiq~~---~~~~~~lk~l~d~~-~~~~ii-~tgS   97 (128)
T PF13173_consen   61 GKKYIFIDEIQYL---PDWEDALKFLVDNG-PNIKII-LTGS   97 (128)
T ss_pred             CCcEEEEehhhhh---ccHHHHHHHHHHhc-cCceEE-EEcc
Confidence            4468999999988   45666777776654 344444 4444

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=96.38  E-value=0.022  Score=56.76  Aligned_cols=40  Identities=8%  Similarity=0.261  Sum_probs=26.3

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEec
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSA  230 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SA  230 (423)
                      ..++++||||+|.+..  .-...+.+.++.-+....+|+.|-
T Consensus       118 gr~KVIIIDEah~LT~--~A~NALLKtLEEPP~~v~FILaTt  157 (830)
T PRK07003        118 ARFKVYMIDEVHMLTN--HAFNAMLKTLEEPPPHVKFILATT  157 (830)
T ss_pred             CCceEEEEeChhhCCH--HHHHHHHHHHHhcCCCeEEEEEEC
Confidence            4678999999998865  223445555666565665665553

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.37  E-value=0.017  Score=54.94  Aligned_cols=48  Identities=10%  Similarity=0.248  Sum_probs=27.9

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhC-CCCceEEEEeccCCccHH
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMT-PHDKQVMMFSATLSKEIR  237 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-~~~~~~v~~SAT~~~~~~  237 (423)
                      +.+++++||+|.+.........+..++..+ ....++|+.|-+.|..+.
T Consensus       202 ~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~  250 (445)
T PRK12422        202 NVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLK  250 (445)
T ss_pred             cCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHh
Confidence            567899999998865333334444443322 234566666655565544

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=96.37  E-value=0.035  Score=52.91  Aligned_cols=38  Identities=13%  Similarity=0.148  Sum_probs=23.0

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      +.+++.||+|+|||..... +...+.....+.+++++..
T Consensus       131 n~l~lyG~~G~GKTHLl~a-i~~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQS-IGNYVVQNEPDLRVMYITS  168 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHH-HHHHHHHhCCCCeEEEEEH
Confidence            3589999999999975432 3333332222226666654

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=96.36  E-value=0.014  Score=51.05  Aligned_cols=40  Identities=13%  Similarity=0.258  Sum_probs=25.2

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      ++|.||||+||+-. +=.++....-.+.+-.+++|+|....
T Consensus        90 ~~VYGPTG~GKSqL-lRNLis~~lI~P~PETVfFItP~~~m  129 (369)
T PF02456_consen   90 GVVYGPTGSGKSQL-LRNLISCQLIQPPPETVFFITPQKDM  129 (369)
T ss_pred             EEEECCCCCCHHHH-HHHhhhcCcccCCCCceEEECCCCCC
Confidence            78999999999942 22222222223333378999988754

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

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.35  E-value=0.033  Score=44.99  Aligned_cols=37  Identities=16%  Similarity=0.200  Sum_probs=22.4

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      +++.|++|+|||......+..... .  +..++++.....
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~-~--~~~v~~~~~e~~   38 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIAT-K--GGKVVYVDIEEE   38 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHh-c--CCEEEEEECCcc
Confidence            578999999999865443333322 1  225666665433

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.

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=96.34  E-value=0.011  Score=60.36  Aligned_cols=82  Identities=20%  Similarity=0.220  Sum_probs=59.5

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC-CCeEEEEEecChHHHHHHHHHHHHHhcc-CCCce
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP-GQVTALVLCHTRELAYQICHEFERFSTY-LPDIK  145 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~L~~q~~~~~~~~~~~-~~~~~  145 (423)
                      .+++-|++++.+.  ...++|.|..|||||.+.+--+...+...+ .+.++|+++-|+..|..+.+++.++... ..++.
T Consensus         4 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~~~~~~~~~   81 (726)
T TIGR01073         4 HLNPEQREAVKTT--EGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLLGPVAEDIW   81 (726)
T ss_pred             ccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHhccccCCcE
Confidence            5889999998753  467999999999999887666655553322 2237999999999999999999877542 12344


Q ss_pred             EEEEEc
Q 014486          146 VAVFYG  151 (423)
Q Consensus       146 ~~~~~~  151 (423)
                      +..+|+
T Consensus        82 i~TFHs   87 (726)
T TIGR01073        82 ISTFHS   87 (726)
T ss_pred             EEcHHH
Confidence            555444

Designed to identify pcrA members of the uvrD/rep subfamily.

>PLN03025 replication factor C subunit; Provisional

Probab=96.33  E-value=0.036  Score=50.62  Aligned_cols=38  Identities=16%  Similarity=0.313  Sum_probs=25.3

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ..+++|+||+|.+..  .....+.+..+..+....+++.+
T Consensus        99 ~~kviiiDE~d~lt~--~aq~aL~~~lE~~~~~t~~il~~  136 (319)
T PLN03025         99 RHKIVILDEADSMTS--GAQQALRRTMEIYSNTTRFALAC  136 (319)
T ss_pred             CeEEEEEechhhcCH--HHHHHHHHHHhcccCCceEEEEe
Confidence            578999999999865  33455566666655555555443

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.32  E-value=0.057  Score=54.63  Aligned_cols=17  Identities=29%  Similarity=0.341  Sum_probs=13.8

Q ss_pred             eEEEccCCCcchhHHHH
Q 014486           86 VICQAKSGMGKTAVFVL  102 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~  102 (423)
                      ++|.|+||+|||.+.-.
T Consensus       784 LYIyG~PGTGKTATVK~  800 (1164)
T PTZ00112        784 LYISGMPGTGKTATVYS  800 (1164)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            35999999999987543

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.28  E-value=0.09  Score=46.32  Aligned_cols=132  Identities=12%  Similarity=0.137  Sum_probs=68.3

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh--HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR--ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKD  160 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~--~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (423)
                      +..+.+.+++|+|||..+...+.... .. +....++-+.+.  ..+.||.......     ++.+.             
T Consensus        75 ~~~i~~~G~~g~GKTtl~~~l~~~l~-~~-~~~v~~i~~D~~ri~~~~ql~~~~~~~-----~~~~~-------------  134 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAKMAWQFH-GK-KKTVGFITTDHSRIGTVQQLQDYVKTI-----GFEVI-------------  134 (270)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHHH-Hc-CCeEEEEecCCCCHHHHHHHHHHhhhc-----CceEE-------------
Confidence            35689999999999986654333322 11 221334444222  4555554333221     22221             


Q ss_pred             HHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCc-cHHHH
Q 014486          161 LLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSK-EIRPV  239 (423)
Q Consensus       161 ~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~-~~~~~  239 (423)
                               ...++..+...+..- ....++++|++|-+=+...+......+..+.....+..-++.+|||... +....
T Consensus       135 ---------~~~~~~~l~~~l~~l-~~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LVl~a~~~~~d~~~~  204 (270)
T PRK06731        135 ---------AVRDEAAMTRALTYF-KEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEI  204 (270)
T ss_pred             ---------ecCCHHHHHHHHHHH-HhcCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEEEcCccCHHHHHHH
Confidence                     112344443333211 0113568999999976532223344455555555555456779998754 55566


Q ss_pred             HHHhc
Q 014486          240 CKKFM  244 (423)
Q Consensus       240 ~~~~~  244 (423)
                      ++.|.
T Consensus       205 ~~~f~  209 (270)
T PRK06731        205 ITNFK  209 (270)
T ss_pred             HHHhC
Confidence            66554

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.26  E-value=0.043  Score=55.11  Aligned_cols=129  Identities=10%  Similarity=0.129  Sum_probs=65.6

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH--HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE--LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDL  161 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~--L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (423)
                      +-+.+.||||+|||.+....+.......+.....++-+.+--  -..|    ++.+.... ++.                
T Consensus       186 ~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQ----L~~~a~~~-gvp----------------  244 (767)
T PRK14723        186 GVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQ----LRIYGRIL-GVP----------------  244 (767)
T ss_pred             eEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHH----HHHHHHhC-CCC----------------
Confidence            347899999999998765433332222222212333333221  2233    33343322 222                


Q ss_pred             HhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCcc-HHHHH
Q 014486          162 LKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKE-IRPVC  240 (423)
Q Consensus       162 ~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~-~~~~~  240 (423)
                            -..+.+|+.+...+..    +.+.++|+||=+=+.-.+......+..+.....+...++.++||.... +...+
T Consensus       245 ------v~~~~~~~~l~~al~~----~~~~D~VLIDTAGRs~~d~~l~eel~~l~~~~~p~e~~LVLsAt~~~~~l~~i~  314 (767)
T PRK14723        245 ------VHAVKDAADLRFALAA----LGDKHLVLIDTVGMSQRDRNVSEQIAMLCGVGRPVRRLLLLNAASHGDTLNEVV  314 (767)
T ss_pred             ------ccccCCHHHHHHHHHH----hcCCCEEEEeCCCCCccCHHHHHHHHHHhccCCCCeEEEEECCCCcHHHHHHHH
Confidence                  1223355555554442    235578888888765432233344444444444555678888887543 33344


Q ss_pred             HHh
Q 014486          241 KKF  243 (423)
Q Consensus       241 ~~~  243 (423)
                      +.|
T Consensus       315 ~~f  317 (767)
T PRK14723        315 HAY  317 (767)
T ss_pred             HHH
Confidence            444

>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=96.22  E-value=0.017  Score=46.84  Aligned_cols=44  Identities=20%  Similarity=0.413  Sum_probs=33.4

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSK  234 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~  234 (423)
                      ...+++|+||+|.+..  .....+.+.++.-+....++++|..+..
T Consensus       101 ~~~KviiI~~ad~l~~--~a~NaLLK~LEepp~~~~fiL~t~~~~~  144 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTE--EAQNALLKTLEEPPENTYFILITNNPSK  144 (162)
T ss_dssp             SSSEEEEEETGGGS-H--HHHHHHHHHHHSTTTTEEEEEEES-GGG
T ss_pred             CCceEEEeehHhhhhH--HHHHHHHHHhcCCCCCEEEEEEECChHH
Confidence            5689999999999875  6677788888888888877777765443

...

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=96.22  E-value=0.016  Score=62.59  Aligned_cols=123  Identities=20%  Similarity=0.160  Sum_probs=78.0

Q ss_pred             CChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEE
Q 014486           69 PSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAV  148 (423)
Q Consensus        69 ~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~  148 (423)
                      +|+-|+++|.  ..+++++|.|..|||||.+.+--++..+..+....++|+++=|+..+..+.+++.+.....  +.   
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            5789999997  3588899999999999998777666655443322368999999999999988887754321  00   


Q ss_pred             EEcCcchHHHHHHHhcCCCcEEEechHHHHH-HHhcCCCCC-CCccEEEEcCcch
Q 014486          149 FYGGVNIKIHKDLLKNECPQIVVGTPGRILA-LARDKDLSL-KNVRHFILDECDK  201 (423)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~-~~~~~~~~~-~~~~~vVvDE~h~  201 (423)
                        .........+.+..- ...-|+|-+.+.. +++.....+ -+..+=|.||...
T Consensus        75 --~~p~~~~L~~q~~~~-~~~~i~Tihsf~~~~~~~~~~~l~ldP~F~i~de~e~  126 (1232)
T TIGR02785        75 --QEPNSKHLRRQLALL-NTANISTLHSFCLKVIRKHYYLLDLDPSFRILTDTEQ  126 (1232)
T ss_pred             --cCchhHHHHHHHhhc-cCCeEeeHHHHHHHHHHHhhhhcCCCCCceeCCHHHH
Confidence              000111122222222 3677999998865 444432221 1223445887764

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=96.19  E-value=0.078  Score=49.74  Aligned_cols=125  Identities=12%  Similarity=0.164  Sum_probs=59.2

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL  162 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (423)
                      +.-+.+.||||+|||......+.......+.....++...+...+  ..+.+..++... ++.+.               
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rig--alEQL~~~a~il-Gvp~~---------------  252 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIG--GHEQLRIYGKLL-GVSVR---------------  252 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchh--HHHHHHHHHHHc-CCcee---------------
Confidence            445889999999999865433222211111122445555553221  122233333332 33322               


Q ss_pred             hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccH
Q 014486          163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEI  236 (423)
Q Consensus       163 ~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~  236 (423)
                             .+.++..+...+.    .+.+.+.+++|.+-+.-........+..+.....+...++.+|||.....
T Consensus       253 -------~v~~~~dl~~al~----~l~~~d~VLIDTaGrsqrd~~~~~~l~~l~~~~~~~~~~LVl~at~~~~~  315 (420)
T PRK14721        253 -------SIKDIADLQLMLH----ELRGKHMVLIDTVGMSQRDQMLAEQIAMLSQCGTQVKHLLLLNATSSGDT  315 (420)
T ss_pred             -------cCCCHHHHHHHHH----HhcCCCEEEecCCCCCcchHHHHHHHHHHhccCCCceEEEEEcCCCCHHH
Confidence                   2223333332222    24556789999864321111122333333332334456788999976543

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.18  E-value=0.026  Score=53.46  Aligned_cols=37  Identities=14%  Similarity=0.161  Sum_probs=22.3

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEe
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLC  121 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  121 (423)
                      +.+++.||+|+|||.... ++...+.....+.+++++.
T Consensus       137 n~l~l~G~~G~GKThL~~-ai~~~l~~~~~~~~v~yi~  173 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLH-AIGNEILENNPNAKVVYVS  173 (405)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHHhCCCCcEEEEE
Confidence            357999999999997543 3333333222222566664

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).

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.17  E-value=0.18  Score=44.18  Aligned_cols=78  Identities=14%  Similarity=0.184  Sum_probs=46.2

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCC-----ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEE
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGM-----DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVL  120 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~-----~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil  120 (423)
                      ..|.+..=-+...++|++.=+.   |+   -+|++..|+     .+++.+|+|+||++.+-  +.+.    ... .+++-
T Consensus       130 VkWsDVAGLE~AKeALKEAVIL---PI---KFPqlFtGkR~PwrgiLLyGPPGTGKSYLAK--AVAT----EAn-STFFS  196 (439)
T KOG0739|consen  130 VKWSDVAGLEGAKEALKEAVIL---PI---KFPQLFTGKRKPWRGILLYGPPGTGKSYLAK--AVAT----EAN-STFFS  196 (439)
T ss_pred             CchhhhccchhHHHHHHhheee---cc---cchhhhcCCCCcceeEEEeCCCCCcHHHHHH--HHHh----hcC-CceEE
Confidence            4576665556666777765221   11   135566653     48999999999996432  2111    111 45777


Q ss_pred             ecChHHHHHHHHHHHH
Q 014486          121 CHTRELAYQICHEFER  136 (423)
Q Consensus       121 ~P~~~L~~q~~~~~~~  136 (423)
                      +.+..|+..|.-+-.+
T Consensus       197 vSSSDLvSKWmGESEk  212 (439)
T KOG0739|consen  197 VSSSDLVSKWMGESEK  212 (439)
T ss_pred             eehHHHHHHHhccHHH
Confidence            8888887766544433

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.09  E-value=0.04  Score=52.06  Aligned_cols=53  Identities=19%  Similarity=0.321  Sum_probs=34.4

Q ss_pred             cEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhc
Q 014486          192 RHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFM  244 (423)
Q Consensus       192 ~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~  244 (423)
                      ++||+|.+-+...+......+..+.....+..-++.++||...+....++.+.
T Consensus       177 DvVIIDTAGr~~~d~~lm~El~~l~~~~~pdevlLVvda~~gq~av~~a~~F~  229 (437)
T PRK00771        177 DVIIVDTAGRHALEEDLIEEMKEIKEAVKPDEVLLVIDATIGQQAKNQAKAFH  229 (437)
T ss_pred             CEEEEECCCcccchHHHHHHHHHHHHHhcccceeEEEeccccHHHHHHHHHHH
Confidence            78999999554332344555666666666666678888887766555555543

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.08  E-value=0.039  Score=47.82  Aligned_cols=34  Identities=18%  Similarity=0.240  Sum_probs=21.4

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEE
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVL  120 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil  120 (423)
                      ..+++.|++|+|||..+.. +...+...+.  .++++
T Consensus       100 ~~~~l~G~~GtGKThLa~a-ia~~l~~~g~--~v~~i  133 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAA-ICNELLLRGK--SVLII  133 (244)
T ss_pred             ceEEEECCCCCCHHHHHHH-HHHHHHhcCC--eEEEE
Confidence            4689999999999976543 3333333222  44444

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.08  E-value=0.036  Score=48.99  Aligned_cols=18  Identities=33%  Similarity=0.541  Sum_probs=15.3

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      .++++.||+|+|||..+-
T Consensus        43 ~~vll~GppGtGKTtlA~   60 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVAR   60 (261)
T ss_pred             ceEEEEcCCCCCHHHHHH
Confidence            568999999999998653

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.06  E-value=0.013  Score=53.35  Aligned_cols=44  Identities=14%  Similarity=0.127  Sum_probs=26.4

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      ++++++.||||+|||..+.. +...+...+  ..+++ .+...|..+.
T Consensus       183 ~~~Lll~G~~GtGKThLa~a-Ia~~l~~~g--~~V~y-~t~~~l~~~l  226 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNC-IAKELLDRG--KSVIY-RTADELIEIL  226 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHH-HHHHHHHCC--CeEEE-EEHHHHHHHH
Confidence            47799999999999975433 333333322  14444 4445554443

>PRK06921 hypothetical protein; Provisional

Probab=96.05  E-value=0.025  Score=49.95  Aligned_cols=44  Identities=16%  Similarity=0.095  Sum_probs=26.0

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQ  129 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  129 (423)
                      +.++++.|++|+|||.... ++...+.... +..++++. ...+..+
T Consensus       117 ~~~l~l~G~~G~GKThLa~-aia~~l~~~~-g~~v~y~~-~~~l~~~  160 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLT-AAANELMRKK-GVPVLYFP-FVEGFGD  160 (266)
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHhhhc-CceEEEEE-HHHHHHH
Confidence            5679999999999997543 3444443321 22555554 3344433

>PRK12377 putative replication protein; Provisional

Probab=96.02  E-value=0.032  Score=48.51  Aligned_cols=44  Identities=9%  Similarity=0.184  Sum_probs=26.1

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQIC  131 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  131 (423)
                      .++++.||+|+|||..+.. +...+...+.  .+ +.++..+|..++.
T Consensus       102 ~~l~l~G~~GtGKThLa~A-Ia~~l~~~g~--~v-~~i~~~~l~~~l~  145 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAA-IGNRLLAKGR--SV-IVVTVPDVMSRLH  145 (248)
T ss_pred             CeEEEECCCCCCHHHHHHH-HHHHHHHcCC--Ce-EEEEHHHHHHHHH
Confidence            5799999999999975433 3333333222  33 4444456655543

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.01  E-value=0.043  Score=53.21  Aligned_cols=39  Identities=8%  Similarity=0.241  Sum_probs=27.0

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ..++++|+||+|.+..  .....+.+.++.-+....+|+.|
T Consensus       118 ~~~kV~iIDE~~~ls~--~a~naLLk~LEepp~~~~fIlat  156 (509)
T PRK14958        118 GRFKVYLIDEVHMLSG--HSFNALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             CCcEEEEEEChHhcCH--HHHHHHHHHHhccCCCeEEEEEE
Confidence            4678999999998865  33344555666666666666655

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.99  E-value=0.0095  Score=53.76  Aligned_cols=66  Identities=23%  Similarity=0.296  Sum_probs=40.8

Q ss_pred             HHHHHhCCCCCCChhhhhccccccc-CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           58 LRAIVDSGFEHPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        58 ~~~l~~~~~~~~~~~Q~~~i~~~~~-~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      ++.+.+.|.  +.+.|...+..+.. +++++++|+||||||... -+++..........+++.+=...+|
T Consensus       120 l~~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll-~aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        120 LDDYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTLA-NAVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             HHHHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHHhcCCCCceEEEecCCccc
Confidence            344555554  56777766655554 678999999999999743 4444444322222266666666665

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=95.97  E-value=0.053  Score=46.81  Aligned_cols=18  Identities=11%  Similarity=0.204  Sum_probs=15.2

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      +..+++.||+|+|||..+
T Consensus        42 ~~~~~l~G~~G~GKT~La   59 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLL   59 (227)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            456999999999999654

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=95.97  E-value=0.071  Score=51.63  Aligned_cols=39  Identities=13%  Similarity=0.294  Sum_probs=27.8

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ...+++|+||+|.+..  .....+.+.+..-++...+|+.+
T Consensus       116 ~~~KVvIIDEad~Lt~--~A~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451        116 ARFKIFIIDEVHMLTK--EAFNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             CCeEEEEEECcccCCH--HHHHHHHHHHhhcCCceEEEEEE
Confidence            5678999999998864  34445566666666667666665

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.95  E-value=0.033  Score=56.61  Aligned_cols=38  Identities=8%  Similarity=0.253  Sum_probs=25.6

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEE
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMF  228 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~  228 (423)
                      ..++++||||+|.+..  .....+.+.++.-+....+|+.
T Consensus       118 gk~KViIIDEAh~LT~--eAqNALLKtLEEPP~~vrFILa  155 (944)
T PRK14949        118 GRFKVYLIDEVHMLSR--SSFNALLKTLEEPPEHVKFLLA  155 (944)
T ss_pred             CCcEEEEEechHhcCH--HHHHHHHHHHhccCCCeEEEEE
Confidence            4678999999998854  3445555566655555655555

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=95.94  E-value=0.0088  Score=54.13  Aligned_cols=67  Identities=21%  Similarity=0.308  Sum_probs=42.1

Q ss_pred             HHHHHHhCCCCCCChhhhhcccccc-cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           57 LLRAIVDSGFEHPSEVQHECIPQAI-LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        57 ~~~~l~~~~~~~~~~~Q~~~i~~~~-~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      .++.|.+.|+  +.+.|.+.+..+. .+++++++|+||||||.. +-+++..........+++++-.+.++
T Consensus       123 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl-l~aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        123 TLDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKTTL-VNAIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             CHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHhhhhcCCCceEEEEcCCCcc
Confidence            3456665555  4577777776544 467899999999999954 44455443211222366777676665

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.93  E-value=0.12  Score=51.74  Aligned_cols=125  Identities=18%  Similarity=0.185  Sum_probs=88.3

Q ss_pred             HHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhC-C-CCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccc
Q 014486          274 EKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVEC-N-FPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVG  349 (423)
Q Consensus       274 ~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~-~-~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~  349 (423)
                      .|.+.+..++...  .++.+||.++.+.....+.+.|+.. + ..+..+|+++++.+|.+.+....+|+.+|+|+|..+.
T Consensus       172 GKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSAv  251 (665)
T PRK14873        172 DWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAV  251 (665)
T ss_pred             cHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcceeE
Confidence            4556666665443  3568999999999999999999875 3 5788999999999999999999999999999997654


Q ss_pred             cCCCCCCCCEEEEccCCCCcchhhhccc-c-------cCCCCCceEEEEEecCcccHHHH
Q 014486          350 RGIDIERVNIVINYDMPDSADTYLHRVG-R-------AGRFGTKGLAITFVSSASDSDIL  401 (423)
Q Consensus       350 ~Gld~~~~~~vi~~~~~~s~~~~~Q~~G-R-------~~R~g~~~~~~~~~~~~~~~~~~  401 (423)
                      . .-+++...||..+.-.  ..|.|--+ |       ..|+...|..+++-+.....+.+
T Consensus       252 F-aP~~~LgLIIvdEEhd--~sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTPSles~  308 (665)
T PRK14873        252 F-APVEDLGLVAIWDDGD--DLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAEAQ  308 (665)
T ss_pred             E-eccCCCCEEEEEcCCc--hhhcCCCCCCccHHHHHHHHHHHcCCcEEEECCCCCHHHH
Confidence            3 5566777777766432  23443322 1       12333456667676655554443

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.93  E-value=0.035  Score=54.53  Aligned_cols=39  Identities=8%  Similarity=0.244  Sum_probs=25.6

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      .+.+++||||+|.+..  .....+.+.++.-+....+|+.+
T Consensus       117 gk~KV~IIDEVh~LS~--~A~NALLKtLEEPP~~v~FILaT  155 (702)
T PRK14960        117 GRFKVYLIDEVHMLST--HSFNALLKTLEEPPEHVKFLFAT  155 (702)
T ss_pred             CCcEEEEEechHhcCH--HHHHHHHHHHhcCCCCcEEEEEE
Confidence            4578999999998864  33344555666555556555554

>PTZ00293 thymidine kinase; Provisional

Probab=95.92  E-value=0.039  Score=46.26  Aligned_cols=39  Identities=13%  Similarity=0.088  Sum_probs=25.5

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      |.--++.||++||||.-.+-. +......+.  +++++-|..
T Consensus         4 G~i~vi~GpMfSGKTteLLr~-i~~y~~ag~--kv~~~kp~~   42 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMRL-VKRFTYSEK--KCVVIKYSK   42 (211)
T ss_pred             eEEEEEECCCCChHHHHHHHH-HHHHHHcCC--ceEEEEecc
Confidence            344688999999999654443 333332222  778888865

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=95.92  E-value=0.029  Score=53.02  Aligned_cols=146  Identities=14%  Similarity=0.188  Sum_probs=77.6

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH-HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhc
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE-LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN  164 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~-L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (423)
                      .++.|+.|||||.+....++..+...+.+.+++++-|+.. +...+...+......+ ++....-.......   -.+.+
T Consensus         4 ~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~-g~~~~~~~~~~~~~---i~~~~   79 (396)
T TIGR01547         4 IIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENLLSIE-GINYEFKKSKSSME---IKILN   79 (396)
T ss_pred             EEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHHHHHc-CChhheeecCCccE---EEecC
Confidence            6788999999999887777766555322348888888876 6666777777655443 22211111110000   00111


Q ss_pred             -CCCcEEEech-HHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHH
Q 014486          165 -ECPQIVVGTP-GRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKK  242 (423)
Q Consensus       165 -~~~~ilv~T~-~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~  242 (423)
                       + ..|++..- +....+     .....+.++.+|||..+.. ..+...+.++ +. +.....+++|.||+.....+.+.
T Consensus        80 ~g-~~i~f~g~~d~~~~i-----k~~~~~~~~~idEa~~~~~-~~~~~l~~rl-r~-~~~~~~i~~t~NP~~~~~w~~~~  150 (396)
T TIGR01547        80 TG-KKFIFKGLNDKPNKL-----KSGAGIAIIWFEEASQLTF-EDIKELIPRL-RE-TGGKKFIIFSSNPESPLHWVKKR  150 (396)
T ss_pred             CC-eEEEeecccCChhHh-----hCcceeeeehhhhhhhcCH-HHHHHHHHHh-hc-cCCccEEEEEcCcCCCccHHHHH
Confidence             2 24554433 211111     1223368899999998754 2333333332 11 12223588999987654444444


Q ss_pred             hc
Q 014486          243 FM  244 (423)
Q Consensus       243 ~~  244 (423)
                      +.
T Consensus       151 f~  152 (396)
T TIGR01547       151 FI  152 (396)
T ss_pred             HH
Confidence            43

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.92  E-value=0.046  Score=50.87  Aligned_cols=39  Identities=8%  Similarity=0.270  Sum_probs=24.0

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ...+++|+||+|.+..  .....+.+....-+....+++.|
T Consensus       118 ~~~kviIIDEa~~l~~--~a~naLLk~lEe~~~~~~fIl~t  156 (363)
T PRK14961        118 SRFKVYLIDEVHMLSR--HSFNALLKTLEEPPQHIKFILAT  156 (363)
T ss_pred             CCceEEEEEChhhcCH--HHHHHHHHHHhcCCCCeEEEEEc
Confidence            4568999999998854  22233444455545555556554

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.92  E-value=0.065  Score=52.68  Aligned_cols=39  Identities=18%  Similarity=0.243  Sum_probs=26.9

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ...+++||||+|.+..  .-...+.+.++.-+....+|+.+
T Consensus       117 ~~~KVvIIDEah~Lt~--~A~NALLK~LEEpp~~~~fIL~t  155 (584)
T PRK14952        117 SRYRIFIVDEAHMVTT--AGFNALLKIVEEPPEHLIFIFAT  155 (584)
T ss_pred             CCceEEEEECCCcCCH--HHHHHHHHHHhcCCCCeEEEEEe
Confidence            5678999999998865  33444555666656666666665

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.90  E-value=0.045  Score=53.72  Aligned_cols=41  Identities=7%  Similarity=0.261  Sum_probs=26.4

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      .+++++||||+|.+..  .....+.+.++.-+....+|+.|-.
T Consensus       123 gr~KViIIDEah~Ls~--~AaNALLKTLEEPP~~v~FILaTte  163 (700)
T PRK12323        123 GRFKVYMIDEVHMLTN--HAFNAMLKTLEEPPEHVKFILATTD  163 (700)
T ss_pred             CCceEEEEEChHhcCH--HHHHHHHHhhccCCCCceEEEEeCC
Confidence            4678999999998865  2233444455554556666666543

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.89  E-value=0.099  Score=48.03  Aligned_cols=121  Identities=15%  Similarity=0.215  Sum_probs=58.2

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec-ChH-HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH-TRE-LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKD  160 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P-~~~-L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (423)
                      ++.+++.||+|+|||....-.+.. +...+ ...++|-+. .+. -+.||.    .+.... ++.+.             
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~-l~~~g-~~V~lItaDtyR~gAveQLk----~yae~l-gvpv~-------------  265 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQ-LLKQN-RTVGFITTDTFRSGAVEQFQ----GYADKL-DVELI-------------  265 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHHcC-CeEEEEeCCccCccHHHHHH----HHhhcC-CCCEE-------------
Confidence            456889999999999765443333 22222 213344443 332 233443    333222 22221             


Q ss_pred             HHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCC
Q 014486          161 LLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLS  233 (423)
Q Consensus       161 ~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~  233 (423)
                               ...+|+.+...+.... ...+.++|++|=+-+.-.+......+..+.....+..-++.+||+..
T Consensus       266 ---------~~~dp~dL~~al~~l~-~~~~~D~VLIDTAGr~~~d~~~l~EL~~l~~~~~p~~~~LVLsag~~  328 (407)
T PRK12726        266 ---------VATSPAELEEAVQYMT-YVNCVDHILIDTVGRNYLAEESVSEISAYTDVVHPDLTCFTFSSGMK  328 (407)
T ss_pred             ---------ecCCHHHHHHHHHHHH-hcCCCCEEEEECCCCCccCHHHHHHHHHHhhccCCceEEEECCCccc
Confidence                     1234554444332111 11346788888886543222334445555555544443556676544

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.87  E-value=0.061  Score=53.11  Aligned_cols=39  Identities=10%  Similarity=0.236  Sum_probs=23.8

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ..++++||||+|.+.. .. ...+.+.++.-+....+|+.|
T Consensus       123 g~~KV~IIDEvh~Ls~-~a-~NaLLKtLEEPP~~~~fIL~T  161 (618)
T PRK14951        123 GRFKVFMIDEVHMLTN-TA-FNAMLKTLEEPPEYLKFVLAT  161 (618)
T ss_pred             CCceEEEEEChhhCCH-HH-HHHHHHhcccCCCCeEEEEEE
Confidence            4678999999998865 22 233444444444455555554

>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=95.86  E-value=0.041  Score=46.37  Aligned_cols=47  Identities=19%  Similarity=0.274  Sum_probs=26.6

Q ss_pred             ccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhccccccc-C---CceEEEccCCCcchhHHH
Q 014486           43 IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL-G---MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        43 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~-~---~~~ii~~~tGsGKT~~~~  101 (423)
                      ..+.+|++|.=.+.+...+.-.            +..... +   .+++++||+|+|||..+-
T Consensus        18 lRP~~L~efiGQ~~l~~~l~i~------------i~aa~~r~~~l~h~lf~GPPG~GKTTLA~   68 (233)
T PF05496_consen   18 LRPKSLDEFIGQEHLKGNLKIL------------IRAAKKRGEALDHMLFYGPPGLGKTTLAR   68 (233)
T ss_dssp             TS-SSCCCS-S-HHHHHHHHHH------------HHHHHCTTS---EEEEESSTTSSHHHHHH
T ss_pred             cCCCCHHHccCcHHHHhhhHHH------------HHHHHhcCCCcceEEEECCCccchhHHHH
Confidence            3455688887666666654411            111111 1   358999999999997543

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.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=95.83  E-value=0.087  Score=49.47  Aligned_cols=54  Identities=11%  Similarity=0.260  Sum_probs=31.0

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHh
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKF  243 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~  243 (423)
                      .+++||+|=+-+.-.+......+..+.....+..-++.++||...+....++.|
T Consensus       182 ~~DvViIDTaGr~~~d~~lm~El~~i~~~~~p~e~lLVlda~~Gq~a~~~a~~F  235 (429)
T TIGR01425       182 NFDIIIVDTSGRHKQEDSLFEEMLQVAEAIQPDNIIFVMDGSIGQAAEAQAKAF  235 (429)
T ss_pred             CCCEEEEECCCCCcchHHHHHHHHHHhhhcCCcEEEEEeccccChhHHHHHHHH
Confidence            356677777765433223444555555555555556777777765555555544

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.

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=95.83  E-value=0.088  Score=50.81  Aligned_cols=127  Identities=13%  Similarity=0.172  Sum_probs=78.3

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHH-HhccCCCceEEEEEcCcchHHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER-FSTYLPDIKVAVFYGGVNIKIHKDLL  162 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (423)
                      +-.+...|--.|||.. +.|++..+...-.+.++.|++..+-.++-+.+++.. ...++|.-.+....++          
T Consensus       203 kaTVFLVPRRHGKTWf-~VpiIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~vi~~k~~----------  271 (668)
T PHA03372        203 KATVFLVPRRHGKTWF-IIPIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHTIENKDN----------  271 (668)
T ss_pred             cceEEEecccCCceeh-HHHHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccceeeecCc----------
Confidence            4577778999999974 556666666555566999999998877776666643 2333333223222221          


Q ss_pred             hcCCCcEEEechHH-----HHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCC-CCceEEEEecc
Q 014486          163 KNECPQIVVGTPGR-----ILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTP-HDKQVMMFSAT  231 (423)
Q Consensus       163 ~~~~~~ilv~T~~~-----l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~-~~~~~v~~SAT  231 (423)
                           -|.+.-|+.     +....+.+...-.++++++|||||-+     -...+..++..+. ++.++|++|.|
T Consensus       272 -----tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI-----~~~a~~tilgfm~q~~~KiIfISS~  336 (668)
T PHA03372        272 -----VISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFI-----KKDAFNTILGFLAQNTTKIIFISST  336 (668)
T ss_pred             -----EEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhcc-----CHHHHHHhhhhhcccCceEEEEeCC
Confidence                 233333321     12223344455678999999999944     3445556665554 46788999887

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=95.82  E-value=0.061  Score=50.81  Aligned_cols=18  Identities=28%  Similarity=0.482  Sum_probs=15.3

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      .+++|.||+|+|||...-
T Consensus        56 ~~~lI~G~~GtGKT~l~~   73 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTVK   73 (394)
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            569999999999997643

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=95.81  E-value=0.036  Score=54.13  Aligned_cols=135  Identities=14%  Similarity=0.128  Sum_probs=78.5

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccC-CCceEEEEEcCcchHHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYL-PDIKVAVFYGGVNIKIHKD  160 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  160 (423)
                      ..+-.++..|--.|||.... +++..+...-.+.++++.+|.+..++.+.+++......+ +.-.+....| ..+   .-
T Consensus       253 kqk~tVflVPRR~GKTwivv-~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG-e~I---~i  327 (738)
T PHA03368        253 RQRATVFLVPRRHGKTWFLV-PLIALALATFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG-ETI---SF  327 (738)
T ss_pred             hccceEEEecccCCchhhHH-HHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC-cEE---EE
Confidence            34668899999999998655 444433322223389999999999999999998875532 2211222222 111   00


Q ss_pred             HHhcCC-CcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHh-CCCCceEEEEeccC
Q 014486          161 LLKNEC-PQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKM-TPHDKQVMMFSATL  232 (423)
Q Consensus       161 ~~~~~~-~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~-~~~~~~~v~~SAT~  232 (423)
                      .+.++. ..|.+++.      .+.+...-..++++|+|||+-+..     ..+..++-. ...++++|++|.|-
T Consensus       328 ~f~nG~kstI~FaSa------rntNsiRGqtfDLLIVDEAqFIk~-----~al~~ilp~l~~~n~k~I~ISS~N  390 (738)
T PHA03368        328 SFPDGSRSTIVFASS------HNTNGIRGQDFNLLFVDEANFIRP-----DAVQTIMGFLNQTNCKIIFVSSTN  390 (738)
T ss_pred             EecCCCccEEEEEec------cCCCCccCCcccEEEEechhhCCH-----HHHHHHHHHHhccCccEEEEecCC
Confidence            112221 24444421      112234445789999999997754     222222222 22378899999884

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=95.81  E-value=0.045  Score=48.35  Aligned_cols=42  Identities=21%  Similarity=0.345  Sum_probs=26.4

Q ss_pred             CCccEEEEcCcchhhccC-CcHHHHHHHHHhCCCC--ceEEEEecc
Q 014486          189 KNVRHFILDECDKMLESL-DMRRDVQEIFKMTPHD--KQVMMFSAT  231 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~-~~~~~~~~~~~~~~~~--~~~v~~SAT  231 (423)
                      .+++++||||+|.++... .-.+.+...++.+.+.  ..+|++ +|
T Consensus       144 ~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~v-Gt  188 (302)
T PF05621_consen  144 LGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGV-GT  188 (302)
T ss_pred             cCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEe-cc
Confidence            456799999999987632 2344555666666554  345544 45

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=95.81  E-value=0.072  Score=48.17  Aligned_cols=140  Identities=16%  Similarity=0.181  Sum_probs=72.7

Q ss_pred             CCCChhhhhccccccc----C---CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH-h
Q 014486           67 EHPSEVQHECIPQAIL----G---MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF-S  138 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~----~---~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~-~  138 (423)
                      ..++|+|..++..+..    +   +..++.||.|.||+..+...+...+........   .|+.          ++.+ .
T Consensus         3 ~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~---~c~~----------c~~~~~   69 (319)
T PRK08769          3 SAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAA---AQRT----------RQLIAA   69 (319)
T ss_pred             ccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCC---cchH----------HHHHhc
Confidence            3577888888877664    2   348999999999998665433333332211100   1121          1111 2


Q ss_pred             ccCCCceEEEEEcC-cchHHHHHHHhcCCCcEEEechHHHHHHHhcCC--CCCCCccEEEEcCcchhhccCCcHHHHHHH
Q 014486          139 TYLPDIKVAVFYGG-VNIKIHKDLLKNECPQIVVGTPGRILALARDKD--LSLKNVRHFILDECDKMLESLDMRRDVQEI  215 (423)
Q Consensus       139 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~--~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~  215 (423)
                      ..+|++.+.....+ .+..       .. ..|.   -+.+..+.+.-.  -.....+++|||+||.+..  .....+.+.
T Consensus        70 g~HPD~~~i~~~p~~~~~k-------~~-~~I~---idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~--~AaNaLLKt  136 (319)
T PRK08769         70 GTHPDLQLVSFIPNRTGDK-------LR-TEIV---IEQVREISQKLALTPQYGIAQVVIVDPADAINR--AACNALLKT  136 (319)
T ss_pred             CCCCCEEEEecCCCccccc-------cc-cccc---HHHHHHHHHHHhhCcccCCcEEEEeccHhhhCH--HHHHHHHHH
Confidence            33455544321111 0000       00 0122   222222222111  1124678999999999864  556667777


Q ss_pred             HHhCCCCceEEEEeccC
Q 014486          216 FKMTPHDKQVMMFSATL  232 (423)
Q Consensus       216 ~~~~~~~~~~v~~SAT~  232 (423)
                      ++.-+....++++|..+
T Consensus       137 LEEPp~~~~fiL~~~~~  153 (319)
T PRK08769        137 LEEPSPGRYLWLISAQP  153 (319)
T ss_pred             hhCCCCCCeEEEEECCh
Confidence            77766677677776543

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=95.81  E-value=0.049  Score=53.31  Aligned_cols=47  Identities=13%  Similarity=0.263  Sum_probs=28.1

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhC-CCCceEEEEeccCCccH
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMT-PHDKQVMMFSATLSKEI  236 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-~~~~~~v~~SAT~~~~~  236 (423)
                      ++++|+|||+|.+.........+..++..+ ....++|+.|-..|..+
T Consensus       377 ~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL  424 (617)
T PRK14086        377 EMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQL  424 (617)
T ss_pred             cCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhh
Confidence            467899999998865333334444444433 33566776555555544

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=95.79  E-value=0.087  Score=51.77  Aligned_cols=137  Identities=10%  Similarity=0.115  Sum_probs=74.8

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhcc------CCCc-eEEEEEcCcc
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTY------LPDI-KVAVFYGGVN  154 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~------~~~~-~~~~~~~~~~  154 (423)
                      ..+-.++.+|-|.|||.+..+.+...+...  +.+++|.+|...-+.++.++++.....      ++.. .+....|+..
T Consensus       186 kq~~tV~taPRqrGKS~iVgi~l~~La~f~--Gi~IlvTAH~~~ts~evF~rv~~~le~lg~~~~fp~~~~iv~vkgg~E  263 (752)
T PHA03333        186 GKCYTAATVPRRCGKTTIMAIILAAMISFL--EIDIVVQAQRKTMCLTLYNRVETVVHAYQHKPWFPEEFKIVTLKGTDE  263 (752)
T ss_pred             hhcceEEEeccCCCcHHHHHHHHHHHHHhc--CCeEEEECCChhhHHHHHHHHHHHHHHhccccccCCCceEEEeeCCee
Confidence            345688999999999987655444333212  248999999999999988888877652      2221 1222223211


Q ss_pred             -hHHHHHHHhc-CCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCC-CCceEEEEecc
Q 014486          155 -IKIHKDLLKN-ECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTP-HDKQVMMFSAT  231 (423)
Q Consensus       155 -~~~~~~~~~~-~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~-~~~~~v~~SAT  231 (423)
                       .......-.. +...+.+++..       .+...-..++++|+|||+-+..     ..+..++-.+. ...+++++|.+
T Consensus       264 ~I~f~~p~gak~G~sti~F~Ars-------~~s~RG~~~DLLIVDEAAfI~~-----~~l~aIlP~l~~~~~k~IiISS~  331 (752)
T PHA03333        264 NLEYISDPAAKEGKTTAHFLASS-------PNAARGQNPDLVIVDEAAFVNP-----GALLSVLPLMAVKGTKQIHISSP  331 (752)
T ss_pred             EEEEecCcccccCcceeEEeccc-------CCCcCCCCCCEEEEECcccCCH-----HHHHHHHHHHccCCCceEEEeCC
Confidence             0000000000 11133332221       1112224568999999997643     33334444333 35667777766


Q ss_pred             C
Q 014486          232 L  232 (423)
Q Consensus       232 ~  232 (423)
                      -
T Consensus       332 ~  332 (752)
T PHA03333        332 V  332 (752)
T ss_pred             C
Confidence            5

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=95.78  E-value=0.068  Score=48.77  Aligned_cols=39  Identities=15%  Similarity=0.299  Sum_probs=26.0

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ..++||+||+|.+.. ......+..+....+...++|+.|
T Consensus       100 ~~~vliiDe~d~l~~-~~~~~~L~~~le~~~~~~~~Ilt~  138 (316)
T PHA02544        100 GGKVIIIDEFDRLGL-ADAQRHLRSFMEAYSKNCSFIITA  138 (316)
T ss_pred             CCeEEEEECcccccC-HHHHHHHHHHHHhcCCCceEEEEc
Confidence            457899999998833 234455666677666666666544

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=95.76  E-value=0.041  Score=54.77  Aligned_cols=152  Identities=14%  Similarity=0.150  Sum_probs=86.2

Q ss_pred             HHHHHhCCCCCCChhhhhcccccccCC--ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHH
Q 014486           58 LRAIVDSGFEHPSEVQHECIPQAILGM--DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFE  135 (423)
Q Consensus        58 ~~~l~~~~~~~~~~~Q~~~i~~~~~~~--~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  135 (423)
                      ...+.....+.+..-|.+.+..++..+  -+++.|.-|-|||.+.-+++........ ...++|..|+.+-++...+.+.
T Consensus       204 ~~~l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~~-~~~iiVTAP~~~nv~~Lf~fa~  282 (758)
T COG1444         204 PRELYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLAG-SVRIIVTAPTPANVQTLFEFAG  282 (758)
T ss_pred             CHHHhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhcC-CceEEEeCCCHHHHHHHHHHHH
Confidence            345666545555555556666666643  4899999999999877655533332222 3488999999999888887776


Q ss_pred             HHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHH
Q 014486          136 RFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEI  215 (423)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~  215 (423)
                      +-.... +.+-.+......   ...........|=+.+|....          ..-+++|||||=-+     -.+.+.++
T Consensus       283 ~~l~~l-g~~~~v~~d~~g---~~~~~~~~~~~i~y~~P~~a~----------~~~DllvVDEAAaI-----plplL~~l  343 (758)
T COG1444         283 KGLEFL-GYKRKVAPDALG---EIREVSGDGFRIEYVPPDDAQ----------EEADLLVVDEAAAI-----PLPLLHKL  343 (758)
T ss_pred             HhHHHh-CCcccccccccc---ceeeecCCceeEEeeCcchhc----------ccCCEEEEehhhcC-----ChHHHHHH
Confidence            544333 222111111100   000000111234455554332          11468999999744     34455555


Q ss_pred             HHhCCCCceEEEEeccCC
Q 014486          216 FKMTPHDKQVMMFSATLS  233 (423)
Q Consensus       216 ~~~~~~~~~~v~~SAT~~  233 (423)
                      ....+    .+++|.|+-
T Consensus       344 ~~~~~----rv~~sTTIh  357 (758)
T COG1444         344 LRRFP----RVLFSTTIH  357 (758)
T ss_pred             HhhcC----ceEEEeeec
Confidence            55443    678888863

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.76  E-value=0.039  Score=62.04  Aligned_cols=62  Identities=27%  Similarity=0.271  Sum_probs=43.7

Q ss_pred             CCCChhhhhcccccccCC--ceEEEccCCCcchhHHH---HHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           67 EHPSEVQHECIPQAILGM--DVICQAKSGMGKTAVFV---LSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~~~--~~ii~~~tGsGKT~~~~---~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      ..+++.|+.++..++.+.  -++|.|+.|+|||...-   -++.......  +.+++.++||..-+.++
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~~--g~~v~glApT~~Aa~~L 1084 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFESE--QLQVIGLAPTHEAVGEL 1084 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHhc--CCeEEEEeChHHHHHHH
Confidence            378999999999988764  47889999999997641   2222322222  23788899997665554

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.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.73  E-value=0.012  Score=50.85  Aligned_cols=134  Identities=13%  Similarity=0.137  Sum_probs=65.0

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCC-CCCCeEEEEEecChHHHHHHHHHHHHHhccCC----CceEEEEEcCcchH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEP-NPGQVTALVLCHTRELAYQICHEFERFSTYLP----DIKVAVFYGGVNIK  156 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~----~~~~~~~~~~~~~~  156 (423)
                      .|..+++.|++|+|||...+-.+.+.+.. +.   ++++++-. +-..++.+.++.+.....    .-....+.......
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge---~vlyvs~e-e~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~~~~~~   93 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNFGE---KVLYVSFE-EPPEELIENMKSFGWDLEEYEDSGKLKIIDAFPERI   93 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHT-----EEEEESS-S-HHHHHHHHHTTTS-HHHHHHTTSEEEEESSGGGS
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCC---cEEEEEec-CCHHHHHHHHHHcCCcHHHHhhcCCEEEEecccccc
Confidence            35669999999999998766555555554 33   67777743 334555555554421110    00111111111000


Q ss_pred             HHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc---cCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          157 IHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE---SLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       157 ~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~---~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      ..         .  -..++.+...+...... .+.+.+|+|-...+..   ...++..+..+...+.....++++++.
T Consensus        94 ~~---------~--~~~~~~l~~~i~~~i~~-~~~~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l~~~~~t~llt~~  159 (226)
T PF06745_consen   94 GW---------S--PNDLEELLSKIREAIEE-LKPDRVVIDSLSALLLYDDPEELRRFLRALIKFLKSRGVTTLLTSE  159 (226)
T ss_dssp             T----------T--SCCHHHHHHHHHHHHHH-HTSSEEEEETHHHHTTSSSGGGHHHHHHHHHHHHHHTTEEEEEEEE
T ss_pred             cc---------c--ccCHHHHHHHHHHHHHh-cCCCEEEEECHHHHhhcCCHHHHHHHHHHHHHHHHHCCCEEEEEEc
Confidence            00         0  11222333322211000 1227899999988821   133455566666666555556666666

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 ....

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=95.73  E-value=0.051  Score=49.76  Aligned_cols=40  Identities=20%  Similarity=0.440  Sum_probs=29.5

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEec
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSA  230 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SA  230 (423)
                      ...++||+|||+.+..  +....+.+....-+....+++.+-
T Consensus       108 ~~~kviiidead~mt~--~A~nallk~lEep~~~~~~il~~n  147 (325)
T COG0470         108 GGYKVVIIDEADKLTE--DAANALLKTLEEPPKNTRFILITN  147 (325)
T ss_pred             CCceEEEeCcHHHHhH--HHHHHHHHHhccCCCCeEEEEEcC
Confidence            6788999999998875  556666777777666676666554

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=95.72  E-value=0.096  Score=46.59  Aligned_cols=55  Identities=18%  Similarity=0.152  Sum_probs=32.6

Q ss_pred             ccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHH
Q 014486           77 IPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEF  134 (423)
Q Consensus        77 i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~  134 (423)
                      +--+..|.-+++.|++|+|||...+..+...+...+  .++++++-- .-..++..++
T Consensus        24 ~gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g--~~vl~iS~E-~~~~~~~~r~   78 (271)
T cd01122          24 TKGLRKGELIILTAGTGVGKTTFLREYALDLITQHG--VRVGTISLE-EPVVRTARRL   78 (271)
T ss_pred             eEEEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcC--ceEEEEEcc-cCHHHHHHHH
Confidence            334555677999999999999765554444433212  267777632 2233444444

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.70  E-value=0.092  Score=49.51  Aligned_cols=22  Identities=23%  Similarity=0.209  Sum_probs=17.1

Q ss_pred             CceEEEccCCCcchhHHHHHHh
Q 014486           84 MDVICQAKSGMGKTAVFVLSTL  105 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~  105 (423)
                      +..++.||.|+|||.++...+-
T Consensus        39 ha~lf~Gp~G~GKtt~A~~~a~   60 (397)
T PRK14955         39 HGYIFSGLRGVGKTTAARVFAK   60 (397)
T ss_pred             eeEEEECCCCCCHHHHHHHHHH
Confidence            3488999999999987755433

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=95.70  E-value=0.095  Score=51.80  Aligned_cols=40  Identities=10%  Similarity=0.212  Sum_probs=26.9

Q ss_pred             CCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      +...++|||||+|.+..  .....+.+.++.-+....+|+.+
T Consensus       130 ~a~~KVvIIDEad~Ls~--~a~naLLKtLEePp~~~~fIl~t  169 (598)
T PRK09111        130 SARYKVYIIDEVHMLST--AAFNALLKTLEEPPPHVKFIFAT  169 (598)
T ss_pred             cCCcEEEEEEChHhCCH--HHHHHHHHHHHhCCCCeEEEEEe
Confidence            45678999999998864  23344555556656666666665

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=95.67  E-value=0.085  Score=48.98  Aligned_cols=48  Identities=15%  Similarity=0.252  Sum_probs=33.4

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhCCC-CceEEEEeccCCccHH
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPH-DKQVMMFSATLSKEIR  237 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~-~~~~v~~SAT~~~~~~  237 (423)
                      +++++++|.++.+..+......+-.++..+.. ..|+++.|..+|.++.
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~  223 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELN  223 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhc
Confidence            56789999999887654556666555555543 4578888877776654

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=95.67  E-value=0.092  Score=51.72  Aligned_cols=49  Identities=16%  Similarity=0.278  Sum_probs=29.2

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTL  105 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~  105 (423)
                      +.+|+++.-.+.+.+.|...            +..-.-++..+++||.|+|||.++-+.+-
T Consensus        12 P~~f~~viGq~~v~~~L~~~------------i~~~~~~hayLf~Gp~GtGKTt~Ak~lAk   60 (559)
T PRK05563         12 PQTFEDVVGQEHITKTLKNA------------IKQGKISHAYLFSGPRGTGKTSAAKIFAK   60 (559)
T ss_pred             CCcHHhccCcHHHHHHHHHH------------HHcCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            44566666666666555432            00001124478899999999987655433

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.65  E-value=0.06  Score=52.13  Aligned_cols=19  Identities=26%  Similarity=0.343  Sum_probs=15.5

Q ss_pred             ceEEEccCCCcchhHHHHH
Q 014486           85 DVICQAKSGMGKTAVFVLS  103 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~~  103 (423)
                      ..++.||.|+|||.++...
T Consensus        38 a~Lf~GppGtGKTTlA~~l   56 (504)
T PRK14963         38 AYLFSGPRGVGKTTTARLI   56 (504)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3699999999999876543

>PRK09183 transposase/IS protein; Provisional

Probab=95.64  E-value=0.071  Score=46.91  Aligned_cols=24  Identities=21%  Similarity=0.267  Sum_probs=18.9

Q ss_pred             cccCCceEEEccCCCcchhHHHHH
Q 014486           80 AILGMDVICQAKSGMGKTAVFVLS  103 (423)
Q Consensus        80 ~~~~~~~ii~~~tGsGKT~~~~~~  103 (423)
                      +..+.++++.||+|+|||..+...
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al  122 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIAL  122 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHH
Confidence            445778999999999999765443

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=95.60  E-value=0.041  Score=45.93  Aligned_cols=40  Identities=13%  Similarity=0.311  Sum_probs=25.2

Q ss_pred             CCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ....++||+||+|.+..  .....+...++..++..-+|+++
T Consensus        94 ~~~~kviiide~~~l~~--~~~~~Ll~~le~~~~~~~~il~~  133 (188)
T TIGR00678        94 ESGRRVVIIEDAERMNE--AAANALLKTLEEPPPNTLFILIT  133 (188)
T ss_pred             cCCeEEEEEechhhhCH--HHHHHHHHHhcCCCCCeEEEEEE
Confidence            35678999999998864  23344555555545455455544

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.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.60  E-value=0.019  Score=51.58  Aligned_cols=74  Identities=22%  Similarity=0.310  Sum_probs=43.0

Q ss_pred             CCCCCHHHHHHHHhCCCCCCChhhhhccccccc-CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           50 DFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        50 ~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~-~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      .++..+.-++.|.+.|.  +.+.|...+..+.. +++++++|+||||||... -+++..+.......+++++=...++
T Consensus       100 k~~~~~~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       100 KKAVAVFTLDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             CcCCCCCCHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHhhccCCCceEEEECCchhh
Confidence            33333333455555554  44556555555444 678999999999999753 3444444332222266777666665

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.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.58  E-value=0.069  Score=51.25  Aligned_cols=19  Identities=32%  Similarity=0.352  Sum_probs=15.6

Q ss_pred             ceEEEccCCCcchhHHHHH
Q 014486           85 DVICQAKSGMGKTAVFVLS  103 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~~  103 (423)
                      ..++.||+|+|||..+-+.
T Consensus        38 ~~Lf~GPpGtGKTTlA~~l   56 (472)
T PRK14962         38 AYIFAGPRGTGKTTVARIL   56 (472)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4799999999999876543

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.58  E-value=0.17  Score=47.24  Aligned_cols=55  Identities=15%  Similarity=0.208  Sum_probs=31.5

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCC---CCceEEEEeccCCc-cHHHHHHHh
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTP---HDKQVMMFSATLSK-EIRPVCKKF  243 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~---~~~~~v~~SAT~~~-~~~~~~~~~  243 (423)
                      .+.++|++|=+-+...+......+..+.....   +...++.+|||... .+......+
T Consensus       298 ~~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~~~~f  356 (432)
T PRK12724        298 DGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTVLKAY  356 (432)
T ss_pred             CCCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHHHHHh
Confidence            45678999976654322233444555555442   23457888999876 444444443

>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=95.58  E-value=0.11  Score=40.25  Aligned_cols=15  Identities=27%  Similarity=0.541  Sum_probs=13.0

Q ss_pred             eEEEccCCCcchhHH
Q 014486           86 VICQAKSGMGKTAVF  100 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~  100 (423)
                      +++.||+|+|||..+
T Consensus         1 ill~G~~G~GKT~l~   15 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLA   15 (132)
T ss_dssp             EEEESSTTSSHHHHH
T ss_pred             CEEECcCCCCeeHHH
Confidence            589999999999754

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 ....

>CHL00181 cbbX CbbX; Provisional

Probab=95.51  E-value=0.11  Score=46.58  Aligned_cols=20  Identities=30%  Similarity=0.493  Sum_probs=16.4

Q ss_pred             CCceEEEccCCCcchhHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~  102 (423)
                      +.++++.||+|+|||..+-.
T Consensus        59 ~~~ill~G~pGtGKT~lAr~   78 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALK   78 (287)
T ss_pred             CceEEEECCCCCCHHHHHHH
Confidence            45689999999999987643

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.49  E-value=0.064  Score=52.73  Aligned_cols=24  Identities=17%  Similarity=0.216  Sum_probs=18.1

Q ss_pred             CceEEEccCCCcchhHHHHHHhhc
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQ  107 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~  107 (423)
                      +..|+.||.|+|||.++.+.+-..
T Consensus        39 ha~Lf~GPpG~GKTtiArilAk~L   62 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIARIFAKAL   62 (624)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhc
Confidence            458899999999998876544333

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=95.47  E-value=0.096  Score=51.97  Aligned_cols=39  Identities=8%  Similarity=0.259  Sum_probs=25.6

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ..++++||||+|.+..  .....+.+.++.-+....+|+.|
T Consensus       118 g~~KV~IIDEah~Ls~--~a~NALLKtLEEPp~~v~FIL~T  156 (647)
T PRK07994        118 GRFKVYLIDEVHMLSR--HSFNALLKTLEEPPEHVKFLLAT  156 (647)
T ss_pred             CCCEEEEEechHhCCH--HHHHHHHHHHHcCCCCeEEEEec
Confidence            4678999999998865  33444555566555555555553

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.46  E-value=0.23  Score=44.03  Aligned_cols=56  Identities=14%  Similarity=0.353  Sum_probs=34.7

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCC------CCceEEEEeccCCccHHHHHHHhc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTP------HDKQVMMFSATLSKEIRPVCKKFM  244 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~------~~~~~v~~SAT~~~~~~~~~~~~~  244 (423)
                      .++++|++|=+-+...+......+..+.....      +...++.++||...+....+..+.
T Consensus       153 ~~~D~ViIDT~G~~~~d~~~~~el~~~~~~~~~~~~~~~~~~~LVl~a~~~~~~~~~~~~f~  214 (272)
T TIGR00064       153 RNIDVVLIDTAGRLQNKVNLMDELKKIKRVIKKVDKDAPDEVLLVLDATTGQNALEQAKVFN  214 (272)
T ss_pred             CCCCEEEEeCCCCCcchHHHHHHHHHHHHHHhcccCCCCceEEEEEECCCCHHHHHHHHHHH
Confidence            45678999988766433344445666655544      455678899987665444444443

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.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=95.45  E-value=0.16  Score=50.89  Aligned_cols=43  Identities=12%  Similarity=0.254  Sum_probs=37.5

Q ss_pred             ccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCc
Q 014486          191 VRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSK  234 (423)
Q Consensus       191 ~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~  234 (423)
                      .-++|+|+.|.+.+ ......+..+.+..|.+...++.|-+-|+
T Consensus       130 pl~LVlDDyHli~~-~~l~~~l~fLl~~~P~~l~lvv~SR~rP~  172 (894)
T COG2909         130 PLYLVLDDYHLISD-PALHEALRFLLKHAPENLTLVVTSRSRPQ  172 (894)
T ss_pred             ceEEEeccccccCc-ccHHHHHHHHHHhCCCCeEEEEEeccCCC
Confidence            35899999999988 67788899999999999999999988653

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.40  E-value=0.12  Score=49.50  Aligned_cols=23  Identities=22%  Similarity=0.184  Sum_probs=17.5

Q ss_pred             CCceEEEccCCCcchhHHHHHHh
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTL  105 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~  105 (423)
                      ++-+.+.||||+|||.+....+.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~  278 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAA  278 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHH
Confidence            44588999999999987655443

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.40  E-value=0.07  Score=51.15  Aligned_cols=85  Identities=19%  Similarity=0.123  Sum_probs=52.3

Q ss_pred             CCHH-HHHHHHhCCCCCC-------ChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC---CCeEEEEEe
Q 014486           53 LKPE-LLRAIVDSGFEHP-------SEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP---GQVTALVLC  121 (423)
Q Consensus        53 l~~~-~~~~l~~~~~~~~-------~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~---~~~~~lil~  121 (423)
                      ..++ ++..|.+.--.++       .+-|-++|.. -.++-++|+|..|||||.+++--+...+....   ....+||+.
T Consensus       189 ~~dEvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~-ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~  267 (747)
T COG3973         189 GRDEVLQRVLEKNSSAKMRDIVETIQKEQNEIIRF-EKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLG  267 (747)
T ss_pred             hHHHHHHHHHHhccchhHHHHHHHhhHhHHHHHhc-cCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEc
Confidence            3344 4566666533333       3445555421 23556899999999999887654443332211   111499999


Q ss_pred             cChHHHHHHHHHHHHHh
Q 014486          122 HTRELAYQICHEFERFS  138 (423)
Q Consensus       122 P~~~L~~q~~~~~~~~~  138 (423)
                      |.+.+..-+.+.+-+++
T Consensus       268 PN~vFleYis~VLPeLG  284 (747)
T COG3973         268 PNRVFLEYISRVLPELG  284 (747)
T ss_pred             CcHHHHHHHHHhchhhc
Confidence            99998888777666553

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=95.39  E-value=0.12  Score=50.59  Aligned_cols=39  Identities=10%  Similarity=0.228  Sum_probs=23.9

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ...+++|+||+|.+..  .....+.+.+..-+....+|++|
T Consensus       118 ~~~KVIIIDEad~Lt~--~A~NaLLKtLEEPp~~tvfIL~T  156 (605)
T PRK05896        118 FKYKVYIIDEAHMLST--SAWNALLKTLEEPPKHVVFIFAT  156 (605)
T ss_pred             CCcEEEEEechHhCCH--HHHHHHHHHHHhCCCcEEEEEEC
Confidence            3568899999998854  23344555555544455455544

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.39  E-value=0.16  Score=47.60  Aligned_cols=79  Identities=18%  Similarity=0.140  Sum_probs=54.0

Q ss_pred             HHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHH
Q 014486           57 LLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER  136 (423)
Q Consensus        57 ~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  136 (423)
                      +++.+++. +..+-..|.++.-..-.|+. .|.|=.|||||....+-+.+.-. .+...++++.+=|+.|+.++.....+
T Consensus       152 ~l~~iesk-IanfD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Kaa~lh~-knPd~~I~~Tfftk~L~s~~r~lv~~  228 (660)
T COG3972         152 LLDTIESK-IANFDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKAAELHS-KNPDSRIAFTFFTKILASTMRTLVPE  228 (660)
T ss_pred             HHHHHHHH-HhcccchhheeeeecCCchh-hhhcccCCCchhHHHHHHHHHhc-CCCCceEEEEeehHHHHHHHHHHHHH
Confidence            44444443 33455778888666666666 77888999999865544433333 33334899999999999998888877


Q ss_pred             Hh
Q 014486          137 FS  138 (423)
Q Consensus       137 ~~  138 (423)
                      |+
T Consensus       229 F~  230 (660)
T COG3972         229 FF  230 (660)
T ss_pred             HH
Confidence            64

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.39  E-value=0.19  Score=48.27  Aligned_cols=21  Identities=24%  Similarity=0.264  Sum_probs=16.9

Q ss_pred             cCCceEEEccCCCcchhHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~  102 (423)
                      .++.+.+.||+|+|||.....
T Consensus       349 ~G~vIaLVGPtGvGKTTtaak  369 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAK  369 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            456788999999999987544

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=95.36  E-value=0.13  Score=51.12  Aligned_cols=39  Identities=10%  Similarity=0.273  Sum_probs=25.4

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      .+.+++||||+|.+..  .....+.+.+..-+....+|+.|
T Consensus       118 gk~KVIIIDEad~Ls~--~A~NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        118 GKYKVYIIDEVHMLSK--SAFNAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             CCcEEEEEECccccCH--HHHHHHHHHHHhCCCCcEEEEEe
Confidence            4678999999998754  22334555555555566666655

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=95.34  E-value=0.089  Score=48.01  Aligned_cols=18  Identities=28%  Similarity=0.322  Sum_probs=15.2

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      .+.|++||+|+|||..+-
T Consensus        49 ~SmIl~GPPG~GKTTlA~   66 (436)
T COG2256          49 HSMILWGPPGTGKTTLAR   66 (436)
T ss_pred             ceeEEECCCCCCHHHHHH
Confidence            469999999999997653

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=95.34  E-value=0.27  Score=42.46  Aligned_cols=52  Identities=6%  Similarity=0.047  Sum_probs=31.3

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .+.-+++.|++|+|||...+..+...+..+   .++++++.. +-..+..+.+.++
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g---~~~~yi~~e-~~~~~~~~~~~~~   74 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGFLQNG---YSVSYVSTQ-LTTTEFIKQMMSL   74 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhCC---CcEEEEeCC-CCHHHHHHHHHHh
Confidence            356699999999999987544444433332   267888743 3334444444443

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.28  E-value=0.089  Score=46.97  Aligned_cols=22  Identities=23%  Similarity=0.312  Sum_probs=16.7

Q ss_pred             CCceEEEccCCCcchhHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLST  104 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~  104 (423)
                      ++.+++.||||+|||.+....+
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa  215 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLA  215 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            3458899999999998754433

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=95.25  E-value=0.032  Score=49.87  Aligned_cols=73  Identities=16%  Similarity=0.189  Sum_probs=48.5

Q ss_pred             CcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCC-ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           48 FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGM-DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        48 ~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~-~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      .+.|+-.+-.+..|.+  |..+++-|...+..+.... +++++|.||||||.. +-++........   +++.+=.+.+|
T Consensus       139 IRKf~k~~ltl~dli~--~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl-LNal~~~i~~~e---RvItiEDtaEL  212 (355)
T COG4962         139 IRKFPKIKLTLLDLII--FGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL-LNALSGFIDSDE---RVITIEDTAEL  212 (355)
T ss_pred             ccccccccccHHHHHH--cCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH-HHHHHhcCCCcc---cEEEEeehhhh
Confidence            3444444444444443  5678899999888888765 899999999999974 223333333333   77888787766

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.24  E-value=0.021  Score=53.80  Aligned_cols=42  Identities=17%  Similarity=0.252  Sum_probs=28.4

Q ss_pred             ChhhhhcccccccCCc--eEEEccCCCcchhHHHHHHhhccCCCC
Q 014486           70 SEVQHECIPQAILGMD--VICQAKSGMGKTAVFVLSTLQQTEPNP  112 (423)
Q Consensus        70 ~~~Q~~~i~~~~~~~~--~ii~~~tGsGKT~~~~~~~~~~~~~~~  112 (423)
                      .+.|...+..++....  +++.||||||||.+ +..++..+....
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~~~  286 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNTPE  286 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcCCC
Confidence            4555666656565433  78999999999976 455666655444

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=95.19  E-value=0.029  Score=57.97  Aligned_cols=98  Identities=13%  Similarity=0.082  Sum_probs=73.9

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCcc-EEEEcCccccCCCCCCCCEEEEccC
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKR-ILVATDLVGRGIDIERVNIVINYDM  365 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~-ili~T~~~~~Gld~~~~~~vi~~~~  365 (423)
                      ...++|+|+......+.+...+...++....-.++   ++-...+..|.+  ++ +++-++..+-|+|+-.+.||+..+|
T Consensus      1220 ~qekvIvfsqws~~ldV~e~~~~~N~I~~~~~~~t---~d~~dc~~~fk~--I~clll~~~~~~~GLNL~eA~Hvfl~eP 1294 (1394)
T KOG0298|consen 1220 EQEKVIVFSQWSVVLDVKELRYLMNLIKKQLDGET---EDFDDCIICFKS--IDCLLLFVSKGSKGLNLIEATHVFLVEP 1294 (1394)
T ss_pred             cCceEEEEEehHHHHHHHHHHHHhhhhHhhhccCC---cchhhhhhhccc--ceEEEEEeccCcccccHHhhhhhheecc
Confidence            34689999998888888877777665554333322   223334455554  44 5567889999999999999999999


Q ss_pred             CCCcchhhhcccccCCCCCceEEE
Q 014486          366 PDSADTYLHRVGRAGRFGTKGLAI  389 (423)
Q Consensus       366 ~~s~~~~~Q~~GR~~R~g~~~~~~  389 (423)
                      .-++..-.|++||++|.||+....
T Consensus      1295 iLN~~~E~QAigRvhRiGQ~~pT~ 1318 (1394)
T KOG0298|consen 1295 ILNPGDEAQAIGRVHRIGQKRPTF 1318 (1394)
T ss_pred             ccCchHHHhhhhhhhhcccccchh
Confidence            999999999999999999976544

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=95.18  E-value=0.069  Score=49.17  Aligned_cols=41  Identities=20%  Similarity=0.320  Sum_probs=28.4

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      ...++|||||+|.+..  .....+.+.++.-+....++++|..
T Consensus       140 g~~rVviIDeAd~l~~--~aanaLLk~LEEpp~~~~fiLit~~  180 (351)
T PRK09112        140 GNWRIVIIDPADDMNR--NAANAILKTLEEPPARALFILISHS  180 (351)
T ss_pred             CCceEEEEEchhhcCH--HHHHHHHHHHhcCCCCceEEEEECC
Confidence            5678999999998864  4445566666665556666666544

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=95.18  E-value=0.093  Score=48.62  Aligned_cols=42  Identities=17%  Similarity=0.278  Sum_probs=28.4

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccC
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATL  232 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~  232 (423)
                      ...+++||||+|.+..  .....+.+.++.-+....++++|..+
T Consensus       140 ~~~kVviIDead~m~~--~aanaLLK~LEepp~~~~~IL~t~~~  181 (365)
T PRK07471        140 GGWRVVIVDTADEMNA--NAANALLKVLEEPPARSLFLLVSHAP  181 (365)
T ss_pred             CCCEEEEEechHhcCH--HHHHHHHHHHhcCCCCeEEEEEECCc
Confidence            5678999999998854  44455666666655566566665554

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=95.18  E-value=0.15  Score=46.37  Aligned_cols=41  Identities=10%  Similarity=0.248  Sum_probs=28.2

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      ...+++|+|++|.+..  .....+.+.++..+....+|++|-.
T Consensus       112 ~~~kV~iiEp~~~Ld~--~a~naLLk~LEep~~~~~~Ilvth~  152 (325)
T PRK08699        112 GGLRVILIHPAESMNL--QAANSLLKVLEEPPPQVVFLLVSHA  152 (325)
T ss_pred             CCceEEEEechhhCCH--HHHHHHHHHHHhCcCCCEEEEEeCC
Confidence            5678999999998864  5566666777766655555555443

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=95.16  E-value=0.12  Score=46.82  Aligned_cols=41  Identities=2%  Similarity=0.106  Sum_probs=29.0

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      ...+++|+|+||.+..  .....+.+.++.=+....++++|..
T Consensus       106 g~~KV~iI~~a~~m~~--~AaNaLLKtLEEPp~~~~fiL~t~~  146 (325)
T PRK06871        106 GGNKVVYIQGAERLTE--AAANALLKTLEEPRPNTYFLLQADL  146 (325)
T ss_pred             CCceEEEEechhhhCH--HHHHHHHHHhcCCCCCeEEEEEECC
Confidence            4678999999999864  5556666777775666656665544

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=95.15  E-value=0.14  Score=46.80  Aligned_cols=41  Identities=12%  Similarity=0.186  Sum_probs=28.6

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      ...+++|||+||.+..  .-...+.+.++.-++...++++|..
T Consensus       131 ~~~kV~iI~~ae~m~~--~AaNaLLKtLEEPp~~t~fiL~t~~  171 (342)
T PRK06964        131 GGARVVVLYPAEALNV--AAANALLKTLEEPPPGTVFLLVSAR  171 (342)
T ss_pred             CCceEEEEechhhcCH--HHHHHHHHHhcCCCcCcEEEEEECC
Confidence            5678999999999864  4555566666665556656666544

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=95.15  E-value=0.26  Score=44.93  Aligned_cols=38  Identities=16%  Similarity=0.394  Sum_probs=25.1

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ..++|++||+|.+..  .....+..+....+....+|+.+
T Consensus       102 ~~~vviiDe~~~l~~--~~~~~L~~~le~~~~~~~lIl~~  139 (319)
T PRK00440        102 PFKIIFLDEADNLTS--DAQQALRRTMEMYSQNTRFILSC  139 (319)
T ss_pred             CceEEEEeCcccCCH--HHHHHHHHHHhcCCCCCeEEEEe
Confidence            457899999998854  23445566666656666666654

>PRK10867 signal recognition particle protein; Provisional

Probab=95.14  E-value=0.26  Score=46.64  Aligned_cols=21  Identities=19%  Similarity=0.104  Sum_probs=16.1

Q ss_pred             ceEEEccCCCcchhHHHHHHh
Q 014486           85 DVICQAKSGMGKTAVFVLSTL  105 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~~~~  105 (423)
                      -++++|++|+|||.+..-.+.
T Consensus       102 vI~~vG~~GsGKTTtaakLA~  122 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAK  122 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHH
Confidence            378999999999987654343

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.14  E-value=0.077  Score=52.49  Aligned_cols=39  Identities=13%  Similarity=0.275  Sum_probs=26.2

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ...+++||||+|.+..  .....+.+.++.-+....+|+.|
T Consensus       118 ~~~KVvIIdev~~Lt~--~a~naLLk~LEepp~~~~fIl~t  156 (576)
T PRK14965        118 SRYKIFIIDEVHMLST--NAFNALLKTLEEPPPHVKFIFAT  156 (576)
T ss_pred             CCceEEEEEChhhCCH--HHHHHHHHHHHcCCCCeEEEEEe
Confidence            5678999999998864  33445555666555566566555

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=95.13  E-value=0.15  Score=47.68  Aligned_cols=41  Identities=10%  Similarity=0.260  Sum_probs=25.8

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      ...+++||||+|.+..  .....+.+.++.-+....+|+.|.+
T Consensus       116 ~~~kViiIDead~m~~--~aanaLLk~LEep~~~~~fIL~a~~  156 (394)
T PRK07940        116 GRWRIVVIEDADRLTE--RAANALLKAVEEPPPRTVWLLCAPS  156 (394)
T ss_pred             CCcEEEEEechhhcCH--HHHHHHHHHhhcCCCCCeEEEEECC
Confidence            4678999999999964  3334455555554545544554444

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=95.12  E-value=0.14  Score=51.93  Aligned_cols=76  Identities=13%  Similarity=0.191  Sum_probs=63.9

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHh----CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc-cccCCCCCCCCEEE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVE----CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL-VGRGIDIERVNIVI  361 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~-~~~Gld~~~~~~vi  361 (423)
                      .+.++++.+++...|.+.++.+++    .++++..++|+++..+|...+....+|+.+|+|+|.. +...+.+.++.+||
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            456899999999999888777654    4688999999999999999999999999999999964 55567788888877


Q ss_pred             E
Q 014486          362 N  362 (423)
Q Consensus       362 ~  362 (423)
                      .
T Consensus       389 I  389 (681)
T PRK10917        389 I  389 (681)
T ss_pred             E
Confidence            4

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=95.05  E-value=0.1  Score=50.46  Aligned_cols=21  Identities=19%  Similarity=0.199  Sum_probs=17.0

Q ss_pred             CceEEEccCCCcchhHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLST  104 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~  104 (423)
                      +..++.||.|+|||.++-+.+
T Consensus        44 ~a~Lf~Gp~G~GKTT~ArilA   64 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSARIIA   64 (507)
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            468999999999998765533

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.05  E-value=0.14  Score=44.56  Aligned_cols=39  Identities=23%  Similarity=0.194  Sum_probs=26.3

Q ss_pred             ccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEe
Q 014486           81 ILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLC  121 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  121 (423)
                      ..|.-++|.|++|+|||...+-.+.......+  ..+++++
T Consensus        11 ~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g--~~vly~s   49 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAFALNIAENIAKKQG--KPVLFFS   49 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCC--CceEEEe
Confidence            44666899999999999765544444444322  2677777

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.

>PRK05580 primosome assembly protein PriA; Validated

Probab=95.01  E-value=0.14  Score=51.75  Aligned_cols=76  Identities=17%  Similarity=0.342  Sum_probs=63.5

Q ss_pred             CCcEEEEEcChhhHHHHHHHHHhC-CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEcc
Q 014486          288 FNQVVIFVKSVSRAAELNKLLVEC-NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYD  364 (423)
Q Consensus       288 ~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~  364 (423)
                      +.++||.++++..+.++.+.|++. +..+..+||+++..+|...+.....|+.+|+|+|..+.. +.+.++.++|.-+
T Consensus       190 g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-~p~~~l~liVvDE  266 (679)
T PRK05580        190 GKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-LPFKNLGLIIVDE  266 (679)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-ccccCCCEEEEEC
Confidence            568999999999999999999764 788999999999999999988889999999999974332 4566777777554

>PRK13342 recombination factor protein RarA; Reviewed

Probab=95.00  E-value=0.19  Score=47.68  Aligned_cols=18  Identities=28%  Similarity=0.320  Sum_probs=15.0

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      .++++.||+|+|||..+-
T Consensus        37 ~~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         37 SSMILWGPPGTGKTTLAR   54 (413)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            368999999999997653

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.94  E-value=0.16  Score=49.61  Aligned_cols=39  Identities=10%  Similarity=0.278  Sum_probs=26.0

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      .+.+++|+||+|.+..  .....+.+.++.-+....+|+.|
T Consensus       118 ~~~kVvIIDEad~ls~--~a~naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969        118 GRFKVYIIDEVHMLSK--SAFNAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             CCceEEEEcCcccCCH--HHHHHHHHHHhCCCCCEEEEEEe
Confidence            5678999999998864  22334555555555566666665

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=94.91  E-value=0.18  Score=46.77  Aligned_cols=51  Identities=18%  Similarity=0.256  Sum_probs=31.9

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      |.-+++.|++|+|||...+..+...... +  .+++|+.-. +-..|+..++.++
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~~-g--~~VlYvs~E-Es~~qi~~Ra~rl  132 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAKR-G--GKVLYVSGE-ESPEQIKLRADRL  132 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhc-C--CeEEEEECC-cCHHHHHHHHHHc
Confidence            3458999999999998655444333322 1  277887654 3445665555554

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.

>TIGR00595 priA primosomal protein N'

Probab=94.91  E-value=0.23  Score=48.29  Aligned_cols=76  Identities=16%  Similarity=0.291  Sum_probs=62.5

Q ss_pred             CCcEEEEEcChhhHHHHHHHHHhC-CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEcc
Q 014486          288 FNQVVIFVKSVSRAAELNKLLVEC-NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYD  364 (423)
Q Consensus       288 ~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~  364 (423)
                      ++++|+.++++..+.++.+.|++. +..+..+||+++..+|........+|+.+|+|+|..+-. ..+.++..||.-+
T Consensus        25 g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf-~p~~~l~lIIVDE  101 (505)
T TIGR00595        25 GKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF-LPFKNLGLIIVDE  101 (505)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc-CcccCCCEEEEEC
Confidence            568999999999999999999864 678889999999999999988888999999999965332 3456777777543

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).

>PRK04195 replication factor C large subunit; Provisional

Probab=94.90  E-value=0.13  Score=49.91  Aligned_cols=49  Identities=10%  Similarity=0.070  Sum_probs=29.0

Q ss_pred             cCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~  101 (423)
                      .+.+++++...+...+.|...-    ..++     .-...+.+++.||+|+|||..+-
T Consensus         9 rP~~l~dlvg~~~~~~~l~~~l----~~~~-----~g~~~~~lLL~GppG~GKTtla~   57 (482)
T PRK04195          9 RPKTLSDVVGNEKAKEQLREWI----ESWL-----KGKPKKALLLYGPPGVGKTSLAH   57 (482)
T ss_pred             CCCCHHHhcCCHHHHHHHHHHH----HHHh-----cCCCCCeEEEECCCCCCHHHHHH
Confidence            3455667766666666555420    0000     00014569999999999997653

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.88  E-value=0.11  Score=50.55  Aligned_cols=39  Identities=8%  Similarity=0.230  Sum_probs=26.6

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      .+.+++|+||+|.+..  .....+.+.++.-+....+|+.|
T Consensus       118 g~~kViIIDEa~~ls~--~a~naLLK~LEepp~~v~fIL~T  156 (546)
T PRK14957        118 GRYKVYLIDEVHMLSK--QSFNALLKTLEEPPEYVKFILAT  156 (546)
T ss_pred             CCcEEEEEechhhccH--HHHHHHHHHHhcCCCCceEEEEE
Confidence            4678999999998864  34445556666655566666655

>TIGR00959 ffh signal recognition particle protein

Probab=94.85  E-value=0.28  Score=46.35  Aligned_cols=22  Identities=18%  Similarity=0.122  Sum_probs=16.8

Q ss_pred             ceEEEccCCCcchhHHHHHHhh
Q 014486           85 DVICQAKSGMGKTAVFVLSTLQ  106 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~~~~~  106 (423)
                      -++++|++|+|||.+..-.+..
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~  122 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYY  122 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHH
Confidence            4889999999999876544433

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.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=94.84  E-value=0.37  Score=41.58  Aligned_cols=52  Identities=17%  Similarity=0.209  Sum_probs=30.9

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .|..+++.|++|+|||..+...+.+.+..+.   .+++++. .....++.+.++.+
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~---~~~~is~-e~~~~~i~~~~~~~   70 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLRDGD---PVIYVTT-EESRESIIRQAAQF   70 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHhcCC---eEEEEEc-cCCHHHHHHHHHHh
Confidence            3567999999999999765544444333222   5666663 33344554444443

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.

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=94.82  E-value=0.18  Score=48.01  Aligned_cols=40  Identities=18%  Similarity=0.182  Sum_probs=25.2

Q ss_pred             cccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEe
Q 014486           80 AILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLC  121 (423)
Q Consensus        80 ~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  121 (423)
                      +..|.-++|.|++|+|||...+-.+.......+.  .+++++
T Consensus       191 ~~~g~liviag~pg~GKT~~al~ia~~~a~~~g~--~v~~fS  230 (421)
T TIGR03600       191 LVKGDLIVIGARPSMGKTTLALNIAENVALREGK--PVLFFS  230 (421)
T ss_pred             CCCCceEEEEeCCCCCHHHHHHHHHHHHHHhCCC--cEEEEE
Confidence            3345568999999999997665544344322222  566665

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.

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=94.81  E-value=0.21  Score=45.01  Aligned_cols=17  Identities=29%  Similarity=0.358  Sum_probs=14.6

Q ss_pred             CceEEEccCCCcchhHH
Q 014486           84 MDVICQAKSGMGKTAVF  100 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~  100 (423)
                      .++|++||+|+|||..+
T Consensus       163 pSmIlWGppG~GKTtlA  179 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLA  179 (554)
T ss_pred             CceEEecCCCCchHHHH
Confidence            45999999999999754

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=94.71  E-value=0.44  Score=41.31  Aligned_cols=51  Identities=10%  Similarity=0.113  Sum_probs=32.2

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      +.-+++.|++|+|||......+...+..+   .+++++.-.. -..++.+.+.++
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~~g---~~~~y~~~e~-~~~~~~~~~~~~   75 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALKQG---KKVYVITTEN-TSKSYLKQMESV   75 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHhCC---CEEEEEEcCC-CHHHHHHHHHHC
Confidence            45589999999999986655555444432   2777777543 334555555554

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=94.71  E-value=0.064  Score=50.38  Aligned_cols=30  Identities=23%  Similarity=0.308  Sum_probs=23.2

Q ss_pred             hhhhcccccccCCceEEEccCCCcchhHHH
Q 014486           72 VQHECIPQAILGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        72 ~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~  101 (423)
                      .....+..+..++++++.||+|+|||..+-
T Consensus       183 ~le~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        183 TIETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             HHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            344455566678999999999999997654

>PHA00729 NTP-binding motif containing protein

Probab=94.70  E-value=0.23  Score=42.24  Aligned_cols=77  Identities=9%  Similarity=0.051  Sum_probs=36.5

Q ss_pred             cEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcH----HHHHHHHHhCCCCceEEEEeccCCccHHHHHHHh
Q 014486          168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMR----RDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKF  243 (423)
Q Consensus       168 ~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~----~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~  243 (423)
                      ..++.+.+.+...+..........+++|+||+-.-.....+.    ..+..+...+.....++.+...-+.++...++..
T Consensus        60 ~~~fid~~~Ll~~L~~a~~~~~~~dlLIIDd~G~~~~~~~wh~~~~~~yf~L~~aLrSR~~l~il~~ls~edL~~~Lr~R  139 (226)
T PHA00729         60 NSYFFELPDALEKIQDAIDNDYRIPLIIFDDAGIWLSKYVWYEDYMKTFYKIYALIRTRVSAVIFTTPSPEDLAFYLREK  139 (226)
T ss_pred             cEEEEEHHHHHHHHHHHHhcCCCCCEEEEeCCchhhcccchhhhccchHHHHHHHHHhhCcEEEEecCCHHHHHHHHHhC
Confidence            555566666655443221122345789999943222211122    1222233333334445666655555555555553


Q ss_pred             c
Q 014486          244 M  244 (423)
Q Consensus       244 ~  244 (423)
                      .
T Consensus       140 g  140 (226)
T PHA00729        140 G  140 (226)
T ss_pred             C
Confidence            3

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.70  E-value=0.57  Score=42.56  Aligned_cols=56  Identities=13%  Similarity=0.334  Sum_probs=33.6

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhC------CCCceEEEEeccCCccHHHHHHHhc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMT------PHDKQVMMFSATLSKEIRPVCKKFM  244 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~------~~~~~~v~~SAT~~~~~~~~~~~~~  244 (423)
                      .++++||+|=+-+..........+..+.+.+      .+...++.++||...+....+..+.
T Consensus       195 ~~~D~ViIDTaGr~~~~~~l~~eL~~~~~v~~~~~~~~p~~~~LVl~a~~g~~~~~~a~~f~  256 (318)
T PRK10416        195 RGIDVLIIDTAGRLHNKTNLMEELKKIKRVIKKADPDAPHEVLLVLDATTGQNALSQAKAFH  256 (318)
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHHHHHHhhhcCCCCceEEEEEECCCChHHHHHHHHHH
Confidence            4568899999987654333444555555432      2344578899997665444444443

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.64  E-value=0.17  Score=50.23  Aligned_cols=40  Identities=13%  Similarity=0.191  Sum_probs=25.0

Q ss_pred             CCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      +.+.++|||||+|.+..  .-...+.+.++.-+...-+|+++
T Consensus       125 ~~~~KVvIIdEad~Lt~--~a~naLLK~LEePp~~tv~IL~t  164 (620)
T PRK14954        125 KGRYRVYIIDEVHMLST--AAFNAFLKTLEEPPPHAIFIFAT  164 (620)
T ss_pred             cCCCEEEEEeChhhcCH--HHHHHHHHHHhCCCCCeEEEEEe
Confidence            35678999999998864  22334455555544455555555

>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=94.64  E-value=0.49  Score=38.73  Aligned_cols=54  Identities=13%  Similarity=0.257  Sum_probs=27.5

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHH
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKK  242 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~  242 (423)
                      .+.++||+|.......+......+..+........-++.++++.+.........
T Consensus        81 ~~~d~viiDt~g~~~~~~~~l~~l~~l~~~~~~~~~~lVv~~~~~~~~~~~~~~  134 (173)
T cd03115          81 ENFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDAMTGQDAVNQAKA  134 (173)
T ss_pred             CCCCEEEEECcccchhhHHHHHHHHHHHhhcCCCeEEEEEECCCChHHHHHHHH
Confidence            355689999988652212233334444333334444566666654444444333

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.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=94.57  E-value=0.22  Score=45.01  Aligned_cols=43  Identities=14%  Similarity=0.279  Sum_probs=30.2

Q ss_pred             CCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccC
Q 014486          188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATL  232 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~  232 (423)
                      ....+++|||+||.+..  .....+.+.++.=+....++++|..+
T Consensus       106 ~~~~kV~iI~~ae~m~~--~AaNaLLKtLEEPp~~t~fiL~t~~~  148 (319)
T PRK06090        106 LNGYRLFVIEPADAMNE--SASNALLKTLEEPAPNCLFLLVTHNQ  148 (319)
T ss_pred             cCCceEEEecchhhhCH--HHHHHHHHHhcCCCCCeEEEEEECCh
Confidence            35678999999999864  45566667777766666666665553

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=94.54  E-value=0.25  Score=50.09  Aligned_cols=18  Identities=28%  Similarity=0.344  Sum_probs=15.1

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      .++++.||+|+|||..+-
T Consensus        53 ~slLL~GPpGtGKTTLA~   70 (725)
T PRK13341         53 GSLILYGPPGVGKTTLAR   70 (725)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            468999999999997653

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=94.50  E-value=0.6  Score=37.45  Aligned_cols=53  Identities=23%  Similarity=0.276  Sum_probs=38.7

Q ss_pred             CCCccEEEEcCcchhhcc-CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHH
Q 014486          188 LKNVRHFILDECDKMLES-LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVC  240 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~-~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~  240 (423)
                      ...+++||+||+=..... .--...+..+++..+...-+|+.+-.+|+++...+
T Consensus        93 ~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~A  146 (159)
T cd00561          93 SGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAA  146 (159)
T ss_pred             cCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhC
Confidence            356789999999877541 23355677777877777778888888888776553

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.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=94.50  E-value=0.24  Score=45.31  Aligned_cols=135  Identities=12%  Similarity=0.109  Sum_probs=67.9

Q ss_pred             CChhhhhccccccc----C---CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH-hcc
Q 014486           69 PSEVQHECIPQAIL----G---MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF-STY  140 (423)
Q Consensus        69 ~~~~Q~~~i~~~~~----~---~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~-~~~  140 (423)
                      ++|+|...+..+.+    +   +-.++.||.|.||+..+...+...+...+.....-=.|++          ++.+ ...
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~s----------C~~~~~g~   72 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRG----------CQLMQAGT   72 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHH----------HHHHHcCC
Confidence            56788777776653    2   3478999999999987654333333322111010001222          2222 123


Q ss_pred             CCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhc--CCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHh
Q 014486          141 LPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARD--KDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKM  218 (423)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~--~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~  218 (423)
                      +|++....-.++..             .|   +-+.+..+.+.  ..-.....+++|+|+||.|..  .....+.+.++.
T Consensus        73 HPD~~~i~p~~~~~-------------~I---~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~--~AaNaLLKtLEE  134 (334)
T PRK07993         73 HPDYYTLTPEKGKS-------------SL---GVDAVREVTEKLYEHARLGGAKVVWLPDAALLTD--AAANALLKTLEE  134 (334)
T ss_pred             CCCEEEEecccccc-------------cC---CHHHHHHHHHHHhhccccCCceEEEEcchHhhCH--HHHHHHHHHhcC
Confidence            35544332111100             11   11222222211  011235678999999999864  455666666666


Q ss_pred             CCCCceEEEEecc
Q 014486          219 TPHDKQVMMFSAT  231 (423)
Q Consensus       219 ~~~~~~~v~~SAT  231 (423)
                      =+...-++++|..
T Consensus       135 Pp~~t~fiL~t~~  147 (334)
T PRK07993        135 PPENTWFFLACRE  147 (334)
T ss_pred             CCCCeEEEEEECC
Confidence            5555655655544

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

Probab=94.46  E-value=0.12  Score=51.88  Aligned_cols=91  Identities=16%  Similarity=0.286  Sum_probs=71.5

Q ss_pred             eChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhC-CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcC
Q 014486          270 LSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVEC-NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD  346 (423)
Q Consensus       270 ~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~  346 (423)
                      +....|-+....++...  .++.+||.++.+.....+.+.|+.+ |.++..+|+++++.+|.....+...|+.+|+|+|.
T Consensus       225 vTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtR  304 (730)
T COG1198         225 VTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTR  304 (730)
T ss_pred             CCCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCceEEEEec
Confidence            44555666666666543  4568999999999999999998865 88999999999999999999999999999999996


Q ss_pred             ccccCCCCCCCCEEE
Q 014486          347 LVGRGIDIERVNIVI  361 (423)
Q Consensus       347 ~~~~Gld~~~~~~vi  361 (423)
                      .+-. .-++++..+|
T Consensus       305 SAlF-~Pf~~LGLII  318 (730)
T COG1198         305 SALF-LPFKNLGLII  318 (730)
T ss_pred             hhhc-CchhhccEEE
Confidence            5332 3344556555

>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]

Probab=94.46  E-value=1.9  Score=35.57  Aligned_cols=34  Identities=3%  Similarity=-0.026  Sum_probs=24.2

Q ss_pred             HHHHHHHHhCCCCceEEEEeccCCccHHHHHHHh
Q 014486          210 RDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKF  243 (423)
Q Consensus       210 ~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~  243 (423)
                      ..+.+-.+..++..+++++|+.-...+..+++..
T Consensus       163 evm~~da~~~np~~~ii~~n~ktg~G~~~~~~~i  196 (202)
T COG0378         163 EVMARDAKEVNPEAPIIFTNLKTGEGLDEWLRFI  196 (202)
T ss_pred             HHHHHHHHHhCCCCCEEEEeCCCCcCHHHHHHHH
Confidence            3455556677888899999998877776665443

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=94.45  E-value=0.034  Score=45.81  Aligned_cols=46  Identities=20%  Similarity=0.221  Sum_probs=26.3

Q ss_pred             ccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           81 ILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      -.++++++.||+|+|||..+...+.+... .+  ..+++ ++..+|...+
T Consensus        45 ~~~~~l~l~G~~G~GKThLa~ai~~~~~~-~g--~~v~f-~~~~~L~~~l   90 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLAVAIANEAIR-KG--YSVLF-ITASDLLDEL   90 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHHHHHHHHHHH-TT----EEE-EEHHHHHHHH
T ss_pred             ccCeEEEEEhhHhHHHHHHHHHHHHHhcc-CC--cceeE-eecCceeccc
Confidence            35678999999999999876543333333 22  14444 4445565543

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.

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=94.43  E-value=0.23  Score=41.58  Aligned_cols=51  Identities=12%  Similarity=0.277  Sum_probs=25.1

Q ss_pred             CccEEEEcCcchhhccCCcH----HHHHHHHHhCCCC-ceEEEEeccCCccHHHHHH
Q 014486          190 NVRHFILDECDKMLESLDMR----RDVQEIFKMTPHD-KQVMMFSATLSKEIRPVCK  241 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~----~~~~~~~~~~~~~-~~~v~~SAT~~~~~~~~~~  241 (423)
                      .-.++|+||||.........    ......+...++. .-++++|-.+ ..+...++
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~~~~~~~l~~hRh~g~diiliTQ~~-~~id~~ir  134 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKVPEIIEFLAQHRHYGWDIILITQSP-SQIDKFIR  134 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T----HHHHGGGGCCCTT-EEEEEES-G-GGB-HHHH
T ss_pred             CCcEEEEECChhhcCCCccccccchHHHHHHHHhCcCCcEEEEEeCCH-HHHhHHHH
Confidence            44689999999987644442    2333555555553 3456665544 33444443

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=94.39  E-value=0.086  Score=46.21  Aligned_cols=27  Identities=11%  Similarity=0.351  Sum_probs=20.3

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCC
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPG  113 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~  113 (423)
                      ++|.||||||||.+ +.+++..+.....
T Consensus       128 ILVTGpTGSGKSTT-lAamId~iN~~~~  154 (353)
T COG2805         128 ILVTGPTGSGKSTT-LAAMIDYINKHKA  154 (353)
T ss_pred             EEEeCCCCCcHHHH-HHHHHHHHhccCC
Confidence            89999999999976 4566666655443

>PF05729 NACHT: NACHT domain

Probab=94.37  E-value=0.85  Score=36.73  Aligned_cols=16  Identities=19%  Similarity=0.420  Sum_probs=13.7

Q ss_pred             eEEEccCCCcchhHHH
Q 014486           86 VICQAKSGMGKTAVFV  101 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~  101 (423)
                      ++|.|++|+|||...-
T Consensus         3 l~I~G~~G~GKStll~   18 (166)
T PF05729_consen    3 LWISGEPGSGKSTLLR   18 (166)
T ss_pred             EEEECCCCCChHHHHH
Confidence            6899999999997653

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.34  E-value=0.26  Score=49.11  Aligned_cols=23  Identities=17%  Similarity=0.167  Sum_probs=17.4

Q ss_pred             CceEEEccCCCcchhHHHHHHhh
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQ  106 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~  106 (423)
                      +..++.||.|+|||..+...+-.
T Consensus        39 ~a~Lf~Gp~G~GKttlA~~lAk~   61 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSARILAKS   61 (620)
T ss_pred             ceEEEECCCCCChHHHHHHHHHH
Confidence            45799999999999876543333

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.30  E-value=0.13  Score=46.97  Aligned_cols=47  Identities=21%  Similarity=0.278  Sum_probs=28.9

Q ss_pred             CCcCCCCCHHHHHHHHhCCCCCC--ChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           47 GFRDFLLKPELLRAIVDSGFEHP--SEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        47 ~~~~~~l~~~~~~~l~~~~~~~~--~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      .|+...|+|.+.+.+......+-  ..+|.       --+|++..||+|+|||+.+
T Consensus       353 pl~~ViL~psLe~Rie~lA~aTaNTK~h~a-------pfRNilfyGPPGTGKTm~A  401 (630)
T KOG0742|consen  353 PLEGVILHPSLEKRIEDLAIATANTKKHQA-------PFRNILFYGPPGTGKTMFA  401 (630)
T ss_pred             CcCCeecCHHHHHHHHHHHHHhcccccccc-------hhhheeeeCCCCCCchHHH
Confidence            46677777777776664422110  11110       1257999999999999754

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=94.28  E-value=0.67  Score=41.07  Aligned_cols=33  Identities=18%  Similarity=0.240  Sum_probs=21.4

Q ss_pred             CChhhhhcccccc----cCC-ceEEEccCCCcchhHHH
Q 014486           69 PSEVQHECIPQAI----LGM-DVICQAKSGMGKTAVFV  101 (423)
Q Consensus        69 ~~~~Q~~~i~~~~----~~~-~~ii~~~tGsGKT~~~~  101 (423)
                      +++.+..++..+.    .+. .+++.||+|+|||...-
T Consensus        24 ~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        24 PSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            4445555554443    223 48899999999997643

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=94.23  E-value=0.082  Score=45.96  Aligned_cols=51  Identities=14%  Similarity=0.141  Sum_probs=34.6

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      |..++|.||+|+|||..++-.+.+.+..+.   ++++++- .+-..++.+.+..+
T Consensus        21 gs~~lI~G~pGsGKT~la~~~l~~~~~~ge---~~lyvs~-ee~~~~i~~~~~~~   71 (237)
T TIGR03877        21 RNVVLLSGGPGTGKSIFSQQFLWNGLQMGE---PGIYVAL-EEHPVQVRRNMAQF   71 (237)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHcCC---cEEEEEe-eCCHHHHHHHHHHh
Confidence            566999999999999876655555553322   6788874 34556666666654

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.

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=94.23  E-value=0.05  Score=49.78  Aligned_cols=41  Identities=20%  Similarity=0.287  Sum_probs=27.5

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      .+++++++||||||||.. +-+++..+....   +++.+=++.+|
T Consensus       161 ~~~nilI~G~tGSGKTTl-l~aLl~~i~~~~---rivtiEd~~El  201 (344)
T PRK13851        161 GRLTMLLCGPTGSGKTTM-SKTLISAIPPQE---RLITIEDTLEL  201 (344)
T ss_pred             cCCeEEEECCCCccHHHH-HHHHHcccCCCC---CEEEECCCccc
Confidence            478899999999999964 344444443322   55666666655

>PRK05973 replicative DNA helicase; Provisional

Probab=94.17  E-value=0.13  Score=44.23  Aligned_cols=65  Identities=15%  Similarity=0.160  Sum_probs=40.6

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .++|.. +..--+..|.-++|.|++|+|||...+..+.+.+..+.   +++|++-- +-..|+.+++..+
T Consensus        50 ~~~p~~-~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge---~vlyfSlE-es~~~i~~R~~s~  114 (237)
T PRK05973         50 ATTPAE-ELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGR---TGVFFTLE-YTEQDVRDRLRAL  114 (237)
T ss_pred             CCCCHH-HhcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCC---eEEEEEEe-CCHHHHHHHHHHc
Confidence            455632 34445556677999999999999876665555544322   66777532 3345666666555

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=94.13  E-value=0.17  Score=50.92  Aligned_cols=76  Identities=14%  Similarity=0.196  Sum_probs=63.1

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHh----CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc-cccCCCCCCCCEEE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVE----CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL-VGRGIDIERVNIVI  361 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~-~~~Gld~~~~~~vi  361 (423)
                      .+.++++.+++...|.+.++.+++    .|+++..++|+++..+|...++...+|+.+|+|+|.. +...+.+.++.+||
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            356899999999999988777664    3788999999999999999999999999999999964 44567777788776


Q ss_pred             E
Q 014486          362 N  362 (423)
Q Consensus       362 ~  362 (423)
                      .
T Consensus       363 I  363 (630)
T TIGR00643       363 I  363 (630)
T ss_pred             E
Confidence            4

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=94.10  E-value=0.1  Score=48.23  Aligned_cols=26  Identities=19%  Similarity=0.153  Sum_probs=18.5

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccC
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTE  109 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~  109 (423)
                      +..++++||||||||... ..++..+.
T Consensus       149 ~GlilI~G~TGSGKTT~l-~al~~~i~  174 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLA-ASIYQHCG  174 (372)
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHHHHH
Confidence            446899999999999753 44555443

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).

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

Probab=94.04  E-value=0.22  Score=50.82  Aligned_cols=71  Identities=20%  Similarity=0.237  Sum_probs=57.0

Q ss_pred             HHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCC-----CCeEE-EcCCCCHHHHHHHHHhhhcCCccEEEEcCc
Q 014486          277 RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECN-----FPSIC-IHSGMSQEERLTRYKGFKEGNKRILVATDL  347 (423)
Q Consensus       277 ~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~-----~~~~~-~~~~~~~~~r~~~~~~f~~~~~~ili~T~~  347 (423)
                      ..+..+.-...++++++.+|+...+.++++.|....     ..+.. ||+.++..+++.++++|.+|..+|||+|+.
T Consensus       114 g~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~  190 (1187)
T COG1110         114 GLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQ  190 (1187)
T ss_pred             HHHHHHHHHhcCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHH
Confidence            344444445556899999999999999988887652     33333 999999999999999999999999998864

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=93.97  E-value=0.18  Score=48.13  Aligned_cols=148  Identities=10%  Similarity=-0.006  Sum_probs=83.8

Q ss_pred             CCChhhhhccccccc------C----CceEEEccCCCcchhHHH-HHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAIL------G----MDVICQAKSGMGKTAVFV-LSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER  136 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~------~----~~~ii~~~tGsGKT~~~~-~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  136 (423)
                      .+-|+|+-++-.++-      +    +.++|..|-+-|||..+. +.....+.....+....|++|+.+-+.+....++.
T Consensus        61 ~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~~F~~ar~  140 (546)
T COG4626          61 SLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAANSFNPARD  140 (546)
T ss_pred             ccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhhhcCCcEEEEeccHHHHHHhhHHHHH
Confidence            567899988877772      1    348999999999996543 22222222234444889999999999999988888


Q ss_pred             HhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhc--CCCCCCCccEEEEcCcchhhccCCcHHHHHH
Q 014486          137 FSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARD--KDLSLKNVRHFILDECDKMLESLDMRRDVQE  214 (423)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~--~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~  214 (423)
                      +....+++....-            .......|...-.......+..  ...+-.+..+.|+||.|....   ....+..
T Consensus       141 mv~~~~~l~~~~~------------~q~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~---~~~~~~~  205 (546)
T COG4626         141 MVKRDDDLRDLCN------------VQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGK---QEDMYSE  205 (546)
T ss_pred             HHHhCcchhhhhc------------cccceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcC---HHHHHHH
Confidence            7765432211100            0000001111111112222222  223345677899999998754   1134444


Q ss_pred             HHHh--CCCCceEEEEec
Q 014486          215 IFKM--TPHDKQVMMFSA  230 (423)
Q Consensus       215 ~~~~--~~~~~~~v~~SA  230 (423)
                      +..-  ..++.+++..|.
T Consensus       206 ~~~g~~ar~~~l~~~ITT  223 (546)
T COG4626         206 AKGGLGARPEGLVVYITT  223 (546)
T ss_pred             HHhhhccCcCceEEEEec
Confidence            4332  244667777775

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.94  E-value=0.43  Score=46.50  Aligned_cols=57  Identities=23%  Similarity=0.254  Sum_probs=39.6

Q ss_pred             ccccCCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           41 VGIHSSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        41 ~~~~~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      .+....+|++.+=-+.+...|++.   ...+|-.+.+-.+   -.-+.+++.||+|+|||+.+
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            555667899998667776666643   4455555555553   23467999999999999864

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=93.93  E-value=1.1  Score=40.31  Aligned_cols=56  Identities=13%  Similarity=0.335  Sum_probs=41.5

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCc------eEEEEeccCCccHHHHHHHhc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK------QVMMFSATLSKEIRPVCKKFM  244 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~------~~v~~SAT~~~~~~~~~~~~~  244 (423)
                      .++++|++|=|-++-+..+.-..+.++.+...+..      -++.+=||...+....++.|.
T Consensus       220 r~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~llvlDAttGqnal~QAk~F~  281 (340)
T COG0552         220 RGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATTGQNALSQAKIFN  281 (340)
T ss_pred             cCCCEEEEeCcccccCchhHHHHHHHHHHHhccccCCCCceEEEEEEcccChhHHHHHHHHH
Confidence            45678999999999877778888888888776654      344558998877666655554

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=93.93  E-value=1.1  Score=41.55  Aligned_cols=110  Identities=13%  Similarity=0.164  Sum_probs=58.3

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL  162 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (423)
                      .+.+.+.|+.|.|||..  +-+.....+.+.+.+    ++.-+...++.+.+.++.            ++.         
T Consensus        62 ~~GlYl~G~vG~GKT~L--md~f~~~lp~~~k~R----~HFh~Fm~~vh~~l~~~~------------~~~---------  114 (362)
T PF03969_consen   62 PKGLYLWGPVGRGKTML--MDLFYDSLPIKRKRR----VHFHEFMLDVHSRLHQLR------------GQD---------  114 (362)
T ss_pred             CceEEEECCCCCchhHH--HHHHHHhCCcccccc----ccccHHHHHHHHHHHHHh------------CCC---------
Confidence            46799999999999974  333333332222112    244466666666666553            100         


Q ss_pred             hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhC-CCCceEEEEeccCCccH
Q 014486          163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMT-PHDKQVMMFSATLSKEI  236 (423)
Q Consensus       163 ~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-~~~~~~v~~SAT~~~~~  236 (423)
                           +-+    ..+.+.+      .....++.+||.|.-.  ..-...+.+++..+ ....-+|..|-++|.++
T Consensus       115 -----~~l----~~va~~l------~~~~~lLcfDEF~V~D--iaDAmil~rLf~~l~~~gvvlVaTSN~~P~~L  172 (362)
T PF03969_consen  115 -----DPL----PQVADEL------AKESRLLCFDEFQVTD--IADAMILKRLFEALFKRGVVLVATSNRPPEDL  172 (362)
T ss_pred             -----ccH----HHHHHHH------HhcCCEEEEeeeeccc--hhHHHHHHHHHHHHHHCCCEEEecCCCChHHH
Confidence                 100    0111111      1244589999999542  23344444444433 44666777777777654

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

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=93.92  E-value=0.17  Score=44.71  Aligned_cols=39  Identities=23%  Similarity=0.238  Sum_probs=27.0

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      .|.=+++.|.+|.|||..++-.+...+...+  ..+++++.
T Consensus        18 ~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~~--~~vly~Sl   56 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFALQIALNAALNGG--YPVLYFSL   56 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHHHHHHHHHHHTTS--SEEEEEES
T ss_pred             cCcEEEEEecccCCchHHHHHHHHHHHHhcC--CeEEEEcC
Confidence            3445899999999999876665555555432  27788874

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 ....

>PRK06904 replicative DNA helicase; Validated

Probab=93.90  E-value=0.42  Score=46.03  Aligned_cols=115  Identities=17%  Similarity=0.157  Sum_probs=55.9

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcC--cchHHHH-
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGG--VNIKIHK-  159 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~-  159 (423)
                      |.=++|.|.||.|||..++-.+...+...+ . .+++++. -.-..|+..++-....   ++....+..|  .+..++. 
T Consensus       221 G~LiiIaarPg~GKTafalnia~~~a~~~g-~-~Vl~fSl-EMs~~ql~~Rlla~~s---~v~~~~i~~g~~l~~~e~~~  294 (472)
T PRK06904        221 SDLIIVAARPSMGKTTFAMNLCENAAMASE-K-PVLVFSL-EMPAEQIMMRMLASLS---RVDQTKIRTGQNLDQQDWAK  294 (472)
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHhcC-C-eEEEEec-cCCHHHHHHHHHHhhC---CCCHHHhccCCCCCHHHHHH
Confidence            444889999999999755433333332222 1 4566543 3445555555443322   2222222222  2222221 


Q ss_pred             -----HHHhcCCCcEEE-----echHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          160 -----DLLKNECPQIVV-----GTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       160 -----~~~~~~~~~ilv-----~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                           ..+... +.+.|     .|+..+....+........+++||||-.+.+..
T Consensus       295 ~~~a~~~l~~~-~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~  348 (472)
T PRK06904        295 ISSTVGMFKQK-PNLYIDDSSGLTPTELRSRARRVYRENGGLSLIMVDYLQLMRA  348 (472)
T ss_pred             HHHHHHHHhcC-CCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEecHHhcCC
Confidence                 112122 34555     244555443322111123578999999998753

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=93.87  E-value=0.31  Score=47.95  Aligned_cols=19  Identities=26%  Similarity=0.258  Sum_probs=15.7

Q ss_pred             CceEEEccCCCcchhHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~  102 (423)
                      +..++.||.|+|||.++..
T Consensus        39 hayLf~Gp~G~GKTt~Ar~   57 (563)
T PRK06647         39 NAYIFSGPRGVGKTSSARA   57 (563)
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            3479999999999987654

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.87  E-value=0.15  Score=45.16  Aligned_cols=93  Identities=11%  Similarity=0.145  Sum_probs=46.6

Q ss_pred             CcCCCCCHHHHHHHHhCCCCCCChhhhhccccccc-CCceEEEccCCCcchhHHHHHHhhcc--CCCCCCeEE-EEEe--
Q 014486           48 FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQT--EPNPGQVTA-LVLC--  121 (423)
Q Consensus        48 ~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~-~~~~ii~~~tGsGKT~~~~~~~~~~~--~~~~~~~~~-lil~--  121 (423)
                      |+.+.+...+.+.|...-...+.-.+...=..+.. ++-+++.||+|+|||... -++.+.+  +.....+++ +|=.  
T Consensus       141 WEsLiyds~lK~~ll~Ya~s~l~fsek~vntnlIt~NRliLlhGPPGTGKTSLC-KaLaQkLSIR~~~~y~~~~liEins  219 (423)
T KOG0744|consen  141 WESLIYDSNLKERLLSYAASALLFSEKKVNTNLITWNRLILLHGPPGTGKTSLC-KALAQKLSIRTNDRYYKGQLIEINS  219 (423)
T ss_pred             HHHHhhcccHHHHHHHHHHHHHHHHhcCCCCceeeeeeEEEEeCCCCCChhHHH-HHHHHhheeeecCccccceEEEEeh
Confidence            55555554444444432222222233333344444 445899999999999632 2233322  122222233 3322  


Q ss_pred             ---------cChHHHHHHHHHHHHHhccC
Q 014486          122 ---------HTRELAYQICHEFERFSTYL  141 (423)
Q Consensus       122 ---------P~~~L~~q~~~~~~~~~~~~  141 (423)
                               -+.-|+.++.+.++++....
T Consensus       220 hsLFSKWFsESgKlV~kmF~kI~ELv~d~  248 (423)
T KOG0744|consen  220 HSLFSKWFSESGKLVAKMFQKIQELVEDR  248 (423)
T ss_pred             hHHHHHHHhhhhhHHHHHHHHHHHHHhCC
Confidence                     34456677777777776653

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.83  E-value=0.15  Score=46.34  Aligned_cols=16  Identities=31%  Similarity=0.453  Sum_probs=14.3

Q ss_pred             CceEEEccCCCcchhH
Q 014486           84 MDVICQAKSGMGKTAV   99 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~   99 (423)
                      +.+++.||+|+|||+.
T Consensus       246 kgvLm~GPPGTGKTlL  261 (491)
T KOG0738|consen  246 KGVLMVGPPGTGKTLL  261 (491)
T ss_pred             ceeeeeCCCCCcHHHH
Confidence            5799999999999964

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

Probab=93.81  E-value=0.89  Score=43.61  Aligned_cols=101  Identities=19%  Similarity=0.163  Sum_probs=74.9

Q ss_pred             ccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchH---HHHHHHhcCC
Q 014486           90 AKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIK---IHKDLLKNEC  166 (423)
Q Consensus        90 ~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~  166 (423)
                      .-.++||+..-++++.+....+ -.|.+||.+-+.+-|.|.+.++.    .++++++.+++|.....   +....+..+.
T Consensus       364 elvF~gse~~K~lA~rq~v~~g-~~PP~lIfVQs~eRak~L~~~L~----~~~~i~v~vIh~e~~~~qrde~~~~FR~g~  438 (593)
T KOG0344|consen  364 ELVFCGSEKGKLLALRQLVASG-FKPPVLIFVQSKERAKQLFEELE----IYDNINVDVIHGERSQKQRDETMERFRIGK  438 (593)
T ss_pred             hheeeecchhHHHHHHHHHhcc-CCCCeEEEEecHHHHHHHHHHhh----hccCcceeeEecccchhHHHHHHHHHhccC
Confidence            3357788877777666655544 44578999999999999988886    33689999999986543   3345667788


Q ss_pred             CcEEEechHHHHHHHhcCCCCCCCccEEEEcCcch
Q 014486          167 PQIVVGTPGRILALARDKDLSLKNVRHFILDECDK  201 (423)
Q Consensus       167 ~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~  201 (423)
                      ..++|||     +++.+ ..++.++++||-+++-.
T Consensus       439 IwvLicT-----dll~R-GiDf~gvn~VInyD~p~  467 (593)
T KOG0344|consen  439 IWVLICT-----DLLAR-GIDFKGVNLVINYDFPQ  467 (593)
T ss_pred             eeEEEeh-----hhhhc-cccccCcceEEecCCCc
Confidence            8999999     33343 47899999999987763

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=93.80  E-value=0.24  Score=46.25  Aligned_cols=17  Identities=47%  Similarity=0.579  Sum_probs=15.0

Q ss_pred             CceEEEccCCCcchhHH
Q 014486           84 MDVICQAKSGMGKTAVF  100 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~  100 (423)
                      .+++|.||+|+|||.+.
T Consensus        41 ~~i~I~G~~GtGKT~l~   57 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT   57 (365)
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            56999999999999764

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.

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.80  E-value=0.4  Score=47.71  Aligned_cols=21  Identities=19%  Similarity=0.281  Sum_probs=16.4

Q ss_pred             CceEEEccCCCcchhHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLST  104 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~  104 (423)
                      +..|+.||.|+|||..+...+
T Consensus        39 ~a~Lf~Gp~G~GKTtlA~~lA   59 (585)
T PRK14950         39 HAYLFTGPRGVGKTSTARILA   59 (585)
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            346999999999998765433

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=93.79  E-value=0.38  Score=50.28  Aligned_cols=76  Identities=20%  Similarity=0.215  Sum_probs=63.4

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhC----CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcC-ccccCCCCCCCCEEE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVEC----NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD-LVGRGIDIERVNIVI  361 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~-~~~~Gld~~~~~~vi  361 (423)
                      .+.+++|.+|+...|.+.++.+++.    ++.+..+++..+..++..+++...+|+.+|+|+|. .+...+.+.++.++|
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            4568999999999999998887753    56777899999999999999999999999999995 455567788888877


Q ss_pred             E
Q 014486          362 N  362 (423)
Q Consensus       362 ~  362 (423)
                      .
T Consensus       579 I  579 (926)
T TIGR00580       579 I  579 (926)
T ss_pred             e
Confidence            4

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.

>PRK07004 replicative DNA helicase; Provisional

Probab=93.76  E-value=0.35  Score=46.47  Aligned_cols=115  Identities=15%  Similarity=0.068  Sum_probs=53.4

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEE-EcCcchHHHH-
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVF-YGGVNIKIHK-  159 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~-  159 (423)
                      .|.-++|.|.+|+|||..++--+.......+.  .+++++. -.-..|+..++-....   ++....+ .|..+..++. 
T Consensus       212 ~g~liviaarpg~GKT~~al~ia~~~a~~~~~--~v~~fSl-EM~~~ql~~R~la~~~---~v~~~~i~~g~l~~~e~~~  285 (460)
T PRK07004        212 GGELIIVAGRPSMGKTAFSMNIGEYVAVEYGL--PVAVFSM-EMPGTQLAMRMLGSVG---RLDQHRMRTGRLTDEDWPK  285 (460)
T ss_pred             CCceEEEEeCCCCCccHHHHHHHHHHHHHcCC--eEEEEeC-CCCHHHHHHHHHHhhc---CCCHHHHhcCCCCHHHHHH
Confidence            34558999999999997655433333322221  4555542 2333444443322111   2222211 1222222221 


Q ss_pred             -----HHHhcCCCcEEEe-----chHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          160 -----DLLKNECPQIVVG-----TPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       160 -----~~~~~~~~~ilv~-----T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                           ..+.+  ..+.|.     |+..+....++.......+++||||=.+.+..
T Consensus       286 ~~~a~~~l~~--~~l~I~d~~~~~~~~i~~~~r~l~~~~~~~~lviIDYLql~~~  338 (460)
T PRK07004        286 LTHAVQKMSE--AQLFIDETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMSG  338 (460)
T ss_pred             HHHHHHHHhc--CCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEChhhhccC
Confidence                 22222  244442     34444333222111123578999999998863

>PRK05748 replicative DNA helicase; Provisional

Probab=93.63  E-value=0.5  Score=45.43  Aligned_cols=113  Identities=13%  Similarity=0.073  Sum_probs=54.2

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEE-EcCcchHHHH--
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVF-YGGVNIKIHK--  159 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~--  159 (423)
                      |.-++|.|+||.|||...+-.+.......+.  .+++++. -.-..|+..++-....   ++....+ .|.....++.  
T Consensus       203 G~livIaarpg~GKT~~al~ia~~~a~~~g~--~v~~fSl-Ems~~~l~~R~l~~~~---~v~~~~i~~~~l~~~e~~~~  276 (448)
T PRK05748        203 NDLIIVAARPSVGKTAFALNIAQNVATKTDK--NVAIFSL-EMGAESLVMRMLCAEG---NIDAQRLRTGQLTDDDWPKL  276 (448)
T ss_pred             CceEEEEeCCCCCchHHHHHHHHHHHHhCCC--eEEEEeC-CCCHHHHHHHHHHHhc---CCCHHHhhcCCCCHHHHHHH
Confidence            4558999999999997655444443322221  4555542 3344555554432211   2222111 1222222211  


Q ss_pred             ----HHHhcCCCcEEEe-----chHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          160 ----DLLKNECPQIVVG-----TPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       160 ----~~~~~~~~~ilv~-----T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                          ..+.+.  .+.|.     |++.+...++.......++++||||=.|.+.
T Consensus       277 ~~a~~~l~~~--~~~i~d~~~~ti~~i~~~~r~~~~~~~~~~~vvIDyL~li~  327 (448)
T PRK05748        277 TIAMGSLSDA--PIYIDDTPGIKVTEIRARCRRLAQEHGGLGLILIDYLQLIQ  327 (448)
T ss_pred             HHHHHHHhcC--CEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccchhcC
Confidence                122222  34442     3444444332211111257899999999885

>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=93.57  E-value=0.15  Score=43.92  Aligned_cols=41  Identities=10%  Similarity=0.224  Sum_probs=23.1

Q ss_pred             cEEEEcCcchhh-cc---CCcHHHHHHHHHhCCC-CceEEEEeccC
Q 014486          192 RHFILDECDKML-ES---LDMRRDVQEIFKMTPH-DKQVMMFSATL  232 (423)
Q Consensus       192 ~~vVvDE~h~~~-~~---~~~~~~~~~~~~~~~~-~~~~v~~SAT~  232 (423)
                      -+||+||+|.+. ..   ..+...+..++..... ....+.++++-
T Consensus       120 ~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~  165 (234)
T PF01637_consen  120 VIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIVITGSS  165 (234)
T ss_dssp             EEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEEEEESS
T ss_pred             EEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEEEECCc
Confidence            579999999998 21   2344556666665322 23334455553

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK10436 hypothetical protein; Provisional

Probab=93.56  E-value=0.087  Score=50.29  Aligned_cols=39  Identities=26%  Similarity=0.287  Sum_probs=26.1

Q ss_pred             Chhhhhccccccc--CCceEEEccCCCcchhHHHHHHhhccC
Q 014486           70 SEVQHECIPQAIL--GMDVICQAKSGMGKTAVFVLSTLQQTE  109 (423)
Q Consensus        70 ~~~Q~~~i~~~~~--~~~~ii~~~tGsGKT~~~~~~~~~~~~  109 (423)
                      .+.|.+.+..++.  +.-++++||||||||.+. ..++..+.
T Consensus       203 ~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~  243 (462)
T PRK10436        203 TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLN  243 (462)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhC
Confidence            3556666655554  344899999999999764 44555544

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=93.54  E-value=0.6  Score=43.23  Aligned_cols=30  Identities=20%  Similarity=0.207  Sum_probs=21.8

Q ss_pred             Chhhhhccccccc---CCceEEEccCCCcchhH
Q 014486           70 SEVQHECIPQAIL---GMDVICQAKSGMGKTAV   99 (423)
Q Consensus        70 ~~~Q~~~i~~~~~---~~~~ii~~~tGsGKT~~   99 (423)
                      .+.-.++|+.+.-   |+..+|.||.|+|||..
T Consensus       153 ~~~~~rvID~l~PIGkGQR~lIvgppGvGKTTL  185 (416)
T PRK09376        153 EDLSTRIIDLIAPIGKGQRGLIVAPPKAGKTVL  185 (416)
T ss_pred             cccceeeeeeecccccCceEEEeCCCCCChhHH
Confidence            3444555555553   67899999999999964

>PRK08006 replicative DNA helicase; Provisional

Probab=93.51  E-value=0.68  Score=44.59  Aligned_cols=114  Identities=15%  Similarity=0.115  Sum_probs=54.5

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEE-cCcchHHHHH-
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFY-GGVNIKIHKD-  160 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~-  160 (423)
                      |.-++|.|.+|.|||..++-.+.......+ . .+++++. -.-..|+..++-....   ++....+. |..+..++.+ 
T Consensus       224 G~LiiIaarPgmGKTafalnia~~~a~~~g-~-~V~~fSl-EM~~~ql~~Rlla~~~---~v~~~~i~~~~l~~~e~~~~  297 (471)
T PRK08006        224 SDLIIVAARPSMGKTTFAMNLCENAAMLQD-K-PVLIFSL-EMPGEQIMMRMLASLS---RVDQTRIRTGQLDDEDWARI  297 (471)
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHhcC-C-eEEEEec-cCCHHHHHHHHHHHhc---CCCHHHhhcCCCCHHHHHHH
Confidence            445899999999999765543433332222 1 4555543 2334455544433221   22222222 2222222221 


Q ss_pred             -----HHhcCCCcEEEe-----chHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          161 -----LLKNECPQIVVG-----TPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       161 -----~~~~~~~~ilv~-----T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                           .+... ..+.|-     |+..+....+........+++||||=.|.+.
T Consensus       298 ~~a~~~~~~~-~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~  349 (471)
T PRK08006        298 SGTMGILLEK-RNMYIDDSSGLTPTEVRSRARRIFREHGGLSLIMIDYLQLMR  349 (471)
T ss_pred             HHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHHcc
Confidence                 12121 234442     3444443332211112357899999999875

>PRK04841 transcriptional regulator MalT; Provisional

Probab=93.48  E-value=0.62  Score=49.37  Aligned_cols=43  Identities=9%  Similarity=0.290  Sum_probs=33.7

Q ss_pred             ccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCc
Q 014486          191 VRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSK  234 (423)
Q Consensus       191 ~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~  234 (423)
                      --+||+|++|.+.+ ......+..+....+....+|+.|-+.|+
T Consensus       122 ~~~lvlDD~h~~~~-~~~~~~l~~l~~~~~~~~~lv~~sR~~~~  164 (903)
T PRK04841        122 PLYLVIDDYHLITN-PEIHEAMRFFLRHQPENLTLVVLSRNLPP  164 (903)
T ss_pred             CEEEEEeCcCcCCC-hHHHHHHHHHHHhCCCCeEEEEEeCCCCC
Confidence            34799999998864 45566788888888888888888888543

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=93.42  E-value=0.12  Score=44.87  Aligned_cols=14  Identities=21%  Similarity=0.608  Sum_probs=12.2

Q ss_pred             eEEEccCCCcchhH
Q 014486           86 VICQAKSGMGKTAV   99 (423)
Q Consensus        86 ~ii~~~tGsGKT~~   99 (423)
                      ++|.|+.|||||..
T Consensus         1 ~vv~G~pGsGKSt~   14 (234)
T PF01443_consen    1 IVVHGVPGSGKSTL   14 (234)
T ss_pred             CEEEcCCCCCHHHH
Confidence            47899999999974

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

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=93.36  E-value=0.5  Score=43.87  Aligned_cols=18  Identities=22%  Similarity=0.324  Sum_probs=14.8

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      +..++.||.|+|||..+.
T Consensus        37 ~~~Ll~G~~G~GKt~~a~   54 (355)
T TIGR02397        37 HAYLFSGPRGTGKTSIAR   54 (355)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            457999999999997653

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.

>PRK08506 replicative DNA helicase; Provisional

Probab=93.35  E-value=0.66  Score=44.83  Aligned_cols=113  Identities=18%  Similarity=0.150  Sum_probs=55.6

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEE-cCcchHHHH--
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFY-GGVNIKIHK--  159 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--  159 (423)
                      |.-+++.|.||.|||..++-.+..... .+  ..+++++. -.-..|+..++-....   ++....+. |..+...+.  
T Consensus       192 G~LivIaarpg~GKT~fal~ia~~~~~-~g--~~V~~fSl-EMs~~ql~~Rlla~~s---~v~~~~i~~~~l~~~e~~~~  264 (472)
T PRK08506        192 GDLIIIAARPSMGKTTLCLNMALKALN-QD--KGVAFFSL-EMPAEQLMLRMLSAKT---SIPLQNLRTGDLDDDEWERL  264 (472)
T ss_pred             CceEEEEcCCCCChHHHHHHHHHHHHh-cC--CcEEEEeC-cCCHHHHHHHHHHHhc---CCCHHHHhcCCCCHHHHHHH
Confidence            445899999999999766554444332 22  25566543 3445555554433222   22221111 222222221  


Q ss_pred             ----HHHhcCCCcEEEe-----chHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          160 ----DLLKNECPQIVVG-----TPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       160 ----~~~~~~~~~ilv~-----T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                          ..+.+.  .+.|.     |+..+...++.......++++||||=.+.+..
T Consensus       265 ~~a~~~l~~~--~l~I~d~~~~ti~~I~~~~r~l~~~~~~~~lvvIDyLql~~~  316 (472)
T PRK08506        265 SDACDELSKK--KLFVYDSGYVNIHQVRAQLRKLKSQHPEIGLAVIDYLQLMSG  316 (472)
T ss_pred             HHHHHHHHcC--CeEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEcChhhccC
Confidence                122232  34332     44455443332111123578999999998763

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=93.33  E-value=0.097  Score=47.79  Aligned_cols=41  Identities=17%  Similarity=0.259  Sum_probs=26.4

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      .+++++++|+||||||.. +-+++.......   +++.+=.+.++
T Consensus       159 ~~~nili~G~tgSGKTTl-l~aL~~~ip~~~---ri~tiEd~~El  199 (332)
T PRK13900        159 SKKNIIISGGTSTGKTTF-TNAALREIPAIE---RLITVEDAREI  199 (332)
T ss_pred             cCCcEEEECCCCCCHHHH-HHHHHhhCCCCC---eEEEecCCCcc
Confidence            478899999999999964 344444443322   55555444444

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=93.33  E-value=0.068  Score=46.83  Aligned_cols=49  Identities=14%  Similarity=0.232  Sum_probs=33.2

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEF  134 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~  134 (423)
                      ++.++++.||+|+|||..+.....+.. ..+   ..++++++.+|+.++...+
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g---~sv~f~~~~el~~~Lk~~~  152 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELL-KAG---ISVLFITAPDLLSKLKAAF  152 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHH-HcC---CeEEEEEHHHHHHHHHHHH
Confidence            678899999999999987544333333 322   4466677778877765433

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=93.32  E-value=0.05  Score=52.81  Aligned_cols=38  Identities=21%  Similarity=0.388  Sum_probs=30.3

Q ss_pred             CCChhhhhccccccc----CCceEEEccCCCcchhHHHHHHh
Q 014486           68 HPSEVQHECIPQAIL----GMDVICQAKSGMGKTAVFVLSTL  105 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~~~~ii~~~tGsGKT~~~~~~~~  105 (423)
                      +|+.+|.+.+..+++    |+-.|...|||+|||+..+=.++
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaal   56 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAAL   56 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHH
Confidence            688899887776664    78899999999999987544444

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.32  E-value=0.55  Score=45.40  Aligned_cols=18  Identities=28%  Similarity=0.405  Sum_probs=14.6

Q ss_pred             ceEEEccCCCcchhHHHH
Q 014486           85 DVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~  102 (423)
                      -.++.||.|+|||.++.+
T Consensus        40 ayLf~Gp~G~GKTtlAr~   57 (486)
T PRK14953         40 AYIFAGPRGTGKTTIARI   57 (486)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            367899999999987654

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=93.31  E-value=0.17  Score=46.74  Aligned_cols=27  Identities=15%  Similarity=0.250  Sum_probs=19.4

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccC
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTE  109 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~  109 (423)
                      .+..++++||||||||... ..++..+.
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i~  159 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIRELA  159 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            3566999999999999753 44555443

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.

>TIGR00665 DnaB replicative DNA helicase

Probab=93.28  E-value=0.64  Score=44.55  Aligned_cols=51  Identities=18%  Similarity=0.076  Sum_probs=29.1

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER  136 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  136 (423)
                      |.-++|.|++|+|||...+-.+.......+.  .+++++. -.-..|+..++..
T Consensus       195 G~l~vi~g~pg~GKT~~~l~~a~~~a~~~g~--~vl~~Sl-Em~~~~i~~R~~~  245 (434)
T TIGR00665       195 SDLIILAARPSMGKTAFALNIAENAAIKEGK--PVAFFSL-EMSAEQLAMRMLS  245 (434)
T ss_pred             CeEEEEEeCCCCChHHHHHHHHHHHHHhCCC--eEEEEeC-cCCHHHHHHHHHH
Confidence            4458999999999997655444443332221  5666653 2334444444433

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.

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=93.28  E-value=1.3  Score=36.73  Aligned_cols=145  Identities=14%  Similarity=0.097  Sum_probs=74.5

Q ss_pred             ccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHH
Q 014486           81 ILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKD  160 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (423)
                      .....+++..++|.|||.+++-.++..+..+.   +++++.=.+--..  ..+...+ ...+++.......+..+...  
T Consensus        20 ~~~g~v~v~~g~GkGKtt~a~g~a~ra~g~G~---~V~ivQFlKg~~~--~GE~~~l-~~l~~v~~~~~g~~~~~~~~--   91 (191)
T PRK05986         20 EEKGLLIVHTGNGKGKSTAAFGMALRAVGHGK---KVGVVQFIKGAWS--TGERNLL-EFGGGVEFHVMGTGFTWETQ--   91 (191)
T ss_pred             ccCCeEEEECCCCCChHHHHHHHHHHHHHCCC---eEEEEEEecCCCc--cCHHHHH-hcCCCcEEEECCCCCcccCC--
Confidence            34567999999999999988776666665543   6666642111000  0111111 11223333322221111000  


Q ss_pred             HHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCC--cHHHHHHHHHhCCCCceEEEEeccCCccHHH
Q 014486          161 LLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLD--MRRDVQEIFKMTPHDKQVMMFSATLSKEIRP  238 (423)
Q Consensus       161 ~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~--~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~  238 (423)
                          . ..--.......+..... .+.-..+++||+||+=...+ .+  ....+..+++..|...-+|+..-.+|+++..
T Consensus        92 ----~-~~e~~~~~~~~~~~a~~-~l~~~~ydlvVLDEi~~Al~-~gli~~eevi~~L~~rp~~~evVlTGR~~p~~Lie  164 (191)
T PRK05986         92 ----D-RERDIAAAREGWEEAKR-MLADESYDLVVLDELTYALK-YGYLDVEEVLEALNARPGMQHVVITGRGAPRELIE  164 (191)
T ss_pred             ----C-cHHHHHHHHHHHHHHHH-HHhCCCCCEEEEehhhHHHH-CCCccHHHHHHHHHcCCCCCEEEEECCCCCHHHHH
Confidence                0 00000001111111111 11235678999999987766 33  3456777777777777777777777777665


Q ss_pred             HH
Q 014486          239 VC  240 (423)
Q Consensus       239 ~~  240 (423)
                      .+
T Consensus       165 ~A  166 (191)
T PRK05986        165 AA  166 (191)
T ss_pred             hC
Confidence            53

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=93.27  E-value=0.22  Score=43.92  Aligned_cols=37  Identities=14%  Similarity=0.055  Sum_probs=26.3

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEe
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLC  121 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  121 (423)
                      .|.-++|.|++|+|||...+..+.+.+..+.   ++++++
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge---~vlyis   71 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQASRGN---PVLFVT   71 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhCCC---cEEEEE
Confidence            3556899999999999876665555444322   678877

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK08840 replicative DNA helicase; Provisional

Probab=93.25  E-value=0.71  Score=44.36  Aligned_cols=54  Identities=17%  Similarity=0.071  Sum_probs=29.6

Q ss_pred             ccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHH
Q 014486           79 QAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFE  135 (423)
Q Consensus        79 ~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  135 (423)
                      -+..|.-+++.|.||.|||..++-.+.......+ . .+++++.- .-..|+..++-
T Consensus       213 G~~~g~LiviaarPg~GKTafalnia~~~a~~~~-~-~v~~fSlE-Ms~~ql~~Rll  266 (464)
T PRK08840        213 GLQGSDLIIVAARPSMGKTTFAMNLCENAAMDQD-K-PVLIFSLE-MPAEQLMMRML  266 (464)
T ss_pred             CCCCCceEEEEeCCCCchHHHHHHHHHHHHHhCC-C-eEEEEecc-CCHHHHHHHHH
Confidence            3334455899999999999765443333332222 1 45565532 33445554443

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=93.18  E-value=0.053  Score=47.80  Aligned_cols=20  Identities=20%  Similarity=0.336  Sum_probs=16.2

Q ss_pred             ccCCceEEEccCCCcchhHH
Q 014486           81 ILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ++..|+++.||||||||+.+
T Consensus        95 L~KSNILLiGPTGsGKTlLA  114 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLLA  114 (408)
T ss_pred             eeeccEEEECCCCCcHHHHH
Confidence            34467999999999999754

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=93.18  E-value=0.15  Score=42.50  Aligned_cols=32  Identities=22%  Similarity=0.289  Sum_probs=24.0

Q ss_pred             CChhhhhccccccc-CCceEEEccCCCcchhHH
Q 014486           69 PSEVQHECIPQAIL-GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        69 ~~~~Q~~~i~~~~~-~~~~ii~~~tGsGKT~~~  100 (423)
                      +.+.|...+..... +..+++.||||||||...
T Consensus        10 ~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130          10 FSPLQAAYLWLAVEARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            45666666655554 677999999999999753

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.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=93.15  E-value=0.58  Score=47.07  Aligned_cols=39  Identities=10%  Similarity=0.255  Sum_probs=23.6

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ...+++|+||||.+..  .....+.+.+..-+....+|+++
T Consensus       117 g~~KV~IIDEa~~LT~--~A~NALLKtLEEPP~~tifILaT  155 (725)
T PRK07133        117 SKYKIYIIDEVHMLSK--SAFNALLKTLEEPPKHVIFILAT  155 (725)
T ss_pred             CCCEEEEEEChhhCCH--HHHHHHHHHhhcCCCceEEEEEc
Confidence            5678999999998864  23334444445444444444444

>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=93.12  E-value=1.8  Score=40.34  Aligned_cols=42  Identities=19%  Similarity=0.201  Sum_probs=25.0

Q ss_pred             EEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHH
Q 014486           87 ICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQ  129 (423)
Q Consensus        87 ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  129 (423)
                      ++.++.|+|||......++..+...+....++++ |+..-+..
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~-~~~~~~~~   42 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIA-STYRQARD   42 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEE-ESSHHHHH
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEe-cCHHHHHH
Confidence            5778999999998877777766555543355555 55544444

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.

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=93.12  E-value=1.4  Score=44.59  Aligned_cols=71  Identities=20%  Similarity=0.277  Sum_probs=50.0

Q ss_pred             CCChhhhhccccccc----CCceEEEccCCCcchhHHHHHHhhc---cC-----------C--------C----------
Q 014486           68 HPSEVQHECIPQAIL----GMDVICQAKSGMGKTAVFVLSTLQQ---TE-----------P--------N----------  111 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~~~~ii~~~tGsGKT~~~~~~~~~~---~~-----------~--------~----------  111 (423)
                      +|++.|..-+..++.    ..++++..|||+|||++.+-..++.   +.           .        .          
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~s~e~  100 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEKSEEA  100 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCchhhh
Confidence            678889877766664    5779999999999998765544431   11           0        0          


Q ss_pred             --C-----CCeEEEEEecChHHHHHHHHHHHHHh
Q 014486          112 --P-----GQVTALVLCHTRELAYQICHEFERFS  138 (423)
Q Consensus       112 --~-----~~~~~lil~P~~~L~~q~~~~~~~~~  138 (423)
                        +     +.|++.|-+-|..-..|+.+++++..
T Consensus       101 ~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~  134 (945)
T KOG1132|consen  101 GEPIACYTGIPKIYYASRTHSQLTQVVRELRRTG  134 (945)
T ss_pred             cCccccccCCceEEEecchHHHHHHHHHHHhhcC
Confidence              0     23677788888888888888887753

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=93.11  E-value=0.11  Score=48.82  Aligned_cols=47  Identities=21%  Similarity=0.116  Sum_probs=35.4

Q ss_pred             ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHH
Q 014486           85 DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER  136 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  136 (423)
                      ++++.||||+|||..+++|-+....     ..++|+=|--++........+.
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~~-----~s~vv~D~Kge~~~~t~~~r~~   47 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTWP-----GSVVVLDPKGENFELTSEHRRA   47 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcCC-----CCEEEEccchhHHHHHHHHHHH
Confidence            4789999999999998877666432     2678888888888776655444

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.

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=92.91  E-value=0.18  Score=51.11  Aligned_cols=70  Identities=16%  Similarity=0.147  Sum_probs=54.5

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC-CCeEEEEEecChHHHHHHHHHHHHHhc
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP-GQVTALVLCHTRELAYQICHEFERFST  139 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~L~~q~~~~~~~~~~  139 (423)
                      .+++-|++++.+.  ...++|.+..|||||.+..--+.......+ .+..++.++=|+-.|.++.+++.++..
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            5789999998766  567888899999999987666666555432 223688888888889999999988875

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=92.88  E-value=0.79  Score=47.06  Aligned_cols=18  Identities=28%  Similarity=0.422  Sum_probs=15.4

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      ..+.++.||+|+|||..+
T Consensus       203 ~~n~lL~G~pG~GKT~l~  220 (731)
T TIGR02639       203 KNNPLLVGEPGVGKTAIA  220 (731)
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            357999999999999764

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=92.78  E-value=0.3  Score=44.72  Aligned_cols=42  Identities=12%  Similarity=0.309  Sum_probs=28.9

Q ss_pred             CCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      ....+++||||+|.+..  .....+.+.++.-+....+|++|..
T Consensus       108 ~~~~kvviI~~a~~~~~--~a~NaLLK~LEEPp~~~~~Il~t~~  149 (329)
T PRK08058        108 ESNKKVYIIEHADKMTA--SAANSLLKFLEEPSGGTTAILLTEN  149 (329)
T ss_pred             ccCceEEEeehHhhhCH--HHHHHHHHHhcCCCCCceEEEEeCC
Confidence            35678999999998864  4455566666666666666665543

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=92.75  E-value=0.099  Score=50.29  Aligned_cols=61  Identities=16%  Similarity=0.205  Sum_probs=41.1

Q ss_pred             cCCcccccCCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           37 KKGYVGIHSSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        37 ~~~~~~~~~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ..+|..++..+|++.+--..+...|+-.   ..++|-.|++-.+..   -..++++||+|+|||+.+
T Consensus       499 REGF~tVPdVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~~---PsGvLL~GPPGCGKTLlA  562 (802)
T KOG0733|consen  499 REGFATVPDVTWDDIGALEEVRLELNMAILAPIKRPDLFKALGIDA---PSGVLLCGPPGCGKTLLA  562 (802)
T ss_pred             cccceecCCCChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCCC---CCceEEeCCCCccHHHHH
Confidence            4467777778899998777776666543   344444444444322   456999999999999743

>PRK09087 hypothetical protein; Validated

Probab=92.63  E-value=0.45  Score=40.90  Aligned_cols=18  Identities=28%  Similarity=0.279  Sum_probs=14.6

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      +..+++.||+|+|||...
T Consensus        44 ~~~l~l~G~~GsGKThLl   61 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLA   61 (226)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            344899999999999743

>PRK11823 DNA repair protein RadA; Provisional

Probab=92.62  E-value=0.64  Score=44.51  Aligned_cols=51  Identities=24%  Similarity=0.287  Sum_probs=32.9

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      |.-+++.|++|+|||...+..+......   +.+++|+.-. +-..|+..++.++
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~---g~~vlYvs~E-es~~qi~~ra~rl  130 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAAA---GGKVLYVSGE-ESASQIKLRAERL  130 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEcc-ccHHHHHHHHHHc
Confidence            3458999999999998655544443322   2277888753 4456666666554

>PRK10689 transcription-repair coupling factor; Provisional

Probab=92.53  E-value=0.48  Score=50.78  Aligned_cols=76  Identities=17%  Similarity=0.182  Sum_probs=61.8

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhC----CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcC-ccccCCCCCCCCEEE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVEC----NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD-LVGRGIDIERVNIVI  361 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~-~~~~Gld~~~~~~vi  361 (423)
                      .+.+++|.+++...|.++++.+++.    ++.+..+++..+..++..+++...+|..+|+|+|. .+...+.+.++.++|
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            4578999999999999998888753    45677789999999999999988899999999995 344456677777766


Q ss_pred             E
Q 014486          362 N  362 (423)
Q Consensus       362 ~  362 (423)
                      .
T Consensus       728 I  728 (1147)
T PRK10689        728 V  728 (1147)
T ss_pred             E
Confidence            3

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.51  E-value=1.3  Score=41.40  Aligned_cols=46  Identities=13%  Similarity=0.359  Sum_probs=26.9

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHH
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~  102 (423)
                      +.+|+++.-.+.+.+.+...       ++..-+     .+..++.||.|+|||..+..
T Consensus        13 P~~~~~iig~~~~~~~l~~~-------i~~~~~-----~~~~L~~G~~G~GKt~~a~~   58 (367)
T PRK14970         13 PQTFDDVVGQSHITNTLLNA-------IENNHL-----AQALLFCGPRGVGKTTCARI   58 (367)
T ss_pred             CCcHHhcCCcHHHHHHHHHH-------HHcCCC-----CeEEEEECCCCCCHHHHHHH
Confidence            44566666565555544432       111000     14688999999999976543

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=92.51  E-value=0.68  Score=44.39  Aligned_cols=39  Identities=10%  Similarity=0.310  Sum_probs=24.2

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ...++||+||+|.+..  .....+.+.+..-+....+|+.+
T Consensus       120 ~~~kvvIIdead~lt~--~~~n~LLk~lEep~~~~~~Il~t  158 (451)
T PRK06305        120 SRYKIYIIDEVHMLTK--EAFNSLLKTLEEPPQHVKFFLAT  158 (451)
T ss_pred             CCCEEEEEecHHhhCH--HHHHHHHHHhhcCCCCceEEEEe
Confidence            4678999999998864  22334455555544455555544

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=92.44  E-value=0.19  Score=48.68  Aligned_cols=49  Identities=24%  Similarity=0.287  Sum_probs=37.1

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .++++.||||||||..+++|.+....   +  .++|.=|-.+|........++.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~~~---~--s~iV~D~KgEl~~~t~~~r~~~   93 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLNYP---G--SMIVTDPKGELYEKTAGYRKKR   93 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHhcc---C--CEEEEECCCcHHHHHHHHHHHC
Confidence            46999999999999999888775422   1  5677778888887776655554

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

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=92.41  E-value=1.2  Score=45.96  Aligned_cols=54  Identities=17%  Similarity=0.166  Sum_probs=32.3

Q ss_pred             cCCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ....|++.+-.+.+.+.|...   .+..+..++...   +...+.+++.||+|+|||+.+
T Consensus       448 ~~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g---~~~~~giLL~GppGtGKT~la  504 (733)
T TIGR01243       448 PNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMG---IRPPKGVLLFGPPGTGKTLLA  504 (733)
T ss_pred             cccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcC---CCCCceEEEECCCCCCHHHHH
Confidence            345677777767776666553   222222222221   223456999999999999754

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.

>PRK04328 hypothetical protein; Provisional

Probab=92.41  E-value=0.23  Score=43.43  Aligned_cols=51  Identities=14%  Similarity=0.141  Sum_probs=32.8

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      |..+++.|++|+|||...+..+.+.+..+.   ++++++ +.+-..++.+.++.+
T Consensus        23 gs~ili~G~pGsGKT~l~~~fl~~~~~~ge---~~lyis-~ee~~~~i~~~~~~~   73 (249)
T PRK04328         23 RNVVLLSGGPGTGKSIFSQQFLWNGLQMGE---PGVYVA-LEEHPVQVRRNMRQF   73 (249)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhcCC---cEEEEE-eeCCHHHHHHHHHHc
Confidence            556899999999999766555555444332   667776 333444555555555

>TIGR00767 rho transcription termination factor Rho

Probab=92.33  E-value=0.49  Score=43.96  Aligned_cols=26  Identities=23%  Similarity=0.171  Sum_probs=18.9

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhcc
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQT  108 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~  108 (423)
                      .|+.++|.||+|+|||..... +...+
T Consensus       167 ~Gq~~~IvG~~g~GKTtL~~~-i~~~I  192 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVLLQK-IAQAI  192 (415)
T ss_pred             CCCEEEEECCCCCChhHHHHH-HHHhh
Confidence            477899999999999975332 44433

Members of this family differ in the specificity of RNA binding.

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=92.32  E-value=0.26  Score=46.74  Aligned_cols=70  Identities=16%  Similarity=0.121  Sum_probs=37.6

Q ss_pred             cCCCCCHHHHHHHHhCCCCCCChhhhhcccc-------ccc-----CCceEEEccCCCcchhHHHHHHhhccCCCCCCeE
Q 014486           49 RDFLLKPELLRAIVDSGFEHPSEVQHECIPQ-------AIL-----GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVT  116 (423)
Q Consensus        49 ~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~-------~~~-----~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~  116 (423)
                      ..|+.+++-++.....|+-.-.+.=.+.+..       +..     -.++++.||.|||||..+.     .+......|-
T Consensus       492 PAFG~see~l~~~~~~Gmi~~g~~v~~il~~G~llv~qvk~s~~s~lvSvLl~Gp~~sGKTaLAA-----~iA~~S~FPF  566 (744)
T KOG0741|consen  492 PAFGISEEDLERFVMNGMINWGPPVTRILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTALAA-----KIALSSDFPF  566 (744)
T ss_pred             cccCCCHHHHHHHHhCCceeecccHHHHHhhHHHHHHHhhccccCcceEEEEecCCCCChHHHHH-----HHHhhcCCCe
Confidence            3577777777777766654222222222211       111     1358999999999995332     2222223345


Q ss_pred             EEEEecC
Q 014486          117 ALVLCHT  123 (423)
Q Consensus       117 ~lil~P~  123 (423)
                      +=+++|.
T Consensus       567 vKiiSpe  573 (744)
T KOG0741|consen  567 VKIISPE  573 (744)
T ss_pred             EEEeChH
Confidence            6666664

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=92.29  E-value=0.87  Score=42.24  Aligned_cols=25  Identities=28%  Similarity=0.482  Sum_probs=17.9

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccC
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTE  109 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~  109 (423)
                      .++++.|+||+|||.+.-. ++.++.
T Consensus        43 ~n~~iyG~~GTGKT~~~~~-v~~~l~   67 (366)
T COG1474          43 SNIIIYGPTGTGKTATVKF-VMEELE   67 (366)
T ss_pred             ccEEEECCCCCCHhHHHHH-HHHHHH
Confidence            3599999999999987543 333333

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=92.29  E-value=1.4  Score=43.94  Aligned_cols=37  Identities=22%  Similarity=0.219  Sum_probs=22.8

Q ss_pred             cccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEE
Q 014486           80 AILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALV  119 (423)
Q Consensus        80 ~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~li  119 (423)
                      +..|..+-+.||+|||||...  -++.++.....+ .+++
T Consensus       352 i~~Ge~vaiVG~sGsGKSTl~--~LL~r~~~~~~G-~I~i  388 (567)
T COG1132         352 IEPGEKVAIVGPSGSGKSTLI--KLLLRLYDPTSG-EILI  388 (567)
T ss_pred             EcCCCEEEEECCCCCCHHHHH--HHHhccCCCCCC-eEEE
Confidence            445777889999999998643  344444333222 4444

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=92.27  E-value=0.18  Score=48.72  Aligned_cols=39  Identities=18%  Similarity=0.208  Sum_probs=24.8

Q ss_pred             ChhhhhcccccccCC--ceEEEccCCCcchhHHHHHHhhccC
Q 014486           70 SEVQHECIPQAILGM--DVICQAKSGMGKTAVFVLSTLQQTE  109 (423)
Q Consensus        70 ~~~Q~~~i~~~~~~~--~~ii~~~tGsGKT~~~~~~~~~~~~  109 (423)
                      .+.|.+.+..++...  -++++||||||||... ..++..+.
T Consensus       227 ~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~  267 (486)
T TIGR02533       227 SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLN  267 (486)
T ss_pred             CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccC
Confidence            344555555555432  3789999999999764 34555554

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.

>PRK13764 ATPase; Provisional

Probab=92.24  E-value=0.22  Score=49.04  Aligned_cols=26  Identities=12%  Similarity=0.175  Sum_probs=19.2

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccC
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTE  109 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~  109 (423)
                      +++++++||||||||... .+++..+.
T Consensus       257 ~~~ILIsG~TGSGKTTll-~AL~~~i~  282 (602)
T PRK13764        257 AEGILIAGAPGAGKSTFA-QALAEFYA  282 (602)
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            567999999999999753 44554444

>cd01131 PilT Pilus retraction ATPase PilT

Probab=92.21  E-value=0.18  Score=42.39  Aligned_cols=35  Identities=17%  Similarity=0.326  Sum_probs=21.2

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      ++++||||||||... ..++..+.....+ +++.+-.
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~~~~~~~-~i~t~e~   38 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYINKNKTH-HILTIED   38 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHhhhcCCc-EEEEEcC
Confidence            789999999999764 3344444332222 4454443

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>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=92.20  E-value=0.13  Score=45.74  Aligned_cols=42  Identities=19%  Similarity=0.319  Sum_probs=28.1

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      .+.+++++|+||||||... ..++......  ..+++++-...++
T Consensus       126 ~~~~ili~G~tGSGKTT~l-~all~~i~~~--~~~iv~iEd~~E~  167 (270)
T PF00437_consen  126 GRGNILISGPTGSGKTTLL-NALLEEIPPE--DERIVTIEDPPEL  167 (270)
T ss_dssp             TTEEEEEEESTTSSHHHHH-HHHHHHCHTT--TSEEEEEESSS-S
T ss_pred             cceEEEEECCCccccchHH-HHHhhhcccc--ccceEEeccccce
Confidence            4678999999999999764 4455554444  1267777666554

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 ....

>PRK08760 replicative DNA helicase; Provisional

Probab=92.20  E-value=0.62  Score=45.00  Aligned_cols=112  Identities=16%  Similarity=0.137  Sum_probs=54.4

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEE-cCcchHHHH--
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFY-GGVNIKIHK--  159 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--  159 (423)
                      |.-++|.|.+|.|||...+-.+.......+.  .+++++. -.-..|+..++......   +....+. |..+..++.  
T Consensus       229 G~LivIaarPg~GKTafal~iA~~~a~~~g~--~V~~fSl-EMs~~ql~~Rl~a~~s~---i~~~~i~~g~l~~~e~~~~  302 (476)
T PRK08760        229 TDLIILAARPAMGKTTFALNIAEYAAIKSKK--GVAVFSM-EMSASQLAMRLISSNGR---INAQRLRTGALEDEDWARV  302 (476)
T ss_pred             CceEEEEeCCCCChhHHHHHHHHHHHHhcCC--ceEEEec-cCCHHHHHHHHHHhhCC---CcHHHHhcCCCCHHHHHHH
Confidence            4458999999999997655444433332222  4555543 23345555555443222   2211111 222222221  


Q ss_pred             ----HHHhcCCCcEEEe-----chHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          160 ----DLLKNECPQIVVG-----TPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       160 ----~~~~~~~~~ilv~-----T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                          ..+.+.  .+.|.     |++.+...++.... -.++++||||=.+.+.
T Consensus       303 ~~a~~~l~~~--~l~I~d~~~~t~~~I~~~~r~l~~-~~~~~lVvIDyLql~~  352 (476)
T PRK08760        303 TGAIKMLKET--KIFIDDTPGVSPEVLRSKCRRLKR-EHDLGLIVIDYLQLMS  352 (476)
T ss_pred             HHHHHHHhcC--CEEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEecHHhcC
Confidence                122222  34433     34444443322111 1357899999999885

>TIGR00602 rad24 checkpoint protein rad24

Probab=92.13  E-value=1.8  Score=43.27  Aligned_cols=52  Identities=8%  Similarity=0.148  Sum_probs=29.8

Q ss_pred             ccccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           41 VGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        41 ~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ....+..++++..++..++.+...       .+...+ ....++-+++.||+|+|||.++
T Consensus        76 eKyrP~~ldel~~~~~ki~~l~~~-------l~~~~~-~~~~~~illL~GP~GsGKTTl~  127 (637)
T TIGR00602        76 EKYKPETQHELAVHKKKIEEVETW-------LKAQVL-ENAPKRILLITGPSGCGKSTTI  127 (637)
T ss_pred             HHhCCCCHHHhcCcHHHHHHHHHH-------HHhccc-ccCCCcEEEEECCCCCCHHHHH
Confidence            334455677777777666555432       000000 1112344899999999999864

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

>PHA00012 I assembly protein

Probab=92.07  E-value=0.54  Score=42.07  Aligned_cols=26  Identities=27%  Similarity=0.253  Sum_probs=20.8

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCC
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPN  111 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~  111 (423)
                      -++.|..|+|||+.++.-+...+..+
T Consensus         4 ylITGkPGSGKSl~aV~~I~~~L~~G   29 (361)
T PHA00012          4 YVVTGKLGAGKTLVAVSRIQDKLVKG   29 (361)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHHcC
Confidence            47899999999998887777766644

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=92.06  E-value=1.1  Score=46.01  Aligned_cols=53  Identities=21%  Similarity=0.176  Sum_probs=31.0

Q ss_pred             CCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           45 SSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ..+|++++-.....+.+.+.   .+.+|..++...   +..++.+++.||+|+|||..+
T Consensus       174 ~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~g---i~~~~giLL~GppGtGKT~la  229 (733)
T TIGR01243       174 KVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLG---IEPPKGVLLYGPPGTGKTLLA  229 (733)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcC---CCCCceEEEECCCCCChHHHH
Confidence            34677776555555555443   222222233222   234567999999999999753

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.

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=92.02  E-value=0.25  Score=48.85  Aligned_cols=49  Identities=22%  Similarity=0.064  Sum_probs=39.1

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .++++.||||||||..+++|-+....     ..++|+=|--++....+...++.
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~~-----~S~VV~DpKGEl~~~Ta~~R~~~  207 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFWE-----DSVVVHDIKLENYELTSGWREKQ  207 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhCC-----CCEEEEeCcHHHHHHHHHHHHHC
Confidence            46999999999999999999887642     15788888889888777666554

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=91.98  E-value=0.24  Score=43.74  Aligned_cols=46  Identities=17%  Similarity=0.248  Sum_probs=29.2

Q ss_pred             HHHhCCCCCCChhhhhccccccc--CCceEEEccCCCcchhHHHHHHhhccC
Q 014486           60 AIVDSGFEHPSEVQHECIPQAIL--GMDVICQAKSGMGKTAVFVLSTLQQTE  109 (423)
Q Consensus        60 ~l~~~~~~~~~~~Q~~~i~~~~~--~~~~ii~~~tGsGKT~~~~~~~~~~~~  109 (423)
                      .|.+.|+   .+.|.+.+..++.  +..+++.|+||||||... ..++..+.
T Consensus        58 ~l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i~  105 (264)
T cd01129          58 DLEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSELN  105 (264)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhhC
Confidence            3445554   4566666666554  334899999999999754 33444443

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.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=91.97  E-value=0.77  Score=41.69  Aligned_cols=40  Identities=5%  Similarity=0.235  Sum_probs=28.3

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      ...+++|+|++|.+..  .....+.+.++.-+ ...++++|..
T Consensus       123 ~~~kVvII~~ae~m~~--~aaNaLLK~LEEPp-~~~fILi~~~  162 (314)
T PRK07399        123 APRKVVVIEDAETMNE--AAANALLKTLEEPG-NGTLILIAPS  162 (314)
T ss_pred             CCceEEEEEchhhcCH--HHHHHHHHHHhCCC-CCeEEEEECC
Confidence            5789999999998864  45556667777666 5656666544

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=91.95  E-value=0.2  Score=46.00  Aligned_cols=64  Identities=19%  Similarity=0.272  Sum_probs=39.2

Q ss_pred             HHHHHHhCCCCCCChhhhhccccccc-CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           57 LLRAIVDSGFEHPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        57 ~~~~l~~~~~~~~~~~Q~~~i~~~~~-~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      -++.|.+.|+  +.+.+...+..+.. +.++++.|+||+|||... -.++..+....   +.+++-.+.+|
T Consensus       153 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTll-~al~~~i~~~~---riv~iEd~~El  217 (340)
T TIGR03819       153 TLDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTLL-SALLALVAPDE---RIVLVEDAAEL  217 (340)
T ss_pred             CHHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHHH-HHHHccCCCCC---cEEEECCccee
Confidence            3456666555  34566666655554 578999999999999643 33444433322   55666555554

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>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=91.91  E-value=0.1  Score=42.86  Aligned_cols=38  Identities=18%  Similarity=0.185  Sum_probs=25.1

Q ss_pred             CcEEEechHHHHHHHhcCCC--CCCCccEEEEcCcchhhc
Q 014486          167 PQIVVGTPGRILALARDKDL--SLKNVRHFILDECDKMLE  204 (423)
Q Consensus       167 ~~ilv~T~~~l~~~~~~~~~--~~~~~~~vVvDE~h~~~~  204 (423)
                      .+|+|+++..|+.-......  ...+-.+|||||||.+.+
T Consensus       120 adivi~~y~yl~~~~~~~~~~~~~~~~~ivI~DEAHNL~~  159 (174)
T PF06733_consen  120 ADIVICNYNYLFDPSIRKSLFGIDLKDNIVIFDEAHNLED  159 (174)
T ss_dssp             -SEEEEETHHHHSHHHHHHHCT--CCCEEEEETTGGGCGG
T ss_pred             CCEEEeCHHHHhhHHHHhhhccccccCcEEEEecccchHH
Confidence            59999999988763222111  123446899999998865

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.

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=91.86  E-value=1.3  Score=46.19  Aligned_cols=61  Identities=13%  Similarity=0.023  Sum_probs=39.7

Q ss_pred             CcccccCCCCcCCCCCHHHHHHHHhCCCC-CCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           39 GYVGIHSSGFRDFLLKPELLRAIVDSGFE-HPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        39 ~~~~~~~~~~~~~~l~~~~~~~l~~~~~~-~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      +...-....|++.+....++..|+++-+. -++|-+-.-+ ++..-+.++..||.|+|||+.+
T Consensus       255 p~~~~~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~-~itpPrgvL~~GppGTGkTl~a  316 (1080)
T KOG0732|consen  255 PLSVDSSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNF-NITPPRGVLFHGPPGTGKTLMA  316 (1080)
T ss_pred             chhhhcccCccccccHHHHHHHHHHHHHhHhhhhhHhhhc-ccCCCcceeecCCCCCchhHHH
Confidence            33333456799999888888888887332 2233222221 2334567999999999999754

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=91.81  E-value=3.4  Score=37.22  Aligned_cols=17  Identities=35%  Similarity=0.419  Sum_probs=14.7

Q ss_pred             CCceEEEccCCCcchhH
Q 014486           83 GMDVICQAKSGMGKTAV   99 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~   99 (423)
                      ++++++.||-|||||..
T Consensus        49 snsviiigprgsgkT~l   65 (408)
T KOG2228|consen   49 SNSVIIIGPRGSGKTIL   65 (408)
T ss_pred             CCceEEEccCCCCceEe
Confidence            46799999999999963

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=91.78  E-value=0.3  Score=42.54  Aligned_cols=51  Identities=14%  Similarity=0.229  Sum_probs=28.2

Q ss_pred             ccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHH
Q 014486           43 IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        43 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~  101 (423)
                      ..+..|++|-=.+.+.++|.-+  -+-...+.+++      .++++.||+|.|||..+.
T Consensus        20 lRP~~l~efiGQ~~vk~~L~if--I~AAk~r~e~l------DHvLl~GPPGlGKTTLA~   70 (332)
T COG2255          20 LRPKTLDEFIGQEKVKEQLQIF--IKAAKKRGEAL------DHVLLFGPPGLGKTTLAH   70 (332)
T ss_pred             cCcccHHHhcChHHHHHHHHHH--HHHHHhcCCCc------CeEEeeCCCCCcHHHHHH
Confidence            3455677776566665555421  00001111121      348999999999997543

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=91.75  E-value=0.69  Score=47.25  Aligned_cols=18  Identities=33%  Similarity=0.455  Sum_probs=15.5

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      ..+.++.||+|+|||..+
T Consensus       207 ~~n~LLvGppGvGKT~la  224 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIA  224 (758)
T ss_pred             CCCeEEECCCCCCHHHHH
Confidence            457999999999999764

>COG1485 Predicted ATPase [General function prediction only]

Probab=91.73  E-value=1.1  Score=40.50  Aligned_cols=109  Identities=11%  Similarity=0.123  Sum_probs=61.0

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHh
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLK  163 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (423)
                      +.+.+.|+.|.|||.  ++-..-...+...+    .-++.-.-+..+.+++..+...                       
T Consensus        66 ~GlYl~GgVGrGKT~--LMD~Fy~~lp~~~k----~R~HFh~FM~~vH~~l~~l~g~-----------------------  116 (367)
T COG1485          66 RGLYLWGGVGRGKTM--LMDLFYESLPGERK----RRLHFHRFMARVHQRLHTLQGQ-----------------------  116 (367)
T ss_pred             ceEEEECCCCccHHH--HHHHHHhhCCcccc----ccccHHHHHHHHHHHHHHHcCC-----------------------
Confidence            568999999999996  34444444433221    1245556667777666655311                       


Q ss_pred             cCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHH-hCCCCceEEEEeccCCccH
Q 014486          164 NECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFK-MTPHDKQVMMFSATLSKEI  236 (423)
Q Consensus       164 ~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~-~~~~~~~~v~~SAT~~~~~  236 (423)
                         .+.+-    .+..-+      ..+.+++.+||.|.-.  ..-.-.+.+++. .+.....++..|-|.|..+
T Consensus       117 ---~dpl~----~iA~~~------~~~~~vLCfDEF~VtD--I~DAMiL~rL~~~Lf~~GV~lvaTSN~~P~~L  175 (367)
T COG1485         117 ---TDPLP----PIADEL------AAETRVLCFDEFEVTD--IADAMILGRLLEALFARGVVLVATSNTAPDNL  175 (367)
T ss_pred             ---CCccH----HHHHHH------HhcCCEEEeeeeeecC--hHHHHHHHHHHHHHHHCCcEEEEeCCCChHHh
Confidence               11111    011111      1345689999999431  222333444433 3455788888888888764

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=91.70  E-value=0.21  Score=49.39  Aligned_cols=39  Identities=23%  Similarity=0.229  Sum_probs=26.3

Q ss_pred             ChhhhhcccccccC--CceEEEccCCCcchhHHHHHHhhccC
Q 014486           70 SEVQHECIPQAILG--MDVICQAKSGMGKTAVFVLSTLQQTE  109 (423)
Q Consensus        70 ~~~Q~~~i~~~~~~--~~~ii~~~tGsGKT~~~~~~~~~~~~  109 (423)
                      .+.|.+.+..++..  ..++++||||||||.+. ..++..+.
T Consensus       301 ~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       301 EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            35566666665553  34789999999999764 44555553

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=91.62  E-value=0.46  Score=49.49  Aligned_cols=18  Identities=28%  Similarity=0.449  Sum_probs=15.4

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      .+.++.||+|+|||...-
T Consensus       200 ~n~lL~G~pGvGKT~l~~  217 (857)
T PRK10865        200 NNPVLIGEPGVGKTAIVE  217 (857)
T ss_pred             CceEEECCCCCCHHHHHH
Confidence            579999999999997653

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

Probab=91.56  E-value=0.57  Score=46.00  Aligned_cols=87  Identities=16%  Similarity=0.197  Sum_probs=67.5

Q ss_pred             HHHHHHHHHhh-cCCcEEEEEcChh----hHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc-cc
Q 014486          276 NRKLNDLLDAL-DFNQVVIFVKSVS----RAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL-VG  349 (423)
Q Consensus       276 ~~~l~~ll~~~-~~~~~ivf~~~~~----~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~-~~  349 (423)
                      .-.+..++... .+.++.+..++.=    +...+.+.|...|+.+..+.|.+....|.+++....+|+++++|.|-+ +.
T Consensus       298 vVA~laml~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQ  377 (677)
T COG1200         298 VVALLAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQ  377 (677)
T ss_pred             HHHHHHHHHHHHcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhh
Confidence            33344444444 3457888888854    555566667777999999999999999999999999999999999965 66


Q ss_pred             cCCCCCCCCEEEE
Q 014486          350 RGIDIERVNIVIN  362 (423)
Q Consensus       350 ~Gld~~~~~~vi~  362 (423)
                      ..+++.++-.||.
T Consensus       378 d~V~F~~LgLVIi  390 (677)
T COG1200         378 DKVEFHNLGLVII  390 (677)
T ss_pred             cceeecceeEEEE
Confidence            7888888887774

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.51  E-value=1.7  Score=43.42  Aligned_cols=40  Identities=10%  Similarity=0.223  Sum_probs=26.6

Q ss_pred             CCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      +...+++|+||+|.+..  .....+.+.++..+....+|+.|
T Consensus       119 ~~~~KVvIIdea~~Ls~--~a~naLLK~LEepp~~tifIL~t  158 (614)
T PRK14971        119 IGKYKIYIIDEVHMLSQ--AAFNAFLKTLEEPPSYAIFILAT  158 (614)
T ss_pred             cCCcEEEEEECcccCCH--HHHHHHHHHHhCCCCCeEEEEEe
Confidence            45788999999998864  34445666666655555455544

>PRK09165 replicative DNA helicase; Provisional

Probab=91.51  E-value=1.9  Score=42.03  Aligned_cols=115  Identities=13%  Similarity=0.102  Sum_probs=55.3

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCC------------CCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEE
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPN------------PGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFY  150 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~------------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~  150 (423)
                      |.-++|.|.||.|||..++-.+.......            ..+..++|++. -.-..|+..++.....   ++....+.
T Consensus       217 g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSl-EMs~~ql~~R~la~~s---~v~~~~i~  292 (497)
T PRK09165        217 SDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSL-EMSAEQLATRILSEQS---EISSSKIR  292 (497)
T ss_pred             CceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeC-cCCHHHHHHHHHHHhc---CCCHHHHh
Confidence            44589999999999976544333332210            01225666643 3445555555543322   22221122


Q ss_pred             -cCcchHHHH------HHHhcCCCcEEEe-----chHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          151 -GGVNIKIHK------DLLKNECPQIVVG-----TPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       151 -~~~~~~~~~------~~~~~~~~~ilv~-----T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                       |..+..++.      ..+..  ..+.|.     |++.+...++.... -.++++||||=.|.+..
T Consensus       293 ~~~l~~~e~~~l~~a~~~l~~--~~l~I~d~~~~ti~~i~~~ir~l~~-~~~~~lvvIDyLqli~~  355 (497)
T PRK09165        293 RGKISEEDFEKLVDASQELQK--LPLYIDDTPALSISQLRARARRLKR-QHGLDLLVVDYLQLIRG  355 (497)
T ss_pred             cCCCCHHHHHHHHHHHHHHhc--CCeEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhccC
Confidence             222222211      11222  234432     34445443332111 13578999999998753

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

Probab=91.48  E-value=0.79  Score=47.97  Aligned_cols=76  Identities=21%  Similarity=0.270  Sum_probs=64.9

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhC----CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEc-CccccCCCCCCCCEEE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVEC----NFPSICIHSGMSQEERLTRYKGFKEGNKRILVAT-DLVGRGIDIERVNIVI  361 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T-~~~~~Gld~~~~~~vi  361 (423)
                      .+.++.|.+++.=.|++-++.++++    ++++..++.-.+..+...+++...+|+++|+|+| ..++.++-+.++..+|
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            4568999999988888777777665    5566678888999999999999999999999998 6788899999999887


Q ss_pred             E
Q 014486          362 N  362 (423)
Q Consensus       362 ~  362 (423)
                      .
T Consensus       722 I  722 (1139)
T COG1197         722 I  722 (1139)
T ss_pred             E
Confidence            4

>PF12846 AAA_10: AAA-like domain

Probab=91.43  E-value=0.19  Score=45.42  Aligned_cols=41  Identities=17%  Similarity=0.233  Sum_probs=26.5

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      +.++++.|+||+|||.... .++......+.  .++++=|..+.
T Consensus         1 n~h~~i~G~tGsGKT~~~~-~l~~~~~~~g~--~~~i~D~~g~~   41 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLK-NLLEQLIRRGP--RVVIFDPKGDY   41 (304)
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHHHcCC--CEEEEcCCchH
Confidence            3578999999999997765 44444333332  55666555443

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=91.34  E-value=0.78  Score=39.43  Aligned_cols=42  Identities=14%  Similarity=0.086  Sum_probs=27.1

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCC---CCCeEEEEEecCh
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPN---PGQVTALVLCHTR  124 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~~  124 (423)
                      |.-+.|.||+|+|||...+..+.......   +...+++++....
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            45689999999999987665444433332   1123677777543

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.

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=91.21  E-value=0.29  Score=52.62  Aligned_cols=57  Identities=23%  Similarity=0.221  Sum_probs=45.6

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCC--CCeEEEEEecChHHHHHHHHHHHHHh
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNP--GQVTALVLCHTRELAYQICHEFERFS  138 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~--~~~~~lil~P~~~L~~q~~~~~~~~~  138 (423)
                      .+++++|.|..|||||.+...-++..+...+  ....+|+++-|++-+..+..++.+-.
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~L   73 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDRL   73 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHHH
Confidence            3678999999999999987777777666642  33489999999999998888887543

>PRK05636 replicative DNA helicase; Provisional

Probab=91.18  E-value=1  Score=43.75  Aligned_cols=22  Identities=27%  Similarity=0.440  Sum_probs=16.2

Q ss_pred             CCceEEEccCCCcchhHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLST  104 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~  104 (423)
                      |.-++|.|.||.|||..++-.+
T Consensus       265 G~Liiiaarpg~GKT~~al~~a  286 (505)
T PRK05636        265 GQMIIVAARPGVGKSTLALDFM  286 (505)
T ss_pred             CceEEEEeCCCCCHHHHHHHHH
Confidence            3447899999999997655433

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=91.17  E-value=0.57  Score=39.10  Aligned_cols=64  Identities=16%  Similarity=0.137  Sum_probs=37.2

Q ss_pred             hhcccccc-cCCceEEEccCCCcchhHHHHHHhhccCCC-------CCCeEEEEEecChHHHHHHHHHHHHHh
Q 014486           74 HECIPQAI-LGMDVICQAKSGMGKTAVFVLSTLQQTEPN-------PGQVTALVLCHTRELAYQICHEFERFS  138 (423)
Q Consensus        74 ~~~i~~~~-~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~-------~~~~~~lil~P~~~L~~q~~~~~~~~~  138 (423)
                      ...++.++ .|.-+++.||+|+|||...+-.+.......       ..+.+++++..-.. ..++.+++....
T Consensus        22 ~~li~g~~~~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~   93 (193)
T PF13481_consen   22 DWLIDGLLPRGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALL   93 (193)
T ss_dssp             -EEETTEE-TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHH
T ss_pred             ceeECCcccCCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHh
Confidence            34444555 466699999999999987655444443211       12347777776544 556677776655

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=91.13  E-value=1.7  Score=38.49  Aligned_cols=16  Identities=19%  Similarity=0.387  Sum_probs=14.2

Q ss_pred             CceEEEccCCCcchhH
Q 014486           84 MDVICQAKSGMGKTAV   99 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~   99 (423)
                      +++++.+|+|+|||..
T Consensus       112 ~~~~i~g~~g~GKttl  127 (270)
T TIGR02858       112 LNTLIISPPQCGKTTL  127 (270)
T ss_pred             eEEEEEcCCCCCHHHH
Confidence            5789999999999974

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=91.09  E-value=0.19  Score=32.95  Aligned_cols=18  Identities=22%  Similarity=0.447  Sum_probs=15.1

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      +...++.+++|+|||...
T Consensus        23 g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            456999999999999753

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=91.08  E-value=0.47  Score=51.40  Aligned_cols=57  Identities=18%  Similarity=0.102  Sum_probs=44.8

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhc
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFST  139 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  139 (423)
                      .++++|.|+.|||||.+.+--++..+..+....++++|+-|+.-+.++.+++.+...
T Consensus        10 ~~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~L~   66 (1141)
T TIGR02784        10 KTSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDRLG   66 (1141)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHHHH
Confidence            467999999999999887666665554444344899999999999999888876653

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.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=90.97  E-value=0.92  Score=41.13  Aligned_cols=41  Identities=12%  Similarity=-0.022  Sum_probs=25.9

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCC---CCCCeEEEEEecCh
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEP---NPGQVTALVLCHTR  124 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~---~~~~~~~lil~P~~  124 (423)
                      .-+.+.||+|+|||...+..++....+   .+.+.+++|+.--.
T Consensus        97 ~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~  140 (313)
T TIGR02238        97 SITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEG  140 (313)
T ss_pred             eEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCC
Confidence            347899999999997665544433222   12233888887443

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=90.94  E-value=0.63  Score=45.94  Aligned_cols=20  Identities=30%  Similarity=0.320  Sum_probs=16.6

Q ss_pred             cccCCceEEEccCCCcchhH
Q 014486           80 AILGMDVICQAKSGMGKTAV   99 (423)
Q Consensus        80 ~~~~~~~ii~~~tGsGKT~~   99 (423)
                      +..|+.+.+.||+|||||..
T Consensus       358 i~~G~~vaIvG~SGsGKSTL  377 (529)
T TIGR02868       358 LPPGERVAILGPSGSGKSTL  377 (529)
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            34577899999999999964

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.

>PHA02542 41 41 helicase; Provisional

Probab=90.92  E-value=0.59  Score=44.96  Aligned_cols=35  Identities=11%  Similarity=0.036  Sum_probs=22.4

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEe
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLC  121 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  121 (423)
                      .-+++.|.+|.|||..++-.+..... .+  ..++++.
T Consensus       191 ~LiiIaarPgmGKTtfalniA~~~a~-~g--~~Vl~fS  225 (473)
T PHA02542        191 TLNVLLAGVNVGKSLGLCSLAADYLQ-QG--YNVLYIS  225 (473)
T ss_pred             cEEEEEcCCCccHHHHHHHHHHHHHh-cC--CcEEEEe
Confidence            34889999999999876554444432 22  2555554

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=90.85  E-value=0.34  Score=41.70  Aligned_cols=36  Identities=22%  Similarity=0.239  Sum_probs=23.9

Q ss_pred             ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           85 DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      .+++.|++|||||.. ++.++..+...-  ..+++++|.
T Consensus        15 r~viIG~sGSGKT~l-i~~lL~~~~~~f--~~I~l~t~~   50 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTL-IKSLLYYLRHKF--DHIFLITPE   50 (241)
T ss_pred             eEEEECCCCCCHHHH-HHHHHHhhcccC--CEEEEEecC
Confidence            689999999999964 444555444333  255666673

This is thought to be an ATPase involved in viral DNA packaging [].

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=90.80  E-value=1.5  Score=37.78  Aligned_cols=41  Identities=22%  Similarity=0.249  Sum_probs=24.6

Q ss_pred             cCC-ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           82 LGM-DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        82 ~~~-~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      .++ -+.++|+.|||||...= ++++....+.   .++++.|-..+
T Consensus        49 d~qg~~~vtGevGsGKTv~~R-al~~s~~~d~---~~~v~i~~~~~   90 (269)
T COG3267          49 DGQGILAVTGEVGSGKTVLRR-ALLASLNEDQ---VAVVVIDKPTL   90 (269)
T ss_pred             cCCceEEEEecCCCchhHHHH-HHHHhcCCCc---eEEEEecCcch
Confidence            344 48899999999998754 3444443222   44445444433

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=90.79  E-value=1.2  Score=41.58  Aligned_cols=17  Identities=24%  Similarity=0.321  Sum_probs=14.3

Q ss_pred             CceEEEccCCCcchhHH
Q 014486           84 MDVICQAKSGMGKTAVF  100 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~  100 (423)
                      +.+++.+|.|+|||...
T Consensus       187 rglLLfGPpgtGKtmL~  203 (428)
T KOG0740|consen  187 RGLLLFGPPGTGKTMLA  203 (428)
T ss_pred             chhheecCCCCchHHHH
Confidence            46899999999999643

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=90.76  E-value=0.33  Score=43.96  Aligned_cols=56  Identities=23%  Similarity=0.200  Sum_probs=36.1

Q ss_pred             CCCChhhhhcccccc-cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           67 EHPSEVQHECIPQAI-LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~-~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      ..+.+.|..-+..+. .+++++++|+||||||.. +.+++.......   +.+.+=-+.++
T Consensus       126 gt~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~-lnall~~Ip~~~---rivtIEdt~E~  182 (312)
T COG0630         126 GTISPEQAAYLWLAIEARKSIIICGGTASGKTTL-LNALLDFIPPEE---RIVTIEDTPEL  182 (312)
T ss_pred             CCCCHHHHHHHHHHHHcCCcEEEECCCCCCHHHH-HHHHHHhCCchh---cEEEEeccccc
Confidence            356677765544444 578899999999999964 444555444333   56666555543

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=90.66  E-value=0.39  Score=44.26  Aligned_cols=41  Identities=15%  Similarity=0.220  Sum_probs=24.5

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      +..++++||||||||... ..++..+...... +++.+-...+
T Consensus       122 ~g~ili~G~tGSGKTT~l-~al~~~i~~~~~~-~i~tiEdp~E  162 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTL-ASMIDYINKNAAG-HIITIEDPIE  162 (343)
T ss_pred             CcEEEEECCCCCCHHHHH-HHHHHhhCcCCCC-EEEEEcCChh
Confidence            456899999999999754 3344444322222 5555544333

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=90.61  E-value=0.3  Score=45.41  Aligned_cols=47  Identities=15%  Similarity=0.283  Sum_probs=33.1

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN  111 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~  111 (423)
                      .+.++|++++.+.+.|.+.                  ...++++||+|+|||. |..++.+.+...
T Consensus       244 ~~ledY~L~dkl~eRL~er------------------aeGILIAG~PGaGKsT-FaqAlAefy~~~  290 (604)
T COG1855         244 LSLEDYGLSDKLKERLEER------------------AEGILIAGAPGAGKST-FAQALAEFYASQ  290 (604)
T ss_pred             echhhcCCCHHHHHHHHhh------------------hcceEEecCCCCChhH-HHHHHHHHHHhc
Confidence            3577888998888877642                  2458999999999995 444444444433

>TIGR00763 lon ATP-dependent protease La

Probab=90.52  E-value=1.5  Score=45.38  Aligned_cols=18  Identities=28%  Similarity=0.309  Sum_probs=15.0

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      +..+++.||+|+|||..+
T Consensus       347 ~~~lll~GppG~GKT~lA  364 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSLG  364 (775)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            456899999999999754

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.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=90.45  E-value=0.49  Score=41.75  Aligned_cols=52  Identities=17%  Similarity=0.203  Sum_probs=35.4

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .|+.++|.|++|+|||.-.+-.+...+..+.   ++++++- .+...++.+.+..+
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge---~vlyvs~-~e~~~~l~~~~~~~   73 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFALQFLYEGAREGE---PVLYVST-EESPEELLENARSF   73 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHHHhcCC---cEEEEEe-cCCHHHHHHHHHHc
Confidence            4577999999999999876665666555522   5677664 34555566666554

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=90.39  E-value=1.7  Score=38.00  Aligned_cols=28  Identities=21%  Similarity=0.137  Sum_probs=19.8

Q ss_pred             ccCCceEEEccCCCcchhHHHHHHhhccC
Q 014486           81 ILGMDVICQAKSGMGKTAVFVLSTLQQTE  109 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~~~~~~~~~~  109 (423)
                      -.|+.+++.||.|+|||... -.+.....
T Consensus        14 ~~Gqr~~I~G~~G~GKTTLl-r~I~n~l~   41 (249)
T cd01128          14 GKGQRGLIVAPPKAGKTTLL-QSIANAIT   41 (249)
T ss_pred             CCCCEEEEECCCCCCHHHHH-HHHHhccc
Confidence            35788999999999999643 33444443

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.

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

Probab=90.31  E-value=1.6  Score=41.97  Aligned_cols=91  Identities=12%  Similarity=0.185  Sum_probs=63.2

Q ss_pred             CCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHH---HhcCCCcE
Q 014486           93 GMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDL---LKNECPQI  169 (423)
Q Consensus        93 GsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~i  169 (423)
                      ...|-.. +..++.... .....++||.|-|+.-|.++...+++.     ++++..+||+.+..+....   +.++.+.|
T Consensus       322 ~~~K~~~-l~~lL~~~~-~~~~~KvIIFc~tkr~~~~l~~~l~~~-----~~~a~~iHGd~sQ~eR~~~L~~FreG~~~v  394 (519)
T KOG0331|consen  322 ETAKLRK-LGKLLEDIS-SDSEGKVIIFCETKRTCDELARNLRRK-----GWPAVAIHGDKSQSERDWVLKGFREGKSPV  394 (519)
T ss_pred             HHHHHHH-HHHHHHHHh-ccCCCcEEEEecchhhHHHHHHHHHhc-----CcceeeecccccHHHHHHHHHhcccCCcce
Confidence            4445432 344555444 333349999999999999988877763     4689999999887766544   45688899


Q ss_pred             EEechHHHHHHHhcCCCCCCCccEEEE
Q 014486          170 VVGTPGRILALARDKDLSLKNVRHFIL  196 (423)
Q Consensus       170 lv~T~~~l~~~~~~~~~~~~~~~~vVv  196 (423)
                      +|+|--      -...+++.++++||-
T Consensus       395 LVATdV------AaRGLDi~dV~lVIn  415 (519)
T KOG0331|consen  395 LVATDV------AARGLDVPDVDLVIN  415 (519)
T ss_pred             EEEccc------ccccCCCccccEEEe
Confidence            999942      234567777777763

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=90.29  E-value=0.48  Score=42.40  Aligned_cols=19  Identities=26%  Similarity=0.361  Sum_probs=16.1

Q ss_pred             cCCceEEEccCCCcchhHH
Q 014486           82 LGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~  100 (423)
                      .+.++++.||+|+|||.++
T Consensus        57 ~~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        57 PTLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CCceEEEEcCCCCCHHHHH
Confidence            3457999999999999865

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.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=90.29  E-value=0.35  Score=43.86  Aligned_cols=18  Identities=28%  Similarity=0.427  Sum_probs=16.0

Q ss_pred             cCCceEEEccCCCcchhH
Q 014486           82 LGMDVICQAKSGMGKTAV   99 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~   99 (423)
                      .+.++++.||||||||..
T Consensus       143 ~~~~ili~G~tGsGKTTl  160 (308)
T TIGR02788       143 SRKNIIISGGTGSGKTTF  160 (308)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            477899999999999974

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=90.06  E-value=0.58  Score=46.96  Aligned_cols=48  Identities=19%  Similarity=0.108  Sum_probs=36.4

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER  136 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  136 (423)
                      .++++.||||||||..+++|-+.....     .++|+=|--++........++
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~~g-----S~VV~DpKGE~~~~Ta~~R~~  187 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTFKG-----SVIALDVKGELFELTSRARKA  187 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcCCC-----CEEEEeCCchHHHHHHHHHHh
Confidence            479999999999999999988776431     567777888877665554443

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=90.00  E-value=3.1  Score=33.89  Aligned_cols=51  Identities=16%  Similarity=0.262  Sum_probs=37.3

Q ss_pred             CCccEEEEcCcchhhccCC--cHHHHHHHHHhCCCCceEEEEeccCCccHHHHH
Q 014486          189 KNVRHFILDECDKMLESLD--MRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVC  240 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~--~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~  240 (423)
                      ..+++||+||+=...+ .+  ....+..+++..|...-+|+..-.+|+.+...+
T Consensus        96 ~~~DlvVLDEi~~A~~-~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~A  148 (173)
T TIGR00708        96 PELDLVLLDELTYALK-YGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELA  148 (173)
T ss_pred             CCCCEEEehhhHHHHH-CCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhC
Confidence            5678999999987765 33  344566777777777778888877887766553

Alternate name: corrinoid adenosyltransferase.

>PRK06321 replicative DNA helicase; Provisional

Probab=89.99  E-value=3.6  Score=39.76  Aligned_cols=112  Identities=14%  Similarity=0.131  Sum_probs=53.0

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEE-cCcchHHHH--
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFY-GGVNIKIHK--  159 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--  159 (423)
                      |.=++|.|.+|.|||.-++-.+.......+ . .+++++. ..-..|+..++-....   ++....+. +..+..++.  
T Consensus       226 G~LiiiaarPgmGKTafal~ia~~~a~~~g-~-~v~~fSL-EMs~~ql~~Rlla~~s---~v~~~~i~~~~l~~~e~~~~  299 (472)
T PRK06321        226 SNLMILAARPAMGKTALALNIAENFCFQNR-L-PVGIFSL-EMTVDQLIHRIICSRS---EVESKKISVGDLSGRDFQRI  299 (472)
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHhcC-C-eEEEEec-cCCHHHHHHHHHHhhc---CCCHHHhhcCCCCHHHHHHH
Confidence            344789999999999765543333222222 1 4555542 2334444444433221   22222222 222222222  


Q ss_pred             ----HHHhcCCCcEEEe-----chHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          160 ----DLLKNECPQIVVG-----TPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       160 ----~~~~~~~~~ilv~-----T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                          ..+.+.  .+.|-     |.+.+....+.... -.++++||||=.+.+.
T Consensus       300 ~~a~~~l~~~--~~~idd~~~~ti~~i~~~~r~~~~-~~~~~lvvIDyLql~~  349 (472)
T PRK06321        300 VSVVNEMQEH--TLLIDDQPGLKITDLRARARRMKE-SYDIQFLIIDYLQLLS  349 (472)
T ss_pred             HHHHHHHHcC--CEEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHHcC
Confidence                222222  35443     34444443332111 1357899999999885

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=89.87  E-value=0.5  Score=45.86  Aligned_cols=59  Identities=12%  Similarity=0.088  Sum_probs=39.9

Q ss_pred             hccccccc-----CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           75 ECIPQAIL-----GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        75 ~~i~~~~~-----~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      ..++.++.     |..+++.+|+|+|||...+..+.+.+..+.   +++|++ .-+-..|+..++..+
T Consensus       250 ~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~ge---~~~y~s-~eEs~~~i~~~~~~l  313 (484)
T TIGR02655       250 VRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLENACANKE---RAILFA-YEESRAQLLRNAYSW  313 (484)
T ss_pred             HhHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEE-eeCCHHHHHHHHHHc
Confidence            44555554     345899999999999876665555544332   778877 446667777777665

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=89.79  E-value=0.86  Score=36.24  Aligned_cols=37  Identities=16%  Similarity=0.295  Sum_probs=24.2

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      ..+++.+++|+|||... .-+.+.+...+-. ..=+++|
T Consensus         6 mki~ITG~PGvGKtTl~-~ki~e~L~~~g~k-vgGf~t~   42 (179)
T COG1618           6 MKIFITGRPGVGKTTLV-LKIAEKLREKGYK-VGGFITP   42 (179)
T ss_pred             eEEEEeCCCCccHHHHH-HHHHHHHHhcCce-eeeEEee
Confidence            35899999999999754 4456555555433 3344555

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=89.76  E-value=0.73  Score=39.60  Aligned_cols=51  Identities=18%  Similarity=0.123  Sum_probs=33.2

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      +..+++.|++|+|||...+..+...+..+.   ++++++.. +-..++.+.+..+
T Consensus        16 g~~~li~G~~G~GKt~~~~~~~~~~~~~g~---~~~y~s~e-~~~~~l~~~~~~~   66 (224)
T TIGR03880        16 GHVIVVIGEYGTGKTTFSLQFLYQGLKNGE---KAMYISLE-EREERILGYAKSK   66 (224)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCC---eEEEEECC-CCHHHHHHHHHHc
Confidence            456899999999999765554544444322   67777654 3456666666554

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.

>TIGR00416 sms DNA repair protein RadA

Probab=89.72  E-value=1.3  Score=42.49  Aligned_cols=51  Identities=20%  Similarity=0.261  Sum_probs=32.8

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      |.-+++.|++|+|||...+..+...... +  .+++|+..- +-..|+..++.++
T Consensus        94 GsvilI~G~pGsGKTTL~lq~a~~~a~~-g--~kvlYvs~E-Es~~qi~~ra~rl  144 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQVACQLAKN-Q--MKVLYVSGE-ESLQQIKMRAIRL  144 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHhc-C--CcEEEEECc-CCHHHHHHHHHHc
Confidence            3458999999999998765544433332 2  267888754 4456666655554

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)).

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=89.58  E-value=0.72  Score=40.52  Aligned_cols=50  Identities=14%  Similarity=0.098  Sum_probs=30.1

Q ss_pred             hcccccccC-----CceEEEccCCCcchhHHHHHHhhccCC---CCCCeEEEEEecCh
Q 014486           75 ECIPQAILG-----MDVICQAKSGMGKTAVFVLSTLQQTEP---NPGQVTALVLCHTR  124 (423)
Q Consensus        75 ~~i~~~~~~-----~~~ii~~~tGsGKT~~~~~~~~~~~~~---~~~~~~~lil~P~~  124 (423)
                      ..++.++.|     .-.=++|+.|+|||-..+..++....+   ++...+++|+.-..
T Consensus        25 ~~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~   82 (256)
T PF08423_consen   25 KSLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEG   82 (256)
T ss_dssp             HHHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSS
T ss_pred             HHHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCC
Confidence            345555553     235589999999997655444443322   23334889986443

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 ....

>PRK14701 reverse gyrase; Provisional

Probab=89.55  E-value=1.7  Score=48.43  Aligned_cols=61  Identities=15%  Similarity=0.185  Sum_probs=52.7

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhC------CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVEC------NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL  347 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~  347 (423)
                      .+.++||.+|++..+.++.+.|+..      +..+..+||+++..++.+.++.+.+|..+|||+|+-
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            4568999999999999998888763      456778999999999998888999999999999964

>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=89.55  E-value=0.5  Score=39.99  Aligned_cols=44  Identities=14%  Similarity=0.213  Sum_probs=22.8

Q ss_pred             ccccCCceEEEccCCCcchhHHHHHHhhccCC-CCCCeEEEEEecC
Q 014486           79 QAILGMDVICQAKSGMGKTAVFVLSTLQQTEP-NPGQVTALVLCHT  123 (423)
Q Consensus        79 ~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~  123 (423)
                      .+....+++|.|.||+|||......+...+.. ++.. .-++++..
T Consensus        34 dl~~~~h~li~G~tgsGKS~~l~~ll~~l~~~~~p~~-~~l~iiD~   78 (205)
T PF01580_consen   34 DLKKNPHLLIAGATGSGKSTLLRTLLLSLALTYSPDD-VQLYIIDP   78 (205)
T ss_dssp             EGGGS-SEEEE--TTSSHHHHHHHHHHHHHTT--TTT-EEEEEE-T
T ss_pred             EcCCCceEEEEcCCCCCccHHHHHHHHHHHHHhcCCc-cEEEEEcC
Confidence            34445689999999999997654333333332 2333 33555543

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.

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=89.51  E-value=2.1  Score=37.44  Aligned_cols=46  Identities=11%  Similarity=0.332  Sum_probs=33.5

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccH
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEI  236 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~  236 (423)
                      ..+++||+-||+.+..  +....+++-.......+++|+.--+..+-+
T Consensus       126 r~fKvvvi~ead~LT~--dAQ~aLRRTMEkYs~~~RlIl~cns~SriI  171 (351)
T KOG2035|consen  126 RPFKVVVINEADELTR--DAQHALRRTMEKYSSNCRLILVCNSTSRII  171 (351)
T ss_pred             cceEEEEEechHhhhH--HHHHHHHHHHHHHhcCceEEEEecCcccch
Confidence            4689999999999875  566667777777777777777665554443

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=89.50  E-value=1.8  Score=45.25  Aligned_cols=18  Identities=28%  Similarity=0.449  Sum_probs=15.3

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      ++.++.||+|+|||...-
T Consensus       195 ~n~lL~G~pGvGKT~l~~  212 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAIVE  212 (852)
T ss_pred             CceEEEcCCCCCHHHHHH
Confidence            579999999999997653

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.

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=89.50  E-value=2.3  Score=42.36  Aligned_cols=74  Identities=20%  Similarity=0.316  Sum_probs=56.3

Q ss_pred             eEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCc
Q 014486          115 VTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNV  191 (423)
Q Consensus       115 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~  191 (423)
                      .++||.|+++..+.++++.+...     ++.+..++|+....+..   ..+.++..+|+|||.-     + ...+++.++
T Consensus       258 ~k~LVF~nt~~~ae~l~~~L~~~-----g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv-----~-arGIDip~V  326 (572)
T PRK04537        258 ARTMVFVNTKAFVERVARTLERH-----GYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDV-----A-ARGLHIDGV  326 (572)
T ss_pred             CcEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehh-----h-hcCCCccCC
Confidence            38899999999999998887654     67899999987665443   4556777899999942     1 246788889


Q ss_pred             cEEEEcCc
Q 014486          192 RHFILDEC  199 (423)
Q Consensus       192 ~~vVvDE~  199 (423)
                      ++||.-+.
T Consensus       327 ~~VInyd~  334 (572)
T PRK04537        327 KYVYNYDL  334 (572)
T ss_pred             CEEEEcCC
Confidence            98886554

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.48  E-value=3  Score=41.52  Aligned_cols=35  Identities=31%  Similarity=0.392  Sum_probs=25.1

Q ss_pred             CCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCc
Q 014486          188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK  223 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~  223 (423)
                      +.+..++|+|||-..++ ......++..+..+.++.
T Consensus       620 lr~P~VLILDEATSALD-aeSE~lVq~aL~~~~~~r  654 (716)
T KOG0058|consen  620 LRNPRVLILDEATSALD-AESEYLVQEALDRLMQGR  654 (716)
T ss_pred             hcCCCEEEEechhhhcc-hhhHHHHHHHHHHhhcCC
Confidence            45677899999998887 566666677766555553

>KOG1806 consensus DEAD box containing helicases [Replication, recombination and repair]

Probab=89.47  E-value=0.51  Score=48.22  Aligned_cols=68  Identities=21%  Similarity=0.183  Sum_probs=53.0

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER  136 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  136 (423)
                      ..+|-|-+++..-.+.+.+.+.+|+|+|||-.+.- ++.-+.+....++++|++.+..-..|..+.+.+
T Consensus       738 ~ft~~qveai~sg~qpgltmvvgppgtgktd~avq-il~~lyhn~p~qrTlivthsnqaln~lfeKi~~  805 (1320)
T KOG1806|consen  738 KFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAVQ-ILSVLYHNSPNQRTLIVTHSNQALNQLFEKIMA  805 (1320)
T ss_pred             ccCHHHHHHHHhcCCCCceeeecCCCCCCcchhhh-hhhhhhhcCCCcceEEEEecccchhHHHHHHHh
Confidence            56889999998888888999999999999987654 444444444555999999998877777766644

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=89.46  E-value=0.47  Score=40.25  Aligned_cols=38  Identities=13%  Similarity=0.196  Sum_probs=25.9

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      |.-+.+.||+|+|||...+..+.+....+   .+++++.-.
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~~g---~~v~yi~~e   49 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAARQG---KKVVYIDTE   49 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCC---CeEEEEECC
Confidence            45589999999999987665554444332   267777654

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=89.18  E-value=0.23  Score=43.85  Aligned_cols=26  Identities=23%  Similarity=0.299  Sum_probs=20.4

Q ss_pred             cccccccCCceEEEccCCCcchhHHH
Q 014486           76 CIPQAILGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        76 ~i~~~~~~~~~ii~~~tGsGKT~~~~  101 (423)
                      ++..+..+.++++.||+|+|||..+.
T Consensus        14 ~l~~l~~g~~vLL~G~~GtGKT~lA~   39 (262)
T TIGR02640        14 ALRYLKSGYPVHLRGPAGTGKTTLAM   39 (262)
T ss_pred             HHHHHhcCCeEEEEcCCCCCHHHHHH
Confidence            33445568899999999999998654

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).

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=89.06  E-value=0.25  Score=37.57  Aligned_cols=15  Identities=27%  Similarity=0.514  Sum_probs=13.1

Q ss_pred             eEEEccCCCcchhHH
Q 014486           86 VICQAKSGMGKTAVF  100 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~  100 (423)
                      ++|.|++|||||..+
T Consensus         2 I~I~G~~gsGKST~a   16 (121)
T PF13207_consen    2 IIISGPPGSGKSTLA   16 (121)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            689999999999754

...

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	423
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		1e-168
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		1e-168
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		1e-167
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		1e-105
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		4e-70
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		4e-63
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		5e-63
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		5e-63
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		6e-63
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		3e-62
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		4e-62
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		2e-59
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		3e-59
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		3e-57
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		6e-56
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		1e-54
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		3e-54
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-51
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-51
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		2e-51
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		2e-51
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		4e-47
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		7e-47
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		4e-46
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		5e-43
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		2e-42
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		4e-41
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		2e-36
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		2e-32
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		1e-30
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		3e-30
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		6e-30
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		8e-30
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		2e-29
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		4e-29
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		5e-28
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		5e-26
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		1e-25
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		1e-24
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		1e-24
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		1e-24
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-24
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		2e-24
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		3e-23
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		2e-22
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		1e-20
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		2e-20
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		2e-20
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		3e-20
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		4e-20
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		2e-18
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		6e-18
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		1e-17
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		3e-17
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		3e-17
2jgn_A	185	Ddx3 Helicase Domain Length = 185		8e-17
3ly5_A	262	Ddx18 Dead-Domain Length = 262		1e-16
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		4e-16
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		5e-16
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		2e-15
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		4e-15
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		6e-14
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		3e-09
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		3e-09
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		3e-09
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		7e-07
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		1e-06
1gm5_A	780	Structure Of Recg Bound To Three-Way Dna Junction L		3e-06
2fwr_A	472	Structure Of Archaeoglobus Fulgidis Xpb Length = 47		3e-05
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		5e-05
2fzl_A	219	Structure Of C-Terminal Domain Of Archaeoglobus Ful		7e-05

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  589 bits (1518), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 280/367 (76%), Positives = 320/367 (87%)
Query: 39  GYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTA 98
           G  G  SSGFRDFLLKPELLRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKSGMGKTA
Sbjct: 1   GSPGHMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTA 60
Query: 99  VFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH 158
           VFVL+TLQQ EP  GQV+ LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG++IK  
Sbjct: 61  VFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKD 120
Query: 159 KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKM 218
           +++LK  CP IVVGTPGRILALAR+K L+LK+++HFILDECDKMLE LDMRRDVQEIF+M
Sbjct: 121 EEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRM 180
Query: 219 TPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRK 278
           TPH+KQVMMFSATLSKEIRPVC+KFMQDPMEI+VDDE KLTLHGL Q+Y+KL + EKNRK
Sbjct: 181 TPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRK 240
Query: 279 LNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN 338
           L DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I IH GM QEERL+RY+ FK+  
Sbjct: 241 LFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQ 300
Query: 339 KRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDS 398
           +RILVAT+L GRG+DIERVNI  NYDMP+ +DTYLHRV RAGRFGTKGLAITFVS  +D+
Sbjct: 301 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDA 360
Query: 399 DILNQVS 405
            ILN V 
Sbjct: 361 KILNDVQ 367

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  588 bits (1517), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 280/367 (76%), Positives = 320/367 (87%)
Query: 39  GYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTA 98
           G  G  SSGFRDFLLKPELLRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKSGMGKTA
Sbjct: 1   GSPGHMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTA 60
Query: 99  VFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH 158
           VFVL+TLQQ EP  GQV+ LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG++IK  
Sbjct: 61  VFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKD 120
Query: 159 KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKM 218
           +++LK  CP IVVGTPGRILALAR+K L+LK+++HFILDECDKMLE LDMRRDVQEIF+M
Sbjct: 121 EEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRM 180
Query: 219 TPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRK 278
           TPH+KQVMMFSATLSKEIRPVC+KFMQDPMEI+VDDE KLTLHGL Q+Y+KL + EKNRK
Sbjct: 181 TPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRK 240
Query: 279 LNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN 338
           L DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I IH GM QEERL+RY+ FK+  
Sbjct: 241 LFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQ 300
Query: 339 KRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDS 398
           +RILVAT+L GRG+DIERVNI  NYDMP+ +DTYLHRV RAGRFGTKGLAITFVS  +D+
Sbjct: 301 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDA 360
Query: 399 DILNQVS 405
            ILN V 
Sbjct: 361 KILNDVQ 367

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  585 bits (1509), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 277/362 (76%), Positives = 317/362 (87%)
Query: 44  HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLS 103
           H SGFRDFLLKPELLRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKSGMGKTAVFVL+
Sbjct: 5   HMSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLA 64
Query: 104 TLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLK 163
           TLQQ EP  GQV+ LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG++IK  +++LK
Sbjct: 65  TLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLK 124
Query: 164 NECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK 223
             CP IVVGTPGRILALAR+K L+LK+++HFILDE DKMLE LDMRRDVQEIF+MTPH+K
Sbjct: 125 KNCPHIVVGTPGRILALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQEIFRMTPHEK 184
Query: 224 QVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLL 283
           QVMMFSATLSKEIRPVC+KFMQDPMEI+VDDE KLTLHGL Q+Y+KL + EKNRKL DLL
Sbjct: 185 QVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLL 244
Query: 284 DALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILV 343
           D L+FNQVVIFVKSV R   L +LLVE NFP+I IH GM QEERL+RY+ FK+  +RILV
Sbjct: 245 DVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILV 304
Query: 344 ATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQ 403
           AT+L GRG+DIERVNI  NYDMP+ +DTYLHRV RAGRFGTKGLAITFVS  +D+ ILN 
Sbjct: 305 ATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILND 364
Query: 404 VS 405
           V 
Sbjct: 365 VQ 366

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score =  377 bits (969), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 175/220 (79%), Positives = 199/220 (90%)
Query: 33  GEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKS 92
           G   K  YV IHSSGFRDFLLKPELLRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKS
Sbjct: 1   GSDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKS 60
Query: 93  GMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGG 152
           GMGKTAVFVL+TLQQ EP  GQV+ LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG
Sbjct: 61  GMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGG 120
Query: 153 VNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDV 212
           ++IK  +++LK  CP IVVGTPGRILALAR+K L+LK+++HFILDECDKMLE LDMRRDV
Sbjct: 121 LSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDV 180
Query: 213 QEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
           QEIF+MTPH+KQVMMFSATLSKEIRPVC+KFMQDPMEI+V
Sbjct: 181 QEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 220

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score =  261 bits (668), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 145/347 (41%), Positives = 205/347 (59%), Gaps = 7/347 (2%)
Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F DF LK ELL  I ++GFE PS +Q E IP AI G D++ +AK+G GKTA FV+ TL++
Sbjct: 23  FEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEK 82
Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLK-NEC 166
            +P   ++ AL++  TRELA Q          +   I   V  GG N++   D+L+ NE 
Sbjct: 83  VKPKLNKIQALIMVPTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLR--DDILRLNET 139
Query: 167 PQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVM 226
             I+VGTPGR+L LA  K   L +   FI+DE DKML S D +  +++I    P   Q +
Sbjct: 140 VHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKML-SRDFKTIIEQILSFLPPTHQSL 198
Query: 227 MFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDAL 286
           +FSAT    ++    K +  P EI + +E  LTL G+ Q+Y  + E +K   LN L   L
Sbjct: 199 LFSATFPLTVKEFMVKHLHKPYEINLMEE--LTLKGITQYYAFVEERQKLHCLNTLFSKL 256
Query: 287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD 346
             NQ +IF  S +R   L K + +  +     H+ M Q+ER   +  F++G  R LV +D
Sbjct: 257 QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD 316
Query: 347 LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVS 393
           L+ RGIDI+ VN+VIN+D P +A+TYLHR+GR+GRFG  GLAI  ++
Sbjct: 317 LLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLIN 363

>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 =  238 bits (607), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 134/357 (37%), Positives = 207/357 (57%), Gaps = 8/357 (2%)
Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP 112
           L+ +LLR I   GFE PS +Q   I Q I G DVI Q++SG GKTA F +S LQ  +   
Sbjct: 45  LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV 104
Query: 113 GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQ-IVV 171
            +  AL+L  TRELA QI         Y+ +++     GG N+   +D+ K +  Q +V 
Sbjct: 105 RETQALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNV--GEDIRKLDYGQHVVA 161
Query: 172 GTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT 231
           GTPGR+  + R + L  + ++  +LDE D+ML     +  + ++++  P   QV++ SAT
Sbjct: 162 GTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPATQVVLISAT 220
Query: 232 LSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLLDALDFNQ 290
           L  EI  +  KFM DP+ I V  + +LTL G+ Q ++ +   E K   L DL D L   Q
Sbjct: 221 LPHEILEMTNKFMTDPIRILVKRD-ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQ 279
Query: 291 VVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGR 350
            VIF  +  +   L + + E NF    +H  M Q+ER +  K F+ G  R+L++TD+  R
Sbjct: 280 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 339
Query: 351 GIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF 407
           G+D+ +V+++INYD+P++ + Y+HR+GR+GR+G KG+AI FV +  D  IL  + ++
Sbjct: 340 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKN-DDIRILRDIEQY 395

>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 =  238 bits (607), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 134/357 (37%), Positives = 207/357 (57%), Gaps = 8/357 (2%)
Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP 112
           L+ +LLR I   GFE PS +Q   I Q I G DVI Q++SG GKTA F +S LQ  +   
Sbjct: 45  LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV 104
Query: 113 GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQ-IVV 171
            +  AL+L  TRELA QI         Y+ +++     GG N+   +D+ K +  Q +V 
Sbjct: 105 RETQALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNV--GEDIRKLDYGQHVVA 161
Query: 172 GTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT 231
           GTPGR+  + R + L  + ++  +LDE D+ML     +  + ++++  P   QV++ SAT
Sbjct: 162 GTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPATQVVLISAT 220
Query: 232 LSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLLDALDFNQ 290
           L  EI  +  KFM DP+ I V  + +LTL G+ Q ++ +   E K   L DL D L   Q
Sbjct: 221 LPHEILEMTNKFMTDPIRILVKRD-ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQ 279
Query: 291 VVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGR 350
            VIF  +  +   L + + E NF    +H  M Q+ER +  K F+ G  R+L++TD+  R
Sbjct: 280 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 339
Query: 351 GIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF 407
           G+D+ +V+++INYD+P++ + Y+HR+GR+GR+G KG+AI FV +  D  IL  + ++
Sbjct: 340 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKN-DDIRILRDIEQY 395

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  238 bits (607), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 134/357 (37%), Positives = 207/357 (57%), Gaps = 8/357 (2%)
Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP 112
           L+ +LLR I   GFE PS +Q   I Q I G DVI Q++SG GKTA F +S LQ  +   
Sbjct: 44  LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV 103
Query: 113 GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQ-IVV 171
            +  AL+L  TRELA QI         Y+ +++     GG N+   +D+ K +  Q +V 
Sbjct: 104 RETQALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNV--GEDIRKLDYGQHVVA 160
Query: 172 GTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT 231
           GTPGR+  + R + L  + ++  +LDE D+ML     +  + ++++  P   QV++ SAT
Sbjct: 161 GTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPATQVVLISAT 219
Query: 232 LSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLLDALDFNQ 290
           L  EI  +  KFM DP+ I V  + +LTL G+ Q ++ +   E K   L DL D L   Q
Sbjct: 220 LPHEILEMTNKFMTDPIRILVKRD-ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQ 278
Query: 291 VVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGR 350
            VIF  +  +   L + + E NF    +H  M Q+ER +  K F+ G  R+L++TD+  R
Sbjct: 279 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 338
Query: 351 GIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF 407
           G+D+ +V+++INYD+P++ + Y+HR+GR+GR+G KG+AI FV +  D  IL  + ++
Sbjct: 339 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKN-DDIRILRDIEQY 394

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  238 bits (606), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 134/357 (37%), Positives = 207/357 (57%), Gaps = 8/357 (2%)
Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP 112
           L+ +LLR I   GFE PS +Q   I Q I G DVI Q++SG GKTA F +S LQ  +   
Sbjct: 23  LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV 82
Query: 113 GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQ-IVV 171
            +  AL+L  TRELA QI         Y+ +++     GG N+   +D+ K +  Q +V 
Sbjct: 83  RETQALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNV--GEDIRKLDYGQHVVA 139
Query: 172 GTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT 231
           GTPGR+  + R + L  + ++  +LDE D+ML     +  + ++++  P   QV++ SAT
Sbjct: 140 GTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPATQVVLISAT 198
Query: 232 LSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLLDALDFNQ 290
           L  EI  +  KFM DP+ I V  + +LTL G+ Q ++ +   E K   L DL D L   Q
Sbjct: 199 LPHEILEMTNKFMTDPIRILVKRD-ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQ 257
Query: 291 VVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGR 350
            VIF  +  +   L + + E NF    +H  M Q+ER +  K F+ G  R+L++TD+  R
Sbjct: 258 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 317
Query: 351 GIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF 407
           G+D+ +V+++INYD+P++ + Y+HR+GR+GR+G KG+AI FV +  D  IL  + ++
Sbjct: 318 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKN-DDIRILRDIEQY 373

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  235 bits (600), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 131/357 (36%), Positives = 207/357 (57%), Gaps = 8/357 (2%)
Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP 112
           L+ +LLR I   GFE PS +Q   I Q I G DVI Q++SG GKTA F +S LQ  +   
Sbjct: 8   LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQV 67
Query: 113 GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQ-IVV 171
            +  AL+L  TRELA Q+         Y+ +++     GG N+   +D+ K +  Q +V 
Sbjct: 68  RETQALILAPTRELAVQVQKGLLALGDYM-NVQCHACIGGTNV--GEDIRKLDYGQHVVA 124
Query: 172 GTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT 231
           GTPGR+  + R + L  + ++  +LDE D+ML     +  + ++++  P   QV++ SAT
Sbjct: 125 GTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPATQVVLISAT 183
Query: 232 LSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLLDALDFNQ 290
           L  EI  +  KFM DP+ I V  + +LTL G+ Q ++ +   E K   L DL D L   Q
Sbjct: 184 LPHEILEMTNKFMTDPIRILVKRD-ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQ 242
Query: 291 VVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGR 350
            VIF  +  +   L + + E NF    +H  M Q+ER +  K F+ G  R+L++TD+  R
Sbjct: 243 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 302
Query: 351 GIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF 407
           G+D+ +V+++INYD+P++ + Y+HR+GR+GR+G KG+A+ FV +  D  +L  + ++
Sbjct: 303 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKN-DDIRVLRDIEQY 358

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  235 bits (599), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 130/357 (36%), Positives = 207/357 (57%), Gaps = 8/357 (2%)
Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP 112
           L+ +LLR I   GFE PS +Q   I Q I G DVI Q++SG GKTA F +S LQ  +   
Sbjct: 8   LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQV 67
Query: 113 GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQ-IVV 171
            +  AL+L  TRELA Q+         Y+ +++     GG N+   +D+ K +  Q +V 
Sbjct: 68  RETQALILAPTRELAVQVQKGLLALGDYM-NVQSHACIGGTNV--GEDIRKLDYGQHVVA 124
Query: 172 GTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT 231
           GTPGR+  + R + L  + ++  +LDE D+ML     +  + ++++  P   QV++ SAT
Sbjct: 125 GTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPATQVVLISAT 183
Query: 232 LSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLLDALDFNQ 290
           L  E+  +  KFM DP+ I V  + +LTL G+ Q ++ +   E K   L DL D L   Q
Sbjct: 184 LPHEVLEMTNKFMTDPIRILVKRD-ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQ 242
Query: 291 VVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGR 350
            VIF  +  +   L + + E NF    +H  M Q+ER +  K F+ G  R+L++TD+  R
Sbjct: 243 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 302
Query: 351 GIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF 407
           G+D+ +V+++INYD+P++ + Y+HR+GR+GR+G KG+A+ FV +  D  +L  + ++
Sbjct: 303 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKN-DDIRVLRDIEQY 358

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  226 bits (575), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 146/362 (40%), Positives = 205/362 (56%), Gaps = 5/362 (1%)
Query: 47  GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQ 106
            F D  L   LLR I   GFE PS +Q   I   I G DVI QA+SG GKTA F +S LQ
Sbjct: 15  SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQ 74
Query: 107 QTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNEC 166
           Q E +     ALVL  TRELA QI         Y+     A   GG N++     L+ E 
Sbjct: 75  QIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACI-GGTNVRAEVQKLQMEA 133
Query: 167 PQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVM 226
           P I+VGTPGR+  +   + LS K ++ F+LDE D+ML S   +  + +IF+    + QV+
Sbjct: 134 PHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEML-SRGFKDQIYDIFQKLNSNTQVV 192
Query: 227 MFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLLDA 285
           + SAT+  ++  V KKFM+DP+ I V  E +LTL G+ Q YI +   E K   L DL + 
Sbjct: 193 LLSATMPSDVLEVTKKFMRDPIRILVKKE-ELTLEGIRQFYINVEREEWKLDTLCDLYET 251
Query: 286 LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVAT 345
           L   Q VIF+ +  +   L + +   +F    +H  M Q+ER    + F+ G+ R+L+ T
Sbjct: 252 LTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITT 311
Query: 346 DLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVS 405
           DL+ RGID+++V++VINYD+P + + Y+HR+GR GRFG KG+AI  V+   D   L  + 
Sbjct: 312 DLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE-EDKRTLRDIE 370
Query: 406 KF 407
            F
Sbjct: 371 TF 372

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  225 bits (574), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 145/362 (40%), Positives = 204/362 (56%), Gaps = 5/362 (1%)
Query: 47  GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQ 106
            F D  L   LLR I   GFE PS +Q   I   I G DVI QA+SG GKTA F +S LQ
Sbjct: 41  SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQ 100
Query: 107 QTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNEC 166
           Q E +     ALVL  TRELA QI         Y+         GG N++     L+ E 
Sbjct: 101 QIELDLKATQALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEA 159
Query: 167 PQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVM 226
           P I+VGTPGR+  +   + LS K ++ F+LDE D+ML S   +  + +IF+    + QV+
Sbjct: 160 PHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEML-SRGFKDQIYDIFQKLNSNTQVV 218
Query: 227 MFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLLDA 285
           + SAT+  ++  V KKFM+DP+ I V  E +LTL G+ Q YI +   E K   L DL + 
Sbjct: 219 LLSATMPSDVLEVTKKFMRDPIRILVKKE-ELTLEGIRQFYINVEREEWKLDTLCDLYET 277
Query: 286 LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVAT 345
           L   Q VIF+ +  +   L + +   +F    +H  M Q+ER    + F+ G+ R+L+ T
Sbjct: 278 LTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITT 337
Query: 346 DLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVS 405
           DL+ RGID+++V++VINYD+P + + Y+HR+GR GRFG KG+AI  V+   D   L  + 
Sbjct: 338 DLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE-EDKRTLRDIE 396
Query: 406 KF 407
            F
Sbjct: 397 TF 398

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  219 bits (557), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 142/361 (39%), Positives = 210/361 (58%), Gaps = 7/361 (1%)
Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  L   LLR +   GFE PS +Q   I   I G DV+ QA+SG GKT  F ++ LQ+
Sbjct: 24  FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 83
Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            + +     AL+L  TRELA QI       + ++ DIKV    GG +     + L++   
Sbjct: 84  IDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--A 140
Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
           QIVVGTPGR+    + +      ++ FILDE D+ML S   +  + +IF + P   QV++
Sbjct: 141 QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSS-GFKEQIYQIFTLLPPTTQVVL 199
Query: 228 FSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLLDAL 286
            SAT+  ++  V  KFM++P+ I V  + +LTL G+ Q Y+ + E E K   L DL D++
Sbjct: 200 LSATMPNDVLEVTTKFMRNPVRILVKKD-ELTLEGIKQFYVNVEEEEYKYECLTDLYDSI 258
Query: 287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD 346
              Q VIF  +  +  EL   L    F    I+S + Q+ER T  K F+ G+ RIL++TD
Sbjct: 259 SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD 318
Query: 347 LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           L+ RGID+++V++VINYD+P + + Y+HR+GR GRFG KG+AI FV++  D   + ++ K
Sbjct: 319 LLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTN-EDVGAMRELEK 377
Query: 407 F 407
           F
Sbjct: 378 F 378

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score =  214 bits (546), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 103/147 (70%), Positives = 120/147 (81%)
Query: 259 TLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICI 318
           +LHGL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I I
Sbjct: 2   SLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 61
Query: 319 HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGR 378
           H GM QEERL+RY+ FK+  +RILVAT+L GRG+DIERVNI  NYDMP+ +DTYLHRV R
Sbjct: 62  HRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVAR 121
Query: 379 AGRFGTKGLAITFVSSASDSDILNQVS 405
           AGRFGTKGLAITFVS  +D+ ILN V 
Sbjct: 122 AGRFGTKGLAITFVSDENDAKILNDVQ 148

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  210 bits (535), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 140/361 (38%), Positives = 204/361 (56%), Gaps = 7/361 (1%)
Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  L   LLR +   GFE PS +Q   I   I G DV+ QA+SG GKT  F ++ LQ+
Sbjct: 23  FDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAALQR 82
Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            + +     AL L  TRELA QI       + +  DIKV    GG +     + L++   
Sbjct: 83  IDTSVKAPQALXLAPTRELALQIQKVVXALA-FHXDIKVHACIGGTSFVEDAEGLRD--A 139
Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
           QIVVGTPGR+    + +      ++ FILDE D+ L S   +  + +IF + P   QV++
Sbjct: 140 QIVVGTPGRVFDNIQRRRFRTDKIKXFILDEADEXLSS-GFKEQIYQIFTLLPPTTQVVL 198
Query: 228 FSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLLDAL 286
            SAT   ++  V  KF ++P+ I V  + +LTL G+ Q Y+ + E E K   L DL D++
Sbjct: 199 LSATXPNDVLEVTTKFXRNPVRILVKKD-ELTLEGIKQFYVNVEEEEYKYECLTDLYDSI 257
Query: 287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD 346
              Q VIF  +  +  EL   L    F    I+S + Q+ER T  K F+ G+ RIL++TD
Sbjct: 258 SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTD 317
Query: 347 LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           L+ RGID+++V++VINYD+P + + Y+HR+GR GRFG KG+AI FV++  D     ++ K
Sbjct: 318 LLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTN-EDVGAXRELEK 376
Query: 407 F 407
           F
Sbjct: 377 F 377

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score =  209 bits (531), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 130/352 (36%), Positives = 199/352 (56%), Gaps = 12/352 (3%)
Query: 43  IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFV 101
           +    F +  L   +L AI + GFE P+++Q + IP  +    +++ QA++G GKTA F 
Sbjct: 3   VEYXNFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFA 62
Query: 102 LSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDL 161
           +  ++    N G + A++L  TRELA Q+  E E       ++K+A  YGG  I      
Sbjct: 63  IPLIELVNENNG-IEAIILTPTRELAIQVADEIESLKGN-KNLKIAKIYGGKAIYPQIKA 120
Query: 162 LKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPH 221
           LKN    IVVGTPGRIL       L+LKNV++FILDE D+ L +    +DV++I      
Sbjct: 121 LKN--ANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXL-NXGFIKDVEKILNACNK 177
Query: 222 DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLND 281
           DK++++FSAT  +EI  + KK+  D    Y   +AK+  + + Q Y++++E E+   L  
Sbjct: 178 DKRILLFSATXPREILNLAKKYXGD----YSFIKAKINAN-IEQSYVEVNENERFEALCR 232
Query: 282 LLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRI 341
           LL   +F  +V F K+     EL   L +  F +  IH  +SQ +R    + FK+   RI
Sbjct: 233 LLKNKEFYGLV-FCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRI 291
Query: 342 LVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVS 393
           L+ATD+  RGID+  +N VINY +P + ++Y HR+GR GR G KG AI+ ++
Sbjct: 292 LIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIIN 343

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score =  200 bits (509), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 124/370 (33%), Positives = 199/370 (53%), Gaps = 15/370 (4%)
Query: 47  GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL--GMDVICQAKSGMGKTAVFVLST 104
            F +  LKP+LL+ +   GF  PS++Q   +P  +     ++I Q++SG GKTA FVL+ 
Sbjct: 93  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152
Query: 105 LQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN 164
           L Q EP       L L  T ELA Q     E+   + P++K+A    G  ++  + +   
Sbjct: 153 LSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI--- 209
Query: 165 ECPQIVVGTPGRILAL-ARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK 223
              QIV+GTPG +L   ++ K +  K ++ F+LDE D M+ +   +     I +M P + 
Sbjct: 210 -SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC 268
Query: 224 QVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEL-EKNRKLNDL 282
           Q+++FSAT    +    +K + DP  I +  E + TL  + Q+Y+  S   EK + L +L
Sbjct: 269 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE-TLDTIKQYYVLCSSRDEKFQALCNL 327
Query: 283 LDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRIL 342
             A+   Q +IF  +   A+ L   L +       +   M  E+R    + F+EG +++L
Sbjct: 328 YGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVL 387
Query: 343 VATDLVGRGIDIERVNIVINYDMPDSAD------TYLHRVGRAGRFGTKGLAITFVSSAS 396
           V T++  RGID+E+V++VIN+D+P   D      TYLHR+GR GRFG +GLA+  V S  
Sbjct: 388 VTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH 447
Query: 397 DSDILNQVSK 406
             +ILN++ +
Sbjct: 448 SMNILNRIQE 457

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score =  200 bits (508), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 124/370 (33%), Positives = 199/370 (53%), Gaps = 15/370 (4%)
Query: 47  GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL--GMDVICQAKSGMGKTAVFVLST 104
            F +  LKP+LL+ +   GF  PS++Q   +P  +     ++I Q++SG GKTA FVL+ 
Sbjct: 63  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 122
Query: 105 LQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN 164
           L Q EP       L L  T ELA Q     E+   + P++K+A    G  ++  + +   
Sbjct: 123 LSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI--- 179
Query: 165 ECPQIVVGTPGRILAL-ARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK 223
              QIV+GTPG +L   ++ K +  K ++ F+LDE D M+ +   +     I +M P + 
Sbjct: 180 -SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC 238
Query: 224 QVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEL-EKNRKLNDL 282
           Q+++FSAT    +    +K + DP  I +  E + TL  + Q+Y+  S   EK + L +L
Sbjct: 239 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE-TLDTIKQYYVLCSSRDEKFQALCNL 297
Query: 283 LDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRIL 342
             A+   Q +IF  +   A+ L   L +       +   M  E+R    + F+EG +++L
Sbjct: 298 YGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVL 357
Query: 343 VATDLVGRGIDIERVNIVINYDMPDSAD------TYLHRVGRAGRFGTKGLAITFVSSAS 396
           V T++  RGID+E+V++VIN+D+P   D      TYLHR+GR GRFG +GLA+  V S  
Sbjct: 358 VTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH 417
Query: 397 DSDILNQVSK 406
             +ILN++ +
Sbjct: 418 SMNILNRIQE 427

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score =  200 bits (508), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 124/370 (33%), Positives = 200/370 (54%), Gaps = 15/370 (4%)
Query: 47  GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL--GMDVICQAKSGMGKTAVFVLST 104
            F +  LKP+LL+ +   GF  PS++Q   +P  +     ++I Q++SG GKTA FVL+ 
Sbjct: 26  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 85
Query: 105 LQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN 164
           L Q EP       L L  T ELA Q     E+   + P++K+A    G  ++  + + + 
Sbjct: 86  LSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE- 144
Query: 165 ECPQIVVGTPGRILAL-ARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK 223
              QIV+GTPG +L   ++ K +  K ++ F+LDE D M+ +   +     I +M P + 
Sbjct: 145 ---QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC 201
Query: 224 QVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEL-EKNRKLNDL 282
           Q+++FSAT    +    +K + DP  I +  E + TL  + Q+Y+  S   EK + L +L
Sbjct: 202 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE-TLDTIKQYYVLCSSRDEKFQALCNL 260
Query: 283 LDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRIL 342
             A+   Q +IF  +   A+ L   L +       +   M  E+R    + F+EG +++L
Sbjct: 261 YGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVL 320
Query: 343 VATDLVGRGIDIERVNIVINYDMPDSAD------TYLHRVGRAGRFGTKGLAITFVSSAS 396
           V T++  RGID+E+V++VIN+D+P   D      TYLHR+GR GRFG +GLA+  V S  
Sbjct: 321 VTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH 380
Query: 397 DSDILNQVSK 406
             +ILN++ +
Sbjct: 381 SMNILNRIQE 390

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score =  199 bits (507), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 124/370 (33%), Positives = 199/370 (53%), Gaps = 15/370 (4%)
Query: 47  GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL--GMDVICQAKSGMGKTAVFVLST 104
            F +  LKP+LL+ +   GF  PS++Q   +P  +     ++I Q++SG GKTA FVL+ 
Sbjct: 42  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 101
Query: 105 LQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN 164
           L Q EP       L L  T ELA Q     E+   + P++K+A    G  ++  + +   
Sbjct: 102 LSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI--- 158
Query: 165 ECPQIVVGTPGRILAL-ARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK 223
              QIV+GTPG +L   ++ K +  K ++ F+LDE D M+ +   +     I +M P + 
Sbjct: 159 -SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC 217
Query: 224 QVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSEL-EKNRKLNDL 282
           Q+++FSAT    +    +K + DP  I +  E + TL  + Q+Y+  S   EK + L +L
Sbjct: 218 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE-TLDTIKQYYVLCSSRDEKFQALCNL 276
Query: 283 LDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRIL 342
             A+   Q +IF  +   A+ L   L +       +   M  E+R    + F+EG +++L
Sbjct: 277 YGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVL 336
Query: 343 VATDLVGRGIDIERVNIVINYDMPDSAD------TYLHRVGRAGRFGTKGLAITFVSSAS 396
           V T++  RGID+E+V++VIN+D+P   D      TYLHR+GR GRFG +GLA+  V S  
Sbjct: 337 VTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH 396
Query: 397 DSDILNQVSK 406
             +ILN++ +
Sbjct: 397 SMNILNRIQE 406

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  185 bits (469), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 120/379 (31%), Positives = 200/379 (52%), Gaps = 24/379 (6%)
Query: 42  GIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG--MDVICQAKSGMGKTAV 99
           G  +  F +  L PELL+ I    F+ PS++Q   +P  +     ++I Q++SG GKTA 
Sbjct: 1   GAMAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAA 60
Query: 100 FVLSTLQQTEPNPGQVTALVLCHTRELAYQ---ICHEFERFSTYLPDIKVAVFYGGVNIK 156
           F L+ L +  P      A+ L  +RELA Q   +  E  +F+     + V   +   N +
Sbjct: 61  FSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEK-NKQ 119
Query: 157 IHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIF 216
           I+         Q++VGTPG +L L R K + L+ ++ F+LDE D ML+   +      + 
Sbjct: 120 INA--------QVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVK 171
Query: 217 KMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL-SELEK 275
           +  P D Q+++FSAT +  +R   KK + +   + +    ++ +  + Q Y+   +E +K
Sbjct: 172 RFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTN-EVNVDAIKQLYMDCKNEADK 230
Query: 276 NRKLNDLLDALDFNQVVIFVKSVSRAAEL-NKLLVECNFPSICIHSGMSQEERLTRYKGF 334
              L +L   +     +IFV +   A  L  KL  E +  SI +H  +  +ER      F
Sbjct: 231 FDVLTELYGVMTIGSSIIFVATKKTANVLYGKLKSEGHEVSI-LHGDLQTQERDRLIDDF 289
Query: 335 KEGNKRILVATDLVGRGIDIERVNIVINYDMPDSAD------TYLHRVGRAGRFGTKGLA 388
           +EG  ++L+ T+++ RGIDI  V++V+NYD+P  A+      TY+HR+GR GRFG KG+A
Sbjct: 290 REGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVA 349
Query: 389 ITFVSSASDSDILNQVSKF 407
           I+FV   +  +IL+ + K+
Sbjct: 350 ISFVHDKNSFNILSAIQKY 368

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  184 bits (467), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 120/379 (31%), Positives = 200/379 (52%), Gaps = 24/379 (6%)
Query: 42  GIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG--MDVICQAKSGMGKTAV 99
           G  +  F +  L PELL+ I    F+ PS++Q   +P  +     ++I Q++SG GKTA 
Sbjct: 1   GAMAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAA 60
Query: 100 FVLSTLQQTEPNPGQVTALVLCHTRELAYQ---ICHEFERFSTYLPDIKVAVFYGGVNIK 156
           F L+ L +  P      A+ L  +RELA Q   +  E  +F+     + V   +   N +
Sbjct: 61  FSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEK-NKQ 119
Query: 157 IHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIF 216
           I+         Q++VGTPG +L L R K + L+ ++ F+LDE D ML+   +      + 
Sbjct: 120 INA--------QVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVK 171
Query: 217 KMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL-SELEK 275
           +  P D Q+++FSAT +  +R   KK + +   + +    ++ +  + Q Y+   +E +K
Sbjct: 172 RFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTN-EVNVDAIKQLYMDCKNEADK 230
Query: 276 NRKLNDLLDALDFNQVVIFVKSVSRAAEL-NKLLVECNFPSICIHSGMSQEERLTRYKGF 334
              L +L   +     +IFV +   A  L  KL  E +  SI +H  +  +ER      F
Sbjct: 231 FDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSI-LHGDLQTQERDRLIDDF 289
Query: 335 KEGNKRILVATDLVGRGIDIERVNIVINYDMPDSAD------TYLHRVGRAGRFGTKGLA 388
           +EG  ++L+ T+++ RGIDI  V++V+NYD+P  A+      TY+HR+GR GRFG KG+A
Sbjct: 290 REGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVA 349
Query: 389 ITFVSSASDSDILNQVSKF 407
           I+FV   +  +IL+ + K+
Sbjct: 350 ISFVHDKNSFNILSAIQKY 368

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  182 bits (461), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 123/410 (30%), Positives = 211/410 (51%), Gaps = 38/410 (9%)
Query: 25  DSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGM 84
           +++  K  G    +      S+  RD ++       +  SG++ P+ +Q   IP    G 
Sbjct: 40  NNIPVKVTGSDVPQPIQHFTSADLRDIIID-----NVNKSGYKIPTPIQKCSIPVISSGR 94
Query: 85  DVICQAKSGMGKTAVFVLSTLQQTEPNP-----GQVTALVLCHTRELAYQICHEFERFS- 138
           D++  A++G GKTA F+L  L +   +P     G+   +++  TRELA QI +E  +F+ 
Sbjct: 95  DLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAF 154
Query: 139 -TYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILD 197
            +YL   K+ + YGG + +   + +   C  +V+ TPGR+L       ++ ++ R  +LD
Sbjct: 155 ESYL---KIGIVYGGTSFRHQNECITRGC-HVVIATPGRLLDFVDRTFITFEDTRFVVLD 210
Query: 198 ECDKMLE---SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVD- 253
           E D+ML+   S DMRR +  +  M P + Q +MFSAT  +EI+ +  +F+++ + + +  
Sbjct: 211 EADRMLDMGFSEDMRRIMTHV-TMRP-EHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGI 268
Query: 254 -----DEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLL 308
                 + K T++       ++++  K  KL ++L     +  ++FV++   A  L   L
Sbjct: 269 VGGACSDVKQTIY-------EVNKYAKRSKLIEILSE-QADGTIVFVETKRGADFLASFL 320
Query: 309 VECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDS 368
            E  FP+  IH    Q +R    + FK G+ ++L+AT +  RG+DI+ +  VINYDMP  
Sbjct: 321 SEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSK 380
Query: 369 ADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSFQCL 418
            D Y+HR+GR GR G  G A +F     D  I   + K   +L GS Q +
Sbjct: 381 IDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVK---ILEGSGQTV 427

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score =  170 bits (430), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 115/343 (33%), Positives = 184/343 (53%), Gaps = 26/343 (7%)
Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP 112
           +  ++ +AI + GF++ +EVQ + IP  + G +V+ +AK+G GKTA + +  L+      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELG---- 56
Query: 113 GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVG 172
             + +LV+  TREL  Q+         Y+ D KVA  YGG+  K   + ++N    IVV 
Sbjct: 57  --MKSLVVTPTRELTRQVASHIRDIGRYM-DTKVAEVYGGMPYKAQINRVRN--ADIVVA 111
Query: 173 TPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATL 232
           TPGR+L L     + L +    I+DE D M E +    D++ I   T + K   +FSAT+
Sbjct: 112 TPGRLLDLWSKGVIDLSSFEIVIIDEADLMFE-MGFIDDIKIILAQTSNRKITGLFSATI 170
Query: 233 SKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQ-- 290
            +EIR V K F+ +  EI    EA + L  +   ++ + +  +++     + AL  N+  
Sbjct: 171 PEEIRKVVKDFITNYEEI----EACIGLANVEHKFVHVKDDWRSK-----VQALRENKDK 221
Query: 291 -VVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVG 349
            V++FV++ +R A+L +L       +I +   + Q  R      F+EG   +L+ TD+  
Sbjct: 222 GVIVFVRTRNRVAKLVRLFDN----AIELRGDLPQSVRNRNIDAFREGEYDMLITTDVAS 277
Query: 350 RGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFV 392
           RG+DI  V  VIN+D P    TY+HR+GR GR G KG AITF+
Sbjct: 278 RGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFI 320

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  165 bits (418), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 117/370 (31%), Positives = 180/370 (48%), Gaps = 25/370 (6%)
Query: 44  HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLS 103
           H   F D  +   ++  I  + +  P+ VQ   IP      D++  A++G GKTA F+L 
Sbjct: 13  HIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLP 72
Query: 104 TLQQTEPN-PGQV-----------------TALVLCHTRELAYQICHEFERFSTYLPDIK 145
            L Q   + PG+                   +LVL  TRELA QI  E  +FS Y   ++
Sbjct: 73  ILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFS-YRSRVR 131
Query: 146 VAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE- 204
             V YGG +I      L+  C  ++V TPGR++ +     + L   ++ +LDE D+ML+ 
Sbjct: 132 PCVVYGGADIGQQIRDLERGC-HLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDM 190
Query: 205 --SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHG 262
                +RR V++        +  MMFSAT  KEI+ + + F+ + + + V      T   
Sbjct: 191 GFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVG-RVGSTSEN 249
Query: 263 LVQHYIKLSELEKNRKLNDLLDALDFNQV-VIFVKSVSRAAELNKLLVECNFPSICIHSG 321
           + Q  + + E +K   L DLL+A   + + ++FV++   A  L   L    +    IH  
Sbjct: 250 ITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGD 309
Query: 322 MSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR 381
            SQ +R      F+ G   ILVAT +  RG+DI  V  VIN+D+P   + Y+HR+GR GR
Sbjct: 310 RSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGR 369
Query: 382 FGTKGLAITF 391
            G  GLA +F
Sbjct: 370 VGNLGLATSF 379

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score =  149 bits (377), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 90/208 (43%), Positives = 115/208 (55%), Gaps = 2/208 (0%)
Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  LK  LLR I   GFE PS +Q   I   I G DVI QA+SG GKTA F +S LQQ
Sbjct: 32  FDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQ 91
Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            E    +  ALVL  TRELA QI         Y+     A   GG N++     L+ E P
Sbjct: 92  LEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACI-GGTNVRNEMQKLQAEAP 150
Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
            IVVGTPGR+  +   + LS K ++ F+LDE D+ML S   +  + EIF+      QV++
Sbjct: 151 HIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEML-SRGFKDQIYEIFQKLNTSIQVVL 209
Query: 228 FSATLSKEIRPVCKKFMQDPMEIYVDDE 255
            SAT+  ++  V KKFM+DP+ I V  E
Sbjct: 210 LSATMPTDVLEVTKKFMRDPIRILVKKE 237

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  136 bits (343), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 81/205 (39%), Positives = 107/205 (52%), Gaps = 2/205 (0%)
Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  L   LLR I   GFE PS +Q   I   I G DVI QA+SG G TA F +S LQQ
Sbjct: 17  FDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISILQQ 76
Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            E +     ALVL  TRELA QI         Y+         GG N++     L+ E P
Sbjct: 77  IELDLXATQALVLAPTRELAQQIQXVVMALGDYM-GASCHACIGGTNVRAEVQXLQMEAP 135
Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
            I+VGTPGR+  +   + LS   +  F+LDE D+ML S      + +IF+    + QV++
Sbjct: 136 HIIVGTPGRVFDMLNRRYLSPXYIXMFVLDEADEML-SRGFXDQIYDIFQXLNSNTQVVL 194
Query: 228 FSATLSKEIRPVCKKFMQDPMEIYV 252
            SAT+  ++  V   FM+DP+ I V
Sbjct: 195 LSATMPSDVLEVTXXFMRDPIRILV 219

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score =  130 bits (328), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 76/208 (36%), Positives = 111/208 (53%), Gaps = 8/208 (3%)
Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F+DF LKPE+L A+   G   P+ +Q   +P A+ G D+I QA++G GKT  F L   ++
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 108 TEPNPG---QVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN 164
             P+     +  ALVL  TRELA Q+  E    +   P +KV   YGG      K+ L  
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASE---LTAVAPHLKVVAVYGGTGYGKQKEALLR 119
Query: 165 ECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQ 224
                VV TPGR L   R   L L  V   +LDE D+ML S+    +V+ +   TP  +Q
Sbjct: 120 GA-DAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEML-SMGFEEEVEALLSATPPSRQ 177
Query: 225 VMMFSATLSKEIRPVCKKFMQDPMEIYV 252
            ++FSATL    + + +++M++P+ I V
Sbjct: 178 TLLFSATLPSWAKRLAERYMKNPVLINV 205

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score =  129 bits (324), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 75/208 (36%), Positives = 111/208 (53%), Gaps = 8/208 (3%)
Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F+DF LKPE+L A+   G   P+ ++   +P A+ G D+I QA++G GKT  F L   ++
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 108 TEPNPG---QVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN 164
             P+     +  ALVL  TRELA Q+  E    +   P +KV   YGG      K+ L  
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASE---LTAVAPHLKVVAVYGGTGYGKQKEALLR 119
Query: 165 ECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQ 224
                VV TPGR L   R   L L  V   +LDE D+ML S+    +V+ +   TP  +Q
Sbjct: 120 GA-DAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEML-SMGFEEEVEALLSATPPSRQ 177
Query: 225 VMMFSATLSKEIRPVCKKFMQDPMEIYV 252
            ++FSATL    + + +++M++P+ I V
Sbjct: 178 TLLFSATLPSWAKRLAERYMKNPVLINV 205

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score =  128 bits (322), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 77/205 (37%), Positives = 113/205 (55%), Gaps = 4/205 (1%)
Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  L  +LLR +   GFE PS +Q   I   I G DV+ QA+SG GKT  F ++ LQ+
Sbjct: 23  FDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 82
Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            + +     AL+L  TRELA QI       + ++ DIKV    GG +     + L++   
Sbjct: 83  IDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--A 139
Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
           QIVVGTPGR+    + +      ++ FILDE D+ML S   +  + +IF + P   QV++
Sbjct: 140 QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSS-GFKEQIYQIFTLLPPTTQVVL 198
Query: 228 FSATLSKEIRPVCKKFMQDPMEIYV 252
            SAT+  ++  V  KFM++P+ I V
Sbjct: 199 LSATMPNDVLEVTTKFMRNPVRILV 223

>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 =  127 bits (320), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 80/214 (37%), Positives = 117/214 (54%), Gaps = 5/214 (2%)
Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  L   LLR +   GFE PS +Q   I   I G DV+ QA+SG GKT  F ++ LQ+
Sbjct: 16  FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 75
Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            + +     AL+L  TRELA QI       + ++ DIKV    GG +     + L++   
Sbjct: 76  IDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--A 132
Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
           QIVVGTPGR+    + +      ++ FILDE D+ML S   +  + +IF + P   QV++
Sbjct: 133 QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSS-GFKEQIYQIFTLLPPTTQVVL 191
Query: 228 FSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLH 261
            SAT+  ++  V  KFM++P+ I V  + +LTL 
Sbjct: 192 LSATMPNDVLEVTTKFMRNPVRILVKKD-ELTLE 224

>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 =  126 bits (317), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 68/149 (45%), Positives = 90/149 (60%), Gaps = 2/149 (1%)
Query: 245 QDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAEL 304
           QDP EI + +E  LTL G+ Q+Y  ++E +K   LN L   L  NQ +IF  S  R   L
Sbjct: 3   QDPYEINLMEE--LTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELL 60
Query: 305 NKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYD 364
            K + +  +    IH+ M QE R   +  F+ G  R LV TDL  RGIDI+ VN+VIN+D
Sbjct: 61  AKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFD 120
Query: 365 MPDSADTYLHRVGRAGRFGTKGLAITFVS 393
            P  A+TYLHR+GR+GRFG  GLAI  ++
Sbjct: 121 FPKLAETYLHRIGRSGRFGHLGLAINLIT 149

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score =  125 bits (314), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 67/210 (31%), Positives = 124/210 (59%), Gaps = 4/210 (1%)
Query: 44  HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLS 103
            +  F+D  +   L  A    G+  P+++Q E IP A+ G D+I  A++G GKT  F L 
Sbjct: 41  ETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALP 100
Query: 104 TLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLK 163
            L      P ++ ALVL  TRELA+QI  +FE   + +  ++ AV  GG++  + + L  
Sbjct: 101 ILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSI-GVQSAVIVGGID-SMSQSLAL 158
Query: 164 NECPQIVVGTPGRILA-LARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHD 222
            + P I++ TPGR++  L   K  +L+ +++ ++DE D++L ++D   +V +I K+ P D
Sbjct: 159 AKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRIL-NMDFETEVDKILKVIPRD 217
Query: 223 KQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
           ++  +FSAT++K+++ + +  +++P++  V
Sbjct: 218 RKTFLFSATMTKKVQKLQRAALKNPVKCAV 247

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score =  122 bits (305), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 66/204 (32%), Positives = 118/204 (57%), Gaps = 4/204 (1%)
Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D+ LK ELL  I + G+E PS +Q E IP A+ G D++ +AK+G GK+  +++  L++
Sbjct: 5   FEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLER 64
Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLK-NEC 166
            +     + A+V+  TRELA Q+     + S ++   KV    GG N++   D+++ ++ 
Sbjct: 65  LDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLR--DDIMRLDDT 122
Query: 167 PQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVM 226
             +V+ TPGRIL L +     + +V+  +LDE DK+L S D  + +++I    P ++Q++
Sbjct: 123 VHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLL-SQDFVQIMEDIILTLPKNRQIL 181
Query: 227 MFSATLSKEIRPVCKKFMQDPMEI 250
           ++SAT    ++      ++ P EI
Sbjct: 182 LYSATFPLSVQKFMNSHLEKPYEI 205

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score =  115 bits (287), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 69/212 (32%), Positives = 114/212 (53%), Gaps = 7/212 (3%)
Query: 45  SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLST 104
            + F  F  +P ++ AI    F  P+E+Q   IP A+ G   + Q+++G GKT  ++L  
Sbjct: 3   ETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPI 62
Query: 105 LQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAV---FYGGVNIKIHKDL 161
            ++ +P   +V A++   TRELA QI HE  + + + P  +  V     GG + +  K L
Sbjct: 63  XEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQ--KAL 120
Query: 162 LK-NECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTP 220
            K N  P IV+GTPGRI    R++ L +      ++DE D  L+      DV +I    P
Sbjct: 121 EKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLXLDX-GFITDVDQIAARXP 179
Query: 221 HDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
            D Q ++FSAT+ ++++P  KK+ ++P  ++V
Sbjct: 180 KDLQXLVFSATIPEKLKPFLKKYXENPTFVHV 211

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score =  114 bits (285), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 73/200 (36%), Positives = 100/200 (50%), Gaps = 2/200 (1%)
Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F   LL   +L  +  +GFE PS VQ + IP    G+D+I QAKSG GKT VF    L  
Sbjct: 26  FESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDS 85
Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
                     L+L  TRE+A QI          +  ++  VF GG  +   K  LK +C 
Sbjct: 86  LVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK-KC- 143
Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
            I VG+PGRI  L     L+  ++R FILDE DK+LE    +  +  I+   P  KQ++ 
Sbjct: 144 HIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLA 203
Query: 228 FSATLSKEIRPVCKKFMQDP 247
            SAT  + +     K+M+DP
Sbjct: 204 VSATYPEFLANALTKYMRDP 223

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score =  111 bits (277), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 97/371 (26%), Positives = 175/371 (47%), Gaps = 32/371 (8%)
Query: 52  LLKPELLRAIVDSGFEHPSEVQHECIPQAILGM---DVICQAKSGMGKTAVFVLSTLQQ- 107
           +L  E+ +AI    F   + VQ + I + IL     DVI +AK+G GKT  F++   Q  
Sbjct: 78  VLDKEIHKAITRMEFPGLTPVQQKTI-KPILSSEDHDVIARAKTGTGKTFAFLIPIFQHL 136
Query: 108 ---TEPNPGQVTALVLCHTRELAYQICHEFERFSTY---LPDIKVAVFYGGVNIKIHKDL 161
                 +   V A+++  TR+LA QI  E ++       L         GG + +   + 
Sbjct: 137 INTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNK 196
Query: 162 LKNECPQIVVGTPGRIL-ALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKM-- 218
           +    P IV+ TPGR++  L +  +   + V + +LDE D++LE +  R D++ I  +  
Sbjct: 197 MNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLE-IGFRDDLETISGILN 255
Query: 219 -----TPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVD--DEAKLTLHGLVQHYIKLS 271
                +  + + ++FSATL  +++ +    M     +++D  D+ +   H  +   + +S
Sbjct: 256 EKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVIS 315
Query: 272 ELEKN------RKLNDLLDALDFN-QVVIFVKSVSRAAELNKLL---VECNFPSICIHSG 321
           E   N        +   +   D N + +IF  +V   + L  +L    + + P +  H  
Sbjct: 316 EKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGK 375
Query: 322 MSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR 381
           ++Q +R +  K FK+    ILV TD+  RG+D   V+ V+   +P     Y+HR+GR  R
Sbjct: 376 ITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTAR 435
Query: 382 FGTKGLAITFV 392
            G +G ++ F+
Sbjct: 436 SGKEGSSVLFI 446

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score =  110 bits (276), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 97/371 (26%), Positives = 175/371 (47%), Gaps = 32/371 (8%)
Query: 52  LLKPELLRAIVDSGFEHPSEVQHECIPQAILGM---DVICQAKSGMGKTAVFVLSTLQQ- 107
           +L  E+ +AI    F   + VQ + I + IL     DVI +AK+G GKT  F++   Q  
Sbjct: 27  VLDKEIHKAITRMEFPGLTPVQQKTI-KPILSSEDHDVIARAKTGTGKTFAFLIPIFQHL 85
Query: 108 ---TEPNPGQVTALVLCHTRELAYQICHEFERFSTY---LPDIKVAVFYGGVNIKIHKDL 161
                 +   V A+++  TR+LA QI  E ++       L         GG + +   + 
Sbjct: 86  INTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNK 145
Query: 162 LKNECPQIVVGTPGRIL-ALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKM-- 218
           +    P IV+ TPGR++  L +  +   + V + +LDE D++LE +  R D++ I  +  
Sbjct: 146 MNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLE-IGFRDDLETISGILN 204
Query: 219 -----TPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVD--DEAKLTLHGLVQHYIKLS 271
                +  + + ++FSATL  +++ +    M     +++D  D+ +   H  +   + +S
Sbjct: 205 EKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVIS 264
Query: 272 ELEKN------RKLNDLLDALDFN-QVVIFVKSVSRAAELNKLL---VECNFPSICIHSG 321
           E   N        +   +   D N + +IF  +V   + L  +L    + + P +  H  
Sbjct: 265 EKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGK 324
Query: 322 MSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR 381
           ++Q +R +  K FK+    ILV TD+  RG+D   V+ V+   +P     Y+HR+GR  R
Sbjct: 325 ITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTAR 384
Query: 382 FGTKGLAITFV 392
            G +G ++ F+
Sbjct: 385 SGKEGSSVLFI 395

>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 =  110 bits (276), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 97/371 (26%), Positives = 175/371 (47%), Gaps = 32/371 (8%)
Query: 52  LLKPELLRAIVDSGFEHPSEVQHECIPQAILGM---DVICQAKSGMGKTAVFVLSTLQQ- 107
           +L  E+ +AI    F   + VQ + I + IL     DVI +AK+G GKT  F++   Q  
Sbjct: 27  VLDKEIHKAITRMEFPGLTPVQQKTI-KPILSSEDHDVIARAKTGTGKTFAFLIPIFQHL 85
Query: 108 ---TEPNPGQVTALVLCHTRELAYQICHEFERFSTY---LPDIKVAVFYGGVNIKIHKDL 161
                 +   V A+++  TR+LA QI  E ++       L         GG + +   + 
Sbjct: 86  INTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNK 145
Query: 162 LKNECPQIVVGTPGRIL-ALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKM-- 218
           +    P IV+ TPGR++  L +  +   + V + +LDE D++LE +  R D++ I  +  
Sbjct: 146 MNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLE-IGFRDDLETISGILN 204
Query: 219 -----TPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVD--DEAKLTLHGLVQHYIKLS 271
                +  + + ++FSATL  +++ +    M     +++D  D+ +   H  +   + +S
Sbjct: 205 EKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVIS 264
Query: 272 ELEKN------RKLNDLLDALDFN-QVVIFVKSVSRAAELNKLL---VECNFPSICIHSG 321
           E   N        +   +   D N + +IF  +V   + L  +L    + + P +  H  
Sbjct: 265 EKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGK 324
Query: 322 MSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR 381
           ++Q +R +  K FK+    ILV TD+  RG+D   V+ V+   +P     Y+HR+GR  R
Sbjct: 325 ITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTAR 384
Query: 382 FGTKGLAITFV 392
            G +G ++ F+
Sbjct: 385 SGKEGSSVLFI 395

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score =  110 bits (276), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 68/212 (32%), Positives = 111/212 (52%), Gaps = 7/212 (3%)
Query: 47  GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL--GMDVICQAKSGMGKTAVFVLST 104
            F +  LKP+LL+ +   GF  PS++Q   +P  +     ++I Q++SG GKTA FVL+ 
Sbjct: 93  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152
Query: 105 LQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN 164
           L Q EP       L L  T ELA Q     E+   + P++K+A    G  ++  + + + 
Sbjct: 153 LSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE- 211
Query: 165 ECPQIVVGTPGRILAL-ARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK 223
              QIV+GTPG +L   ++ K +  K ++ F+LDE D M+ +   +     I +M P + 
Sbjct: 212 ---QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC 268
Query: 224 QVMMFSATLSKEIRPVCKKFMQDPMEIYVDDE 255
           Q+++FSAT    +    +K + DP  I +  E
Sbjct: 269 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 300

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score =  109 bits (273), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 68/212 (32%), Positives = 111/212 (52%), Gaps = 7/212 (3%)
Query: 47  GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL--GMDVICQAKSGMGKTAVFVLST 104
            F +  LKP+LL+ +   GF  PS++Q   +P  +     ++I Q++SG GKTA FVL+ 
Sbjct: 26  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 85
Query: 105 LQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN 164
           L Q EP       L L  T ELA Q     E+   + P++K+A    G  ++  + + + 
Sbjct: 86  LSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE- 144
Query: 165 ECPQIVVGTPGRILAL-ARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK 223
              QIV+GTPG +L   ++ K +  K ++ F+LDE D M+ +   +     I +M P + 
Sbjct: 145 ---QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC 201
Query: 224 QVMMFSATLSKEIRPVCKKFMQDPMEIYVDDE 255
           Q+++FSAT    +    +K + DP  I +  E
Sbjct: 202 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 233

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score =  106 bits (264), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 56/139 (40%), Positives = 80/139 (57%)
Query: 256 AKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPS 315
           A LT   +    I++ E  K   L D+L   + +  +IF ++     +L   L +  +P 
Sbjct: 3   AGLTTRNIEHAVIQVREENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPC 62
Query: 316 ICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHR 375
             IH GM QE+R      FK G  R LVATD+  RGIDIE +++VINYD+P   ++Y+HR
Sbjct: 63  DKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHR 122
Query: 376 VGRAGRFGTKGLAITFVSS 394
            GR GR G KG AI+FV++
Sbjct: 123 TGRTGRAGNKGKAISFVTA 141

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score =  103 bits (256), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 64/205 (31%), Positives = 105/205 (51%), Gaps = 14/205 (6%)
Query: 45  SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG--MDVICQAKSGMGKTAVFVL 102
           +  F +  L PELL+ I    F+ PS++Q   +P  +     ++I Q++SG GKTA F L
Sbjct: 21  AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSL 80
Query: 103 STLQQTEPNPGQVTALVLCHTRELAYQ---ICHEFERFSTYLPDIKVAVFYGGVNIKIHK 159
           + L +  P      A+ L  +RELA Q   +  E  +F+     + V   +   N +I+ 
Sbjct: 81  TMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEK-NKQINA 139
Query: 160 DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMT 219
                   Q++VGTPG +L L R K + L+ ++ F+LDE D ML+   +      + +  
Sbjct: 140 --------QVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFL 191
Query: 220 PHDKQVMMFSATLSKEIRPVCKKFM 244
           P D Q+++FSAT +  +R   KK +
Sbjct: 192 PKDTQLVLFSATFADAVRQYAKKIV 216

>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 = 97.8 bits (242), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 107/210 (50%), Gaps = 14/210 (6%)
Query: 47  GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTL- 105
            F +  L P +   I+ + ++ P+ +Q   IP  +   D++  A++G GKTA F++  + 
Sbjct: 24  NFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIIN 83
Query: 106 --------QQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKI 157
                   QQ          L+L  TRELA QI  E ++FS   P ++  V YGG +   
Sbjct: 84  HLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTP-LRSCVVYGGADTHS 142
Query: 158 HKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE---SLDMRRDVQE 214
               ++  C  ++V TPGR++       +SL+  ++ +LDE D+ML+      +R+ ++E
Sbjct: 143 QIREVQMGC-HLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEE 201
Query: 215 IFKMTPHDKQVMMFSATLSKEIRPVCKKFM 244
               +  ++Q +MFSAT  KEI+ +   F+
Sbjct: 202 SNMPSGINRQTLMFSATFPKEIQKLAADFL 231

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 97.1 bits (240), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 118/227 (51%), Gaps = 13/227 (5%)
Query: 34  EAAKKGYVGIHSSGFRD-FLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKS 92
           ++ +K  +   +  F+D F   P+LL++I+  G   P+ +Q +  P  + G+D+I  A++
Sbjct: 7   KSGEKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQT 66
Query: 93  GMGKTAVFVLSTLQQTEPNP------GQVTALVLCHTRELAYQICHEFERFSTYLPDIKV 146
           G GKT  +++      +  P           LVL  TRELA  +  E  ++S     +K 
Sbjct: 67  GTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYS--YKGLKS 124
Query: 147 AVFYGGVNIKIH-KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES 205
              YGG N     +D+ K     I++ TPGR+  L  +  ++L+++ + ++DE DKML+ 
Sbjct: 125 ICIYGGRNRNGQIEDISKGV--DIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLD- 181
Query: 206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
           ++    +++I      D+Q +M SAT    +R +   +++DPM +YV
Sbjct: 182 MEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 96.7 bits (239), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 63/149 (42%), Positives = 94/149 (63%), Gaps = 2/149 (1%)
Query: 260 LHGLVQHYIKLSELE-KNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICI 318
           L G+ Q Y+ + E E K   L DL D++   Q VIF  +  +  EL   L    F    I
Sbjct: 1   LEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 60
Query: 319 HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGR 378
           +S + Q+ER T  K F+ G+ RIL++TDL+ RGID+++V++VINYD+P + + Y+HR+GR
Sbjct: 61  YSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGR 120
Query: 379 AGRFGTKGLAITFVSSASDSDILNQVSKF 407
            GRFG KG+AI FV++  D   + ++ KF
Sbjct: 121 GGRFGRKGVAINFVTN-EDVGAMRELEKF 148

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 96.3 bits (238), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 43/119 (36%), Positives = 69/119 (57%)
Query: 291 VVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGR 350
           V+IF +  +    +++ L+     ++ IH G  QEER    + F+EG K +LVATD+  +
Sbjct: 57  VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK 116
Query: 351 GIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMF 409
           G+D   +  VINYDMP+  + Y+HR+GR G  G  G+A TF++ A D  +L  +   + 
Sbjct: 117 GLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLL 175

>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 = 95.9 bits (237), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 57/145 (39%), Positives = 78/145 (53%), Gaps = 2/145 (1%)
Query: 265 QHYIKLSELE-KNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMS 323
           Q Y +  +LE K   L  LL   +  + ++FV+   R  EL   L E    +  +   M 
Sbjct: 6   QWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMV 65
Query: 324 QEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFG 383
           Q +R    K   EG   +LVATD+  RGIDI  V+ V N+DMP S DTYLHR+GR  R G
Sbjct: 66  QGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAG 125
Query: 384 TKGLAITFVSSASDSDILNQVSKFM 408
            KG AI+ V  A D  +L +V +++
Sbjct: 126 RKGTAISLV-EAHDHLLLGKVGRYI 149

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 90.5 bits (223), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 53/144 (36%), Positives = 84/144 (58%), Gaps = 8/144 (5%)
Query: 271 SELEKNRKLNDLLDALDFNQVVIFVKSVSRAAEL-NKLLVECNFPSICIHSGMSQEERLT 329
           +E +K   L +L   +     +IFV +   A  L  KL  E +  SI +H  +  +ER  
Sbjct: 18  NEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSI-LHGDLQTQERDR 76
Query: 330 RYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSAD------TYLHRVGRAGRFG 383
               F+EG  ++L+ T+++ RGIDI  V++V+NYD+P  A+      TY+HR+GR GRFG
Sbjct: 77  LIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFG 136
Query: 384 TKGLAITFVSSASDSDILNQVSKF 407
            KG+AI+FV   +  +IL+ + K+
Sbjct: 137 RKGVAISFVHDKNSFNILSAIQKY 160

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 88.6 bits (218), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 53/145 (36%), Positives = 82/145 (56%), Gaps = 8/145 (5%)
Query: 271 SELEKNRKLNDLLDALDFNQVVIFVKSVSRAAEL-NKLLVECNFPSICIHSGMSQEERLT 329
           +E +K   L +L         +IFV +   A  L  KL  E +  SI +H  +  +ER  
Sbjct: 19  NEADKFDVLTELYGVXTIGSSIIFVATKKTANVLYGKLKSEGHEVSI-LHGDLQTQERDR 77
Query: 330 RYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSAD------TYLHRVGRAGRFG 383
               F+EG  ++L+ T+++ RGIDI  V+ V+NYD+P  A+      TY+HR+GR GRFG
Sbjct: 78  LIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFG 137
Query: 384 TKGLAITFVSSASDSDILNQVSKFM 408
            KG+AI+FV   +  +IL+ + K+ 
Sbjct: 138 RKGVAISFVHDKNSFNILSAIQKYF 162

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 87.8 bits (216), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 53/145 (36%), Positives = 82/145 (56%), Gaps = 8/145 (5%)
Query: 271 SELEKNRKLNDLLDALDFNQVVIFVKSVSRAAEL-NKLLVECNFPSICIHSGMSQEERLT 329
           +E +K   L +L         +IFV +   A  L  KL  E +  SI +H  +  +ER  
Sbjct: 20  NEADKFDVLTELYGLXTIGSSIIFVATKKTANVLYGKLKSEGHEVSI-LHGDLQTQERDR 78
Query: 330 RYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSAD------TYLHRVGRAGRFG 383
               F+EG  ++L+ T+++ RGIDI  V+ V+NYD+P  A+      TY+HR+GR GRFG
Sbjct: 79  LIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFG 138
Query: 384 TKGLAITFVSSASDSDILNQVSKFM 408
            KG+AI+FV   +  +IL+ + K+ 
Sbjct: 139 RKGVAISFVHDKNSFNILSAIQKYF 163

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 86.3 bits (212), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 59/216 (27%), Positives = 113/216 (52%), Gaps = 13/216 (6%)
Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQ- 106
           F DF L  + L+ + ++ +   +E+Q + I  A+ G DV+  AK+G GKT  F++  L+ 
Sbjct: 27  FSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEA 86
Query: 107 ----QTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL 162
               Q     G +  L++  TRELAYQ      +      D    +  GG ++K   + +
Sbjct: 87  LYRLQWTSTDG-LGVLIISPTRELAYQTFEVLRKVGKN-HDFSAGLIIGGKDLKHEAERI 144
Query: 163 KNECPQIVVGTPGRILALARDKDLSL--KNVRHFILDECDKMLESLDMRRDVQEIFKMTP 220
            N    I+V TPGR+L    D+ +S    +++  +LDE D++L+ +     +  + +  P
Sbjct: 145 NN--INILVCTPGRLLQ-HMDETVSFHATDLQMLVLDEADRILD-MGFADTMNAVIENLP 200
Query: 221 HDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEA 256
             +Q ++FSAT +K ++ + +  +++P  ++V ++A
Sbjct: 201 KKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHEKA 236

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 86.3 bits (212), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 45/143 (31%), Positives = 84/143 (58%), Gaps = 9/143 (6%)
Query: 258 LTLHGLVQHYIKLSELEKNR--KLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPS 315
           LTL+ + Q+Y+ L E  K++   L ++  ++   Q +IF ++   A  L   +++     
Sbjct: 3   LTLNNIRQYYV-LCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQV 61
Query: 316 ICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMP------DSA 369
             +   ++ E+R +  + F++G +++L+ T++  RGID+++V IV+N+D+P         
Sbjct: 62  SLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDY 121
Query: 370 DTYLHRVGRAGRFGTKGLAITFV 392
           +TYLHR+GR GRFG KGLA   +
Sbjct: 122 ETYLHRIGRTGRFGKKGLAFNMI 144

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 84.7 bits (208), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 48/134 (35%), Positives = 70/134 (52%), Gaps = 1/134 (0%)
Query: 259 TLHGLVQHYIKLSELEKNRKLNDLLDALDFNQV-VIFVKSVSRAAELNKLLVECNFPSIC 317
           T   + Q  + + E +K   L DLL+A   + + ++FV++   A  L   L    +    
Sbjct: 16  TSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTS 75
Query: 318 IHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVG 377
           IH   SQ +R      F+ G   ILVAT +  RG+DI  V  VIN+D+P   + Y+HR+G
Sbjct: 76  IHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIG 135
Query: 378 RAGRFGTKGLAITF 391
           R GR G  GLA +F
Sbjct: 136 RTGRVGNLGLATSF 149

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 84.0 bits (206), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 57/196 (29%), Positives = 101/196 (51%), Gaps = 10/196 (5%)
Query: 52  LLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQ----- 106
           L+    L+AI + GF + +E+QH+ I   + G D++  AK+G GKT  F++  ++     
Sbjct: 60  LVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKL 119
Query: 107 QTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNEC 166
           +  P  G    L+L  TRELA Q     +   T+       +  GG N       L N  
Sbjct: 120 RFMPRNG-TGVLILSPTRELAMQTFGVLKELMTHHVHT-YGLIMGGSNRSAEAQKLGNGI 177
Query: 167 PQIVVGTPGRIL-ALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQV 225
             I+V TPGR+L  +        KN++  ++DE D++L+ +    ++++I K+ P  +Q 
Sbjct: 178 -NIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILD-VGFEEELKQIIKLLPTRRQT 235
Query: 226 MMFSATLSKEIRPVCK 241
           M+FSAT ++++  + +
Sbjct: 236 MLFSATQTRKVEDLAR 251

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 82.8 bits (203), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 56/203 (27%), Positives = 100/203 (49%), Gaps = 12/203 (5%)
Query: 57  LLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP---- 112
           ++  I    F  P+ +Q +  P A+ G+D++  A++G GKT  ++L  +      P    
Sbjct: 40  VMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLER 99
Query: 113 --GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH-KDLLKNECPQI 169
             G +  LVL  TRELA Q+      +      +K    YGG       +DL +    +I
Sbjct: 100 GDGPI-CLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLERGV--EI 155
Query: 170 VVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS 229
            + TPGR++        +L+   + +LDE D+ML+ +     +++I      D+Q +M+S
Sbjct: 156 CIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLD-MGFEPQIRKIVDQIRPDRQTLMWS 214
Query: 230 ATLSKEIRPVCKKFMQDPMEIYV 252
           AT  KE+R + + F++D + I +
Sbjct: 215 ATWPKEVRQLAEDFLKDYIHINI 237

>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 = 82.4 bits (202), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 56/203 (27%), Positives = 100/203 (49%), Gaps = 12/203 (5%)
Query: 57  LLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP---- 112
           ++  I    F  P+ +Q +  P A+ G+D++  A++G GKT  ++L  +      P    
Sbjct: 54  VMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLER 113
Query: 113 --GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH-KDLLKNECPQI 169
             G +  LVL  TRELA Q+      +      +K    YGG       +DL +    +I
Sbjct: 114 GDGPI-CLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLERGV--EI 169
Query: 170 VVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS 229
            + TPGR++        +L+   + +LDE D+ML+ +     +++I      D+Q +M+S
Sbjct: 170 CIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLD-MGFEPQIRKIVDQIRPDRQTLMWS 228
Query: 230 ATLSKEIRPVCKKFMQDPMEIYV 252
           AT  KE+R + + F++D + I +
Sbjct: 229 ATWPKEVRQLAEDFLKDYIHINI 251

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/207 (30%), Positives = 101/207 (48%), Gaps = 23/207 (11%)
Query: 49  RDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ- 107
           +++ +   LL+ I+D+GF+ P+ +Q + IP  + G +++  A +G GKT  F +  L Q 
Sbjct: 32  QEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQL 91
Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL--KNE 165
            +P      AL++  TRELA QI  E          IK++   G     IHK  +  K  
Sbjct: 92  KQPANKGFRALIISPTRELASQIHREL---------IKISEGTGFRIHMIHKAAVAAKKF 142
Query: 166 CPQ------IVVGTPGRILALARD--KDLSLKNVRHFILDECDKMLE--SLDMRRDVQEI 215
            P+      I+V TP R++ L +     + L +V   ++DE DK+ E      R  +  I
Sbjct: 143 GPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASI 202
Query: 216 F-KMTPHDKQVMMFSATLSKEIRPVCK 241
           F   T H  +  MFSAT + ++   CK
Sbjct: 203 FLACTSHKVRRAMFSATFAYDVEQWCK 229

>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 = 79.0 bits (193), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 35/96 (36%), Positives = 59/96 (61%)
Query: 279 LNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN 338
           L+DLL     ++ ++F ++ +   E+ + L+    P+  +H  MSQ ER      F++G 
Sbjct: 19  LSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGE 78
Query: 339 KRILVATDLVGRGIDIERVNIVINYDMPDSADTYLH 374
            R+LVATD+  RG+DI +V++V++Y MPD A+ Y H
Sbjct: 79  VRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQH 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 = 75.5 bits (184), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 33/96 (34%), Positives = 59/96 (61%)
Query: 279 LNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN 338
           L+DLL     ++ ++F ++ +   E+ + L+    P+  +H  +SQ ER      F++G 
Sbjct: 22  LSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGE 81
Query: 339 KRILVATDLVGRGIDIERVNIVINYDMPDSADTYLH 374
            R+LVATD+  RG+DI +V++V++Y +PD A+ Y H
Sbjct: 82  VRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQH 117

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/106 (30%), Positives = 56/106 (52%), Gaps = 3/106 (2%)
Query: 290 QVVIFVKSVSRAAELNKLL---VECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD 346
           + +IF  +V   + L  +L    + + P +  H  ++Q +R +  K FK+    ILV TD
Sbjct: 35  KAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD 94
Query: 347 LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFV 392
           +  RG+D   V+ V+   +P     Y+HR+GR  R G +G ++ F+
Sbjct: 95  VGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 140

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/106 (30%), Positives = 56/106 (52%), Gaps = 3/106 (2%)
Query: 290 QVVIFVKSVSRAAELNKLL---VECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD 346
           + +IF  +V   + L  +L    + + P +  H  ++Q +R +  K FK+    ILV TD
Sbjct: 35  KAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD 94
Query: 347 LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFV 392
           +  RG+D   V+ V+   +P     Y+HR+GR  R G +G ++ F+
Sbjct: 95  VGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 140

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/106 (30%), Positives = 56/106 (52%), Gaps = 3/106 (2%)
Query: 290 QVVIFVKSVSRAAELNKLL---VECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD 346
           + +IF  +V   + L  +L    + + P +  H  ++Q +R +  K FK+    ILV TD
Sbjct: 35  KAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD 94
Query: 347 LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFV 392
           +  RG+D   V+ V+   +P     Y+HR+GR  R G +G ++ F+
Sbjct: 95  VGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 140

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 52.0 bits (123), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 28/104 (26%), Positives = 50/104 (48%)
Query: 292 VIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRG 351
           +I+  S ++  +    L      +   H+G+    R    + F+  + +I+VAT   G G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMG 299
Query: 352 IDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSA 395
           I+   V  V+++D+P + ++Y    GRAGR G    A+ F   A
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPA 343

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/104 (26%), Positives = 49/104 (47%)
Query: 292 VIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRG 351
           +I+  S ++  +    L      +   H+G+    R    + F+  + +I+VAT   G G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXG 299
Query: 352 IDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSA 395
           I+   V  V+++D+P + ++Y    GRAGR G    A  F   A
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFYDPA 343

>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction Length = 780

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 89/340 (26%), Positives = 140/340 (41%), Gaps = 54/340 (15%)
Query: 84  MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQ-ICHEFERFSTYLP 142
           M+ + Q   G GKT V  L+ L   E   G  TA  +  T  LA Q      E FS +  
Sbjct: 390 MNRLLQGDVGSGKTVVAQLAILDNYEA--GFQTAF-MVPTSILAIQHYRRTVESFSKF-- 444
Query: 143 DIKVAVFYGGVNIKIHKDL---LKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDEC 199
           +I VA+  G       + +   L+N    +V+GT   I      +D+  KN+   I+DE 
Sbjct: 445 NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALI-----QEDVHFKNLGLVIIDEQ 499
Query: 200 D----KMLESLDMRRDVQEIFKM--TPHDKQVMM-----FSATLSKEIRPVCKKF--MQD 246
                K  E+L  +  + +   M  TP  + + +        T+  E+ P  K+   M  
Sbjct: 500 HRFGVKQREALMNKGKMVDTLVMSATPIPRSMALAFYGDLDVTVIDEMPPGRKEVQTMLV 559
Query: 247 PM----EIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAA 302
           PM    E+Y     ++   G  Q +I    +E++ KLN                 V  A 
Sbjct: 560 PMDRVNEVYEFVRQEVMRGG--QAFIVYPLIEESDKLN-----------------VKSAV 600
Query: 303 ELNKLLVECNFPSI---CIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI 359
           E+ + L +  FP      +H  +SQEE+      F EG   ILV+T ++  GID+ R N+
Sbjct: 601 EMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANV 660
Query: 360 VINYDMPDSADTYLHRV-GRAGRFGTKGLAITFVSSASDS 398
           ++  +        LH++ GR GR G +      V    + 
Sbjct: 661 MVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEE 700

>pdb|2FWR|A Chain A, Structure Of Archaeoglobus Fulgidis Xpb Length = 472

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 30/111 (27%), Positives = 58/111 (52%), Gaps = 5/111 (4%)
Query: 268 IKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEER 327
           I  +   K RKL ++L+    ++++IF +       ++K+ +    P+I   +  S+EER
Sbjct: 329 IAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL---IPAITHRT--SREER 383
Query: 328 LTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGR 378
               +GF+ G  R +V++ ++  GID+   N+ +      SA  Y+ R+GR
Sbjct: 384 EEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGR 434

>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase Length = 591

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 37/73 (50%)
Query: 319 HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGR 378
           H+ +  E++ T ++ +     +++VAT   G GID   V  VI++ M  S + Y    GR
Sbjct: 298 HANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGR 357
Query: 379 AGRFGTKGLAITF 391
           AGR   K   I +
Sbjct: 358 AGRDDMKADCILY 370

>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus Xpb Length = 219

Iteration: 1
 Score = 45.4 bits (106), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 29/104 (27%), Positives = 56/104 (53%), Gaps = 5/104 (4%)
Query: 275 KNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGF 334
           K RKL ++L+    ++++IF +       ++K+ +    P+I   +  S+EER    +GF
Sbjct: 101 KIRKLREILERHRKDKIIIFTRHNELVYRISKVFL---IPAITHRT--SREEREEILEGF 155
Query: 335 KEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGR 378
           + G  R +V++ ++  GID+   N+ +      SA  Y+ R+GR
Sbjct: 156 RTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGR 199

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	423
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	0.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	0.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-141
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-141
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-140
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-132
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-131
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	1e-130
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	1e-129
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-128
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-115
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	1e-114
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-110
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-108
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	1e-104
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-97
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	7e-92
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	1e-82
3bor_A	237	Human initiation factor 4A-II; translation initiat	2e-79
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	4e-78
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	2e-77
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	3e-76
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	8e-76
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	3e-74
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	9e-69
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	3e-68
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	5e-68
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	3e-60
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	1e-56
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	4e-52
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	1e-51
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	3e-51
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	3e-51
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	7e-49
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	2e-48
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	1e-44
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	4e-42
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	6e-39
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	6e-37
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	1e-35
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	1e-17
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-17
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	5e-15
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	6e-17
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	4e-14
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	2e-12
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	4e-12
1yks_A	440	Genome polyprotein [contains: flavivirin protease	3e-11
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	4e-11
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	6e-11
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	9e-09
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	8e-11
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	2e-08
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	7e-10
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	8e-10
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	8e-09
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	1e-09
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	2e-09
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	5e-09
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	1e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	1e-08
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	2e-08
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	6e-08
3b6e_A	216	Interferon-induced helicase C domain-containing P;	1e-07
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	2e-07
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	1e-06
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	4e-05
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	2e-04

>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 =  614 bits (1586), Expect = 0.0
 Identities = 280/369 (75%), Positives = 320/369 (86%)

Query: 39  GYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTA 98
           G  G  SSGFRDFLLKPELLRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKSGMGKTA
Sbjct: 1   GSPGHMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTA 60

Query: 99  VFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH 158
           VFVL+TLQQ EP  GQV+ LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG++IK  
Sbjct: 61  VFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKD 120

Query: 159 KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKM 218
           +++LK  CP IVVGTPGRILALAR+K L+LK+++HFILDECDKMLE LDMRRDVQEIF+M
Sbjct: 121 EEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRM 180

Query: 219 TPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRK 278
           TPH+KQVMMFSATLSKEIRPVC+KFMQDPMEI+VDDE KLTLHGL Q+Y+KL + EKNRK
Sbjct: 181 TPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRK 240

Query: 279 LNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN 338
           L DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I IH GM QEERL+RY+ FK+  
Sbjct: 241 LFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQ 300

Query: 339 KRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDS 398
           +RILVAT+L GRG+DIERVNI  NYDMP+ +DTYLHRV RAGRFGTKGLAITFVS  +D+
Sbjct: 301 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDA 360

Query: 399 DILNQVSKF 407
            ILN V   
Sbjct: 361 KILNDVQDR 369

>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 =  520 bits (1342), Expect = 0.0
 Identities = 144/376 (38%), Positives = 209/376 (55%), Gaps = 6/376 (1%)

Query: 32  NGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAK 91
           +        +    + F DF LK ELL  I ++GFE PS +Q E IP AI G D++ +AK
Sbjct: 7   DTRPQTDDVLNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAK 66

Query: 92  SGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYG 151
           +G GKTA FV+ TL++ +P   ++ AL++  TRELA Q          +   I   V  G
Sbjct: 67  NGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHC-GISCMVTTG 125

Query: 152 GVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRD 211
           G N++     L      I+VGTPGR+L LA  K   L +   FI+DE DKML S D +  
Sbjct: 126 GTNLRDDILRLNE-TVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKML-SRDFKTI 183

Query: 212 VQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS 271
           +++I    P   Q ++FSAT    ++    K +  P EI + +E  LTL G+ Q+Y  + 
Sbjct: 184 IEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEE--LTLKGITQYYAFVE 241

Query: 272 ELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRY 331
           E +K   LN L   L  NQ +IF  S +R   L K + +  +     H+ M Q+ER   +
Sbjct: 242 ERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVF 301

Query: 332 KGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITF 391
             F++G  R LV +DL+ RGIDI+ VN+VIN+D P +A+TYLHR+GR+GRFG  GLAI  
Sbjct: 302 HEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINL 361

Query: 392 VSSASDSDILNQVSKF 407
           ++  +D   L ++ + 
Sbjct: 362 INW-NDRFNLYKIEQE 376

>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 =  409 bits (1053), Expect = e-141
 Identities = 145/361 (40%), Positives = 204/361 (56%), Gaps = 5/361 (1%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  L   LLR I   GFE PS +Q   I   I G DVI QA+SG GKTA F +S LQQ
Sbjct: 42  FDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQ 101

Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            E +     ALVL  TRELA QI         Y+         GG N++     L+ E P
Sbjct: 102 IELDLKATQALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAP 160

Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
            I+VGTPGR+  +   + LS K ++ F+LDE D+ML S   +  + +IF+    + QV++
Sbjct: 161 HIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEML-SRGFKDQIYDIFQKLNSNTQVVL 219

Query: 228 FSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS-ELEKNRKLNDLLDAL 286
            SAT+  ++  V KKFM+DP+ I V  E +LTL G+ Q YI +  E  K   L DL + L
Sbjct: 220 LSATMPSDVLEVTKKFMRDPIRILVKKE-ELTLEGIRQFYINVEREEWKLDTLCDLYETL 278

Query: 287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD 346
              Q VIF+ +  +   L + +   +F    +H  M Q+ER    + F+ G+ R+L+ TD
Sbjct: 279 TITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTD 338

Query: 347 LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           L+ RGID+++V++VINYD+P + + Y+HR+GR GRFG KG+AI  V+   D   L  +  
Sbjct: 339 LLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE-EDKRTLRDIET 397

Query: 407 F 407
           F
Sbjct: 398 F 398

>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 =  407 bits (1049), Expect = e-141
 Identities = 142/361 (39%), Positives = 210/361 (58%), Gaps = 7/361 (1%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  L   LLR +   GFE PS +Q   I   I G DV+ QA+SG GKT  F ++ LQ+
Sbjct: 23  FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 82

Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            + +     AL+L  TRELA QI       + ++ DIKV    GG +     + L++   
Sbjct: 83  IDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--A 139

Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
           QIVVGTPGR+    + +      ++ FILDE D+ML S   +  + +IF + P   QV++
Sbjct: 140 QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEML-SSGFKEQIYQIFTLLPPTTQVVL 198

Query: 228 FSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLLDAL 286
            SAT+  ++  V  KFM++P+ I V  + +LTL G+ Q Y+ + E E K   L DL D++
Sbjct: 199 LSATMPNDVLEVTTKFMRNPVRILVKKD-ELTLEGIKQFYVNVEEEEYKYECLTDLYDSI 257

Query: 287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD 346
              Q VIF  +  +  EL   L    F    I+S + Q+ER T  K F+ G+ RIL++TD
Sbjct: 258 SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD 317

Query: 347 LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSK 406
           L+ RGID+++V++VINYD+P + + Y+HR+GR GRFG KG+AI FV++  D   + ++ K
Sbjct: 318 LLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTN-EDVGAMRELEK 376

Query: 407 F 407
           F
Sbjct: 377 F 377

>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 =  405 bits (1043), Expect = e-140
 Identities = 137/396 (34%), Positives = 213/396 (53%), Gaps = 13/396 (3%)

Query: 15  DYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQH 74
                     +   TK   E +++  V   +  F    L+ +LLR I   GFE PS +Q 
Sbjct: 9   SGSARKRLLKEEDMTKVEFETSEEVDV---TPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 65

Query: 75  ECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEF 134
             I Q I G DVI Q++SG GKTA F +S LQ  +    +  AL+L  TRELA QI    
Sbjct: 66  RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 125

Query: 135 ERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHF 194
                Y+ +++     GG N+      L      +V GTPGR+  + R + L  + ++  
Sbjct: 126 LALGDYM-NVQCHACIGGTNVGEDIRKLD-YGQHVVAGTPGRVFDMIRRRSLRTRAIKML 183

Query: 195 ILDECDKMLESLDM--RRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
           +LDE D+ML   +   +  + ++++  P   QV++ SATL  EI  +  KFM DP+ I V
Sbjct: 184 VLDEADEML---NKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILV 240

Query: 253 DDEAKLTLHGLVQHYIKLS-ELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC 311
             + +LTL G+ Q ++ +  E  K   L DL D L   Q VIF  +  +   L + + E 
Sbjct: 241 KRD-ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREA 299

Query: 312 NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADT 371
           NF    +H  M Q+ER +  K F+ G  R+L++TD+  RG+D+ +V+++INYD+P++ + 
Sbjct: 300 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 359

Query: 372 YLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF 407
           Y+HR+GR+GR+G KG+AI FV +  D  IL  + ++
Sbjct: 360 YIHRIGRSGRYGRKGVAINFVKN-DDIRILRDIEQY 394

>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 =  386 bits (995), Expect = e-132
 Identities = 124/370 (33%), Positives = 199/370 (53%), Gaps = 15/370 (4%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGM--DVICQAKSGMGKTAVFVLSTL 105
           F +  LKP+LL+ +   GF  PS++Q   +P  +     ++I Q++SG GKTA FVL+ L
Sbjct: 27  FEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAML 86

Query: 106 QQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNE 165
            Q EP       L L  T ELA Q     E+   + P++K+A    G  ++  +    + 
Sbjct: 87  SQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE--RGQKIS- 143

Query: 166 CPQIVVGTPGRIL-ALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQ 224
             QIV+GTPG +L   ++ K +  K ++ F+LDE D M+ +   +     I +M P + Q
Sbjct: 144 -EQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQ 202

Query: 225 VMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL-SELEKNRKLNDLL 283
           +++FSAT    +    +K + DP  I +  E + TL  + Q+Y+   S  EK + L +L 
Sbjct: 203 MLLFSATFEDSVWKFAQKVVPDPNVIKLKRE-EETLDTIKQYYVLCSSRDEKFQALCNLY 261

Query: 284 DALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILV 343
            A+   Q +IF  +   A+ L   L +       +   M  E+R    + F+EG +++LV
Sbjct: 262 GAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLV 321

Query: 344 ATDLVGRGIDIERVNIVINYDMPDSAD------TYLHRVGRAGRFGTKGLAITFVSSASD 397
            T++  RGID+E+V++VIN+D+P   D      TYLHR+GR GRFG +GLA+  V S   
Sbjct: 322 TTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHS 381

Query: 398 SDILNQVSKF 407
            +ILN++ + 
Sbjct: 382 MNILNRIQEH 391

>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 =  386 bits (993), Expect = e-131
 Identities = 124/370 (33%), Positives = 199/370 (53%), Gaps = 15/370 (4%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGM--DVICQAKSGMGKTAVFVLSTL 105
           F +  LKP+LL+ +   GF  PS++Q   +P  +     ++I Q++SG GKTA FVL+ L
Sbjct: 94  FEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAML 153

Query: 106 QQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNE 165
            Q EP       L L  T ELA Q     E+   + P++K+A    G  ++  +    + 
Sbjct: 154 SQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE--RGQKIS- 210

Query: 166 CPQIVVGTPGRIL-ALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQ 224
             QIV+GTPG +L   ++ K +  K ++ F+LDE D M+ +   +     I +M P + Q
Sbjct: 211 -EQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQ 269

Query: 225 VMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL-SELEKNRKLNDLL 283
           +++FSAT    +    +K + DP  I +  E + TL  + Q+Y+   S  EK + L +L 
Sbjct: 270 MLLFSATFEDSVWKFAQKVVPDPNVIKLKRE-EETLDTIKQYYVLCSSRDEKFQALCNLY 328

Query: 284 DALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILV 343
            A+   Q +IF  +   A+ L   L +       +   M  E+R    + F+EG +++LV
Sbjct: 329 GAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLV 388

Query: 344 ATDLVGRGIDIERVNIVINYDMPDSAD------TYLHRVGRAGRFGTKGLAITFVSSASD 397
            T++  RGID+E+V++VIN+D+P   D      TYLHR+GR GRFG +GLA+  V S   
Sbjct: 389 TTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHS 448

Query: 398 SDILNQVSKF 407
            +ILN++ + 
Sbjct: 449 MNILNRIQEH 458

>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 =  372 bits (957), Expect = e-130
 Identities = 175/220 (79%), Positives = 199/220 (90%)

Query: 33  GEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKS 92
           G   K  YV IHSSGFRDFLLKPELLRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKS
Sbjct: 1   GSDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKS 60

Query: 93  GMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGG 152
           GMGKTAVFVL+TLQQ EP  GQV+ LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG
Sbjct: 61  GMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGG 120

Query: 153 VNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDV 212
           ++IK  +++LK  CP IVVGTPGRILALAR+K L+LK+++HFILDECDKMLE LDMRRDV
Sbjct: 121 LSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDV 180

Query: 213 QEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
           QEIF+MTPH+KQVMMFSATLSKEIRPVC+KFMQDPMEI+V
Sbjct: 181 QEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 220

>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 =  376 bits (969), Expect = e-129
 Identities = 111/379 (29%), Positives = 188/379 (49%), Gaps = 19/379 (5%)

Query: 39  GYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGM--DVICQAKSGMGK 96
           G +   +  F +  L PELL+ I    F+ PS++Q   +P  +     ++I Q++SG GK
Sbjct: 1   GAM---AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGK 57

Query: 97  TAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIK 156
           TA F L+ L +  P      A+ L  +RELA Q     +    +       +        
Sbjct: 58  TAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKN 117

Query: 157 IHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIF 216
              +       Q++VGTPG +L L R K + L+ ++ F+LDE D ML+   +      + 
Sbjct: 118 KQIN------AQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVK 171

Query: 217 KMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL-SELEK 275
           +  P D Q+++FSAT +  +R   KK + +   + +    ++ +  + Q Y+   +E +K
Sbjct: 172 RFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTN-EVNVDAIKQLYMDCKNEADK 230

Query: 276 NRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFK 335
              L +L   +     +IFV +   A  L   L         +H  +  +ER      F+
Sbjct: 231 FDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFR 290

Query: 336 EGNKRILVATDLVGRGIDIERVNIVINYDMPDSAD------TYLHRVGRAGRFGTKGLAI 389
           EG  ++L+ T+++ RGIDI  V++V+NYD+P  A+      TY+HR+GR GRFG KG+AI
Sbjct: 291 EGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI 350

Query: 390 TFVSSASDSDILNQVSKFM 408
           +FV   +  +IL+ + K+ 
Sbjct: 351 SFVHDKNSFNILSAIQKYF 369

>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 =  341 bits (876), Expect = e-115
 Identities = 131/349 (37%), Positives = 201/349 (57%), Gaps = 16/349 (4%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFVLSTLQ 106
           F +  L   +L AI + GFE P+++Q + IP  +    +++ QA++G GKTA F +  ++
Sbjct: 8   FNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIE 67

Query: 107 QTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNEC 166
               N G + A++L  TRELA Q+  E E       ++K+A  YGG  I      LKN  
Sbjct: 68  LVNENNG-IEAIILTPTRELAIQVADEIESLKGN-KNLKIAKIYGGKAIYPQIKALKN-- 123

Query: 167 PQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDM--RRDVQEIFKMTPHDKQ 224
             IVVGTPGRIL       L+LKNV++FILDE D+ML   +M   +DV++I      DK+
Sbjct: 124 ANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEML---NMGFIKDVEKILNACNKDKR 180

Query: 225 VMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLD 284
           +++FSAT+ +EI  + KK+M D   I     A +      Q Y++++E E+   L  LL 
Sbjct: 181 ILLFSATMPREILNLAKKYMGDYSFIKAKINANIE-----QSYVEVNENERFEALCRLLK 235

Query: 285 ALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVA 344
             +F   ++F K+     EL  +L +  F +  IH  +SQ +R    + FK+   RIL+A
Sbjct: 236 NKEF-YGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIA 294

Query: 345 TDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVS 393
           TD++ RGID+  +N VINY +P + ++Y+HR+GR GR G KG AI+ ++
Sbjct: 295 TDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIIN 343

>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 =  336 bits (864), Expect = e-114
 Identities = 111/343 (32%), Positives = 175/343 (51%), Gaps = 24/343 (6%)

Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP 112
           +  ++ +AI + GF++ +EVQ + IP  + G +V+ +AK+G GKTA + +  L+      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55

Query: 113 GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVG 172
             + +LV+  TREL  Q+         Y+   KVA  YGG+  K   + ++N    IVV 
Sbjct: 56  -GMKSLVVTPTRELTRQVASHIRDIGRYMD-TKVAEVYGGMPYKAQINRVRN--ADIVVA 111

Query: 173 TPGRILALARDKDLSLKNVRHFILDECDKMLESLDM--RRDVQEIFKMTPHDKQVMMFSA 230
           TPGR+L L     + L +    I+DE D M    +M    D++ I   T + K   +FSA
Sbjct: 112 TPGRLLDLWSKGVIDLSSFEIVIIDEADLMF---EMGFIDDIKIILAQTSNRKITGLFSA 168

Query: 231 TLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQ 290
           T+ +EIR V K F+ +  EI       + L  +   ++ + +    R     L       
Sbjct: 169 TIPEEIRKVVKDFITNYEEIEA----CIGLANVEHKFVHVKD--DWRSKVQALRENKDKG 222

Query: 291 VVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGR 350
           V++FV++ +R A+L +L       +I +   + Q  R      F+EG   +L+ TD+  R
Sbjct: 223 VIVFVRTRNRVAKLVRLF----DNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASR 278

Query: 351 GIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVS 393
           G+DI  V  VIN+D P    TY+HR+GR GR G KG AITF+ 
Sbjct: 279 GLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL 321

>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 =  334 bits (857), Expect = e-110
 Identities = 92/422 (21%), Positives = 177/422 (41%), Gaps = 40/422 (9%)

Query: 3   ETRDNEYEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIV 62
               +  +D+ + +++        V  + N +           S   + +L  E+ +AI 
Sbjct: 35  PRTRSREDDDEVHFDKTTFSKLIHVPKEDNSKEVTL------DSLLEEGVLDKEIHKAIT 88

Query: 63  DSGFEHPSEVQHECIPQAILG--MDVICQAKSGMGKTAVFVLSTLQ----QTEPNPGQVT 116
              F   + VQ + I   +     DVI +AK+G GKT  F++   Q        +   V 
Sbjct: 89  RMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVK 148

Query: 117 ALVLCHTRELAYQICHEFERFSTY---LPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGT 173
           A+++  TR+LA QI  E ++       L         GG + +   + +    P IV+ T
Sbjct: 149 AVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIAT 208

Query: 174 PGRILA-LARDKDLSLKNVRHFILDECDKMLESLDM--RRDVQEIFKMTP-------HDK 223
           PGR++  L +  +   + V + +LDE D++L   ++  R D++ I  +          + 
Sbjct: 209 PGRLIDVLEKYSNKFFRFVDYKVLDEADRLL---EIGFRDDLETISGILNEKNSKSADNI 265

Query: 224 QVMMFSATLSKEIRPVCKKFMQDPMEIYV---DDEAKLTLHGLVQHYIKLSELEKNRK-- 278
           + ++FSATL  +++ +    M     +++   D         + Q  +   +   +    
Sbjct: 266 KTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAA 325

Query: 279 ----LNDLLDALDFNQVVIFVKSVSRAAELNKLLVECN---FPSICIHSGMSQEERLTRY 331
                  + +     + +IF  +V   + L  +L        P +  H  ++Q +R +  
Sbjct: 326 VEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLV 385

Query: 332 KGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITF 391
           K FK+    ILV TD+  RG+D   V+ V+   +P     Y+HR+GR  R G +G ++ F
Sbjct: 386 KRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLF 445

Query: 392 VS 393
           + 
Sbjct: 446 IC 447

>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 =  330 bits (848), Expect = e-108
 Identities = 89/380 (23%), Positives = 165/380 (43%), Gaps = 34/380 (8%)

Query: 45  SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG--MDVICQAKSGMGKTAVFVL 102
            S   + +L  E+ +AI    F   + VQ + I   +     DVI +AK+G GKT  F++
Sbjct: 20  DSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLI 79

Query: 103 STLQ----QTEPNPGQVTALVLCHTRELAYQICHEFERFSTY---LPDIKVAVFYGGVNI 155
              Q        +   V A+++  TR+LA QI  E ++       L         GG + 
Sbjct: 80  PIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDF 139

Query: 156 KIHKDLLKNECPQIVVGTPGRILA-LARDKDLSLKNVRHFILDECDKMLESLDM--RRDV 212
           +   + +    P IV+ TPGR++  L +  +   + V + +LDE D++L   ++  R D+
Sbjct: 140 RAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLL---EIGFRDDL 196

Query: 213 QEIFKMTP-------HDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV---DDEAKLTLHG 262
           + I  +          + + ++FSATL  +++ +    M     +++   D         
Sbjct: 197 ETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHER 256

Query: 263 LVQHYIKLSELEKNRK------LNDLLDALDFNQVVIFVKSVSRAAELNKLLVECN---F 313
           + Q  +   +   +           + +     + +IF  +V   + L  +L        
Sbjct: 257 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 316

Query: 314 PSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYL 373
           P +  H  ++Q +R +  K FK+    ILV TD+  RG+D   V+ V+   +P     Y+
Sbjct: 317 PILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYI 376

Query: 374 HRVGRAGRFGTKGLAITFVS 393
           HR+GR  R G +G ++ F+ 
Sbjct: 377 HRIGRTARSGKEGSSVLFIC 396

>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 =  308 bits (791), Expect = e-104
 Identities = 72/223 (32%), Positives = 105/223 (47%), Gaps = 2/223 (0%)

Query: 31  ANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQA 90
           ++        +    + F   LL   +L  +  +GFE PS VQ + IP    G+D+I QA
Sbjct: 9   SSPRTRTGDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQA 68

Query: 91  KSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFY 150
           KSG GKT VF    L            L+L  TRE+A QI          +  ++  VF 
Sbjct: 69  KSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFI 128

Query: 151 GGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRR 210
           GG  +   K  LK     I VG+PGRI  L     L+  ++R FILDE DK+LE    + 
Sbjct: 129 GGTPLSQDKTRLKK--CHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQE 186

Query: 211 DVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVD 253
            +  I+   P  KQ++  SAT  + +     K+M+DP  + ++
Sbjct: 187 QINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRLN 229

>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 =  297 bits (762), Expect = 2e-97
 Identities = 109/364 (29%), Positives = 186/364 (51%), Gaps = 20/364 (5%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVL----S 103
           F    L+  ++  +  SG++ P+ +Q   IP    G D++  A++G GKTA F+L     
Sbjct: 58  FTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSK 117

Query: 104 TLQQTEPNPGQV-TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL 162
            L+            +++  TRELA QI +E  +F+ +   +K+ + YGG + +   + +
Sbjct: 118 LLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFA-FESYLKIGIVYGGTSFRHQNECI 176

Query: 163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDM------RRDVQEIF 216
              C  +V+ TPGR+L       ++ ++ R  +LDE D+ML   DM      RR +  + 
Sbjct: 177 TRGC-HVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRML---DMGFSEDMRRIMTHV- 231

Query: 217 KMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKN 276
            M P + Q +MFSAT  +EI+ +  +F+++ + + +          + Q   ++++  K 
Sbjct: 232 TMRP-EHQTLMFSATFPEEIQRMAGEFLKNYVFVAIG-IVGGACSDVKQTIYEVNKYAKR 289

Query: 277 RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKE 336
            KL ++L     +  ++FV++   A  L   L E  FP+  IH    Q +R    + FK 
Sbjct: 290 SKLIEILSEQA-DGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKN 348

Query: 337 GNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSAS 396
           G+ ++L+AT +  RG+DI+ +  VINYDMP   D Y+HR+GR GR G  G A +F     
Sbjct: 349 GSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEK 408

Query: 397 DSDI 400
           D  I
Sbjct: 409 DRAI 412

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  282 bits (724), Expect = 7e-92
 Identities = 116/371 (31%), Positives = 176/371 (47%), Gaps = 31/371 (8%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVL---ST 104
           F D  +   ++  I  + +  P+ VQ   IP      D++  A++G GKTA F+L   S 
Sbjct: 17  FSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQ 76

Query: 105 LQQTEPNPGQV---------------TALVLCHTRELAYQICHEFERFSTYLPDIKVAVF 149
           +    P                     +LVL  TRELA QI  E  +FS Y   ++  V 
Sbjct: 77  IYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFS-YRSRVRPCVV 135

Query: 150 YGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDM- 208
           YGG +I      L+  C  ++V TPGR++ +     + L   ++ +LDE D+ML   DM 
Sbjct: 136 YGGADIGQQIRDLERGC-HLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRML---DMG 191

Query: 209 -----RRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGL 263
                RR V++        +  MMFSAT  KEI+ + + F+ + + + V      T   +
Sbjct: 192 FEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVG-RVGSTSENI 250

Query: 264 VQHYIKLSELEKNRKLNDLLDALDFNQ-VVIFVKSVSRAAELNKLLVECNFPSICIHSGM 322
            Q  + + E +K   L DLL+A   +   ++FV++   A  L   L    +    IH   
Sbjct: 251 TQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDR 310

Query: 323 SQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRF 382
           SQ +R      F+ G   ILVAT +  RG+DI  V  VIN+D+P   + Y+HR+GR GR 
Sbjct: 311 SQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRV 370

Query: 383 GTKGLAITFVS 393
           G  GLA +F +
Sbjct: 371 GNLGLATSFFN 381

>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 =  249 bits (639), Expect = 1e-82
 Identities = 103/149 (69%), Positives = 120/149 (80%)

Query: 259 TLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICI 318
           +LHGL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I I
Sbjct: 2   SLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 61

Query: 319 HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGR 378
           H GM QEERL+RY+ FK+  +RILVAT+L GRG+DIERVNI  NYDMP+ +DTYLHRV R
Sbjct: 62  HRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVAR 121

Query: 379 AGRFGTKGLAITFVSSASDSDILNQVSKF 407
           AGRFGTKGLAITFVS  +D+ ILN V   
Sbjct: 122 AGRFGTKGLAITFVSDENDAKILNDVQDR 150

>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 =  244 bits (625), Expect = 2e-79
 Identities = 88/210 (41%), Positives = 113/210 (53%), Gaps = 6/210 (2%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  LK  LLR I   GFE PS +Q   I   I G DVI QA+SG GKTA F +S LQQ
Sbjct: 32  FDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQ 91

Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            E    +  ALVL  TRELA QI         Y+         GG N++     L+ E P
Sbjct: 92  LEIEFKETQALVLAPTRELAQQIQKVILALGDYM-GATCHACIGGTNVRNEMQKLQAEAP 150

Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDM--RRDVQEIFKMTPHDKQV 225
            IVVGTPGR+  +   + LS K ++ F+LDE D+M   L    +  + EIF+      QV
Sbjct: 151 HIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEM---LSRGFKDQIYEIFQKLNTSIQV 207

Query: 226 MMFSATLSKEIRPVCKKFMQDPMEIYVDDE 255
           ++ SAT+  ++  V KKFM+DP+ I V  E
Sbjct: 208 VLLSATMPTDVLEVTKKFMRDPIRILVKKE 237

>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 =  239 bits (613), Expect = 4e-78
 Identities = 66/203 (32%), Positives = 114/203 (56%), Gaps = 2/203 (0%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D+ LK ELL  I + G+E PS +Q E IP A+ G D++ +AK+G GK+  +++  L++
Sbjct: 5   FEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLER 64

Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            +     + A+V+  TRELA Q+     + S ++   KV    GG N++     L  +  
Sbjct: 65  LDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLD-DTV 123

Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
            +V+ TPGRIL L +     + +V+  +LDE DK+L S D  + +++I    P ++Q+++
Sbjct: 124 HVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLL-SQDFVQIMEDIILTLPKNRQILL 182

Query: 228 FSATLSKEIRPVCKKFMQDPMEI 250
           +SAT    ++      ++ P EI
Sbjct: 183 YSATFPLSVQKFMNSHLEKPYEI 205

>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 =  238 bits (610), Expect = 2e-77
 Identities = 80/213 (37%), Positives = 117/213 (54%), Gaps = 5/213 (2%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  L   LLR +   GFE PS +Q   I   I G DV+ QA+SG GKT  F ++ LQ+
Sbjct: 16  FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 75

Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            + +     AL+L  TRELA QI       + ++ DIKV    GG +     + L++   
Sbjct: 76  IDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--A 132

Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
           QIVVGTPGR+    + +      ++ FILDE D+ML S   +  + +IF + P   QV++
Sbjct: 133 QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEML-SSGFKEQIYQIFTLLPPTTQVVL 191

Query: 228 FSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTL 260
            SAT+  ++  V  KFM++P+ I V  + +LTL
Sbjct: 192 LSATMPNDVLEVTTKFMRNPVRILVKKD-ELTL 223

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  241 bits (618), Expect = 3e-76
 Identities = 65/392 (16%), Positives = 129/392 (32%), Gaps = 56/392 (14%)

Query: 56  ELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQV 115
           +          +  +  Q     + + G      A +G+GKT   +++ L          
Sbjct: 9   DFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGK--- 65

Query: 116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLK---NECPQIVVG 172
            + ++  T  L  Q     ++ +     +K+  FY  +  +  +   K    +   I+V 
Sbjct: 66  KSALVFPTVTLVKQTLERLQKLADE--KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVF 123

Query: 173 TPGRILALARDKD-LSLKNVRHFILDECDKMLESLDM--RRDVQEIFKMTPHDKQVMMFS 229
           +      ++++++ LS K      +D+ D +   L      D   +    P +     FS
Sbjct: 124 STQF---VSKNREKLSQKRFDFVFVDDVDAV---LKASRNIDTLLMMVGIPEEIIRKAFS 177

Query: 230 ATLSKEIRPVCKKFMQDPMEIYVD-----DEAKLTLHGLV---------------QHYIK 269
                +I    K      + +            L    L+                  I 
Sbjct: 178 TIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRIS 237

Query: 270 LSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLT 329
               EK  +L ++      + ++IF ++     EL + L    F      S   +     
Sbjct: 238 SRSKEKLVELLEIFR----DGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFE-- 291

Query: 330 RYKGFKEGNKRILVATD----LVGRGIDI-ERVNIVINYDMPDSAD--TYLHRVGRAGRF 382
               FK G   IL+        + RG+D+ ER+  VI +  P   D  TY+   GR+ R 
Sbjct: 292 ---DFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRI 348

Query: 383 GTKGL--AITFVSSASDSDILNQVSKFMFLLI 412
               L   ++ +    D +I   +   + L+ 
Sbjct: 349 LNGVLVKGVSVIFE-EDEEIFESLKTRLLLIA 379

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  234 bits (599), Expect = 8e-76
 Identities = 70/212 (33%), Positives = 118/212 (55%), Gaps = 9/212 (4%)

Query: 46  SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTL 105
           + F  F  +P ++ AI    F  P+E+Q   IP A+ G  ++ Q+++G GKT  ++L  +
Sbjct: 4   TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIM 63

Query: 106 QQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD---IKVAVFYGGVNIKIHKDLL 162
           ++ +P   +V A++   TRELA QI HE  + + + P    I      GG + +   + L
Sbjct: 64  EKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKL 123

Query: 163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDM--RRDVQEIFKMTP 220
             + P IV+GTPGRI    R++ L +      ++DE D M   LDM    DV +I    P
Sbjct: 124 NVQ-PHIVIGTPGRINDFIREQALDVHTAHILVVDEADLM---LDMGFITDVDQIAARMP 179

Query: 221 HDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
            D Q+++FSAT+ ++++P  KK+M++P  ++V
Sbjct: 180 KDLQMLVFSATIPEKLKPFLKKYMENPTFVHV 211

>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 =  233 bits (596), Expect = 3e-74
 Identities = 68/211 (32%), Positives = 110/211 (52%), Gaps = 7/211 (3%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGM--DVICQAKSGMGKTAVFVLSTL 105
           F +  LKP+LL+ +   GF  PS++Q   +P  +     ++I Q++SG GKTA FVL+ L
Sbjct: 94  FEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAML 153

Query: 106 QQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNE 165
            Q EP       L L  T ELA Q     E+   + P++K+A    G  ++  +    + 
Sbjct: 154 SQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE--RGQKIS- 210

Query: 166 CPQIVVGTPGRIL-ALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQ 224
             QIV+GTPG +L   ++ K +  K ++ F+LDE D M+ +   +     I +M P + Q
Sbjct: 211 -EQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQ 269

Query: 225 VMMFSATLSKEIRPVCKKFMQDPMEIYVDDE 255
           +++FSAT    +    +K + DP  I +  E
Sbjct: 270 MLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 300

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score =  215 bits (551), Expect = 9e-69
 Identities = 76/210 (36%), Positives = 110/210 (52%), Gaps = 12/210 (5%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F+DF LKPE+L A+   G   P+ +Q   +P A+ G D+I QA++G GKT  F L   ++
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62

Query: 108 TEPNPGQ---VTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN 164
             P+  +     ALVL  TRELA Q+  E    + +L   KV   YGG      K+ L  
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASELTAVAPHL---KVVAVYGGTGYGKQKEALLR 119

Query: 165 ECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDM--RRDVQEIFKMTPHD 222
                VV TPGR L   R   L L  V   +LDE D+M   L M    +V+ +   TP  
Sbjct: 120 -GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEM---LSMGFEEEVEALLSATPPS 175

Query: 223 KQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
           +Q ++FSATL    + + +++M++P+ I V
Sbjct: 176 RQTLLFSATLPSWAKRLAERYMKNPVLINV 205

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  212 bits (543), Expect = 3e-68
 Identities = 63/149 (42%), Positives = 94/149 (63%), Gaps = 2/149 (1%)

Query: 260 LHGLVQHYIKLSELE-KNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICI 318
           L G+ Q Y+ + E E K   L DL D++   Q VIF  +  +  EL   L    F    I
Sbjct: 1   LEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 60

Query: 319 HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGR 378
           +S + Q+ER T  K F+ G+ RIL++TDL+ RGID+++V++VINYD+P + + Y+HR+GR
Sbjct: 61  YSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGR 120

Query: 379 AGRFGTKGLAITFVSSASDSDILNQVSKF 407
            GRFG KG+AI FV++  D   + ++ KF
Sbjct: 121 GGRFGRKGVAINFVTN-EDVGAMRELEKF 148

>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 =  215 bits (550), Expect = 5e-68
 Identities = 71/249 (28%), Positives = 132/249 (53%), Gaps = 4/249 (1%)

Query: 6   DNEYEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSG 65
            + +    +D   E+          +  EA++       +  F+D  +   L  A    G
Sbjct: 3   HHHHHSSGVDLGTENLYFQSMEEHDSPTEASQPIVEEEETKTFKDLGVTDVLCEACDQLG 62

Query: 66  FEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE 125
           +  P+++Q E IP A+ G D+I  A++G GKT  F L  L      P ++ ALVL  TRE
Sbjct: 63  WTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRE 122

Query: 126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL-ALARDK 184
           LA+QI  +FE   + +  ++ AV  GG++       L  + P I++ TPGR++  L   K
Sbjct: 123 LAFQISEQFEALGSSIG-VQSAVIVGGIDSMSQSLALAKK-PHIIIATPGRLIDHLENTK 180

Query: 185 DLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFM 244
             +L+ +++ ++DE D++L  +D   +V +I K+ P D++  +FSAT++K+++ + +  +
Sbjct: 181 GFNLRALKYLVMDEADRILN-MDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAAL 239

Query: 245 QDPMEIYVD 253
           ++P++  V 
Sbjct: 240 KNPVKCAVS 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 =  195 bits (497), Expect = 3e-60
 Identities = 59/245 (24%), Positives = 114/245 (46%), Gaps = 18/245 (7%)

Query: 17  EEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHEC 76
           E E          K N     +         F DF L  + L+ + ++ +   +E+Q + 
Sbjct: 5   ERESISRLMQNYEKINVNEITR---------FSDFPLSKKTLKGLQEAQYRLVTEIQKQT 55

Query: 77  IPQAILGMDVICQAKSGMGKTAVFVLSTLQ---QTEPNPGQVT-ALVLCHTRELAYQICH 132
           I  A+ G DV+  AK+G GKT  F++  L+   + +         L++  TRELAYQ   
Sbjct: 56  IGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFE 115

Query: 133 EFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILA-LARDKDLSLKNV 191
              +      D    +  GG ++K   + + N    I+V TPGR+L  +         ++
Sbjct: 116 VLRKVGKNH-DFSAGLIIGGKDLKHEAERINN--INILVCTPGRLLQHMDETVSFHATDL 172

Query: 192 RHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIY 251
           +  +LDE D++L+ +     +  + +  P  +Q ++FSAT +K ++ + +  +++P  ++
Sbjct: 173 QMLVLDEADRILD-MGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVW 231

Query: 252 VDDEA 256
           V ++A
Sbjct: 232 VHEKA 236

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score =  185 bits (473), Expect = 1e-56
 Identities = 56/207 (27%), Positives = 97/207 (46%), Gaps = 9/207 (4%)

Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ-TEPN 111
           +   LL+ I+D+GF+ P+ +Q + IP  + G +++  A +G GKT  F +  L Q  +P 
Sbjct: 36  INSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA 95

Query: 112 PGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH-KDLLKNECPQIV 170
                AL++  TRELA QI  E  + S      ++ + +               +   I+
Sbjct: 96  NKGFRALIISPTRELASQIHRELIKISEGTG-FRIHMIHKAAVAAKKFGPKSSKKF-DIL 153

Query: 171 VGTPGRILAL--ARDKDLSLKNVRHFILDECDKMLESLDM--RRDVQEIFKM-TPHDKQV 225
           V TP R++ L       + L +V   ++DE DK+ E      R  +  IF   T H  + 
Sbjct: 154 VTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRR 213

Query: 226 MMFSATLSKEIRPVCKKFMQDPMEIYV 252
            MFSAT + ++   CK  + + + + +
Sbjct: 214 AMFSATFAYDVEQWCKLNLDNVISVSI 240

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score =  173 bits (441), Expect = 4e-52
 Identities = 63/214 (29%), Positives = 109/214 (50%), Gaps = 15/214 (7%)

Query: 48  FRD-FLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQ 106
           F+D F   P+LL++I+  G   P+ +Q +  P  + G+D+I  A++G GKT  +++    
Sbjct: 21  FKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFI 80

Query: 107 QTEPNPGQ------VTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKD 160
             +  P           LVL  TRELA  +  E  ++S     +K    YGG N     +
Sbjct: 81  HLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSY--KGLKSICIYGGRNRNGQIE 138

Query: 161 LLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDM--RRDVQEIFKM 218
            +      I++ TPGR+  L  +  ++L+++ + ++DE DKM   LDM     +++I   
Sbjct: 139 DISKGV-DIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKM---LDMEFEPQIRKILLD 194

Query: 219 TPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
              D+Q +M SAT    +R +   +++DPM +YV
Sbjct: 195 VRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

>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 =  170 bits (432), Expect = 1e-51
 Identities = 44/159 (27%), Positives = 86/159 (54%), Gaps = 8/159 (5%)

Query: 256 AKLTLHGLVQHYIKL-SELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFP 314
           + LTL+ + Q+Y+      +K + L ++  ++   Q +IF ++   A  L   +++    
Sbjct: 1   SMLTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQ 60

Query: 315 SICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSAD---- 370
              +   ++ E+R +  + F++G +++L+ T++  RGID+++V IV+N+D+P        
Sbjct: 61  VSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPD 120

Query: 371 --TYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKF 407
             TYLHR+GR GRFG KGLA   +    +   L ++   
Sbjct: 121 YETYLHRIGRTGRFGKKGLAFNMIEV-DELPSLMKIQDH 158

>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 =  172 bits (438), Expect = 3e-51
 Identities = 61/217 (28%), Positives = 111/217 (51%), Gaps = 14/217 (6%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQ- 106
           F +  L P +   I+ + ++ P+ +Q   IP  +   D++  A++G GKTA F++  +  
Sbjct: 25  FDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINH 84

Query: 107 -------QTEPNPGQV-TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH 158
                  Q   +       L+L  TRELA QI  E ++FS   P ++  V YGG +    
Sbjct: 85  LVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTP-LRSCVVYGGADTHSQ 143

Query: 159 KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES---LDMRRDVQEI 215
              ++  C  ++V TPGR++       +SL+  ++ +LDE D+ML+      +R+ ++E 
Sbjct: 144 IREVQMGC-HLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEES 202

Query: 216 FKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
              +  ++Q +MFSAT  KEI+ +   F+ + + + V
Sbjct: 203 NMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV 239

>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 =  172 bits (438), Expect = 3e-51
 Identities = 64/257 (24%), Positives = 121/257 (47%), Gaps = 12/257 (4%)

Query: 3   ETRDNEYEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSS-GFRDF--LLKPELLR 59
            +  +   + L      + + PD+   ++   +   G  G      F     L+    L+
Sbjct: 8   SSGVDLGTENLYFQSMNNVEKPDNDEDESEVPSLPLGLTGAFEDTSFASLCNLVNENTLK 67

Query: 60  AIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQ---QTEPNPGQVT 116
           AI + GF + +E+QH+ I   + G D++  AK+G GKT  F++  ++   +    P   T
Sbjct: 68  AIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGT 127

Query: 117 -ALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPG 175
             L+L  TRELA Q     +   T+       +  GG N       L N    I+V TPG
Sbjct: 128 GVLILSPTRELAMQTFGVLKELMTHH-VHTYGLIMGGSNRSAEAQKLGNG-INIIVATPG 185

Query: 176 RIL-ALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSK 234
           R+L  +        KN++  ++DE D++L+ +    ++++I K+ P  +Q M+FSAT ++
Sbjct: 186 RLLDHMQNTPGFMYKNLQCLVIDEADRILD-VGFEEELKQIIKLLPTRRQTMLFSATQTR 244

Query: 235 EIRPVCKK-FMQDPMEI 250
           ++  + +    ++P+ +
Sbjct: 245 KVEDLARISLKKEPLYV 261

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  162 bits (413), Expect = 7e-49
 Identities = 56/150 (37%), Positives = 84/150 (56%), Gaps = 1/150 (0%)

Query: 258 LTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSIC 317
           LT   +    I++ E  K   L D+L   + +  +IF ++     +L   L +  +P   
Sbjct: 5   LTTRNIEHAVIQVREENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDK 64

Query: 318 IHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVG 377
           IH GM QE+R      FK G  R LVATD+  RGIDIE +++VINYD+P   ++Y+HR G
Sbjct: 65  IHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTG 124

Query: 378 RAGRFGTKGLAITFVSSASDSDILNQVSKF 407
           R GR G KG AI+FV++  +   L  + ++
Sbjct: 125 RTGRAGNKGKAISFVTA-FEKRFLADIEEY 153

>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 =  164 bits (418), Expect = 2e-48
 Identities = 58/212 (27%), Positives = 98/212 (46%), Gaps = 12/212 (5%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVL----S 103
           F +      ++  I    F  P+ +Q +  P A+ G+D++  A++G GKT  ++L     
Sbjct: 31  FYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVH 90

Query: 104 TLQQTEPNPGQV-TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL 162
              Q     G     LVL  TRELA Q+      +      +K    YGG         L
Sbjct: 91  INHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYC-RACRLKSTCIYGGAPKGPQIRDL 149

Query: 163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDM--RRDVQEIFKMTP 220
           +    +I + TPGR++        +L+   + +LDE D+M   LDM     +++I     
Sbjct: 150 ERGV-EICIATPGRLIDFLECGKTNLRRTTYLVLDEADRM---LDMGFEPQIRKIVDQIR 205

Query: 221 HDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
            D+Q +M+SAT  KE+R + + F++D + I +
Sbjct: 206 PDRQTLMWSATWPKEVRQLAEDFLKDYIHINI 237

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  152 bits (387), Expect = 1e-44
 Identities = 49/165 (29%), Positives = 79/165 (47%), Gaps = 7/165 (4%)

Query: 243 FMQDPMEIYVDDE------AKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVK 296
                  + +  E             ++Q    + E  K   L + L       V+IF +
Sbjct: 4   HHHHSSGVDLGTENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECLQKTP-PPVLIFAE 62

Query: 297 SVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIER 356
             +    +++ L+     ++ IH G  QEER    + F+EG K +LVATD+  +G+D   
Sbjct: 63  KKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPA 122

Query: 357 VNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDIL 401
           +  VINYDMP+  + Y+HR+GR G  G  G+A TF++ A D  +L
Sbjct: 123 IQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVL 167

>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 =  145 bits (368), Expect = 4e-42
 Identities = 57/145 (39%), Positives = 78/145 (53%), Gaps = 2/145 (1%)

Query: 265 QHYIKLSELE-KNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMS 323
           Q Y +  +LE K   L  LL   +  + ++FV+   R  EL   L E    +  +   M 
Sbjct: 6   QWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMV 65

Query: 324 QEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFG 383
           Q +R    K   EG   +LVATD+  RGIDI  V+ V N+DMP S DTYLHR+GR  R G
Sbjct: 66  QGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAG 125

Query: 384 TKGLAITFVSSASDSDILNQVSKFM 408
            KG AI+ V  A D  +L +V +++
Sbjct: 126 RKGTAISLV-EAHDHLLLGKVGRYI 149

>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 =  137 bits (347), Expect = 6e-39
 Identities = 47/130 (36%), Positives = 68/130 (52%), Gaps = 1/130 (0%)

Query: 265 QHYIKLSELEKNRKLNDLLDALDFNQ-VVIFVKSVSRAAELNKLLVECNFPSICIHSGMS 323
           Q  + + E +K   L DLL+A   +   ++FV++   A  L   L    +    IH   S
Sbjct: 22  QKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRS 81

Query: 324 QEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFG 383
           Q +R      F+ G   ILVAT +  RG+DI  V  VIN+D+P   + Y+HR+GR GR G
Sbjct: 82  QRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG 141

Query: 384 TKGLAITFVS 393
             GLA +F +
Sbjct: 142 NLGLATSFFN 151

>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 =  133 bits (336), Expect = 6e-37
 Identities = 40/129 (31%), Positives = 70/129 (54%)

Query: 265 QHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQ 324
           +  +      +   L+DLL     ++ ++F ++ +   E+ + L+    P+  +H  +SQ
Sbjct: 8   EEAVPAPVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQ 67

Query: 325 EERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGT 384
            ER      F++G  R+LVATD+  RG+DI +V++V++Y +PD A+ Y HR GR GR G 
Sbjct: 68  GERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGR 127

Query: 385 KGLAITFVS 393
            G  +    
Sbjct: 128 GGRVVLLYG 136

>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 =  132 bits (334), Expect = 1e-35
 Identities = 42/130 (32%), Positives = 70/130 (53%)

Query: 265 QHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQ 324
           +  +      +   L+DLL     ++ ++F ++ +   E+ + L+    P+  +H  MSQ
Sbjct: 5   EEAVPAPVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQ 64

Query: 325 EERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGT 384
            ER      F++G  R+LVATD+  RG+DI +V++V++Y MPD A+ Y HR GR GR G 
Sbjct: 65  GERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGR 124

Query: 385 KGLAITFVSS 394
            G  +     
Sbjct: 125 GGRVVLLYGP 134

>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 = 84.1 bits (208), Expect = 1e-17
 Identities = 76/417 (18%), Positives = 149/417 (35%), Gaps = 89/417 (21%)

Query: 50  DFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQT 108
           +  +   +   + + G E     Q E +   IL G + +    +  GKT +  ++ + + 
Sbjct: 5   ELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRI 64

Query: 109 EPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQ 168
               G+   + +   + LA +   EF+ +      ++VA+  G  + K  + L K     
Sbjct: 65  LTQGGKA--VYIVPLKALAEEKFQEFQDWEKI--GLRVAMATGDYDSKD-EWLGKY---D 116

Query: 169 IVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQE--IFKMTPHDKQVM 226
           I++ T  +  +L R     +K+V+  + DE   ++ S D R    E  +  M    + + 
Sbjct: 117 IIIATAEKFDSLLRHGSSWIKDVKILVADEI-HLIGSRD-RGATLEVILAHMLGKAQIIG 174

Query: 227 MFSATLS--KEI-------------RPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS 271
           + SAT+   +E+             RPV        +   V  +  +T           S
Sbjct: 175 L-SATIGNPEELAEWLNAELIVSDWRPV-------KLRRGVFYQGFVTWE-------DGS 219

Query: 272 ELEKNRKLNDLLDALDFN-QVVIFV---KSVSRAAE------------------------ 303
               +     + DA+      +IFV   +   R A                         
Sbjct: 220 IDRFSSWEELVYDAIRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADS 279

Query: 304 -----LNKLLVECNFPSICIH-SGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDI--E 355
                 N+ L +     +  H +G+ ++ER+   + F++G  + +VAT  +  GI+    
Sbjct: 280 LEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAF 339

Query: 356 RVNIVINYDMPD-------SADTYLHRVGRAGRFG--TKGLAITFVSSASDSDILNQ 403
           RV I+ +                    +GRAGR      G  I   +S    +++N 
Sbjct: 340 RV-IIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVMNH 395

>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 = 83.7 bits (206), Expect = 1e-17
 Identities = 38/167 (22%), Positives = 66/167 (39%), Gaps = 12/167 (7%)

Query: 227 MFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDAL 286
              A + K          +   EI+ D   K  +  LVQ      +  K  KL +++   
Sbjct: 296 ALRAYIKKLYEEAKAGSTKASKEIFSDKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQ 355

Query: 287 ----DFNQVVIFVKSVSRAAELNKLLVECNFPSICIH--------SGMSQEERLTRYKGF 334
                 +++++F      A ++   LV+    +             G+SQ E+      F
Sbjct: 356 LQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEF 415

Query: 335 KEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR 381
             G   +LVAT +   G+D+  V++V+ Y+   SA   + R GR GR
Sbjct: 416 ARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR 462

>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 = 76.0 bits (186), Expect = 5e-15
 Identities = 37/210 (17%), Positives = 79/210 (37%), Gaps = 19/210 (9%)

Query: 52  LLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN 111
           +L+ +L++         P   Q   I       + +    +G+GKT + ++    +    
Sbjct: 2   VLRRDLIQ---------PRIYQEV-IYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKY 51

Query: 112 PGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVV 171
            G+V  L+L  T+ L  Q    F R    LP  K+    G  + +           +++V
Sbjct: 52  GGKV--LMLAPTKPLVLQHAESFRRL-FNLPPEKIVALTGEKSPEERSKAWARA--KVIV 106

Query: 172 GTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT 231
            TP  I        +SL++V   + DE  + + +      +   +K    +  V+  +A+
Sbjct: 107 ATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGN-YAYVFIAREYKRQAKNPLVIGLTAS 165

Query: 232 LS---KEIRPVCKKFMQDPMEIYVDDEAKL 258
                ++I  V      + +E   ++   +
Sbjct: 166 PGSTPEKIMEVINNLGIEHIEYRSENSPDV 195

>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 = 82.2 bits (203), Expect = 6e-17
 Identities = 74/416 (17%), Positives = 146/416 (35%), Gaps = 94/416 (22%)

Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP 112
           +    +  + + G E     Q E + +   G +++    +  GKT +  ++ +++     
Sbjct: 10  ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG- 68

Query: 113 GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVG 172
               +L +   R LA +    F+++      +++ +  G    +  + L       I+V 
Sbjct: 69  --GKSLYVVPLRALAGEKYESFKKWEKI--GLRIGISTGDYESRD-EHLGDC---DIIVT 120

Query: 173 TPGRILALARDKDLSLKNVRHFILDEC----DKM----LESLDMRRDVQEIFKMTPHDKQ 224
           T  +  +L R++   +K V   ++DE      +     LE L  +       +      +
Sbjct: 121 TSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTK------MRRMNKALR 174

Query: 225 VMMFSATLS--KEI-------------RPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIK 269
           V+  SAT     EI             RPV       P+   V  E        ++ +  
Sbjct: 175 VIGLSATAPNVTEIAEWLDADYYVSDWRPV-------PLVEGVLCEGT------LELFDG 221

Query: 270 LSELEKNRKLNDLLDAL--DFNQVVIFV---KSVSRAA---------------------- 302
                +  K  +L++    +   V++F    +   + A                      
Sbjct: 222 AFSTSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILE 281

Query: 303 ----ELNKLLVECNFPSICIH-SGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDI--E 355
               E+++ L EC       H +G+   +R      F+ GN +++VAT  +  G+++   
Sbjct: 282 ENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPAR 341

Query: 356 RVNIVINYDMPD------SADTYLHRVGRAGRFG--TKGLAITFVSSASDSDILNQ 403
           RV IV +    D          Y    GRAGR G   +G AI  V        + +
Sbjct: 342 RV-IVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVKR 396

>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 = 73.6 bits (180), Expect = 4e-14
 Identities = 34/217 (15%), Positives = 78/217 (35%), Gaps = 11/217 (5%)

Query: 179 ALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRP 238
           A   D + +    +  +    D+   S  + R+ +   K  P  +++      L  + + 
Sbjct: 388 AANSDSEDAQSARQELVSMLMDRHGTSRVLFRNTRNGVKGFPK-RELHTIKLPLPTQYQT 446

Query: 239 VCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDAL-------DFNQV 291
             K           +D A+  L+    +     +       +  ++ L          +V
Sbjct: 447 AIKVSGIMGARKSAEDRARDMLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTSHRSQKV 506

Query: 292 VIFVKSVSRAAEL-NKLLVECNFPSICIHSGMSQEERLTRYKGF--KEGNKRILVATDLV 348
           ++     + A +L   L       +   H GMS  ER      F  ++   ++L+ +++ 
Sbjct: 507 LVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIG 566

Query: 349 GRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTK 385
             G + +  + ++ +D+P + D    R+GR  R G  
Sbjct: 567 SEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQA 603

>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 = 67.9 bits (166), Expect = 2e-12
 Identities = 54/330 (16%), Positives = 102/330 (30%), Gaps = 91/330 (27%)

Query: 93  GMGKT--AVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFY 150
           G GKT  A+  ++ L            L++  T  LA Q       F     +  V  F 
Sbjct: 118 GSGKTHVAMAAINELSTP--------TLIVVPTLALAEQWKERLGIF----GEEYVGEFS 165

Query: 151 GGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDEC-----DKMLES 205
           G             E   + V T     +   + +         I DE      +  ++ 
Sbjct: 166 GR----------IKELKPLTVSTYD---SAYVNAEKLGNRFMLLIFDEVHHLPAESYVQI 212

Query: 206 LDM--------------RRDVQE----------IFKMTPHDKQ--------VMMFSATLS 233
             M              R D +           +F++ P            +      L+
Sbjct: 213 AQMSIAPFRLGLTATFEREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLA 272

Query: 234 KEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE------------------- 274
           ++ R   +K  +   +        L         +  S  +                   
Sbjct: 273 EDERVEYEKREKVYKQFLRARGITLRRAEDFNKIVMASGYDERAYEALRAWEEARRIAFN 332

Query: 275 ---KNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRY 331
              K RKL ++L+    ++++IF +       ++K+     F    I    S+EER    
Sbjct: 333 SKNKIRKLREILERHRKDKIIIFTRHNELVYRISKV-----FLIPAITHRTSREEREEIL 387

Query: 332 KGFKEGNKRILVATDLVGRGIDIERVNIVI 361
           +GF+ G  R +V++ ++  GID+   N+ +
Sbjct: 388 EGFRTGRFRAIVSSQVLDEGIDVPDANVGV 417

>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 = 67.0 bits (163), Expect = 4e-12
 Identities = 57/345 (16%), Positives = 97/345 (28%), Gaps = 73/345 (21%)

Query: 60  AIVDSGFEHPSEVQHECIPQAI-LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTAL 118
             +++    P    +   P            A +G GK+     +   Q     G    L
Sbjct: 208 ESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ-----GYKV-L 261

Query: 119 VLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL 178
           VL  +                              NI+     +    P +   T G+ L
Sbjct: 262 VLNPSVAATLGFGAYMS-----------KAHGIDPNIRTGVRTITTGAP-VTYSTYGKFL 309

Query: 179 ALARDKDLSLKNVRHFILDECDKM-LESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIR 237
           A   D   S       I DEC      ++     V +  +       V+  +AT      
Sbjct: 310 A---DGGCSGGAYDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLA-TATPPGS-- 363

Query: 238 PVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKS 297
                       I   +E  L+  G +  Y K             ++A+   + +IF  S
Sbjct: 364 -----VTVPHPNI---EEVALSNTGEIPFYGKAIP----------IEAIRGGRHLIFCHS 405

Query: 298 VSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRG--IDIE 355
             +  EL   L      ++  + G+                  ++VATD +  G   D +
Sbjct: 406 KKKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGDFD 458

Query: 356 RVNI--------VINYD-----------MPDSADTYLHRVGRAGR 381
            V I         +++            +P  A +   R GR GR
Sbjct: 459 SV-IDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR 502

>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 = 64.1 bits (156), Expect = 3e-11
 Identities = 42/313 (13%), Positives = 79/313 (25%), Gaps = 62/313 (19%)

Query: 93  GMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGG 152
           G GKT  F+   L +      +   LVL  TR +                 + V      
Sbjct: 18  GAGKTRRFLPQILAECARRRLRT--LVLAPTRVVL-------SEMKEAFHGLDVKFHTQA 68

Query: 153 VNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDV 212
            +       +      I       +     +    + N    I+DE   +  +    R  
Sbjct: 69  FSAHGSGREV------IDAMCHATLTYRMLE-PTRVVNWEVIIMDEAHFLDPASIAARGW 121

Query: 213 QEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV--DDEAKLTLHGLVQHYIKL 270
                       ++M +AT               P       D +  +        +  +
Sbjct: 122 AAHRARANESATILM-TATPPGTSDEF-------PHSNGEIEDVQTDIPSEPWNTGHDWI 173

Query: 271 SELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTR 330
              ++                  F+ S+  A  +   L +     + ++    + E    
Sbjct: 174 LADKRP--------------TAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFERE---- 215

Query: 331 YKGFKEGNKRILVATDLVGRG--IDIERV-----NIVINYDMPDSADTYLH--------- 374
           Y   K+     ++ATD+   G  + +ERV                               
Sbjct: 216 YPTIKQKKPDFILATDIAEMGANLCVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSA 275

Query: 375 --RVGRAGRFGTK 385
             R GR GR   +
Sbjct: 276 AQRRGRIGRNPNR 288

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 63.8 bits (154), Expect = 4e-11
 Identities = 43/344 (12%), Positives = 96/344 (27%), Gaps = 45/344 (13%)

Query: 68  HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELA 127
            P   Q + + + ++    I    +  G++ +  L      E   G++  L++  T  L 
Sbjct: 113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKI--LIIVPTTALT 170

Query: 128 YQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLS 187
            Q+  +F  +        +    GG           ++         G    + +     
Sbjct: 171 TQMADDFVDYR-LFSHAMIKKIGGG-------ASKDDKYKNDAPVVVGTWQTVVKQPKEW 222

Query: 188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDP 247
                  + DEC          + +  I     +       S +L      + +      
Sbjct: 223 FSQFGMMMNDECHLA-----TGKSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFG 277

Query: 248 MEIYVDDEAKLTLHG----------LVQHYIKLSELEKNRKLNDLLDALDFNQ------- 290
                   +KL   G           +++  + +   K +   + +  +           
Sbjct: 278 EIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKWIA 337

Query: 291 ------------VVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN 338
                         +  K VS    +  L+         +   +  E R       + G 
Sbjct: 338 KLAIKLAQKDENAFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGK 397

Query: 339 KRILVAT-DLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR 381
             I+VA+  +   GI ++ ++ V+      S    L  +GR  R
Sbjct: 398 GIIIVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLR 441

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 63.4 bits (153), Expect = 6e-11
 Identities = 35/194 (18%), Positives = 71/194 (36%), Gaps = 16/194 (8%)

Query: 199 CDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKL 258
               L   +    + E  +MT     +  F   + +      ++ +    E  +++  K+
Sbjct: 303 YTSHLRKYNDALIISEDAQMTDALNYLKAFFHDVREAAFDETERELTRRFEEKLEELEKV 362

Query: 259 TLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNF----- 313
           +     ++  KL +L     L +        + ++FVK+ +    L K + E        
Sbjct: 363 SRDPSNENP-KLRDLY--LVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLK 419

Query: 314 -------PSICIHSGMSQEERLTRYKGFKE-GNKRILVATDLVGRGIDIERVNIVINYDM 365
                        +GM+   +    + F+  G+  IL+AT +   GIDI   N+VI Y+ 
Sbjct: 420 PGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEY 479

Query: 366 PDSADTYLHRVGRA 379
             +    +   GR 
Sbjct: 480 VGNVIKMIQTRGRG 493

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 56.4 bits (135), Expect = 9e-09
 Identities = 33/186 (17%), Positives = 65/186 (34%), Gaps = 10/186 (5%)

Query: 73  QHECIPQAILGMDVICQAKSGMGKT--AVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI 130
           Q E    A  G + I  A +G GKT  ++ +     +  P   +   +   +   +  Q 
Sbjct: 9   QLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQ 68

Query: 131 CHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL-ALARDKDLSLK 189
              F R+        +A   G  +  +    +  +   I++ TP  ++  L      SL 
Sbjct: 69  ATVFSRY-FERLGYNIASISGATSDSVSVQHIIEDN-DIIILTPQILVNNLNNGAIPSLS 126

Query: 190 NVRHFILDECDKMLES----LDMRRDVQEIFKMTPHDK-QVMMFSATLSKEIRPVCKKFM 244
                I DEC    ++      M R +      +     QV+  +A++        ++ M
Sbjct: 127 VFTLMIFDECHNTSKNHPYNQIMFRYLDHKLGESRDPLPQVVGLTASVGVGDAKTAEEAM 186

Query: 245 QDPMEI 250
           Q   ++
Sbjct: 187 QHICKL 192

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 63.1 bits (152), Expect = 8e-11
 Identities = 36/223 (16%), Positives = 77/223 (34%), Gaps = 16/223 (7%)

Query: 176 RILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKE 235
           +   + +  D   ++     L      L   +    + E  +M      +  F + +   
Sbjct: 289 KACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAA 348

Query: 236 IRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFV 295
                ++ +    E  + +   ++     ++  KL +L     L +          ++FV
Sbjct: 349 GFDEIEQDLTQRFEEKLQELESVSRDPSNENP-KLEDLCFI--LQEEYHLNPETITILFV 405

Query: 296 KSVSRAAELNKLLVEC-NFPSI-----------CIHSGMSQEERLTRYKGFKE-GNKRIL 342
           K+ +    L   +        +             ++GM+   +      FK  G+  IL
Sbjct: 406 KTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNIL 465

Query: 343 VATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTK 385
           +AT +   GIDI + N+VI Y+   +    +   GR    G+K
Sbjct: 466 IATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSK 508

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 55.4 bits (132), Expect = 2e-08
 Identities = 25/133 (18%), Positives = 47/133 (35%), Gaps = 5/133 (3%)

Query: 73  QHECIPQAILGMDVICQAKSGMGKT--AVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI 130
           Q E    A+ G + I  A +G GKT  ++ +     +  P   +   +   +   +  Q 
Sbjct: 18  QLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQN 77

Query: 131 CHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL-ALARDKDLSLK 189
              F ++       +V    G     +  + +      I++ TP  ++  L +    SL 
Sbjct: 78  KSVFSKY-FERHGYRVTGISGATAENVPVEQIVENN-DIIILTPQILVNNLKKGTIPSLS 135

Query: 190 NVRHFILDECDKM 202
                I DEC   
Sbjct: 136 IFTLMIFDECHNT 148

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 60.1 bits (146), Expect = 7e-10
 Identities = 81/420 (19%), Positives = 146/420 (34%), Gaps = 89/420 (21%)

Query: 50  DFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMD--VICQAKSGMGKTAVFVLSTLQQ 107
           D  L   ++  I   G +  +  Q E + + +L  +  ++  + +G GKT +  +  +  
Sbjct: 12  DLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLT-SPTGSGKTLIAEMGIISF 70

Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
              N G+   + +   R L  +    F+ +       KVA+  G  +      L      
Sbjct: 71  LLKNGGKA--IYVTPLRALTNEKYLTFKDWELI--GFKVAMTSGDYDTDD-AWLKNY--- 122

Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
            I++ T  ++ +L R +   L  V +F+LDE    L   + R  V E   +    + ++ 
Sbjct: 123 DIIITTYEKLDSLWRHRPEWLNEVNYFVLDEL-HYLNDPE-RGPVVESVTIRAKRRNLLA 180

Query: 228 FSATLS--KEI-------------RPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE 272
            SAT+S  K+I             RPV       P+   V    +      V      ++
Sbjct: 181 LSATISNYKQIAKWLGAEPVATNWRPV-------PLIEGVIYPERKKKEYNVIFKDNTTK 233

Query: 273 LEK--NRKLNDLLDAL-DFNQVVIFVKS----VSRAAELNKLLVECNFPSICI------- 318
                +  +   LD+L    QV++F  S     S A ++   +   +     +       
Sbjct: 234 KVHGDDAIIAYTLDSLSKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQL 293

Query: 319 -------------------------HSGMSQEERLTRYKGFKEGNKRILVATD------- 346
                                    H+G+S+  R    +GF++   +++VAT        
Sbjct: 294 DDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVN 353

Query: 347 -----LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR--FGTKGLAITFVSSASDSD 399
                ++   I      I   YD     + Y    GRAGR  F   G +I  V    D D
Sbjct: 354 LPARTVIIGDIYRFNKKIAGYYDEIPIME-YKQMSGRAGRPGFDQIGESIVVVRDKEDVD 412

>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 = 60.0 bits (144), Expect = 8e-10
 Identities = 37/203 (18%), Positives = 73/203 (35%), Gaps = 16/203 (7%)

Query: 196 LDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDE 255
           L  C + L   +    + E  ++      +  F   +        ++ +    +    + 
Sbjct: 542 LFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPEL 601

Query: 256 AKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC-NFP 314
             L+     ++  KL EL     L+D        + ++F K+ +  + L K + E     
Sbjct: 602 IALSKDETNENP-KLEELV--CILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILN 658

Query: 315 SIC-----------IHSGMSQEERLTRYKGFKEGNK-RILVATDLVGRGIDIERVNIVIN 362
            I              +GM+   +      FK     R+L+AT +   GIDI + N+V+ 
Sbjct: 659 YIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVL 718

Query: 363 YDMPDSADTYLHRVGRAGRFGTK 385
           Y+   +    +   GR    G+K
Sbjct: 719 YEYSGNVTKMIQVRGRGRAAGSK 741

>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 = 56.9 bits (136), Expect = 8e-09
 Identities = 41/255 (16%), Positives = 87/255 (34%), Gaps = 18/255 (7%)

Query: 3   ETRDNEYEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIV 62
           E    + + E+ D  E+  +A  + + +A  +      +G  + G        E  +   
Sbjct: 192 EDNAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYETKK--- 248

Query: 63  DSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKT--AVFVLSTLQQTEPNPGQVTALVL 120
                     Q E    AI G + +  A +G GKT  ++ +     Q  P   +   + L
Sbjct: 249 ------ARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFL 302

Query: 121 CHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL-A 179
                +  Q  + F+          V    G     +  + +  +   I+V TP  ++ +
Sbjct: 303 ATKVPVYEQQKNVFKHH-FERQGYSVQGISGENFSNVSVEKVIEDS-DIIVVTPQILVNS 360

Query: 180 LARDKDLSLKNVRHFILDECDKML----ESLDMRRDVQEIFKMTPHDKQVMMFSATLSKE 235
                  SL      I DEC         ++ M R +++ F       Q++  +A++   
Sbjct: 361 FEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVG 420

Query: 236 IRPVCKKFMQDPMEI 250
                ++ ++    +
Sbjct: 421 NAKNIEETIEHICSL 435

>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 = 59.6 bits (143), Expect = 1e-09
 Identities = 41/255 (16%), Positives = 86/255 (33%), Gaps = 18/255 (7%)

Query: 3   ETRDNEYEDELLDYEEEDAQAPDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIV 62
           E    + + E+ D  E+  +A  + + +A  +      +G  + G        E  +   
Sbjct: 192 EDNAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYETKK--- 248

Query: 63  DSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKT--AVFVLSTLQQTEPNPGQVTALVL 120
                     Q E    AI G + +  A +G GKT  ++ +     Q  P   +   + L
Sbjct: 249 ------ARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFL 302

Query: 121 CHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL-A 179
                +  Q  + F+          V    G     +  + +  +   I+V TP  ++ +
Sbjct: 303 ATKVPVYEQQKNVFKHH-FERQGYSVQGISGENFSNVSVEKVIEDS-DIIVVTPQILVNS 360

Query: 180 LARDKDLSLKNVRHFILDECDKMLESLD----MRRDVQEIFKMTPHDKQVMMFSATLSKE 235
                  SL      I DEC     +      M R +++ F       Q++  +A++   
Sbjct: 361 FEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVG 420

Query: 236 IRPVCKKFMQDPMEI 250
                ++ ++    +
Sbjct: 421 NAKNIEETIEHICSL 435

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos} Length = 797

 Score = 58.8 bits (141), Expect = 2e-09
 Identities = 44/259 (16%), Positives = 89/259 (34%), Gaps = 17/259 (6%)

Query: 140 YLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDEC 199
               ++       ++    KD         +V T  R   L + +D   ++     L  C
Sbjct: 487 TEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQ-RKCRLLQLEDKEEESRICRALFIC 545

Query: 200 DKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLT 259
            + L   +    + E  ++      +  F   +        ++ +    +    +   L+
Sbjct: 546 TEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALS 605

Query: 260 LHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC-NFPSICI 318
                ++  KL EL     L+D        + ++F K+ +  + L K + E      I  
Sbjct: 606 KDETNENP-KLEELVCI--LDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKP 662

Query: 319 H-----------SGMSQEERLTRYKGFKEGNK-RILVATDLVGRGIDIERVNIVINYDMP 366
                       +GM+   +      FK     R+L+AT +   GIDI + N+V+ Y+  
Sbjct: 663 GVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYS 722

Query: 367 DSADTYLHRVGRAGRFGTK 385
            +    +   GR    G+K
Sbjct: 723 GNVTKMIQVRGRGRAAGSK 741

>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 = 57.3 bits (137), Expect = 5e-09
 Identities = 39/239 (16%), Positives = 80/239 (33%), Gaps = 16/239 (6%)

Query: 156 KIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEI 215
           +  K     +  +  +    R   L + +D   ++     L  C + L   +    + E 
Sbjct: 261 QNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISED 320

Query: 216 FKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEK 275
            ++      +  F   +        ++ +    +    +   L+         KL EL  
Sbjct: 321 ARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALS-KDETNENPKLEELVC 379

Query: 276 NRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC-NFPSICIH-----------SGMS 323
              L+D        + ++F K+ +  + L K + E      I              +GM+
Sbjct: 380 I--LDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMT 437

Query: 324 QEERLTRYKGFKEGNK-RILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR 381
              +      FK     R+L+AT +   GIDI + N+V+ Y+   +    +   GR   
Sbjct: 438 LPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRA 496

>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 = 55.7 bits (133), Expect = 1e-08
 Identities = 28/185 (15%), Positives = 61/185 (32%), Gaps = 9/185 (4%)

Query: 73  QHECIPQAILGMDVICQAKSGMGKT--AVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI 130
           Q E    AI G + +  A +G GKT  ++ +     Q  P   +   + L     +  Q 
Sbjct: 12  QIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQ 71

Query: 131 CHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL-ALARDKDLSLK 189
            + F+          V    G     +  + +  +   I+V TP  ++ +       SL 
Sbjct: 72  KNVFKHH-FERQGYSVQGISGENFSNVSVEKVIEDS-DIIVVTPQILVNSFEDGTLTSLS 129

Query: 190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQ----VMMFSATLSKEIRPVCKKFMQ 245
                I DEC     +      +    +   +       ++  +A++        ++ ++
Sbjct: 130 IFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIE 189

Query: 246 DPMEI 250
               +
Sbjct: 190 HICSL 194

>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 = 57.6 bits (138), Expect = 5e-09
 Identities = 36/252 (14%), Positives = 80/252 (31%), Gaps = 61/252 (24%)

Query: 184 KDLSLKNVRHFILD-ECDKMLESLD---MRRDVQEIFKMTPHDKQV-MMFSATLSKEIRP 238
           KD+       F+ + +C  + +       + ++  I            +F   LSK+   
Sbjct: 19  KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM 78

Query: 239 VCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALD--FNQVVIFVK 296
           V +KF+++ +     +      +  +   IK  + + +      ++  D  +N   +F K
Sbjct: 79  V-QKFVEEVLR---IN------YKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK 128

Query: 297 -SVSRAAELNKL---LVECN-FPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRG 351
            +VSR     KL   L+E     ++ I  G+          G   G K  +     V   
Sbjct: 129 YNVSRLQPYLKLRQALLELRPAKNVLID-GV---------LGS--G-KTWVAL--DVCLS 173

Query: 352 IDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLL 411
             ++                         +   K   +   +  S   +L  + K ++ +
Sbjct: 174 YKVQC------------------------KMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209

Query: 412 IGSFQCLVLGSF 423
             ++      S 
Sbjct: 210 DPNWTSRSDHSS 221

>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 = 52.5 bits (125), Expect = 2e-07
 Identities = 53/382 (13%), Positives = 113/382 (29%), Gaps = 104/382 (27%)

Query: 5   RDNEYEDEL--LD--YEEEDAQAPD------------SVATKANGEAAKKGYVGIHSSGF 48
           +   YE+ L  L      +   A +             V    +        +  HS   
Sbjct: 239 KSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTL 298

Query: 49  RDFLLKPELLRAIVDSGFEH-PSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
               +K  LL   +D   +  P EV     P+ +    +I ++           L+T   
Sbjct: 299 TPDEVK-SLLLKYLDCRPQDLPREV-LTTNPRRL---SIIAESIRDG-------LATWDN 346

Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH------KDL 161
            +     V    L    E +  +    E    +    +++VF    +I          D+
Sbjct: 347 WK----HVNCDKLTTIIESSLNVLEPAEYRKMFD---RLSVFPPSAHIPTILLSLIWFDV 399

Query: 162 LKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMT-- 219
           +K++   +V       L + +    S  ++    L+   K+     + R + + + +   
Sbjct: 400 IKSDVMVVVNKLHKYSL-VEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKT 458

Query: 220 --PHDKQVM-------------MFSATLSKEIRPVCKKFMQDPMEIYVDD---EAKL--- 258
               D                 + +    + +      F      +++D    E K+   
Sbjct: 459 FDSDDLIPPYLDQYFYSHIGHHLKNIEHPERM----TLFRM----VFLDFRFLEQKIRHD 510

Query: 259 ------------TLHGLVQH--YIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAEL 304
                       TL  L  +  YI  ++ +  R +N +LD         F+       E 
Sbjct: 511 STAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILD---------FLPK----IEE 557

Query: 305 NKLLVECNFPSICIHSGMSQEE 326
           N  L+   +  + +   +  E+
Sbjct: 558 N--LICSKYTDL-LRIALMAED 576

>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 = 41.8 bits (97), Expect = 4e-04
 Identities = 54/385 (14%), Positives = 108/385 (28%), Gaps = 125/385 (32%)

Query: 49  RDFLLK--PELLRAI-----VDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFV 101
            +F  K   ++ ++I     +D        V        +     +   +  M     FV
Sbjct: 31  DNFDCKDVQDMPKSILSKEEIDHIIMSKDAVS-----GTLRLFWTLLSKQEEM--VQKFV 83

Query: 102 LSTLQ----------QTEPN-PGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFY 150
              L+          +TE   P  +T + +   R+  Y     F +++            
Sbjct: 84  EEVLRINYKFLMSPIKTEQRQPSMMTRMYI-EQRDRLYNDNQVFAKYNVSRLQPY----- 137

Query: 151 GGVNIKIHKDLLK-NECPQIVV-GTPG---RILAL--ARDKD-----------LSLKNVR 192
               +K+ + LL+      +++ G  G     +AL                  L+LKN  
Sbjct: 138 ----LKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCN 193

Query: 193 HFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
               +   +ML+ L        ++++ P+       S+ +   I                
Sbjct: 194 --SPETVLEMLQKL--------LYQIDPNWTSRSDHSSNIKLRI---------------- 227

Query: 253 DDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC- 311
               +           +L  L K++   + L  L          +V  A   N   + C 
Sbjct: 228 -HSIQA----------ELRRLLKSKPYENCLLVLL---------NVQNAKAWNAFNLSCK 267

Query: 312 -----------NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIV 360
                      +F S    + +S +              + L+   L  R  D+ R  + 
Sbjct: 268 ILLTTRFKQVTDFLSAATTTHISLDHHS---MTLTPDEVKSLLLKYLDCRPQDLPREVLT 324

Query: 361 IN-----------YDMPDSADTYLH 374
            N            D   + D + H
Sbjct: 325 TNPRRLSIIAESIRDGLATWDNWKH 349

>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 = 56.1 bits (135), Expect = 1e-08
 Identities = 50/342 (14%), Positives = 90/342 (26%), Gaps = 71/342 (20%)

Query: 66  FEHPSEVQHECIPQAIL--GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT 123
                      + + I       I     G GKT   + S +++      +   L+L  T
Sbjct: 167 QAERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRT--LILAPT 224

Query: 124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQ---IVVGTPGRILAL 180
           R +A                  +     G+ I+     +K++      + +         
Sbjct: 225 RVVA-------AE---------MEEALRGLPIRYQTPAVKSDHTGREIVDLMCHA-TFTT 267

Query: 181 ARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVC 240
                  + N    ++DE           R              + M +AT      P  
Sbjct: 268 RLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAAAIFM-TATPPGSTDPF- 325

Query: 241 KKFMQDPMEIYV--DDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSV 298
                 P       D E ++        +  +++ +                 V FV S+
Sbjct: 326 ------PQSNSPIEDIEREIPERSWNTGFDWITDYQGK--------------TVWFVPSI 365

Query: 299 SRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRG--IDIER 356
               ++   L +     I +       E    Y   K  +   +V TD+   G      R
Sbjct: 366 KAGNDIANCLRKSGKRVIQLSRKTFDTE----YPKTKLTDWDFVVTTDISEMGANFRAGR 421

Query: 357 V-------NIVINYD----------MPDSADTYLHRVGRAGR 381
           V         VI  D          +P +  +   R GR GR
Sbjct: 422 VIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGR 463

>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 = 54.9 bits (132), Expect = 2e-08
 Identities = 53/354 (14%), Positives = 90/354 (25%), Gaps = 63/354 (17%)

Query: 67  EHPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE 125
               E  +E            I     G GKT   + S +++      +   L+L  TR 
Sbjct: 2   SAMGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLRRLRT--LILAPTRV 59

Query: 126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD 185
           +A             L  + +          +  D    E   + +              
Sbjct: 60  VA-------AEMEEALRGLPI----RYQTPAVKSDHTGRE--IVDLMCHA-TFTTRLLSS 105

Query: 186 LSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVC-KKFM 244
             + N    ++DE           R              + M +AT      P       
Sbjct: 106 TRVPNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAAAIFM-TATPPGSTDPFPQSNSP 164

Query: 245 QDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAEL 304
            + +E  + + +  T    +  Y                      + V FV S+    ++
Sbjct: 165 IEDIEREIPERSWNTGFDWITDYQG--------------------KTVWFVPSIKAGNDI 204

Query: 305 NKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRG--IDIERV----- 357
              L +     I +       E    Y   K  +   +V TD+   G      RV     
Sbjct: 205 ANCLRKSGKRVIQLSRKTFDTE----YPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRR 260

Query: 358 --NIVINYD----------MPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSD 399
               VI  D          +P +  +   R GR GR         +V S     
Sbjct: 261 CLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNP-AQEDDQYVFSGDPLK 313

>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 = 53.7 bits (130), Expect = 6e-08
 Identities = 30/107 (28%), Positives = 49/107 (45%), Gaps = 5/107 (4%)

Query: 299 SRAA--ELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIER 356
           SRA   +    L      +   H+G+    R    + F+  + +I+VAT   G GI+   
Sbjct: 245 SRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPN 304

Query: 357 VNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQ 403
           V  V+++D+P + ++Y    GRAGR G    A+ F   A   D+   
Sbjct: 305 VRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPA---DMAWL 348

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 51.4 bits (123), Expect = 1e-07
 Identities = 28/136 (20%), Positives = 50/136 (36%), Gaps = 11/136 (8%)

Query: 73  QHECIPQAILGMDVICQAKSGMGKT--AVFVLSTLQQTEPNPGQVT-ALVLCHTRELAYQ 129
           Q E    A+ G ++I    +G GKT  AV++       +    +    +VL +   L  Q
Sbjct: 38  QMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQ 97

Query: 130 ICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRIL------ALARD 183
           +  +  +        +V    G   +KI    +   C  I++ T   +           D
Sbjct: 98  LFRKEFQP-FLKKWYRVIGLSGDTQLKISFPEVVKSC-DIIISTAQILENSLLNLENGED 155

Query: 184 KDLSLKNVRHFILDEC 199
             + L +    I+DEC
Sbjct: 156 AGVQLSDFSLIIIDEC 171

>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 = 51.9 bits (125), Expect = 2e-07
 Identities = 27/107 (25%), Positives = 47/107 (43%), Gaps = 4/107 (3%)

Query: 303 ELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN 362
           ++   L      +   H+ +  E++ T ++ +     +++VAT   G GID   V  VI+
Sbjct: 282 QVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIH 341

Query: 363 YDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMF 409
           + M  S + Y    GRAGR   K   I +       DI  ++S  + 
Sbjct: 342 HSMSKSMENYYQESGRAGRDDMKADCILYYGFG---DIF-RISSMVV 384

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431

 Score = 49.5 bits (118), Expect = 1e-06
 Identities = 35/259 (13%), Positives = 70/259 (27%), Gaps = 44/259 (16%)

Query: 146 VAVFYGG---VNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM 202
           +     G     +       +     +          +   + + + N   +I+DE   +
Sbjct: 47  MYEALRGEPIRYMTPAVQSERTGNEIVDFMCHS-TFTMKLLQGVRVPNYNLYIMDEAHFL 105

Query: 203 LESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHG 262
             +    R   E          + M +AT               P       +       
Sbjct: 106 DPASVAARGYIETRVSMGDAGAIFM-TATPPGTTEAF-------PPSNSPIID------- 150

Query: 263 LVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGM 322
                 ++ +   N     + +     + V FV S+ + AE+   L +     + ++   
Sbjct: 151 ---EETRIPDKAWNSGYEWITEFD--GRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRKT 205

Query: 323 SQEERLTRYKGFKEGNKRILVATDLVGRG--IDIERV---NIVINYDMPDSADTYL---- 373
            + E    Y   K      ++ TD+   G     +RV      I   + D   +      
Sbjct: 206 FESE----YPKCKSEKWDFVITTDISEMGANFKADRVIDPRKTIKPILLDGRVSMQGPIA 261

Query: 374 -------HRVGRAGRFGTK 385
                   R GR GR   K
Sbjct: 262 ITPASAAQRRGRIGRNPEK 280

>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 = 44.8 bits (106), Expect = 4e-05
 Identities = 48/316 (15%), Positives = 80/316 (25%), Gaps = 61/316 (19%)

Query: 86  VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIK 145
            +     G GKT   +   ++       +    VL  TR +A          +  L  + 
Sbjct: 24  TVLDLHPGSGKTRKILPQIIKDAIQQRLRT--AVLAPTRVVA-------AEMAEALRGLP 74

Query: 146 VAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES 205
           V            +   +     + V     +          + N   F++DE      +
Sbjct: 75  V-----RYQTSAVQREHQGNEI-VDVMCHATLTHRLMS-PNRVPNYNLFVMDEAHFTDPA 127

Query: 206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVC-KKFMQDPMEIYVDDEAKLTLHGLV 264
               R              + M +AT      P          ++  + D A  + +  +
Sbjct: 128 SIAARGYIATKVELGEAAAIFM-TATPPGTTDPFPDSNAPIHDLQDEIPDRAWSSGYEWI 186

Query: 265 QHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQ 324
                    E   K             V FV SV    E+   L       I ++     
Sbjct: 187 T--------EYAGK------------TVWFVASVKMGNEIAMCLQRAGKKVIQLNRKSYD 226

Query: 325 EERLTRYKGFKEGNKRILVATDLVGRG--IDIERV-------NIVINYDMPDSADTYLH- 374
            E    Y   K G+   ++ TD+   G      RV          I  +           
Sbjct: 227 TE----YPKCKNGDWDFVITTDISEMGANFGASRVIDCRKSVKPTILEEGEGRVILGNPS 282

Query: 375 ---------RVGRAGR 381
                    R GR GR
Sbjct: 283 PITSASAAQRRGRVGR 298

>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 = 43.0 bits (101), Expect = 2e-04
 Identities = 36/234 (15%), Positives = 59/234 (25%), Gaps = 46/234 (19%)

Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
            + V      L       L + N   F++DE      +    R              + M
Sbjct: 311 IVDVMCHA-TLTHRLMSPLRVPNYNLFVMDEAHFTDPASIAARGYIATRVEAGEAAAIFM 369

Query: 228 FSATLSKEIRPV-CKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDAL 286
            +AT      P          +   + D A  +          +++              
Sbjct: 370 -TATPPGTSDPFPDTNSPVHDVSSEIPDRAWSSGFEW------ITDYAGK---------- 412

Query: 287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD 346
                V FV SV  + E+ + L       I ++      E        K G+   ++ TD
Sbjct: 413 ----TVWFVASVKMSNEIAQCLQRAGKRVIQLNRKSYDTEYPKC----KNGDWDFVITTD 464

Query: 347 LV--GRGIDIERV------NIVINYDMPDSADTYLH-----------RVGRAGR 381
           +   G      RV            D  +                  R GR GR
Sbjct: 465 ISEMGANFGASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGR 518

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	423
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	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
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	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
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	100.0
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	100.0
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	100.0
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	100.0
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	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
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	100.0
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	100.0
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	100.0
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	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
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	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
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	100.0
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	100.0
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	100.0
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
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	100.0
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	100.0
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	100.0
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	100.0
1yks_A	440	Genome polyprotein [contains: flavivirin protease	100.0
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	100.0
3h1t_A	590	Type I site-specific restriction-modification syst	100.0
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	100.0
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	100.0
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	100.0
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	100.0
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	100.0
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	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
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	100.0
3jux_A	822	Protein translocase subunit SECA; protein transloc	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.97
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.96
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.96
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.95
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.95
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.95
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.95
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.95
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.94
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	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
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.91
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.9
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.89
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.87
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.87
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.83
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.83
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.83
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.84
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.47
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	98.46
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	98.39
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.37
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.27
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.26
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.26
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.22
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.66
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.54
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.32
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.11
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.08
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.01
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	96.96
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.94
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.94
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.8
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	96.79
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	96.77
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	96.66
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	96.62
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.6
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.55
3bos_A	242	Putative DNA replication factor; P-loop containing	96.47
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.38
2chg_A	226	Replication factor C small subunit; DNA-binding pr	96.33
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.32
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.09
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	96.06
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.04
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.0
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	95.94
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	95.87
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	95.53
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	95.45
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	95.44
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	95.37
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	95.24
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	95.16
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.08
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	95.0
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	94.78
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	94.77
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	94.59
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	94.54
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	94.51
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	94.23
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	94.2
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	94.12
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	94.06
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	93.92
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	93.8
2chq_A	319	Replication factor C small subunit; DNA-binding pr	93.53
3pvs_A	447	Replication-associated recombination protein A; ma	93.48
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	93.45
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	93.41
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	93.16
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	93.02
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	92.87
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	92.8
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	92.73
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	92.66
2r6a_A	454	DNAB helicase, replicative helicase; replication,	92.56
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	92.49
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	92.4
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	92.31
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	92.05
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	91.83
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	91.76
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	91.59
2fna_A	357	Conserved hypothetical protein; structural genomic	91.45
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	91.29
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	90.93
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	90.84
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	90.72
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	90.04
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	90.02
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	89.99
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	89.91
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	89.79
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	89.74
3co5_A	143	Putative two-component system transcriptional RES	89.67
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	89.35
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	89.3
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	89.27
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	88.4
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	88.29
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	88.12
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	88.1
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	88.09
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	87.88
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	87.82
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	87.73
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	87.65
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	87.31
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	87.11
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	86.99
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	86.86
3io5_A	333	Recombination and repair protein; storage dimer, i	86.59
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	86.57
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	86.53
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	86.17
1p9r_A	418	General secretion pathway protein E; bacterial typ	86.06
2z43_A	324	DNA repair and recombination protein RADA; archaea	86.06
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	86.04
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	85.83
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	85.82
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	85.68
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	85.63
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	85.36
2qgz_A	308	Helicase loader, putative primosome component; str	85.22
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	85.11
2l82_A	162	Designed protein OR32; structural genomics, northe	84.95
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	84.93
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	84.86
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	84.78
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	84.47
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	84.45
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	84.4
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	84.31
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	83.97
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	84.32
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	83.83
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	83.76
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	83.59
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	83.59
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	83.58
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	83.47
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	83.35
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	83.27
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	83.14
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	83.13
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	83.03
2eyu_A	261	Twitching motility protein PILT; pilus retraction	82.92
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	82.88
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	82.85
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	82.8
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	82.74
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	82.68
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	82.58
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	82.57
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	82.57
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	82.52
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	82.41
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	82.4
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	82.36
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	82.16
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	82.11
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	81.99
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	81.87
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	81.85
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	81.66
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	81.55
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	81.53
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	81.5
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	81.4
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	81.33
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	81.32
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	81.28
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	81.22
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	81.17
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	81.14
2cvh_A	220	DNA repair and recombination protein RADB; filamen	81.06
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	81.02
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	81.01
3bfn_A	388	Kinesin-like protein KIF22; limited proteolysis, s	80.95
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	80.95
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	80.94
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	80.92
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	80.86
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	80.76
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	80.61
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	80.59
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	80.56
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	80.3
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	80.28
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	80.2
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	80.2
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	80.17
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	80.11
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	80.02

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=100.00  E-value=1.7e-61  Score=458.66  Aligned_cols=364  Identities=29%  Similarity=0.510  Sum_probs=324.9

Q ss_pred             cCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC-----CCCeEEE
Q 014486           44 HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN-----PGQVTAL  118 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~-----~~~~~~l  118 (423)
                      ...+|+++++++.++++|.++||..|+|+|+++++.++.++++++++|||||||++|++|++..+...     ..++++|
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            44579999999999999999999999999999999999999999999999999999999999875432     2356899


Q ss_pred             EEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcC
Q 014486          119 VLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDE  198 (423)
Q Consensus       119 il~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE  198 (423)
                      |++|+++|+.|++++++++.... ++++..++||.....+...+..+ ++|+|+||++|.+++......+.+++++|+||
T Consensus       134 il~PtreLa~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~-~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVlDE  211 (434)
T 2db3_A          134 IVSPTRELAIQIFNEARKFAFES-YLKIGIVYGGTSFRHQNECITRG-CHVVIATPGRLLDFVDRTFITFEDTRFVVLDE  211 (434)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTS-SCCCCEECTTSCHHHHHHHHTTC-CSEEEECHHHHHHHHHTTSCCCTTCCEEEEET
T ss_pred             EEecCHHHHHHHHHHHHHHhccC-CcEEEEEECCCCHHHHHHHhhcC-CCEEEEChHHHHHHHHhCCcccccCCeEEEcc
Confidence            99999999999999999987664 78889999999988877777766 59999999999999998888899999999999


Q ss_pred             cchhhccCCcHHHHHHHHHhC--CCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHH
Q 014486          199 CDKMLESLDMRRDVQEIFKMT--PHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKN  276 (423)
Q Consensus       199 ~h~~~~~~~~~~~~~~~~~~~--~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  276 (423)
                      ||++.+ .+|...+..+...+  ++..|++++|||+|+.+..++..++.++..+...... .....+.+.+..+....+.
T Consensus       212 ah~~~~-~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~-~~~~~i~~~~~~~~~~~k~  289 (434)
T 2db3_A          212 ADRMLD-MGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVG-GACSDVKQTIYEVNKYAKR  289 (434)
T ss_dssp             HHHHTS-TTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTT-CCCTTEEEEEEECCGGGHH
T ss_pred             Hhhhhc-cCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEecccc-ccccccceEEEEeCcHHHH
Confidence            999998 68999999998875  5688999999999999999988888877766554433 2334556677778888888


Q ss_pred             HHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCC
Q 014486          277 RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIER  356 (423)
Q Consensus       277 ~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~  356 (423)
                      ..+.+++..... ++||||++++.++.+++.|...++++..+||++++.+|..+++.|++|+.+|||||+++++|+|+|+
T Consensus       290 ~~l~~~l~~~~~-~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~  368 (434)
T 2db3_A          290 SKLIEILSEQAD-GTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKN  368 (434)
T ss_dssp             HHHHHHHHHCCT-TEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTT
T ss_pred             HHHHHHHHhCCC-CEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCccc
Confidence            889998887764 4999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcch
Q 014486          357 VNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLI  412 (423)
Q Consensus       357 ~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (423)
                      +++||+|++|.++.+|+||+||+||.|+.|.+++|+++..+......+.+.+....
T Consensus       369 v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~~~~~~~~l~~~l~~~~  424 (434)
T 2db3_A          369 IKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSG  424 (434)
T ss_dssp             CCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTTCGGGHHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccccHHHHHHHHHHHHHcC
Confidence            99999999999999999999999999999999999998778788888888876543

>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=1e-60  Score=449.75  Aligned_cols=371  Identities=75%  Similarity=1.189  Sum_probs=339.1

Q ss_pred             cCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           44 HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      .+..|+++++++.+.++|.++||..|+|+|.++++.++.++++++.+|||+|||++++++++..+.....++++||++|+
T Consensus         6 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~   85 (391)
T 1xti_A            6 MSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHT   85 (391)
T ss_dssp             ---CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSC
T ss_pred             CCCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCC
Confidence            34679999999999999999999999999999999999999999999999999999999999887766666689999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                      ++|+.|+.+.++++....+++++..++|+.........+.++.++|+|+||+++..++......+.++++||+||||.+.
T Consensus        86 ~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~  165 (391)
T 1xti_A           86 RELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKML  165 (391)
T ss_dssp             HHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHT
T ss_pred             HHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHh
Confidence            99999999999999888778999999999988887777777767999999999999988888888999999999999998


Q ss_pred             ccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHH
Q 014486          204 ESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLL  283 (423)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll  283 (423)
                      ++.++...+..+....++..|++++|||+++.....+..++..+..+................+.......+...+..++
T Consensus       166 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l  245 (391)
T 1xti_A          166 EQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLL  245 (391)
T ss_dssp             SSHHHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEECCGGGHHHHHHHHH
T ss_pred             hccchHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEcCchhHHHHHHHHH
Confidence            75578888888999998899999999999999999888888888777766655555666777778888888889999999


Q ss_pred             HhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEc
Q 014486          284 DALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINY  363 (423)
Q Consensus       284 ~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~  363 (423)
                      .....+++||||++.+.+..+++.|...++.+..+||+++..+|..+++.|++|+.+|||||+++++|+|+|++++||++
T Consensus       246 ~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~  325 (391)
T 1xti_A          246 DVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNY  325 (391)
T ss_dssp             HHSCCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEEES
T ss_pred             HhcCCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEEEe
Confidence            98888999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhh
Q 014486          364 DMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGS  414 (423)
Q Consensus       364 ~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  414 (423)
                      ++|+++..|.||+||+||.|++|.+++++++.++..+++.+++.++..+..
T Consensus       326 ~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  376 (391)
T 1xti_A          326 DMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISE  376 (391)
T ss_dssp             SCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHHHHHHHHHHHHTTCCCEE
T ss_pred             CCCCCHHHHHHhcccccCCCCceEEEEEEcccchHHHHHHHHHHhcCChhh
Confidence            999999999999999999999999999999888889999999999877654

>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=2.2e-58  Score=436.47  Aligned_cols=364  Identities=37%  Similarity=0.639  Sum_probs=324.0

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      .+|+++++++.+.++|.+.||..|+|+|+++++.++.++++++.+|||+|||++|+++++..+.....+.++||++|+++
T Consensus        37 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~  116 (410)
T 2j0s_A           37 PTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRE  116 (410)
T ss_dssp             CSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHH
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCcHH
Confidence            46999999999999999999999999999999999999999999999999999999999998876555569999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~  205 (423)
                      |+.|+.+.++++.... ++.+..+.|+.....+...+..+ ++|+|+||+++..++......+.++++||+||||++.+ 
T Consensus       117 L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~-  193 (410)
T 2j0s_A          117 LAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDYG-QHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLN-  193 (410)
T ss_dssp             HHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHHHC-CSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTS-
T ss_pred             HHHHHHHHHHHHhccC-CeEEEEEECCCCHHHHHHHhhcC-CCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHHHh-
Confidence            9999999999987665 78899999999888877777666 59999999999999988888889999999999999987 


Q ss_pred             CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeCh-HHHHHHHHHHHH
Q 014486          206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE-LEKNRKLNDLLD  284 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~ll~  284 (423)
                      .++...+..+...+++..|++++|||+++........++..+..+...... .....+.+.+..... ..+...+.+++.
T Consensus       194 ~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~k~~~l~~~~~  272 (410)
T 2j0s_A          194 KGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDE-LTLEGIKQFFVAVEREEWKFDTLCDLYD  272 (410)
T ss_dssp             TTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGG-CSCTTEEEEEEEESSTTHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCcc-ccCCCceEEEEEeCcHHhHHHHHHHHHH
Confidence            688999999999999999999999999998877777777777666544332 233445555555544 347788888888


Q ss_pred             hhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEcc
Q 014486          285 ALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYD  364 (423)
Q Consensus       285 ~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~  364 (423)
                      ....+++||||++.+.++.+++.|...++.+..+||++++.+|..+++.|++|+.+|||||+++++|+|+|++++||+++
T Consensus       273 ~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~  352 (410)
T 2j0s_A          273 TLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYD  352 (410)
T ss_dssp             HHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESS
T ss_pred             hcCCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEEC
Confidence            88888999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhh
Q 014486          365 MPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGS  414 (423)
Q Consensus       365 ~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  414 (423)
                      +|+++..|.||+||+||.|++|.+++|+++ .+...+..++++++..+..
T Consensus       353 ~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~-~~~~~~~~i~~~~~~~~~~  401 (410)
T 2j0s_A          353 LPNNRELYIHRIGRSGRYGRKGVAINFVKN-DDIRILRDIEQYYSTQIDE  401 (410)
T ss_dssp             CCSSHHHHHHHHTTSSGGGCCEEEEEEEEG-GGHHHHHHHHHHTTCCCEE
T ss_pred             CCCCHHHHHHhcccccCCCCceEEEEEecH-HHHHHHHHHHHHhCCCcee
Confidence            999999999999999999999999999985 6778888999999876654

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=100.00  E-value=1.1e-57  Score=430.28  Aligned_cols=366  Identities=39%  Similarity=0.637  Sum_probs=323.4

Q ss_pred             cCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           44 HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      ...+|+++++++.+.++|.++||.+|+|+|.++++.++.++++++.+|||+|||++++++++..+.....+.++||++|+
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            34579999999999999999999999999999999999999999999999999999999999988766556689999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                      ++|+.|+.+.++++.... ++++..+.|+.....+...+... ++|+|+||+++..++......+.++++||+||||++.
T Consensus        99 ~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~  176 (400)
T 1s2m_A           99 RELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLNET-VHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKML  176 (400)
T ss_dssp             HHHHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHTTSC-CSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHS
T ss_pred             HHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHHHhcCC-CCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhh
Confidence            999999999999987665 78888999988877666555444 6999999999999888877888999999999999987


Q ss_pred             ccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHH
Q 014486          204 ESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLL  283 (423)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll  283 (423)
                      + ..+...+..+...+++..|++++|||++......+...+..+..+.....  .....+...+.......+...+..++
T Consensus       177 ~-~~~~~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~k~~~l~~~~  253 (400)
T 1s2m_A          177 S-RDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEE--LTLKGITQYYAFVEERQKLHCLNTLF  253 (400)
T ss_dssp             S-HHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCSS--CBCTTEEEEEEECCGGGHHHHHHHHH
T ss_pred             h-hchHHHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEeccc--cccCCceeEEEEechhhHHHHHHHHH
Confidence            7 57888888898888889999999999999988888888877765544332  33345556666677778888888898


Q ss_pred             HhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEc
Q 014486          284 DALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINY  363 (423)
Q Consensus       284 ~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~  363 (423)
                      .....+++||||++.+.++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||||+++++|+|+|++++||++
T Consensus       254 ~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi~~  333 (400)
T 1s2m_A          254 SKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINF  333 (400)
T ss_dssp             HHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEES
T ss_pred             hhcCCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEEEe
Confidence            88888999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhhh
Q 014486          364 DMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSF  415 (423)
Q Consensus       364 ~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (423)
                      ++|+++..|.||+||+||.|++|.+++++++ .+...+..+++.++..+..+
T Consensus       334 ~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~-~~~~~~~~i~~~~~~~~~~~  384 (400)
T 1s2m_A          334 DFPKTAETYLHRIGRSGRFGHLGLAINLINW-NDRFNLYKIEQELGTEIAAI  384 (400)
T ss_dssp             SCCSSHHHHHHHHCBSSCTTCCEEEEEEECG-GGHHHHHHHHHHHTCCCEEC
T ss_pred             CCCCCHHHHHHhcchhcCCCCCceEEEEecc-chHHHHHHHHHHhCCCcccc
Confidence            9999999999999999999999999999986 46677888999998776543

>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=5.6e-58  Score=434.43  Aligned_cols=366  Identities=39%  Similarity=0.651  Sum_probs=311.6

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ..+|+++++++.+.+.|.+.|+..|+++|.++++.++.++++++.+|||+|||++|++++++.+.....+.++||++|++
T Consensus        39 ~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  118 (414)
T 3eiq_A           39 VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTR  118 (414)
T ss_dssp             CCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             hcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChH
Confidence            35699999999999999999999999999999999999999999999999999999999999887665566899999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      +|+.|+.+.++++.... +..+....|+.........+..+.++|+|+||++|...+......+.++++||+||||++.+
T Consensus       119 ~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~~~  197 (414)
T 3eiq_A          119 ELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLS  197 (414)
T ss_dssp             HHHHHHHHHHHHHGGGS-CCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHHHHH
T ss_pred             HHHHHHHHHHHHHhccc-CceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHHhhc
Confidence            99999999999988765 78888889998888777777766689999999999999988888888999999999999987


Q ss_pred             cCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeCh-HHHHHHHHHHH
Q 014486          205 SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSE-LEKNRKLNDLL  283 (423)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~ll  283 (423)
                       .++...+..++..+++..|++++|||++.........++..+..+...... .....+...+..... ..+...+..++
T Consensus       198 -~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~  275 (414)
T 3eiq_A          198 -RGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEE-LTLEGIRQFYINVEREEWKLDTLCDLY  275 (414)
T ss_dssp             -TTTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCC-CCTTSCCEEEEECSSSTTHHHHHHHHH
T ss_pred             -cCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCc-cCCCCceEEEEEeChHHhHHHHHHHHH
Confidence             688999999999999999999999999999888888888877766554433 233444455555443 34778888888


Q ss_pred             HhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEc
Q 014486          284 DALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINY  363 (423)
Q Consensus       284 ~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~  363 (423)
                      .....+++||||++++.++.+++.|...++.+..+||++++.+|..+++.|++|+.+|||||+++++|+|+|++++||++
T Consensus       276 ~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~  355 (414)
T 3eiq_A          276 ETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY  355 (414)
T ss_dssp             HSSCCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEEES
T ss_pred             HhCCCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEEEe
Confidence            88888999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhh
Q 014486          364 DMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGS  414 (423)
Q Consensus       364 ~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  414 (423)
                      ++|+++..|.||+||+||.|++|.+++++++ .+...+..+++.++..+..
T Consensus       356 ~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~-~~~~~~~~~~~~~~~~~~~  405 (414)
T 3eiq_A          356 DLPTNRENYIHRIGRGGRFGRKGVAINMVTE-EDKRTLRDIETFYNTSIEE  405 (414)
T ss_dssp             SCCSSTHHHHHHSCCC-------CEEEEECS-THHHHHHHHHHHTTCCCEE
T ss_pred             CCCCCHHHhhhhcCcccCCCCCceEEEEEcH-HHHHHHHHHHHHHcCCccc
Confidence            9999999999999999999999999999985 5677788999998876654

>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=2.3e-57  Score=430.01  Aligned_cols=367  Identities=34%  Similarity=0.559  Sum_probs=322.3

Q ss_pred             cCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccC--CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEe
Q 014486           44 HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG--MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLC  121 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~--~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  121 (423)
                      ...+|+++++++.++++|.+.||..|+|+|.++++.++.+  +++++.+|||+|||++|++|++..+.....++++||++
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            3457999999999999999999999999999999999997  89999999999999999999999888777677999999


Q ss_pred             cChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhc-CCCCCCCccEEEEcCcc
Q 014486          122 HTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARD-KDLSLKNVRHFILDECD  200 (423)
Q Consensus       122 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~-~~~~~~~~~~vVvDE~h  200 (423)
                      |+++|+.|+++.++++....+++.+....++.......    ...++|+|+||+++..++.. ....+.++++||+||||
T Consensus       103 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah  178 (412)
T 3fht_A          103 PTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ----KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEAD  178 (412)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTC----CCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHH
T ss_pred             CCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhhh----cCCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHH
Confidence            99999999999999998877788888888876544322    23369999999999998865 55667899999999999


Q ss_pred             hhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeC-hHHHHHHH
Q 014486          201 KMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS-ELEKNRKL  279 (423)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l  279 (423)
                      .+.+...+...+..+...++...|++++|||+++........++..+..+....... ....+...+.... ...+...+
T Consensus       179 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l  257 (412)
T 3fht_A          179 VMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE-TLDTIKQYYVLCSSRDEKFQAL  257 (412)
T ss_dssp             HHHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGS-SCTTEEEEEEECSSHHHHHHHH
T ss_pred             HHhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccc-cccCceEEEEEcCChHHHHHHH
Confidence            998766888889999999999999999999999999888888888877665554432 3334444444443 45677888


Q ss_pred             HHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCE
Q 014486          280 NDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI  359 (423)
Q Consensus       280 ~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~  359 (423)
                      ..++.....+++||||++.+.+..+++.|...++.+..+||++++.+|..+++.|++|+.+|||||+++++|+|+|++++
T Consensus       258 ~~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~  337 (412)
T 3fht_A          258 CNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSV  337 (412)
T ss_dssp             HHHHHHHSSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEE
T ss_pred             HHHHhhcCCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCE
Confidence            88888888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccCCC------CcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhhh
Q 014486          360 VINYDMPD------SADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSF  415 (423)
Q Consensus       360 vi~~~~~~------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (423)
                      ||++++|+      +...|+||+||+||.|+.|.+++++++.++...++.+++.++..+...
T Consensus       338 Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~  399 (412)
T 3fht_A          338 VINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL  399 (412)
T ss_dssp             EEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHHTCCCEEC
T ss_pred             EEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChhhHHHHHHHHHHHCCccccC
Confidence            99999995      568999999999999999999999998888999999999999776554

>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=1.7e-57  Score=431.47  Aligned_cols=363  Identities=31%  Similarity=0.507  Sum_probs=312.6

Q ss_pred             ccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC-----------
Q 014486           43 IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN-----------  111 (423)
Q Consensus        43 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~-----------  111 (423)
                      ....+|+++++++.+.++|...||..|+|+|.++++.++.++++++.+|||+|||++|++|++..+...           
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            345579999999999999999999999999999999999999999999999999999999998765321           


Q ss_pred             -------CCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC
Q 014486          112 -------PGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK  184 (423)
Q Consensus       112 -------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~  184 (423)
                             ...+++||++|+++|+.|+++.++++.... ++++..++|+.....+...+..+ ++|+|+||++|..++...
T Consensus        92 ~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~I~v~Tp~~l~~~l~~~  169 (417)
T 2i4i_A           92 NGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRS-RVRPCVVYGGADIGQQIRDLERG-CHLLVATPGRLVDMMERG  169 (417)
T ss_dssp             CBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCHHHHHHHHTTC-CSEEEECHHHHHHHHHTT
T ss_pred             ccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcC-CceEEEEECCCCHHHHHHHhhCC-CCEEEEChHHHHHHHHcC
Confidence                   122579999999999999999999987654 78999999999888777777665 699999999999999888


Q ss_pred             CCCCCCccEEEEcCcchhhccCCcHHHHHHHHHh--CCC--CceEEEEeccCCccHHHHHHHhccCCceeeecccccccc
Q 014486          185 DLSLKNVRHFILDECDKMLESLDMRRDVQEIFKM--TPH--DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTL  260 (423)
Q Consensus       185 ~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~--~~~--~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (423)
                      ...+.++++||+||||.+.+ .++...+..+...  ++.  ..|++++|||+++........++..+..+...... ...
T Consensus       170 ~~~~~~~~~iViDEah~~~~-~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~  247 (417)
T 2i4i_A          170 KIGLDFCKYLVLDEADRMLD-MGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVG-STS  247 (417)
T ss_dssp             SBCCTTCCEEEESSHHHHHH-TTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC-----CC
T ss_pred             CcChhhCcEEEEEChhHhhc-cCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCCC-CCc
Confidence            88889999999999999988 6789999888874  332  57899999999999888888888877655543332 233


Q ss_pred             ccceEEEEEeChHHHHHHHHHHHHhh-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCc
Q 014486          261 HGLVQHYIKLSELEKNRKLNDLLDAL-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNK  339 (423)
Q Consensus       261 ~~~~~~~~~~~~~~~~~~l~~ll~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~  339 (423)
                      ..+...+.......+...+.++++.. ..+++||||++++.++.+++.|...++.+..+||++++.+|..+++.|++|+.
T Consensus       248 ~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~  327 (417)
T 2i4i_A          248 ENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKS  327 (417)
T ss_dssp             SSEEEEEEECCGGGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSS
T ss_pred             cCceEEEEEeccHhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCC
Confidence            45566677777888888888988877 46789999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhc
Q 014486          340 RILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFL  410 (423)
Q Consensus       340 ~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (423)
                      +|||||+++++|+|+|++++||++++|+++..|.||+||+||.|+.|.+++|+++ .+......+.+.+..
T Consensus       328 ~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~-~~~~~~~~l~~~~~~  397 (417)
T 2i4i_A          328 PILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNE-RNINITKDLLDLLVE  397 (417)
T ss_dssp             CEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECG-GGGGGHHHHHHHHHH
T ss_pred             CEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEcc-ccHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999985 455556667666653

>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=1e-56  Score=423.14  Aligned_cols=358  Identities=31%  Similarity=0.556  Sum_probs=314.7

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccC--CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG--MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~--~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      ..+|+++++++.+.++|.+.|+..|+|+|.++++.++.+  +++++.+|||+|||++++++++..+.....++++||++|
T Consensus         4 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P   83 (395)
T 3pey_A            4 AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAP   83 (395)
T ss_dssp             CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECS
T ss_pred             ccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECC
Confidence            357999999999999999999999999999999999998  899999999999999999999998877666669999999


Q ss_pred             ChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchh
Q 014486          123 TRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM  202 (423)
Q Consensus       123 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~  202 (423)
                      +++|+.|+++.++++.... ++.+....++......     ...++|+|+||+++...+......+.++++||+||||.+
T Consensus        84 ~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-----~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~  157 (395)
T 3pey_A           84 SRELARQTLEVVQEMGKFT-KITSQLIVPDSFEKNK-----QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNM  157 (395)
T ss_dssp             SHHHHHHHHHHHHHHTTTS-CCCEEEESTTSSCTTS-----CBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHH
T ss_pred             CHHHHHHHHHHHHHHhccc-CeeEEEEecCchhhhc-----cCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhh
Confidence            9999999999999987654 6777777766433221     123699999999999999888888999999999999999


Q ss_pred             hccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEe-ChHHHHHHHHH
Q 014486          203 LESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKL-SELEKNRKLND  281 (423)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~  281 (423)
                      .+..++...+..+...+++..|++++|||+++........++..+..+...... .........+... ....+...+..
T Consensus       158 ~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~  236 (395)
T 3pey_A          158 LDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNE-VNVDAIKQLYMDCKNEADKFDVLTE  236 (395)
T ss_dssp             HHSTTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGG-CSCTTEEEEEEECSSHHHHHHHHHH
T ss_pred             cCccccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEccccc-cccccccEEEEEcCchHHHHHHHHH
Confidence            886788889999999999999999999999999888888888777665544433 2233444444444 45567777888


Q ss_pred             HHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEE
Q 014486          282 LLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVI  361 (423)
Q Consensus       282 ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi  361 (423)
                      ++.....+++||||++++.++.+++.|+..++.+..+||+++..+|..+++.|++|+.+|||||+++++|+|+|++++||
T Consensus       237 ~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi  316 (395)
T 3pey_A          237 LYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVV  316 (395)
T ss_dssp             HHTTTTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEE
T ss_pred             HHHhccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEE
Confidence            88877889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EccCCC------CcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHh
Q 014486          362 NYDMPD------SADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       362 ~~~~~~------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                      ++++|+      ++..|.||+||+||.|++|.+++++.+.++...++.+++.++
T Consensus       317 ~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~  370 (395)
T 3pey_A          317 NYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFG  370 (395)
T ss_dssp             ESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHTT
T ss_pred             EcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHHHHHHHHHHHHhC
Confidence            999999      999999999999999999999999998888899999999887

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=100.00  E-value=1.3e-55  Score=411.40  Aligned_cols=361  Identities=36%  Similarity=0.591  Sum_probs=317.0

Q ss_pred             ccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccC-CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEe
Q 014486           43 IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLC  121 (423)
Q Consensus        43 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~-~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~  121 (423)
                      .+..+|+++++++.+.++|.+.|+..|+|+|.++++.++.+ +++++.+|||+|||++++++++..+...+ +.++||++
T Consensus         3 ~~~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~~-~~~~lil~   81 (367)
T 1hv8_A            3 VEYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENN-GIEAIILT   81 (367)
T ss_dssp             CCCCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSS-SCCEEEEC
T ss_pred             cccCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcccC-CCcEEEEc
Confidence            34567999999999999999999999999999999999988 68999999999999999999988776543 34899999


Q ss_pred             cChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcch
Q 014486          122 HTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDK  201 (423)
Q Consensus       122 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~  201 (423)
                      |+++|+.|+++.+.++.... ++.+..+.|+.........+.+  ++|+|+||+++...+......+.++++||+||||.
T Consensus        82 P~~~L~~q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~--~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~  158 (367)
T 1hv8_A           82 PTRELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALKN--ANIVVGTPGRILDHINRGTLNLKNVKYFILDEADE  158 (367)
T ss_dssp             SCHHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHHT--CSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHH
T ss_pred             CCHHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHhhcCC--CCEEEecHHHHHHHHHcCCcccccCCEEEEeCchH
Confidence            99999999999999987654 7788899999887766666653  59999999999999988888889999999999999


Q ss_pred             hhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHH
Q 014486          202 MLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLND  281 (423)
Q Consensus       202 ~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  281 (423)
                      +.+ .++...+..+...+++..+++++|||+++........++..+..+.....     ..+...+.......+...+..
T Consensus       159 ~~~-~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~l~~  232 (367)
T 1hv8_A          159 MLN-MGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKIN-----ANIEQSYVEVNENERFEALCR  232 (367)
T ss_dssp             HHT-TTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECCSS-----SSSEEEEEECCGGGHHHHHHH
T ss_pred             hhh-hchHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEecCC-----CCceEEEEEeChHHHHHHHHH
Confidence            987 67888999999999899999999999999888887777766544333221     244556667777788888888


Q ss_pred             HHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEE
Q 014486          282 LLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVI  361 (423)
Q Consensus       282 ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi  361 (423)
                      ++. ....++||||++.+.++.+++.|++.++.+..+||+++..+|..+++.|++|+.+|||||+++++|+|+|++++||
T Consensus       233 ~l~-~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi  311 (367)
T 1hv8_A          233 LLK-NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVI  311 (367)
T ss_dssp             HHC-STTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEE
T ss_pred             HHh-cCCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEE
Confidence            776 3567899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhhh
Q 014486          362 NYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSF  415 (423)
Q Consensus       362 ~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (423)
                      ++++|+++..|.||+||+||.|++|.+++++++ .+...+..+++.++..+..+
T Consensus       312 ~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~-~~~~~~~~i~~~~~~~~~~~  364 (367)
T 1hv8_A          312 NYHLPQNPESYMHRIGRTGRAGKKGKAISIINR-REYKKLRYIERAMKLKIKKL  364 (367)
T ss_dssp             ESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECT-TSHHHHHHHHHHHTCCCCCB
T ss_pred             EecCCCCHHHhhhcccccccCCCccEEEEEEcH-HHHHHHHHHHHHhCCCCcee
Confidence            999999999999999999999999999999985 56778899999999877643

>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=6.9e-58  Score=440.88  Aligned_cols=366  Identities=34%  Similarity=0.561  Sum_probs=179.8

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccC--CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG--MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~--~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      ..+|+++++++.++++|.++||..|+|+|.++++.++.+  +++++.+|||||||++|++|++..+......+++||++|
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            357999999999999999999999999999999999997  889999999999999999999999887777779999999


Q ss_pred             ChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhc-CCCCCCCccEEEEcCcch
Q 014486          123 TRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARD-KDLSLKNVRHFILDECDK  201 (423)
Q Consensus       123 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~-~~~~~~~~~~vVvDE~h~  201 (423)
                      +++|+.|+++.++++....+++.+....++.......    ....+|+|+||+++..++.+ ..+.+.++++||+||+|+
T Consensus       171 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~  246 (479)
T 3fmp_B          171 TYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ----KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV  246 (479)
T ss_dssp             SHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTC----CCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHH
T ss_pred             hHHHHHHHHHHHHHHHhhCCCceEEEEeCCccccccc----cCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHH
Confidence            9999999999999998877788888888876543221    22358999999999998865 456678999999999999


Q ss_pred             hhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeC-hHHHHHHHH
Q 014486          202 MLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS-ELEKNRKLN  280 (423)
Q Consensus       202 ~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~  280 (423)
                      +.+..++...+..+...++...|++++|||++.....+...++..+..+....... ....+.+.+..+. ...+...+.
T Consensus       247 ~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~  325 (479)
T 3fmp_B          247 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE-TLDTIKQYYVLCSSRDEKFQALC  325 (479)
T ss_dssp             HHTSTTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC----------------------------
T ss_pred             HhhcCCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEecccccc-CcCCceEEEEEeCCHHHHHHHHH
Confidence            98756888889999999999999999999999999888888888877666554332 2233333333333 245566677


Q ss_pred             HHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEE
Q 014486          281 DLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIV  360 (423)
Q Consensus       281 ~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~v  360 (423)
                      .++.....+++||||++...++.+++.|...++.+..+||++++.+|..+++.|++|+.+|||||+++++|+|+|++++|
T Consensus       326 ~~~~~~~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~V  405 (479)
T 3fmp_B          326 NLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVV  405 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHhhccCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEE
Confidence            77777777899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEccCCC------CcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhhh
Q 014486          361 INYDMPD------SADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSF  415 (423)
Q Consensus       361 i~~~~~~------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (423)
                      |++++|.      +...|+||+||+||.|+.|.+++|+++..+...++.+++.++..+...
T Consensus       406 I~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~~~~~~l  466 (479)
T 3fmp_B          406 INFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL  466 (479)
T ss_dssp             -------------------------------------------------------------
T ss_pred             EEecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchHHHHHHHHHHhCCCceEC
Confidence            9999994      668999999999999999999999998888899999999998776544

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=100.00  E-value=4.1e-57  Score=425.72  Aligned_cols=365  Identities=39%  Similarity=0.652  Sum_probs=183.6

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ...|+++++++.+.++|.+.|+..|+|+|+++++.++.++++++.+|||+|||++|+++++..+.....++++||++|++
T Consensus        20 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~   99 (394)
T 1fuu_A           20 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTR   99 (394)
T ss_dssp             CCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSSH
T ss_pred             cCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCCH
Confidence            45699999999999999999999999999999999999999999999999999999999999887766666999999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      +|+.|+.+.+.++.... ++++..++|+.........+..  ++|+|+||+++...+......+.++++||+||||.+.+
T Consensus       100 ~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~--~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~~  176 (394)
T 1fuu_A          100 ELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLS  176 (394)
T ss_dssp             HHHHHHHHHHHHHTTTS-CCCEEEECSSCCHHHHHHHHHH--CSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHH
T ss_pred             HHHHHHHHHHHHHhccC-CeeEEEEeCCCchHHHHhhcCC--CCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHHhhC
Confidence            99999999999987664 7889999999887766665553  59999999999998888778888999999999999987


Q ss_pred             cCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHH-HHHHHHHHH
Q 014486          205 SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELE-KNRKLNDLL  283 (423)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~~ll  283 (423)
                       .++...+..+...+++..|++++|||+++........++..+..+...... .....+...+....... +...+..++
T Consensus       177 -~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~  254 (394)
T 1fuu_A          177 -SGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDE-LTLEGIKQFYVNVEEEEYKYECLTDLY  254 (394)
T ss_dssp             -TTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC------------------------------
T ss_pred             -CCcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCcc-ccCCCceEEEEEcCchhhHHHHHHHHH
Confidence             688999999999999999999999999998888888888877766554332 12223333333333322 556677777


Q ss_pred             HhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEc
Q 014486          284 DALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINY  363 (423)
Q Consensus       284 ~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~  363 (423)
                      +....+++||||++++.++.+++.|++.++.+..+||+++..+|..+++.|++|+.+|||||+++++|+|+|++++||++
T Consensus       255 ~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~Vi~~  334 (394)
T 1fuu_A          255 DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINY  334 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hcCCCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEEEEe
Confidence            77777899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhhh
Q 014486          364 DMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSF  415 (423)
Q Consensus       364 ~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (423)
                      ++|+++..|.||+||+||.|++|.+++++++ .+...+..+++.++..+...
T Consensus       335 ~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~-~~~~~~~~l~~~~~~~~~~~  385 (394)
T 1fuu_A          335 DLPANKENYIHRIGRGGRFGRKGVAINFVTN-EDVGAMRELEKFYSTQIEEL  385 (394)
T ss_dssp             ----------------------------------------------------
T ss_pred             CCCCCHHHHHHHcCcccCCCCCceEEEEEch-hHHHHHHHHHHHhCCccccc
Confidence            9999999999999999999999999999975 46667888888888766543

>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=2.4e-54  Score=424.67  Aligned_cols=358  Identities=25%  Similarity=0.426  Sum_probs=294.2

Q ss_pred             CCHHHHHHHHhCCCCCCChhhhhcccccc--cCCceEEEccCCCcchhHHHHHHhhccCCC----CCCeEEEEEecChHH
Q 014486           53 LKPELLRAIVDSGFEHPSEVQHECIPQAI--LGMDVICQAKSGMGKTAVFVLSTLQQTEPN----PGQVTALVLCHTREL  126 (423)
Q Consensus        53 l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~--~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~----~~~~~~lil~P~~~L  126 (423)
                      +++.++++|.++||..|+|+|.++++.++  .++++++.+|||+|||++|++|++..+...    ...+++||++|+++|
T Consensus        28 l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~L  107 (579)
T 3sqw_A           28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  107 (579)
T ss_dssp             SCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHH
Confidence            99999999999999999999999999999  678999999999999999999999765433    234589999999999


Q ss_pred             HHHHHHHHHHHhcc---CCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC-CCCCCCccEEEEcCcchh
Q 014486          127 AYQICHEFERFSTY---LPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK-DLSLKNVRHFILDECDKM  202 (423)
Q Consensus       127 ~~q~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~-~~~~~~~~~vVvDE~h~~  202 (423)
                      +.|+++.++++...   .+.+.+..+.|+.........+....++|+|+||++|..++... ...+..+++||+||||++
T Consensus       108 a~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l  187 (579)
T 3sqw_A          108 ALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRL  187 (579)
T ss_dssp             HHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHH
T ss_pred             HHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccCCEEEEEChHHh
Confidence            99999999988642   24567888899988887777776655799999999999877654 345678999999999999


Q ss_pred             hccCCcHHHHHHHHHhCC-------CCceEEEEeccCCccHHHHHHHhccCCceeeeccc---cccccccceEEEEEeCh
Q 014486          203 LESLDMRRDVQEIFKMTP-------HDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDE---AKLTLHGLVQHYIKLSE  272 (423)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~-------~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~  272 (423)
                      .+ .+|...+..+...++       ...|++++|||+++.+...+..++..+..+.....   .......+...+.....
T Consensus       188 ~~-~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  266 (579)
T 3sqw_A          188 LE-IGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEK  266 (579)
T ss_dssp             TS-TTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESS
T ss_pred             hc-CCCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEEEecc
Confidence            98 678888877766543       36799999999999988888888877665544321   11222333444444332


Q ss_pred             H-HHH----HHHHHHHHh-hcCCcEEEEEcChhhHHHHHHHHHhC---CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEE
Q 014486          273 L-EKN----RKLNDLLDA-LDFNQVVIFVKSVSRAAELNKLLVEC---NFPSICIHSGMSQEERLTRYKGFKEGNKRILV  343 (423)
Q Consensus       273 ~-~~~----~~l~~ll~~-~~~~~~ivf~~~~~~~~~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili  343 (423)
                      . .+.    ..+...+.. ....++||||+++..++.+++.|...   ++.+..+||++++.+|..+++.|++|+.+|||
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            1 221    222333332 45679999999999999999999887   89999999999999999999999999999999


Q ss_pred             EcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcch
Q 014486          344 ATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLI  412 (423)
Q Consensus       344 ~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (423)
                      ||+++++|+|+|++++||++++|.++..|+||+||+||.|+.|.+++++.+ .+...+..+++..+..+
T Consensus       347 aT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~-~e~~~~~~l~~~~~~~~  414 (579)
T 3sqw_A          347 CTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICK-DELPFVRELEDAKNIVI  414 (579)
T ss_dssp             ECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEG-GGHHHHHHHHHHHCCCC
T ss_pred             EcchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcc-cHHHHHHHHHHHhCCCc
Confidence            999999999999999999999999999999999999999999999999985 57777888887765444

>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=4.3e-54  Score=422.84  Aligned_cols=358  Identities=25%  Similarity=0.427  Sum_probs=292.6

Q ss_pred             CCHHHHHHHHhCCCCCCChhhhhcccccc--cCCceEEEccCCCcchhHHHHHHhhccCCCC----CCeEEEEEecChHH
Q 014486           53 LKPELLRAIVDSGFEHPSEVQHECIPQAI--LGMDVICQAKSGMGKTAVFVLSTLQQTEPNP----GQVTALVLCHTREL  126 (423)
Q Consensus        53 l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~--~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~----~~~~~lil~P~~~L  126 (423)
                      +++.++++|.+.||..|+|+|.++++.++  .++++++++|||+|||++|++|++..+...+    ..+++||++|+++|
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            99999999999999999999999999999  5789999999999999999999998764332    33589999999999


Q ss_pred             HHHHHHHHHHHhcc---CCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC-CCCCCCccEEEEcCcchh
Q 014486          127 AYQICHEFERFSTY---LPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK-DLSLKNVRHFILDECDKM  202 (423)
Q Consensus       127 ~~q~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~-~~~~~~~~~vVvDE~h~~  202 (423)
                      +.|+++.++++...   .+...+..+.|+.........+....++|+|+||++|..++... ...+.++++||+||||++
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            99999999987543   23567888899988877777765545799999999999877654 235678999999999999


Q ss_pred             hccCCcHHHHHHHHHhC-------CCCceEEEEeccCCccHHHHHHHhccCCceeeeccc---cccccccceEEEEEeCh
Q 014486          203 LESLDMRRDVQEIFKMT-------PHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDE---AKLTLHGLVQHYIKLSE  272 (423)
Q Consensus       203 ~~~~~~~~~~~~~~~~~-------~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~  272 (423)
                      .+ .+|...+..+...+       ....|++++|||+++.+......++..+..+.....   .......+...+.....
T Consensus       239 ~~-~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  317 (563)
T 3i5x_A          239 LE-IGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEK  317 (563)
T ss_dssp             TS-TTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESS
T ss_pred             hc-cchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEEECch
Confidence            88 67888877776554       336789999999999988888888777665544321   11222333344444332


Q ss_pred             H-HHH----HHHHHHHHh-hcCCcEEEEEcChhhHHHHHHHHHhC---CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEE
Q 014486          273 L-EKN----RKLNDLLDA-LDFNQVVIFVKSVSRAAELNKLLVEC---NFPSICIHSGMSQEERLTRYKGFKEGNKRILV  343 (423)
Q Consensus       273 ~-~~~----~~l~~ll~~-~~~~~~ivf~~~~~~~~~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili  343 (423)
                      . .+.    ..+...+.. ....++||||+++..++.+++.|...   ++.+..+||++++.+|..+++.|++|+.+|||
T Consensus       318 ~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLv  397 (563)
T 3i5x_A          318 FANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILV  397 (563)
T ss_dssp             TTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEE
T ss_pred             hHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEE
Confidence            1 222    222222322 45679999999999999999999886   89999999999999999999999999999999


Q ss_pred             EcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcch
Q 014486          344 ATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLI  412 (423)
Q Consensus       344 ~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (423)
                      ||+++++|+|+|++++||++++|.++..|+||+||+||.|+.|.+++++.+ .+...+..+++.++..+
T Consensus       398 aT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~-~e~~~~~~l~~~~~~~~  465 (563)
T 3i5x_A          398 CTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICK-DELPFVRELEDAKNIVI  465 (563)
T ss_dssp             ECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEG-GGHHHHHHHHHHHCCCC
T ss_pred             EcchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEch-hHHHHHHHHHHHhCCCc
Confidence            999999999999999999999999999999999999999999999999985 56778888888776444

>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=3e-53  Score=390.84  Aligned_cols=336  Identities=34%  Similarity=0.543  Sum_probs=286.4

Q ss_pred             CCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHH
Q 014486           53 LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICH  132 (423)
Q Consensus        53 l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~  132 (423)
                      +++.+.++|.++|+..|+|+|.++++.++.++++++.+|||+|||++++++++..      +.++||++|+++|+.|+++
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            4688999999999999999999999999999999999999999999999998875      2389999999999999999


Q ss_pred             HHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHH
Q 014486          133 EFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDV  212 (423)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~  212 (423)
                      .++++.... ++++..++|+.........+.+  ++|+|+||+++...+......+.++++||+||||.+.+ .++...+
T Consensus        75 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~--~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~-~~~~~~~  150 (337)
T 2z0m_A           75 HIRDIGRYM-DTKVAEVYGGMPYKAQINRVRN--ADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFE-MGFIDDI  150 (337)
T ss_dssp             HHHHHTTTS-CCCEEEECTTSCHHHHHHHHTT--CSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHH-TTCHHHH
T ss_pred             HHHHHhhhc-CCcEEEEECCcchHHHHhhcCC--CCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhc-cccHHHH
Confidence            999987664 7789999998887766666554  59999999999998888777888999999999999988 6888899


Q ss_pred             HHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEE
Q 014486          213 QEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVV  292 (423)
Q Consensus       213 ~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~i  292 (423)
                      ..+....+...+++++|||+++.....+..++..+..+...    .........+.......+  .....+.....+++|
T Consensus       151 ~~~~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~l  224 (337)
T 2z0m_A          151 KIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEAC----IGLANVEHKFVHVKDDWR--SKVQALRENKDKGVI  224 (337)
T ss_dssp             HHHHHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEECS----GGGGGEEEEEEECSSSSH--HHHHHHHTCCCSSEE
T ss_pred             HHHHhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeeecc----cccCCceEEEEEeChHHH--HHHHHHHhCCCCcEE
Confidence            99999999999999999999999888888887766554322    122333444444443322  223556666778999


Q ss_pred             EEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchh
Q 014486          293 IFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTY  372 (423)
Q Consensus       293 vf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~  372 (423)
                      |||++.+.++.+++.|.    .+..+||+++..+|.++++.|++|+.+|||||+++++|+|+|++++||++++|+|+..|
T Consensus       225 vf~~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~  300 (337)
T 2z0m_A          225 VFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTY  300 (337)
T ss_dssp             EECSCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSCCSSHHHH
T ss_pred             EEEcCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecCCCCHHHh
Confidence            99999999999998887    57899999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhc
Q 014486          373 LHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFL  410 (423)
Q Consensus       373 ~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (423)
                      .||+||+||.|++|.+++++.  .+....+.+++.++.
T Consensus       301 ~Q~~GR~gR~g~~g~~~~~~~--~~~~~~~~i~~~~~~  336 (337)
T 2z0m_A          301 IHRIGRTGRMGRKGEAITFIL--NEYWLEKEVKKVSQK  336 (337)
T ss_dssp             HHHHTTBCGGGCCEEEEEEES--SCHHHHHHHC-----
T ss_pred             hHhcCccccCCCCceEEEEEe--CcHHHHHHHHHHhcc
Confidence            999999999999999999998  677778888877754

>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=2.7e-52  Score=406.22  Aligned_cols=339  Identities=18%  Similarity=0.214  Sum_probs=271.6

Q ss_pred             cCCCCcCCCCCHHHHHHHHh-CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           44 HSSGFRDFLLKPELLRAIVD-SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      ..+.+.++++++.+.+.|++ +||..|+|+|.++++.++.++++++.+|||+|||++|++|++...      .++||++|
T Consensus        19 ~~w~~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~~------g~~lVisP   92 (591)
T 2v1x_A           19 AAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSD------GFTLVICP   92 (591)
T ss_dssp             GGGCCSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTSS------SEEEEECS
T ss_pred             hccccccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHcC------CcEEEEeC
Confidence            34456679999999999998 599999999999999999999999999999999999999998742      28999999


Q ss_pred             ChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHH-----hcCCCcEEEechHHHH------HHHhcCCCCCCCc
Q 014486          123 TRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL-----KNECPQIVVGTPGRIL------ALARDKDLSLKNV  191 (423)
Q Consensus       123 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~ilv~T~~~l~------~~~~~~~~~~~~~  191 (423)
                      +++|+.|+.+.+.++     ++++..++++.........+     ..+.++|+|+||++|.      ..+.. ...+.++
T Consensus        93 ~~~L~~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~-~~~~~~i  166 (591)
T 2v1x_A           93 LISLMEDQLMVLKQL-----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEK-AYEARRF  166 (591)
T ss_dssp             CHHHHHHHHHHHHHH-----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHH-HHHTTCE
T ss_pred             HHHHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHh-hhhccCC
Confidence            999999999999887     67888888887765544332     2455799999999874      22222 2345688


Q ss_pred             cEEEEcCcchhhcc-CCcHHHHHH--HHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEE
Q 014486          192 RHFILDECDKMLES-LDMRRDVQE--IFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYI  268 (423)
Q Consensus       192 ~~vVvDE~h~~~~~-~~~~~~~~~--~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (423)
                      ++||+||||++..+ .+|+..+..  .+....+..+++++|||+++.+...+..++..+....+...  .....+.....
T Consensus       167 ~~iViDEAH~is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~~--~~r~nl~~~v~  244 (591)
T 2v1x_A          167 TRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTAS--FNRPNLYYEVR  244 (591)
T ss_dssp             EEEEEETGGGGSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEECC--CCCTTEEEEEE
T ss_pred             cEEEEECcccccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEecC--CCCcccEEEEE
Confidence            99999999999874 336665543  23333446889999999999887777766654433322221  11122222222


Q ss_pred             EeC--hHHHHHHHHHHHHh-hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEc
Q 014486          269 KLS--ELEKNRKLNDLLDA-LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVAT  345 (423)
Q Consensus       269 ~~~--~~~~~~~l~~ll~~-~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T  345 (423)
                      ...  ...+...+.+++.. ..++++||||++++.++.+++.|...|+.+..+|+++++.+|..+++.|++|+.+|||||
T Consensus       245 ~~~~~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT  324 (591)
T 2v1x_A          245 QKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVAT  324 (591)
T ss_dssp             ECCSSHHHHHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEEC
T ss_pred             eCCCcHHHHHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEe
Confidence            221  23445566666653 356899999999999999999999999999999999999999999999999999999999


Q ss_pred             CccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcc
Q 014486          346 DLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSAS  396 (423)
Q Consensus       346 ~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  396 (423)
                      +++++|+|+|++++||++++|.|+..|.|++||+||.|++|.+++++++.+
T Consensus       325 ~a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~D  375 (591)
T 2v1x_A          325 VAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGD  375 (591)
T ss_dssp             TTSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHH
T ss_pred             chhhcCCCcccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChHH
Confidence            999999999999999999999999999999999999999999999997543

>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=2.3e-51  Score=396.04  Aligned_cols=335  Identities=17%  Similarity=0.236  Sum_probs=270.3

Q ss_pred             CCCcCCCCCHHHHHHHHh-CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           46 SGFRDFLLKPELLRAIVD-SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      .+|+++++++.+.+.|.+ +|+..|+|+|.++++.++.++++++.+|||+|||++|++|++...      .++||++|++
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 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLN------GLTVVVSPLI   75 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHSS------SEEEEECSCH
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHhC------CCEEEECChH
Confidence            368999999999999998 799999999999999999999999999999999999999998652      2899999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcch
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDK  201 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~  201 (423)
                      +|+.|+.+.++++     ++.+..++++.......   ..+..+.++|+++||+++........+...++++||+||||+
T Consensus        76 aL~~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~  150 (523)
T 1oyw_A           76 SLMKDQVDQLQAN-----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHC  150 (523)
T ss_dssp             HHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGG
T ss_pred             HHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCccc
Confidence            9999999998875     67888888877654433   334456689999999998532111123347889999999999


Q ss_pred             hhcc-CCcHHHHHHH---HHhCCCCceEEEEeccCCccHHHHHHHhcc-CCceeeeccccccccccceEEEEEeChHHHH
Q 014486          202 MLES-LDMRRDVQEI---FKMTPHDKQVMMFSATLSKEIRPVCKKFMQ-DPMEIYVDDEAKLTLHGLVQHYIKLSELEKN  276 (423)
Q Consensus       202 ~~~~-~~~~~~~~~~---~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  276 (423)
                      +..+ .+|+..+..+   ...++ ..+++++|||+++.....+...+. ....+......   ...+.  +.......+.
T Consensus       151 i~~~g~~fr~~~~~l~~l~~~~~-~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~~~~~---r~~l~--~~v~~~~~~~  224 (523)
T 1oyw_A          151 ISQWGHDFRPEYAALGQLRQRFP-TLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFD---RPNIR--YMLMEKFKPL  224 (523)
T ss_dssp             GCTTSSCCCHHHHGGGGHHHHCT-TSCEEEEESCCCHHHHHHHHHHHTCCSCEEEECCCC---CTTEE--EEEEECSSHH
T ss_pred             cCcCCCccHHHHHHHHHHHHhCC-CCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEeCCCC---CCceE--EEEEeCCCHH
Confidence            9874 3466555443   44443 578999999999876654443332 22222222221   12222  2222334556


Q ss_pred             HHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCC
Q 014486          277 RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIER  356 (423)
Q Consensus       277 ~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~  356 (423)
                      ..+.+++....++++||||++++.++.+++.|...|+.+..+||++++.+|..+++.|++|+.+|||||+++++|+|+|+
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            67888888777889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          357 VNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       357 ~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      +++||++++|+|+..|.||+||+||.|++|.+++++++.+.
T Consensus       305 v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d~  345 (523)
T 1oyw_A          305 VRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADM  345 (523)
T ss_dssp             CCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHH
T ss_pred             ccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCHHHH
Confidence            99999999999999999999999999999999999976443

>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=1.4e-49  Score=376.12  Aligned_cols=327  Identities=19%  Similarity=0.311  Sum_probs=259.4

Q ss_pred             HHHHHHhC-CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHH
Q 014486           57 LLRAIVDS-GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFE  135 (423)
Q Consensus        57 ~~~~l~~~-~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  135 (423)
                      +.+.+++. |+ +|+|+|.++++.++.++++++.+|||+|||++++++++.....   ++++||++|+++|+.|+++.++
T Consensus        10 ~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~~---~~~~lil~Pt~~L~~q~~~~~~   85 (414)
T 3oiy_A           10 FRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARK---GKKSALVFPTVTLVKQTLERLQ   85 (414)
T ss_dssp             HHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHTT---TCCEEEEESSHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhcC---CCEEEEEECCHHHHHHHHHHHH
Confidence            34455553 56 7999999999999999999999999999999999988877633   3389999999999999999999


Q ss_pred             HHhccCCCceEEEEEcCcch---HHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc-------
Q 014486          136 RFSTYLPDIKVAVFYGGVNI---KIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES-------  205 (423)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~-------  205 (423)
                      ++..  .++++..++|+.+.   ......+..+.++|+|+||+++..++..  ..+.++++||+||||++..+       
T Consensus        86 ~~~~--~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~iViDEaH~~~~~~~~~d~~  161 (414)
T 3oiy_A           86 KLAD--EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTL  161 (414)
T ss_dssp             HHCC--SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCCSEEEESCHHHHHHCHHHHHHH
T ss_pred             HHcc--CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccccEEEEeChHhhhhccchhhhH
Confidence            9876  48899999999987   4455666666679999999999887764  55678999999999987642       


Q ss_pred             ---CCcHHH-HHHHHHhCC-----------CCceEEEEecc-CCccHH-HHHHHhccCCceeeeccccccccccceEEEE
Q 014486          206 ---LDMRRD-VQEIFKMTP-----------HDKQVMMFSAT-LSKEIR-PVCKKFMQDPMEIYVDDEAKLTLHGLVQHYI  268 (423)
Q Consensus       206 ---~~~~~~-~~~~~~~~~-----------~~~~~v~~SAT-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (423)
                         .+|... +..++..++           ...|++++||| +|.... ........    +.... .......+.+.+.
T Consensus       162 l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~----~~~~~-~~~~~~~i~~~~~  236 (414)
T 3oiy_A          162 LMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGR-LVSVARNITHVRI  236 (414)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS----CCSSC-CCCCCCSEEEEEE
T ss_pred             HhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc----cCcCc-cccccccchheee
Confidence               355555 677777665           78899999999 565543 22232222    11111 1112233333333


Q ss_pred             EeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeE-EEcCCCCHHHHHHHHHhhhcCCccEEEE---
Q 014486          269 KLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSI-CIHSGMSQEERLTRYKGFKEGNKRILVA---  344 (423)
Q Consensus       269 ~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~-~~~~~~~~~~r~~~~~~f~~~~~~ili~---  344 (423)
                      ..   .+...+..+++.. ++++||||+++..++.+++.|...|+.+. .+||.    +|.  ++.|++|+.+||||   
T Consensus       237 ~~---~~~~~l~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~vLvat~s  306 (414)
T 3oiy_A          237 SS---RSKEKLVELLEIF-RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINILIGVQA  306 (414)
T ss_dssp             SS---CCHHHHHHHHHHH-CSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSEEEEECC
T ss_pred             cc---CHHHHHHHHHHHc-CCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeEEEEecC
Confidence            33   3455667777764 48999999999999999999999999998 88884    444  99999999999999   


Q ss_pred             -cCccccCCCCCC-CCEEEEccCC--CCcchhhhcccccCCCC----CceEEEEEecCcccHHHHHHHHHHHh
Q 014486          345 -TDLVGRGIDIER-VNIVINYDMP--DSADTYLHRVGRAGRFG----TKGLAITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       345 -T~~~~~Gld~~~-~~~vi~~~~~--~s~~~~~Q~~GR~~R~g----~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                       |+++++|+|+|+ +++||++++|  .++..|+||+||+||.|    ..|.+++++   .+...+..+++.++
T Consensus       307 ~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~---~~~~~~~~l~~~~~  376 (414)
T 3oiy_A          307 YYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE---EDEEIFESLKTRLL  376 (414)
T ss_dssp             TTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC---CCHHHHHHHHHHHH
T ss_pred             cCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE---ccHHHHHHHHHHhc
Confidence             999999999999 9999999999  99999999999999987    478999888   56777888888887

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=100.00  E-value=6.6e-48  Score=388.37  Aligned_cols=334  Identities=20%  Similarity=0.261  Sum_probs=217.4

Q ss_pred             HHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC--CCeEEEEEecChHHHHHHHHHHH
Q 014486           58 LRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP--GQVTALVLCHTRELAYQICHEFE  135 (423)
Q Consensus        58 ~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~--~~~~~lil~P~~~L~~q~~~~~~  135 (423)
                      .+++..+|+..|+++|.++++.++.++++++++|||+|||++|+++++..+...+  .+.++||++|+++|+.||.+.++
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            3567788999999999999999999999999999999999999999987654332  22489999999999999999999


Q ss_pred             HHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCC-CCCCccEEEEcCcchhhccCCcHHHHHH
Q 014486          136 RFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDL-SLKNVRHFILDECDKMLESLDMRRDVQE  214 (423)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~-~~~~~~~vVvDE~h~~~~~~~~~~~~~~  214 (423)
                      ++.... ++++..++|+.........+..+ ++|+|+||++|.+.+....+ .+.++++||+||||++.+...+...+..
T Consensus        83 ~~~~~~-~~~v~~~~g~~~~~~~~~~~~~~-~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i~~~  160 (696)
T 2ykg_A           83 KYFERH-GYRVTGISGATAENVPVEQIVEN-NDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFN  160 (696)
T ss_dssp             HHTTTT-TCCEEEECSSSCSSSCHHHHHHT-CSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHHHHH
T ss_pred             HHhccC-CceEEEEeCCccccccHHHhccC-CCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHHHHH
Confidence            988653 78999999988665555555444 69999999999998887766 6889999999999999875444444433


Q ss_pred             HHHh-----CCCCceEEEEeccCCc-------cH-HHHHHH---------------------hccCCceeeeccccccc-
Q 014486          215 IFKM-----TPHDKQVMMFSATLSK-------EI-RPVCKK---------------------FMQDPMEIYVDDEAKLT-  259 (423)
Q Consensus       215 ~~~~-----~~~~~~~v~~SAT~~~-------~~-~~~~~~---------------------~~~~~~~~~~~~~~~~~-  259 (423)
                      .+..     .++.++++++|||+..       .. ..+...                     +...|............ 
T Consensus       161 ~l~~~~~~~~~~~~~il~LTATp~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~l~~~~~~p~~~~~~~~~~~~~  240 (696)
T 2ykg_A          161 YLDQKLGGSSGPLPQVIGLTASVGVGDAKTTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISD  240 (696)
T ss_dssp             HHHHHHTTCCSCCCEEEEEESCCCCSSCCSHHHHHHHHHHHHHHTTCCEEECCCTTHHHHHHHSCCCEEEEEECCCCSCC
T ss_pred             HHHHhhcccCCCCCeEEEEeCccccCccccHHHHHHHHHHHHHhcCCceEeecccchHHHHhhcCCCceeEEecCcccCC
Confidence            3332     3467899999999972       11 111111                     11111100000000000 


Q ss_pred             --------------------------------------------------------------------------------
Q 014486          260 --------------------------------------------------------------------------------  259 (423)
Q Consensus       260 --------------------------------------------------------------------------------  259 (423)
                                                                                                      
T Consensus       241 ~fs~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~  320 (696)
T 2ykg_A          241 KFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYN  320 (696)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSTTGGGSSSCCSCCSSSHHHHHHHHHHHHTSCC------CCHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHHHHHHhhcccchhhhHHHHHHHHHHHHHHHHh
Confidence                                                                                            


Q ss_pred             -----------------------------cccceEEEEE----------------eChHHHHHHHHHHHHhh----cCCc
Q 014486          260 -----------------------------LHGLVQHYIK----------------LSELEKNRKLNDLLDAL----DFNQ  290 (423)
Q Consensus       260 -----------------------------~~~~~~~~~~----------------~~~~~~~~~l~~ll~~~----~~~~  290 (423)
                                                   ...+.+.+..                .....+...+.+++...    ++++
T Consensus       321 ~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~ll~~~~~~~~~~~  400 (696)
T 2ykg_A          321 DALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETI  400 (696)
T ss_dssp             HHHHHHHHSCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHTTCTTCC
T ss_pred             HHHhccchhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhccCCCCc
Confidence                                         0000000000                01234556667777665    5689


Q ss_pred             EEEEEcChhhHHHHHHHHHhCC----CCeEEE--------cCCCCHHHHHHHHHhhhc-CCccEEEEcCccccCCCCCCC
Q 014486          291 VVIFVKSVSRAAELNKLLVECN----FPSICI--------HSGMSQEERLTRYKGFKE-GNKRILVATDLVGRGIDIERV  357 (423)
Q Consensus       291 ~ivf~~~~~~~~~l~~~L~~~~----~~~~~~--------~~~~~~~~r~~~~~~f~~-~~~~ili~T~~~~~Gld~~~~  357 (423)
                      +||||+++..++.+++.|...+    +++..+        |+++++.+|.++++.|++ |+.+|||||+++++|+|+|++
T Consensus       401 ~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~GiDip~v  480 (696)
T 2ykg_A          401 TILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQC  480 (696)
T ss_dssp             EEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEESSCCC---CCC
T ss_pred             EEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcCCcCccC
Confidence            9999999999999999999987    888888        559999999999999998 999999999999999999999


Q ss_pred             CEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCc
Q 014486          358 NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       358 ~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      ++||+||+|+++..|+||+|| ||. +.|.++++++..
T Consensus       481 ~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~  516 (696)
T 2ykg_A          481 NLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNA  516 (696)
T ss_dssp             SEEEEESCC--CCCC-----------CCCEEEEEESCH
T ss_pred             CEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCC
Confidence            999999999999999999999 998 778998888754

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=100.00  E-value=2.9e-46  Score=367.39  Aligned_cols=325  Identities=21%  Similarity=0.239  Sum_probs=223.8

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC--CCeEEEEEecChHHHHHHHHHHHHHhccCCCce
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP--GQVTALVLCHTRELAYQICHEFERFSTYLPDIK  145 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~--~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  145 (423)
                      +|+|+|.++++.++.++++++++|||+|||++|++|++..+...+  .++++||++|+++|+.||.+.++++.... +++
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-~~~   82 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERL-GYN   82 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTT-TCC
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccC-CcE
Confidence            799999999999999999999999999999999999988766543  14489999999999999999999998765 789


Q ss_pred             EEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCC-CCCCccEEEEcCcchhhccCCcHHHHHHHHHhC-----
Q 014486          146 VAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDL-SLKNVRHFILDECDKMLESLDMRRDVQEIFKMT-----  219 (423)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~-~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-----  219 (423)
                      +..++|+.........+..+ ++|+|+||+++...+..... .+.++++||+||||++.+...+...+..+....     
T Consensus        83 ~~~~~g~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~  161 (555)
T 3tbk_A           83 IASISGATSDSVSVQHIIED-NDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKLGESR  161 (555)
T ss_dssp             EEEECTTTGGGSCHHHHHHH-CSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHHTSSCC
T ss_pred             EEEEcCCCcchhhHHHHhcC-CCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcchHHHHHHHHHHhhhcccc
Confidence            99999998776655555544 59999999999998888776 788999999999999987444444443443332     


Q ss_pred             CCCceEEEEeccCCccH----HHHH------HHhccCCceeeeccccc----cccccceEEEEEe---------------
Q 014486          220 PHDKQVMMFSATLSKEI----RPVC------KKFMQDPMEIYVDDEAK----LTLHGLVQHYIKL---------------  270 (423)
Q Consensus       220 ~~~~~~v~~SAT~~~~~----~~~~------~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~---------------  270 (423)
                      .+..+++++|||++...    ....      ...+... .+.......    .............               
T Consensus       162 ~~~~~~l~lSAT~~~~~~~~~~~~~~~~~~l~~~l~~~-~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (555)
T 3tbk_A          162 DPLPQVVGLTASVGVGDAKTAEEAMQHICKLCAALDAS-VIATVRDNVAELEQVVYKPQKISRKVASRTSNTFKCIISQL  240 (555)
T ss_dssp             SCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHTTCS-EEECCCSCHHHHHTTCCCCCEEEEECCCCSCCHHHHHHHHH
T ss_pred             CCCCeEEEEecCcccCccccHHHHHHHHHHHHHhcCCe-eeeccccCHHHHHhhcCCCceEEEEecCcccChHHHHHHHH
Confidence            24578999999996421    1111      1111100 010000000    0000000000000               


Q ss_pred             --------------------------------------------------------------------------------
Q 014486          271 --------------------------------------------------------------------------------  270 (423)
Q Consensus       271 --------------------------------------------------------------------------------  270 (423)
                                                                                                      
T Consensus       241 ~~~~~~~~~~~~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  320 (555)
T 3tbk_A          241 MKETEKLAKDVSEELGKLFQIQNREFGTQKYEQWIVGVHKACSVFQMADKEEESRVCKALFLYTSHLRKYNDALIISEDA  320 (555)
T ss_dssp             HHHHHHHHHTSCHHHHGGGGCCSCCSSSHHHHHHHHHHHHHHHTCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHhhhhhhhcccccccchhhhHHHHHHHHHhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence                                                                                            


Q ss_pred             -----------------------------------------------ChHHHHHHHHHHHHh----hcCCcEEEEEcChh
Q 014486          271 -----------------------------------------------SELEKNRKLNDLLDA----LDFNQVVIFVKSVS  299 (423)
Q Consensus       271 -----------------------------------------------~~~~~~~~l~~ll~~----~~~~~~ivf~~~~~  299 (423)
                                                                     ....|...+.+++..    .+.+++||||+++.
T Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~  400 (555)
T 3tbk_A          321 QMTDALNYLKAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRDLYLVLQEEYHLKPETKTILFVKTRA  400 (555)
T ss_dssp             CHHHHHHHHHHHHHHHCC-----HHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHHHCTTCCEEEECSSHH
T ss_pred             hHHHHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhccCCCcCCHHHHHHHHHHHHHhccCCCceEEEEeCcHH
Confidence                                                           012344455555544    25689999999999


Q ss_pred             hHHHHHHHHHhCC------------CCeEEEcCCCCHHHHHHHHHhhhc-CCccEEEEcCccccCCCCCCCCEEEEccCC
Q 014486          300 RAAELNKLLVECN------------FPSICIHSGMSQEERLTRYKGFKE-GNKRILVATDLVGRGIDIERVNIVINYDMP  366 (423)
Q Consensus       300 ~~~~l~~~L~~~~------------~~~~~~~~~~~~~~r~~~~~~f~~-~~~~ili~T~~~~~Gld~~~~~~vi~~~~~  366 (423)
                      .++.+++.|...+            .....+||++++.+|..+++.|++ |+++|||||+++++|+|+|++++||+|++|
T Consensus       401 ~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p  480 (555)
T 3tbk_A          401 LVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYV  480 (555)
T ss_dssp             HHHHHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECCCTTCCEETTSCSEEEEESCC
T ss_pred             HHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCCccccCCEEEEeCCC
Confidence            9999999998864            344455679999999999999999 999999999999999999999999999999


Q ss_pred             CCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          367 DSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       367 ~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      +|+..|+||+|| ||. +.|.+++|+++...
T Consensus       481 ~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~  509 (555)
T 3tbk_A          481 GNVIKMIQTRGR-GRA-RDSKCFLLTSSADV  509 (555)
T ss_dssp             SSCCCEECSSCC-CTT-TSCEEEEEESCHHH
T ss_pred             CCHHHHHHhcCc-CcC-CCceEEEEEcCCCH
Confidence            999999999999 998 88999999986544

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=100.00  E-value=1.5e-46  Score=381.54  Aligned_cols=331  Identities=21%  Similarity=0.251  Sum_probs=205.8

Q ss_pred             hCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC--CCeEEEEEecChHHHHHHHHHHHHHhcc
Q 014486           63 DSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP--GQVTALVLCHTRELAYQICHEFERFSTY  140 (423)
Q Consensus        63 ~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~--~~~~~lil~P~~~L~~q~~~~~~~~~~~  140 (423)
                      .+|+..|+|+|.++++.++.++++++++|||+|||++|+++++..+...+  .+.++||++|+++|+.||.+.++++...
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            34788999999999999999999999999999999999999998766543  1448999999999999999999999876


Q ss_pred             CCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCC-CCCCccEEEEcCcchhhccCCcHHHHHHHHHh-
Q 014486          141 LPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDL-SLKNVRHFILDECDKMLESLDMRRDVQEIFKM-  218 (423)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~-~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~-  218 (423)
                      . ++++..++|+.........+..+ ++|+|+||++|...+..... .+.++++||+||||++.....+...+..+... 
T Consensus       323 ~-~~~v~~~~g~~~~~~~~~~~~~~-~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~~~~~i~~~~~~~~  400 (797)
T 4a2q_A          323 Q-GYSVQGISGENFSNVSVEKVIED-SDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQK  400 (797)
T ss_dssp             G-TCCEEEECCC-----CHHHHHHT-CSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTSHHHHHHHHHHHHH
T ss_pred             C-CceEEEEeCCcchhhhHHHhhCC-CCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCccHHHHHHHHHHHh
Confidence            5 78999999998776665555555 69999999999998887766 78899999999999998743334333333332 


Q ss_pred             ---CCCCceEEEEeccCCcc-----------HHHHH------------------HHhccCCceeeecccccc--c-----
Q 014486          219 ---TPHDKQVMMFSATLSKE-----------IRPVC------------------KKFMQDPMEIYVDDEAKL--T-----  259 (423)
Q Consensus       219 ---~~~~~~~v~~SAT~~~~-----------~~~~~------------------~~~~~~~~~~~~~~~~~~--~-----  259 (423)
                         ..+..+++++|||++..           +..+.                  ..+...+...........  .     
T Consensus       401 ~~~~~~~~~~l~lSATp~~~~~~~~~~~~~~i~~l~~~L~~~~i~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  480 (797)
T 4a2q_A          401 FNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAII  480 (797)
T ss_dssp             HTTCCCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHSCCCCCEEEECCCCSCCHHHHHH
T ss_pred             hccCCCCCeEEEEcCCccccccccHHHHHHHHHHHHHhcCCcEEecccccHHHHHHhcCCCceEEEecCCCCCcHHHHHH
Confidence               25568999999999531           11111                  111111111100000000  0     


Q ss_pred             ---------c-cc---------ceEEEEE-------e-------------------------------------------
Q 014486          260 ---------L-HG---------LVQHYIK-------L-------------------------------------------  270 (423)
Q Consensus       260 ---------~-~~---------~~~~~~~-------~-------------------------------------------  270 (423)
                               . ..         .......       +                                           
T Consensus       481 ~~l~~~i~~~~~~~~~l~~l~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~  560 (797)
T 4a2q_A          481 SNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISE  560 (797)
T ss_dssp             HHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhHHhhhhccccccchhHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHhhhc
Confidence                     0 00         0000000       0                                           


Q ss_pred             -------------------------------------------------ChHHHHHHHHHHHHh----hcCCcEEEEEcC
Q 014486          271 -------------------------------------------------SELEKNRKLNDLLDA----LDFNQVVIFVKS  297 (423)
Q Consensus       271 -------------------------------------------------~~~~~~~~l~~ll~~----~~~~~~ivf~~~  297 (423)
                                                                       ....|...+..++..    .++.++||||++
T Consensus       561 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~kvLIF~~~  640 (797)
T 4a2q_A          561 DARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKT  640 (797)
T ss_dssp             HSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHTTHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHHCSSCCEEEEESS
T ss_pred             cccHHHHHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHHHhccCCCCeEEEEECc
Confidence                                                             012233445555543    456899999999


Q ss_pred             hhhHHHHHHHHHhC------------CCCeEEEcCCCCHHHHHHHHHhhhc-CCccEEEEcCccccCCCCCCCCEEEEcc
Q 014486          298 VSRAAELNKLLVEC------------NFPSICIHSGMSQEERLTRYKGFKE-GNKRILVATDLVGRGIDIERVNIVINYD  364 (423)
Q Consensus       298 ~~~~~~l~~~L~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-~~~~ili~T~~~~~Gld~~~~~~vi~~~  364 (423)
                      +..++.+.+.|...            |.....+||++++.+|..+++.|++ |+++|||||+++++|+|+|++++||+|+
T Consensus       641 ~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GIDlp~v~~VI~yd  720 (797)
T 4a2q_A          641 RALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYE  720 (797)
T ss_dssp             HHHHHHHHHHHHTCSTTCSCCCEEC----------------------------CCSEEEEECC-------CCCSEEEEES
T ss_pred             HHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCCCchhCCEEEEeC
Confidence            99999999999873            5556677899999999999999999 9999999999999999999999999999


Q ss_pred             CCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          365 MPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       365 ~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      +|+|+..|+||+|| ||. ++|.+++|++....
T Consensus       721 ~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~~  751 (797)
T 4a2q_A          721 YSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEV  751 (797)
T ss_dssp             CCSCHHHHHTC---------CCCEEEEECCHHH
T ss_pred             CCCCHHHHHHhcCC-CCC-CCceEEEEEeCCcH
Confidence            99999999999999 999 88999999986543

>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=9.2e-47  Score=389.43  Aligned_cols=342  Identities=18%  Similarity=0.188  Sum_probs=264.7

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      ..|..+++++.+...+...+...|+++|.++++.+..++++++++|||||||++|.++++..+..++   +++|++|+++
T Consensus       162 ~~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~g~---rvlvl~Ptra  238 (1108)
T 3l9o_A          162 PNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQ---RVIYTSPIKA  238 (1108)
T ss_dssp             SCCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHTTC---EEEEEESSHH
T ss_pred             CCcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhcCC---eEEEEcCcHH
Confidence            3567777777776677666677899999999999999999999999999999999999998875433   8999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~  205 (423)
                      |+.|+++.+.++..     .+..++|+.+..        +.++|+|+||++|.+++......+.++++||+||||++.+ 
T Consensus       239 La~Q~~~~l~~~~~-----~VglltGd~~~~--------~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d-  304 (1108)
T 3l9o_A          239 LSNQKYRELLAEFG-----DVGLMTGDITIN--------PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRD-  304 (1108)
T ss_dssp             HHHHHHHHHHHHTS-----SEEEECSSCBCC--------CSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTS-
T ss_pred             HHHHHHHHHHHHhC-----CccEEeCccccC--------CCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccc-
Confidence            99999999998753     677788877632        3369999999999998888777788999999999999987 


Q ss_pred             CCcHHHHHHHHHhCCCCceEEEEeccCCccH--HHHHHHhccCCceeeeccccccccccce--------EEEEEeC----
Q 014486          206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEI--RPVCKKFMQDPMEIYVDDEAKLTLHGLV--------QHYIKLS----  271 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~----  271 (423)
                      .++...+..+...+++..|++++|||+|+..  ..++......+..+..............        .......    
T Consensus       305 ~~rg~~~e~ii~~l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~rp~pl~~~~~~~~~~~~~~~vd~~~~~~  384 (1108)
T 3l9o_A          305 KERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFR  384 (1108)
T ss_dssp             HHHHHHHHHHHHHSCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECCCSSCEEEEEEETTSSCCEEEEETTTEEC
T ss_pred             cchHHHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCCcccceEEEeecCCcceeeeeccccchh
Confidence            5788888999999999999999999998753  3455555544444332221111110000        0000000    


Q ss_pred             ----------------------------------------hHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC
Q 014486          272 ----------------------------------------ELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC  311 (423)
Q Consensus       272 ----------------------------------------~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~  311 (423)
                                                              ...+...+...+......++||||+++..++.++..|...
T Consensus       385 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~  464 (1108)
T 3l9o_A          385 EENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKL  464 (1108)
T ss_dssp             HHHHHHHHTTC-----------------------------CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSH
T ss_pred             hhhHHHHHHHHHhhhcccccccccccccccccccccccccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhc
Confidence                                                    0222333444455556679999999999999999998653


Q ss_pred             CCC---------------------------------------eEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCC
Q 014486          312 NFP---------------------------------------SICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGI  352 (423)
Q Consensus       312 ~~~---------------------------------------~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gl  352 (423)
                      ++.                                       +..+||++++.+|..+++.|++|.++|||||+++++|+
T Consensus       465 ~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GI  544 (1108)
T 3l9o_A          465 DFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGL  544 (1108)
T ss_dssp             HHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCC
T ss_pred             cCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCC
Confidence            322                                       68899999999999999999999999999999999999


Q ss_pred             CCCCCCEEEEccCCC--------CcchhhhcccccCCCC--CceEEEEEecCcccHHHHHHH
Q 014486          353 DIERVNIVINYDMPD--------SADTYLHRVGRAGRFG--TKGLAITFVSSASDSDILNQV  404 (423)
Q Consensus       353 d~~~~~~vi~~~~~~--------s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~~~~~~~~~~  404 (423)
                      |+|++++||+++.|+        |+.+|+||+||+||.|  ..|.+++++++..+...+..+
T Consensus       545 DiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~~~~~~~~~l  606 (1108)
T 3l9o_A          545 NMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGM  606 (1108)
T ss_dssp             CC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCCCCHHHHHHH
T ss_pred             CCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCCcCHHHHHHH
Confidence            999999999877654        5566999999999999  679999999877665544443

>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=1.3e-46  Score=378.63  Aligned_cols=335  Identities=19%  Similarity=0.249  Sum_probs=260.0

Q ss_pred             CCcCCCCCHHHHHHHHhCCCCCCChhhhhcccc-cccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           47 GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQ-AILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        47 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~-~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      +|+++++++.+.+.+.+.||.+|+|+|.++++. +..++++++++|||||||+++.++++..+...+  .+++|++|+++
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 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQG--GKAVYIVPLKA   79 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHHC--SEEEEECSSGG
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhCC--CEEEEEcCcHH
Confidence            488999999999999999999999999999998 788999999999999999999999987665222  39999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~  205 (423)
                      |+.|++++++++...  ++++..++|+.......  +  +.++|+|+||+++..++......+.++++||+||+|.+.+ 
T Consensus        80 La~q~~~~~~~l~~~--g~~v~~~~G~~~~~~~~--~--~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~-  152 (720)
T 2zj8_A           80 LAEEKFQEFQDWEKI--GLRVAMATGDYDSKDEW--L--GKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGS-  152 (720)
T ss_dssp             GHHHHHHHTGGGGGG--TCCEEEECSCSSCCCGG--G--GGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGC-
T ss_pred             HHHHHHHHHHHHHhc--CCEEEEecCCCCccccc--c--CCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCC-
Confidence            999999999755443  78999999976544321  1  2369999999999998887666688999999999999976 


Q ss_pred             CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccce--EEEEEeC------hHHHHH
Q 014486          206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLV--QHYIKLS------ELEKNR  277 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~------~~~~~~  277 (423)
                      ......+..++..++...|+|++|||+++. ..+.. ++.... +.... .........  .......      ......
T Consensus       153 ~~r~~~~~~ll~~l~~~~~ii~lSATl~n~-~~~~~-~l~~~~-~~~~~-rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~  228 (720)
T 2zj8_A          153 RDRGATLEVILAHMLGKAQIIGLSATIGNP-EELAE-WLNAEL-IVSDW-RPVKLRRGVFYQGFVTWEDGSIDRFSSWEE  228 (720)
T ss_dssp             TTTHHHHHHHHHHHBTTBEEEEEECCCSCH-HHHHH-HTTEEE-EECCC-CSSEEEEEEEETTEEEETTSCEEECSSTTH
T ss_pred             CcccHHHHHHHHHhhcCCeEEEEcCCcCCH-HHHHH-HhCCcc-cCCCC-CCCcceEEEEeCCeeeccccchhhhhHHHH
Confidence            567777777777776689999999999862 33333 332111 11000 000000000  0000010      112233


Q ss_pred             HHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC---------------------------------CCCeEEEcCCCCH
Q 014486          278 KLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC---------------------------------NFPSICIHSGMSQ  324 (423)
Q Consensus       278 ~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~---------------------------------~~~~~~~~~~~~~  324 (423)
                      .+.+.+.  +++++||||++++.++.++..|.+.                                 ...+..+|+++++
T Consensus       229 ~~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~  306 (720)
T 2zj8_A          229 LVYDAIR--KKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGR  306 (720)
T ss_dssp             HHHHHHH--TTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCH
T ss_pred             HHHHHHh--CCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCH
Confidence            4444443  4589999999999999999888753                                 1248899999999


Q ss_pred             HHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE----cc----CCCCcchhhhcccccCCCC--CceEEEEEecC
Q 014486          325 EERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN----YD----MPDSADTYLHRVGRAGRFG--TKGLAITFVSS  394 (423)
Q Consensus       325 ~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~----~~----~~~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~  394 (423)
                      .+|..+++.|++|.++|||||+++++|+|+|++++||+    |+    .|.++.+|.||+|||||.|  ..|.|++++++
T Consensus       307 ~~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~  386 (720)
T 2zj8_A          307 DERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTS  386 (720)
T ss_dssp             HHHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSS
T ss_pred             HHHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecC
Confidence            99999999999999999999999999999999999998    66    5889999999999999988  47889999886


Q ss_pred             cc
Q 014486          395 AS  396 (423)
Q Consensus       395 ~~  396 (423)
                      .+
T Consensus       387 ~~  388 (720)
T 2zj8_A          387 DD  388 (720)
T ss_dssp             SC
T ss_pred             cc
Confidence            55

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=100.00  E-value=2.5e-46  Score=367.92  Aligned_cols=328  Identities=20%  Similarity=0.241  Sum_probs=196.9

Q ss_pred             CCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC--CCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           66 FEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP--GQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        66 ~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~--~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      ..+|+|+|.++++.++.++++++++|||+|||++|++|++..+...+  .++++||++|+++|+.||.+.++++.... +
T Consensus         5 ~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-~   83 (556)
T 4a2p_A            5 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ-G   83 (556)
T ss_dssp             ---CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGG-T
T ss_pred             CCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhccc-C
Confidence            44899999999999999999999999999999999999988765543  14489999999999999999999998765 7


Q ss_pred             ceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCC-CCCCccEEEEcCcchhhccCCcHHHHHHHHHh----
Q 014486          144 IKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDL-SLKNVRHFILDECDKMLESLDMRRDVQEIFKM----  218 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~-~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~----  218 (423)
                      +++..++|+.........+..+ ++|+|+||+++...+..... .+.++++||+||||++.++..+...+..+...    
T Consensus        84 ~~~~~~~g~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~  162 (556)
T 4a2p_A           84 YSVQGISGENFSNVSVEKVIED-SDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNS  162 (556)
T ss_dssp             CCEEECCCC-----CHHHHHHH-CSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTSHHHHHHHHHHHHHHCC
T ss_pred             ceEEEEeCCCCcchhHHHhhCC-CCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcchHHHHHHHHHHhhhcc
Confidence            8999999998766655555444 59999999999999988777 78999999999999998743333333233322    


Q ss_pred             CCCCceEEEEeccCCcc----HH-------HHHHHh------------------ccCCceeeecccc--ccccc------
Q 014486          219 TPHDKQVMMFSATLSKE----IR-------PVCKKF------------------MQDPMEIYVDDEA--KLTLH------  261 (423)
Q Consensus       219 ~~~~~~~v~~SAT~~~~----~~-------~~~~~~------------------~~~~~~~~~~~~~--~~~~~------  261 (423)
                      ..+..+++++|||++..    ..       .+...+                  ...+.........  .....      
T Consensus       163 ~~~~~~~l~lSAT~~~~~~~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (556)
T 4a2p_A          163 ASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNL  242 (556)
T ss_dssp             ---CCEEEEEESCCCCTTCSSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHTCCCCEEEEECCCCSCCHHHHHHHHH
T ss_pred             cCCCCeEEEEeCCcccCchhhHHHHHHHHHHHHHhcCCeEecchhcchHHHHhcCCCCceEEEEcCCCcCChHHHHHHHH
Confidence            24568899999999532    11       111111                  1111100000000  00000      


Q ss_pred             ---------cce--EEEEE-------------------------------------------------------------
Q 014486          262 ---------GLV--QHYIK-------------------------------------------------------------  269 (423)
Q Consensus       262 ---------~~~--~~~~~-------------------------------------------------------------  269 (423)
                               ...  .....                                                             
T Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  322 (556)
T 4a2p_A          243 MSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISEDAR  322 (556)
T ss_dssp             HHHHHHHHHHHCC---------CCCSSHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHhhhhhhhcccccccchhhHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence                     000  00000                                                             


Q ss_pred             ---------------------------------------------eChHHHHHHHHHHHHh----hcCCcEEEEEcChhh
Q 014486          270 ---------------------------------------------LSELEKNRKLNDLLDA----LDFNQVVIFVKSVSR  300 (423)
Q Consensus       270 ---------------------------------------------~~~~~~~~~l~~ll~~----~~~~~~ivf~~~~~~  300 (423)
                                                                   .....|...+.+++..    .+..++||||+++..
T Consensus       323 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~~l~~~~~~~~~~k~lVF~~~~~~  402 (556)
T 4a2p_A          323 IIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRAL  402 (556)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTHHHHHHHHHCSSSCCHHHHHHHHHHHHHHHHCTTCCEEEEESSHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhHHHHhhhhccCCCCCChHHHHHHHHHHHHhcCCCCceEEEEEccHHH
Confidence                                                         0012244445555543    356899999999999


Q ss_pred             HHHHHHHHHhC------------CCCeEEEcCCCCHHHHHHHHHhhhc-CCccEEEEcCccccCCCCCCCCEEEEccCCC
Q 014486          301 AAELNKLLVEC------------NFPSICIHSGMSQEERLTRYKGFKE-GNKRILVATDLVGRGIDIERVNIVINYDMPD  367 (423)
Q Consensus       301 ~~~l~~~L~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~  367 (423)
                      ++.+.+.|...            |.....+||++++.+|..+++.|++ |+++|||||+++++|+|+|++++||+|++|+
T Consensus       403 ~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~  482 (556)
T 4a2p_A          403 VSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSG  482 (556)
T ss_dssp             HHHHHHHHTTCSGGGSCCEEC------------------------------CCEEEEEC-----------CEEEEETCCS
T ss_pred             HHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCCCchhCCEEEEeCCCC
Confidence            99999999875            4555667888999999999999999 9999999999999999999999999999999


Q ss_pred             CcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          368 SADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       368 s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      |+..|+||+|| ||. ++|.++++++....
T Consensus       483 s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~  510 (556)
T 4a2p_A          483 NVTKMIQVRGR-GRA-AGSKCILVTSKTEV  510 (556)
T ss_dssp             CHHHHHHC----------CCEEEEESCHHH
T ss_pred             CHHHHHHhcCC-CCC-CCceEEEEEeCcch
Confidence            99999999999 998 78999999987544

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=100.00  E-value=8.5e-46  Score=372.91  Aligned_cols=337  Identities=20%  Similarity=0.238  Sum_probs=256.3

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccc-cccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQ-AILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~-~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      ..+|+++++++.+.+.+.+.||..|+|+|.++++. +..++++++++|||||||+++.++++..+...+  .+++|++|+
T Consensus         7 ~~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~--~~il~i~P~   84 (715)
T 2va8_A            7 WMPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNG--GKAIYVTPL   84 (715)
T ss_dssp             CCBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHSC--SEEEEECSC
T ss_pred             cCcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHCC--CeEEEEeCc
Confidence            35699999999999999999999999999999999 778899999999999999999999987655222  399999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                      ++|+.|+++.++.+...  ++++...+|+.......  +.  .++|+|+||++|..++......+.++++||+||+|.+.
T Consensus        85 r~La~q~~~~~~~~~~~--g~~v~~~~G~~~~~~~~--~~--~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~  158 (715)
T 2va8_A           85 RALTNEKYLTFKDWELI--GFKVAMTSGDYDTDDAW--LK--NYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLN  158 (715)
T ss_dssp             HHHHHHHHHHHGGGGGG--TCCEEECCSCSSSCCGG--GG--GCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGG
T ss_pred             HHHHHHHHHHHHHhhcC--CCEEEEEeCCCCCchhh--cC--CCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcC
Confidence            99999999999655432  77888888876544321  22  36999999999999888766668899999999999987


Q ss_pred             ccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeecccccccccc---------ceEEEEE-----
Q 014486          204 ESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHG---------LVQHYIK-----  269 (423)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~-----  269 (423)
                      + ..+...+..+...++ ..|+|++|||+++. ..+... +..+. +..... ......         .......     
T Consensus       159 ~-~~~~~~l~~i~~~~~-~~~ii~lSATl~n~-~~~~~~-l~~~~-~~~~~r-~~~l~~~~~~~~~~~~~~~~~~~~~~~  232 (715)
T 2va8_A          159 D-PERGPVVESVTIRAK-RRNLLALSATISNY-KQIAKW-LGAEP-VATNWR-PVPLIEGVIYPERKKKEYNVIFKDNTT  232 (715)
T ss_dssp             C-TTTHHHHHHHHHHHH-TSEEEEEESCCTTH-HHHHHH-HTCEE-EECCCC-SSCEEEEEEEECSSTTEEEEEETTSCE
T ss_pred             C-cccchHHHHHHHhcc-cCcEEEEcCCCCCH-HHHHHH-hCCCc-cCCCCC-CCCceEEEEecCCcccceeeecCcchh
Confidence            5 566667777666655 78999999999852 333333 32211 110000 000000         0000000     


Q ss_pred             --eC-hHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCC----------------------------------
Q 014486          270 --LS-ELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECN----------------------------------  312 (423)
Q Consensus       270 --~~-~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~----------------------------------  312 (423)
                        .. .......+.+.+.  .++++||||++++.++.+++.|.+..                                  
T Consensus       233 ~~~~~~~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~  310 (715)
T 2va8_A          233 KKVHGDDAIIAYTLDSLS--KNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSL  310 (715)
T ss_dssp             EEEESSSHHHHHHHHHHT--TTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHH
T ss_pred             hhcccchHHHHHHHHHHh--cCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHH
Confidence              00 1233344444442  46899999999999999999988642                                  


Q ss_pred             --CCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE----cc-------CCCCcchhhhccccc
Q 014486          313 --FPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN----YD-------MPDSADTYLHRVGRA  379 (423)
Q Consensus       313 --~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~----~~-------~~~s~~~~~Q~~GR~  379 (423)
                        ..+..+||+++..+|..+++.|++|.++|||||+++++|+|+|++++||+    |+       .|.|..+|.||+|||
T Consensus       311 ~~~~v~~~h~~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRa  390 (715)
T 2va8_A          311 ISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRA  390 (715)
T ss_dssp             HTTTEEEECTTSCHHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTB
T ss_pred             HhcCEEEECCCCCHHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhc
Confidence              24889999999999999999999999999999999999999999999999    88       799999999999999


Q ss_pred             CCCCC--ceEEEEEecCccc
Q 014486          380 GRFGT--KGLAITFVSSASD  397 (423)
Q Consensus       380 ~R~g~--~~~~~~~~~~~~~  397 (423)
                      ||.|.  .|.|++++++.++
T Consensus       391 GR~g~~~~G~~~~l~~~~~~  410 (715)
T 2va8_A          391 GRPGFDQIGESIVVVRDKED  410 (715)
T ss_dssp             CCTTTCSCEEEEEECSCGGG
T ss_pred             CCCCCCCCceEEEEeCCchH
Confidence            99884  7899999876543

>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=1.8e-46  Score=376.56  Aligned_cols=334  Identities=17%  Similarity=0.261  Sum_probs=253.4

Q ss_pred             CCcCCC--CCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           47 GFRDFL--LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        47 ~~~~~~--l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      +|++++  +++.+.+.+.+.||.+|+|+|.++++.++.++++++++|||||||+++.++++..+..+   .+++|++|++
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 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG---GKSLYVVPLR   78 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTT---CCEEEEESSH
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHhC---CcEEEEeCcH
Confidence            477788  89999999999999999999999999999999999999999999999999999876532   3899999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      +|+.|+++.++.+.. . ++++..++|+.......  +  +.++|+|+||+++..++......+.++++||+||+|.+.+
T Consensus        79 ~La~q~~~~~~~~~~-~-g~~v~~~~G~~~~~~~~--~--~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~  152 (702)
T 2p6r_A           79 ALAGEKYESFKKWEK-I-GLRIGISTGDYESRDEH--L--GDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDS  152 (702)
T ss_dssp             HHHHHHHHHHTTTTT-T-TCCEEEECSSCBCCSSC--S--TTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGC
T ss_pred             HHHHHHHHHHHHHHh-c-CCEEEEEeCCCCcchhh--c--cCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCC
Confidence            999999999865433 2 78899999877554321  1  2369999999999998888666688999999999999876


Q ss_pred             cCCcHHHHHHHHHh---CCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccc-----cceEEEEEe-----C
Q 014486          205 SLDMRRDVQEIFKM---TPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLH-----GLVQHYIKL-----S  271 (423)
Q Consensus       205 ~~~~~~~~~~~~~~---~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~-----~  271 (423)
                       ......+..+...   .++..|++++|||+++ ...+.. ++..+. +..... .....     .....+...     .
T Consensus       153 -~~r~~~~~~ll~~l~~~~~~~~ii~lSATl~n-~~~~~~-~l~~~~-~~~~~r-~~~l~~~~~~~~~~~~~~~~~~~~~  227 (702)
T 2p6r_A          153 -EKRGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAE-WLDADY-YVSDWR-PVPLVEGVLCEGTLELFDGAFSTSR  227 (702)
T ss_dssp             -TTTHHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHH-HTTCEE-EECCCC-SSCEEEEEECSSEEEEEETTEEEEE
T ss_pred             -CCcccHHHHHHHHHHhcCcCceEEEECCCcCC-HHHHHH-HhCCCc-ccCCCC-CccceEEEeeCCeeeccCcchhhhh
Confidence             4555555544433   3568999999999986 333433 333221 111000 00000     000011110     0


Q ss_pred             hHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC------------------------------CCCeEEEcCC
Q 014486          272 ELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC------------------------------NFPSICIHSG  321 (423)
Q Consensus       272 ~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~------------------------------~~~~~~~~~~  321 (423)
                      .......+.+.+.  +++++||||++++.+..+++.|.+.                              +..+..+||+
T Consensus       228 ~~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~  305 (702)
T 2p6r_A          228 RVKFEELVEECVA--ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAG  305 (702)
T ss_dssp             ECCHHHHHHHHHH--TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTT
T ss_pred             hhhHHHHHHHHHh--cCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCC
Confidence            0013344444443  4689999999999999999888753                              1357789999


Q ss_pred             CCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE----cc---CCCCcchhhhcccccCCCC--CceEEEEEe
Q 014486          322 MSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN----YD---MPDSADTYLHRVGRAGRFG--TKGLAITFV  392 (423)
Q Consensus       322 ~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~----~~---~~~s~~~~~Q~~GR~~R~g--~~~~~~~~~  392 (423)
                      +++.+|..+++.|++|.++|||||+++++|+|+|++++||+    |+   .|.|+.+|.||+||+||.|  ..|.|++++
T Consensus       306 l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~  385 (702)
T 2p6r_A          306 LLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIV  385 (702)
T ss_dssp             SCHHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEEC
T ss_pred             CCHHHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEe
Confidence            99999999999999999999999999999999999999998    55   7899999999999999988  478999998


Q ss_pred             cCcc
Q 014486          393 SSAS  396 (423)
Q Consensus       393 ~~~~  396 (423)
                      ++.+
T Consensus       386 ~~~~  389 (702)
T 2p6r_A          386 GKRD  389 (702)
T ss_dssp             CGGG
T ss_pred             cCcc
Confidence            8654

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=100.00  E-value=1.3e-45  Score=378.40  Aligned_cols=330  Identities=21%  Similarity=0.245  Sum_probs=205.6

Q ss_pred             CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCC--CeEEEEEecChHHHHHHHHHHHHHhccC
Q 014486           64 SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPG--QVTALVLCHTRELAYQICHEFERFSTYL  141 (423)
Q Consensus        64 ~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~L~~q~~~~~~~~~~~~  141 (423)
                      .|+..|+++|.++++.++.|+++++++|||+|||++|+++++..+...+.  +.++||++|+++|+.||.++++++....
T Consensus       244 ~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~  323 (936)
T 4a2w_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ  323 (936)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhccc
Confidence            36779999999999999999999999999999999999999988766431  3489999999999999999999998765


Q ss_pred             CCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCC-CCCCccEEEEcCcchhhccCCcHHHHHHHHHh--
Q 014486          142 PDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDL-SLKNVRHFILDECDKMLESLDMRRDVQEIFKM--  218 (423)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~-~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~--  218 (423)
                       ++++..++|+.........+..+ ++|+|+||++|...+..... .+.++++||+||||++.....+...+..+...  
T Consensus       324 -~~~v~~~~G~~~~~~~~~~~~~~-~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~~~~~i~~~~~~~~~  401 (936)
T 4a2w_A          324 -GYSVQGISGENFSNVSVEKVIED-SDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKF  401 (936)
T ss_dssp             -TCCEEEECCC-----CCHHHHHH-CSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTCHHHHHHHHHHHHHH
T ss_pred             -CceEEEEECCcchhhHHHHhccC-CCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCccHHHHHHHHHHHhh
Confidence             78999999998666544444444 59999999999998887766 68889999999999998743444444344332  


Q ss_pred             --CCCCceEEEEeccCCcc-----------HHHHH------------------HHhccCCceeeeccccccc--------
Q 014486          219 --TPHDKQVMMFSATLSKE-----------IRPVC------------------KKFMQDPMEIYVDDEAKLT--------  259 (423)
Q Consensus       219 --~~~~~~~v~~SAT~~~~-----------~~~~~------------------~~~~~~~~~~~~~~~~~~~--------  259 (423)
                        ..+..+++++|||+...           +..+.                  ..+...+............        
T Consensus       402 ~~~~~~~~~l~LSATp~~~~~~~l~~~~~~i~~L~~~L~~~~i~~~~~~~~~l~~~~~~p~~~~~~~~~~~~~~~~~~l~  481 (936)
T 4a2w_A          402 NSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIIS  481 (936)
T ss_dssp             TTCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCSSHHHHHHHSCCCCEEEEECCCCSCCHHHHHHH
T ss_pred             ccCCCcCeEEEecCCcccccchhHHHHHHHHHHHHHhcCCceeecccccHHHHHHhccCCcceEEecccccCcHHHHHHH
Confidence              25568899999999531           11111                  1111111111100000000        


Q ss_pred             --------c-ccc--------eEEEEEe----------------------------------------------------
Q 014486          260 --------L-HGL--------VQHYIKL----------------------------------------------------  270 (423)
Q Consensus       260 --------~-~~~--------~~~~~~~----------------------------------------------------  270 (423)
                              . ...        .......                                                    
T Consensus       482 ~l~~~i~~~~~~~l~~~~l~~~~~~~~g~~~y~~~l~~l~k~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~al~i~~~  561 (936)
T 4a2w_A          482 NLMSETEALMRTIAYVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISED  561 (936)
T ss_dssp             HHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhhhhhccccccchHHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence                    0 000        0000000                                                    


Q ss_pred             ------------------------------------------------ChHHHHHHHHHHHHh----hcCCcEEEEEcCh
Q 014486          271 ------------------------------------------------SELEKNRKLNDLLDA----LDFNQVVIFVKSV  298 (423)
Q Consensus       271 ------------------------------------------------~~~~~~~~l~~ll~~----~~~~~~ivf~~~~  298 (423)
                                                                      ....|...+.+++..    .++.++||||+++
T Consensus       562 ~~~~~~~~~l~~~~~~~~~~~~~~~e~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~rvLIF~~t~  641 (936)
T 4a2w_A          562 ARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTR  641 (936)
T ss_dssp             SCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTSTTCCCHHHHHHHHHHHHTTTSCTTCCEEEEESSH
T ss_pred             hhHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHhhhccCCCCHHHHHHHHHHHHHhccCCCCeEEEEeCCH
Confidence                                                            011233444555554    2468999999999


Q ss_pred             hhHHHHHHHHHhC------------CCCeEEEcCCCCHHHHHHHHHhhhc-CCccEEEEcCccccCCCCCCCCEEEEccC
Q 014486          299 SRAAELNKLLVEC------------NFPSICIHSGMSQEERLTRYKGFKE-GNKRILVATDLVGRGIDIERVNIVINYDM  365 (423)
Q Consensus       299 ~~~~~l~~~L~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-~~~~ili~T~~~~~Gld~~~~~~vi~~~~  365 (423)
                      ..++.+.+.|...            |.....+||++++.+|.++++.|++ |+++|||||+++++|+|+|++++||+|++
T Consensus       642 ~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~eGIDlp~v~~VI~yD~  721 (936)
T 4a2w_A          642 ALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEY  721 (936)
T ss_dssp             HHHHHHHHHHHHCSTTSSCCCEEC----------------------------CCSEEEEECC------CCCCSEEEEESC
T ss_pred             HHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhcCCcchhCCEEEEeCC
Confidence            9999999999986            5556667889999999999999999 99999999999999999999999999999


Q ss_pred             CCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          366 PDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       366 ~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      |+|+..|+||+|| ||. ..|.++++++....
T Consensus       722 p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~  751 (936)
T 4a2w_A          722 SGNVTKMIQVRGR-GRA-AGSKCILVTSKTEV  751 (936)
T ss_dssp             CSCSHHHHCC---------CCCEEEEESCHHH
T ss_pred             CCCHHHHHHhcCC-CCC-CCCEEEEEEeCCCH
Confidence            9999999999999 998 77889988876443

>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=3.4e-45  Score=354.34  Aligned_cols=324  Identities=19%  Similarity=0.285  Sum_probs=247.1

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .|+|+|.++++.++.+ ++++++|||+|||++++++++..+.  ..+.++||++|+++|+.||.+++.++... +..++.
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~--~~~~~~liv~P~~~L~~q~~~~~~~~~~~-~~~~v~   84 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLT--KYGGKVLMLAPTKPLVLQHAESFRRLFNL-PPEKIV   84 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHH--HSCSCEEEECSSHHHHHHHHHHHHHHBCS-CGGGEE
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHh--cCCCeEEEEECCHHHHHHHHHHHHHHhCc-chhheE
Confidence            7999999999999998 9999999999999999998887765  22238999999999999999999998632 355888


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEE
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM  227 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~  227 (423)
                      .++|+.........+.+  ++|+|+||+.+...+....+.+.++++||+||||++.+. .....+...+....+..++++
T Consensus        85 ~~~g~~~~~~~~~~~~~--~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~-~~~~~~~~~~~~~~~~~~~l~  161 (494)
T 1wp9_A           85 ALTGEKSPEERSKAWAR--AKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGN-YAYVFIAREYKRQAKNPLVIG  161 (494)
T ss_dssp             EECSCSCHHHHHHHHHH--CSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTT-CHHHHHHHHHHHHCSSCCEEE
T ss_pred             EeeCCcchhhhhhhccC--CCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCC-CcHHHHHHHHHhcCCCCeEEE
Confidence            99998876655444433  599999999999988887778899999999999999863 344444455555566788999


Q ss_pred             EeccCCccHHH---HHHHhccCCceeeeccccc--cccccceEEEE--Ee------------------------------
Q 014486          228 FSATLSKEIRP---VCKKFMQDPMEIYVDDEAK--LTLHGLVQHYI--KL------------------------------  270 (423)
Q Consensus       228 ~SAT~~~~~~~---~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~--~~------------------------------  270 (423)
                      +|||+......   ++..+..............  ...........  ..                              
T Consensus       162 lTaTp~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  241 (494)
T 1wp9_A          162 LTASPGSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVRKLLREMLRDALKPLAETGLLES  241 (494)
T ss_dssp             EESCSCSSHHHHHHHHHHTTCCEEEECCTTSTTTGGGCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHTSSSC
T ss_pred             EecCCCCCcHHHHHHHHhcChheeeccCCCcHHHHHhcCCCceeEEecCCcHHHHHHHHHHHHHHHHHHHHHHHhccccc
Confidence            99999854332   2222211111110000000  00000000000  00                              


Q ss_pred             --------------------------------------------------------------------------------
Q 014486          271 --------------------------------------------------------------------------------  270 (423)
Q Consensus       271 --------------------------------------------------------------------------------  270 (423)
                                                                                                      
T Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  321 (494)
T 1wp9_A          242 SSPDIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEIFS  321 (494)
T ss_dssp             CCTTSCHHHHHHHHHHHHHHHTTTCCSTTTHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTCCHHHHHHHT
T ss_pred             cCCCcchhHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHHHhhccccchhhhhhhh
Confidence                                                                                            


Q ss_pred             ------------------ChHHHHHHHHHHHHh----hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcC--------
Q 014486          271 ------------------SELEKNRKLNDLLDA----LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHS--------  320 (423)
Q Consensus       271 ------------------~~~~~~~~l~~ll~~----~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~--------  320 (423)
                                        ....|...+.+++..    .+++++||||+++..++.+++.|...|+.+..+||        
T Consensus       322 ~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~  401 (494)
T 1wp9_A          322 DKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDR  401 (494)
T ss_dssp             SHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC----
T ss_pred             hHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccc
Confidence                              122344555666655    36789999999999999999999999999999999        


Q ss_pred             CCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHH
Q 014486          321 GMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSD  399 (423)
Q Consensus       321 ~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~  399 (423)
                      +++..+|..+++.|++|+.+|||+|+++++|+|+|++++||++++|+++..|.||+||+||.|+ |.++.++.+...++
T Consensus       402 ~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t~ee  479 (494)
T 1wp9_A          402 GLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTRDE  479 (494)
T ss_dssp             ---CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTSHHH
T ss_pred             cCCHHHHHHHHHHHhcCCceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCCHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999998 99999988765443

>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=3.5e-44  Score=367.19  Aligned_cols=320  Identities=20%  Similarity=0.235  Sum_probs=251.9

Q ss_pred             hCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           63 DSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        63 ~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      ..+| .|+++|.++++.+..++++++++|||+|||+++.++++..+..+   .++||++|+++|+.|+++.+.++..   
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 TYPF-TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNK---QRVIYTSPIKALSNQKYRELLAEFG---  154 (1010)
T ss_dssp             CCSS-CCCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHTT---CEEEEEESSHHHHHHHHHHHHHHHS---
T ss_pred             hCCC-CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhccC---CeEEEECChHHHHHHHHHHHHHHhC---
Confidence            3466 59999999999999999999999999999999999888776433   3999999999999999999998763   


Q ss_pred             CceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCC
Q 014486          143 DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHD  222 (423)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~  222 (423)
                        ++..++|+.....        ..+|+|+||++|..++.+....+.++++||+||+|++.+ ..+...+..+...++..
T Consensus       155 --~vglltGd~~~~~--------~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d-~~rg~~~e~il~~l~~~  223 (1010)
T 2xgj_A          155 --DVGLMTGDITINP--------DAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRD-KERGVVWEETIILLPDK  223 (1010)
T ss_dssp             --CEEEECSSCEECT--------TCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGC-TTTHHHHHHHHHHSCTT
T ss_pred             --CEEEEeCCCccCC--------CCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcc-cchhHHHHHHHHhcCCC
Confidence              6778888776432        369999999999998887777889999999999999987 56778888888999999


Q ss_pred             ceEEEEeccCCccHH--HHHHHhccCCceeeeccccccccccceEEEEE---------eCh-------------------
Q 014486          223 KQVMMFSATLSKEIR--PVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIK---------LSE-------------------  272 (423)
Q Consensus       223 ~~~v~~SAT~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~-------------------  272 (423)
                      .|++++|||+++...  ..+......+..+.........   +..++..         ...                   
T Consensus       224 ~~il~LSATi~n~~e~a~~l~~~~~~~~~vi~~~~rp~p---l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  300 (1010)
T 2xgj_A          224 VRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTP---LQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQ  300 (1010)
T ss_dssp             CEEEEEECCCTTHHHHHHHHHHHHTSCEEEEEECCCSSC---EEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHTCC--
T ss_pred             CeEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCCccc---ceEEEEecCCcceeeeeccccccchHHHHHHHHHHhhh
Confidence            999999999987532  3333333333333222111110   1111110         000                   


Q ss_pred             ---------------------------HHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCC-----------
Q 014486          273 ---------------------------LEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFP-----------  314 (423)
Q Consensus       273 ---------------------------~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-----------  314 (423)
                                                 ......+...+......++||||+++..++.+++.|...++.           
T Consensus       301 ~~~~~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~  380 (1010)
T 2xgj_A          301 IGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKI  380 (1010)
T ss_dssp             ----------------------------CHHHHHHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHH
T ss_pred             hcccccccccccccccccccccccccchHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHH
Confidence                                       111223444445556679999999999999999999775442           


Q ss_pred             ----------------------------eEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE----
Q 014486          315 ----------------------------SICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN----  362 (423)
Q Consensus       315 ----------------------------~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~----  362 (423)
                                                  +..+||++++.+|..+++.|++|.++|||||+++++|+|+|++++||+    
T Consensus       381 ~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~k  460 (1010)
T 2xgj_A          381 FNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRK  460 (1010)
T ss_dssp             HHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEE
T ss_pred             HHHHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcc
Confidence                                        678999999999999999999999999999999999999999999999    


Q ss_pred             ccC----CCCcchhhhcccccCCCCC--ceEEEEEecCcccHHHHHH
Q 014486          363 YDM----PDSADTYLHRVGRAGRFGT--KGLAITFVSSASDSDILNQ  403 (423)
Q Consensus       363 ~~~----~~s~~~~~Q~~GR~~R~g~--~~~~~~~~~~~~~~~~~~~  403 (423)
                      |+.    |.++.+|.||+||+||.|+  .|.+++++++..+...+..
T Consensus       461 fd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~~e~~~~~~  507 (1010)
T 2xgj_A          461 WDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKG  507 (1010)
T ss_dssp             ECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSCCCHHHHHH
T ss_pred             cCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCCCCHHHHHH
Confidence            998    8899999999999999997  4999999987655544433

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=100.00  E-value=1.1e-44  Score=373.75  Aligned_cols=320  Identities=20%  Similarity=0.320  Sum_probs=254.8

Q ss_pred             CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           64 SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        64 ~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      .|| +|+|+|.++++.++.|+++++++|||||||++++++++..+..   ++++||++|+++|+.|+++.++++.  ..+
T Consensus        75 ~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~~---~~~~Lil~PtreLa~Q~~~~l~~l~--~~~  148 (1104)
T 4ddu_A           75 FGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARK---GKKSALVFPTVTLVKQTLERLQKLA--DEK  148 (1104)
T ss_dssp             SSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHTT---TCCEEEEESSHHHHHHHHHHHHTTS--CTT
T ss_pred             cCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHhc---CCeEEEEechHHHHHHHHHHHHHhh--CCC
Confidence            577 6999999999999999999999999999999888888777633   3389999999999999999999976  348


Q ss_pred             ceEEEEEcCcch---HHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc----------CCcHH
Q 014486          144 IKVAVFYGGVNI---KIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES----------LDMRR  210 (423)
Q Consensus       144 ~~~~~~~~~~~~---~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~----------~~~~~  210 (423)
                      +++..++|+.+.   ..+...+.++.++|+|+||++|.+++..  +.+.++++||+||||++..+          .+|..
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            899999999987   5566677777689999999999887664  55678999999999987641          35555


Q ss_pred             H-HHHHHHhCC-----------CCceEEEEecc-CCccHHH-HHHHhccCCceeeeccccccccccceEEEEEeChHHHH
Q 014486          211 D-VQEIFKMTP-----------HDKQVMMFSAT-LSKEIRP-VCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKN  276 (423)
Q Consensus       211 ~-~~~~~~~~~-----------~~~~~v~~SAT-~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  276 (423)
                      . +..++..++           ...|++++||| .|..+.. .....+.    +.+... ......+.+.+...   .+.
T Consensus       227 ~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~~-~~~~~~i~~~~~~~---~k~  298 (1104)
T 4ddu_A          227 EIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRL-VSVARNITHVRISS---RSK  298 (1104)
T ss_dssp             HHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCBC-CCCCCCEEEEEESC---CCH
T ss_pred             HHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEeccC-CCCcCCceeEEEec---CHH
Confidence            5 777777666           78899999999 5555432 2232222    111111 12233344444433   355


Q ss_pred             HHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeE-EEcCCCCHHHHHHHHHhhhcCCccEEEE----cCccccC
Q 014486          277 RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSI-CIHSGMSQEERLTRYKGFKEGNKRILVA----TDLVGRG  351 (423)
Q Consensus       277 ~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~-~~~~~~~~~~r~~~~~~f~~~~~~ili~----T~~~~~G  351 (423)
                      ..+..++... ++++||||++++.++.++..|...|+++. .+||     +|.+ ++.|++|+.+||||    |+++++|
T Consensus       299 ~~L~~ll~~~-~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg-----~rr~-l~~F~~G~~~VLVatas~TdvlarG  371 (1104)
T 4ddu_A          299 EKLVELLEIF-RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSE-----FEKN-FEDFKVGKINILIGVQAYYGKLTRG  371 (1104)
T ss_dssp             HHHHHHHHHH-CSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSS-----HHHH-HHHHHHTSCSEEEEETTTHHHHCCS
T ss_pred             HHHHHHHHhc-CCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecC-----cHHH-HHHHHCCCCCEEEEecCCCCeeEec
Confidence            6667777774 48999999999999999999999999998 8999     2555 99999999999999    9999999


Q ss_pred             CCCCC-CCEEEEccCCC---------------------------------------------------------------
Q 014486          352 IDIER-VNIVINYDMPD---------------------------------------------------------------  367 (423)
Q Consensus       352 ld~~~-~~~vi~~~~~~---------------------------------------------------------------  367 (423)
                      +|+|+ +++||+||+|.                                                               
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             ---------CcchhhhcccccCCCCC----ceEEEEEecCcccHHHHHHHHHHHh
Q 014486          368 ---------SADTYLHRVGRAGRFGT----KGLAITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       368 ---------s~~~~~Q~~GR~~R~g~----~~~~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                               ++.+|+||+||+||.|.    .|..++++   ++...++.|++.+.
T Consensus       452 ~~~~~~~~pd~~tYihr~GRtgR~~~gg~~~Glsi~~~---~d~~~~~~l~~~~~  503 (1104)
T 4ddu_A          452 DEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSVIFE---EDEEIFESLKTRLL  503 (1104)
T ss_dssp             TTTTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEEC---CCHHHHHHHHHHHH
T ss_pred             CCeeEEEecChhhhhcccCchhcccCCCcccceEEEEE---ecHHHHHHHHHHHh
Confidence                     77789999999999653    45556665   57778888888886

>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=6.5e-43  Score=340.36  Aligned_cols=323  Identities=19%  Similarity=0.227  Sum_probs=249.5

Q ss_pred             hCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           63 DSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        63 ~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      ..|+ +|+|+|..+++.++.|+  |..++||+|||++|++|++.....+   +.++|++||++||.|.++++..+.... 
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~g---~~vlVltptreLA~qd~e~~~~l~~~l-  151 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTG---KGVHVVTVNEYLASRDAEQMGKIFEFL-  151 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTS---SCEEEEESSHHHHHHHHHHHHHHHHHT-
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHcC---CCEEEEeCCHHHHHHHHHHHHHHHhhc-
Confidence            4699 99999999999999998  9999999999999999998554432   379999999999999999999998887 


Q ss_pred             CceEEEEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcC------CCCCCCccEEEEcCcchhhccC---------
Q 014486          143 DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDK------DLSLKNVRHFILDECDKMLESL---------  206 (423)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~------~~~~~~~~~vVvDE~h~~~~~~---------  206 (423)
                      ++++.++.||.+........  + ++|+|+||+.| ++++..+      ...+..++++|+||||+++.+.         
T Consensus       152 gl~v~~i~gg~~~~~r~~~~--~-~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIisg  228 (844)
T 1tf5_A          152 GLTVGLNLNSMSKDEKREAY--A-ADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISG  228 (844)
T ss_dssp             TCCEEECCTTSCHHHHHHHH--H-SSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEE
T ss_pred             CCeEEEEeCCCCHHHHHHhc--C-CCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhcC
Confidence            89999999998765443332  3 59999999999 6666543      2456889999999999998323         


Q ss_pred             ------CcHHHHHHHHHhCC---------CCceEE-----------------EEeccCCcc---HHHHHHH--hcc-CCc
Q 014486          207 ------DMRRDVQEIFKMTP---------HDKQVM-----------------MFSATLSKE---IRPVCKK--FMQ-DPM  248 (423)
Q Consensus       207 ------~~~~~~~~~~~~~~---------~~~~~v-----------------~~SAT~~~~---~~~~~~~--~~~-~~~  248 (423)
                            ++...+..+...++         +.+|+.                 ++|||.+..   +...++.  ++. +..
T Consensus       229 ~~~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~~~~~i~~al~A~~l~~~d~d  308 (844)
T 1tf5_A          229 QAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVD  308 (844)
T ss_dssp             EEECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHHHHHHHHHHHHHHHTCCBTTT
T ss_pred             CcccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccchhHHHHHHHHHHHHHhhcCCc
Confidence                  26778888888886         356776                 889997642   2222111  111 111


Q ss_pred             ee------------------------------------eecccc------------------------------------
Q 014486          249 EI------------------------------------YVDDEA------------------------------------  256 (423)
Q Consensus       249 ~~------------------------------------~~~~~~------------------------------------  256 (423)
                      .+                                    .+....                                    
T Consensus       309 Yiv~dg~v~ivDe~tgr~m~grr~sdGLhqaieake~v~I~~e~~t~a~It~q~~fr~y~kl~GmTGTa~te~~e~~~iY  388 (844)
T 1tf5_A          309 YVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIY  388 (844)
T ss_dssp             EEEETTEEEEBCTTTCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEEEHHHHHTTSSEEEEEESCCGGGHHHHHHHH
T ss_pred             eEEecCeeEEeecccccccCCCccchhhHHHHhhcccceecccccccceeeHHHHHHHHhhhccCCcccchhHHHHHHHh
Confidence            11                                    000000                                    


Q ss_pred             ---------ccccccc-eEEEEEeChHHHHHHHHHHHHh--hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCH
Q 014486          257 ---------KLTLHGL-VQHYIKLSELEKNRKLNDLLDA--LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQ  324 (423)
Q Consensus       257 ---------~~~~~~~-~~~~~~~~~~~~~~~l~~ll~~--~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~  324 (423)
                               ..+.... ....+.....+|...+...+..  ..+.++||||++++.++.++..|...|+++..+|+++.+
T Consensus       389 ~l~vv~IPtn~p~~r~d~~d~v~~~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~  468 (844)
T 1tf5_A          389 NMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHE  468 (844)
T ss_dssp             CCCEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHH
T ss_pred             CCceEEecCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccH
Confidence                     0000000 0113445677788888877754  256789999999999999999999999999999999988


Q ss_pred             HHHHHHHHhhhcCCccEEEEcCccccCCCCC--------CCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcc
Q 014486          325 EERLTRYKGFKEGNKRILVATDLVGRGIDIE--------RVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSAS  396 (423)
Q Consensus       325 ~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~--------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  396 (423)
                      .+|..+...|+.|  .|+|||++++||+|++        ++.+||+++.|.|...|.||+||+||.|.+|.++.|++..+
T Consensus       469 rEr~ii~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD  546 (844)
T 1tf5_A          469 REAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  546 (844)
T ss_dssp             HHHHHHTTTTSTT--CEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             HHHHHHHHcCCCC--eEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHH
Confidence            8877665555554  6999999999999999        78899999999999999999999999999999999998765


Q ss_pred             c
Q 014486          397 D  397 (423)
Q Consensus       397 ~  397 (423)
                      +
T Consensus       547 ~  547 (844)
T 1tf5_A          547 E  547 (844)
T ss_dssp             S
T ss_pred             H
Confidence            4

>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=1e-44  Score=365.30  Aligned_cols=321  Identities=20%  Similarity=0.245  Sum_probs=221.4

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC---CCeEEEEEecChHHHHHH-HHHHHHHhccCCC
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP---GQVTALVLCHTRELAYQI-CHEFERFSTYLPD  143 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~---~~~~~lil~P~~~L~~q~-~~~~~~~~~~~~~  143 (423)
                      .|+|+|.++++.++.++++++++|||+|||++|+++++..+....   .+.++||++|+++|+.|| .++++++...  +
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~--~   84 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK--W   84 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTT--T
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCc--C
Confidence            799999999999999999999999999999999999987654321   123889999999999999 9999998754  4


Q ss_pred             ceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHH------hcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHH
Q 014486          144 IKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALA------RDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFK  217 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~------~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~  217 (423)
                      +++..++|+.........+... ++|+|+||++|...+      ....+.+.++++||+||||++.....+...+..+..
T Consensus        85 ~~v~~~~g~~~~~~~~~~~~~~-~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~~~~l~  163 (699)
T 4gl2_A           85 YRVIGLSGDTQLKISFPEVVKS-CDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLM  163 (699)
T ss_dssp             SCEEEEC----CCCCHHHHHHS-CSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHHHHHHH
T ss_pred             ceEEEEeCCcchhhHHHhhhcC-CCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHHHHHHH
Confidence            7999999987766554444444 699999999999877      444567789999999999988653333333332222


Q ss_pred             h-------------CCCCceEEEEeccCCcc-------H----HHHHHHhccCCceeeeccccc--cccccceEEEEEeC
Q 014486          218 M-------------TPHDKQVMMFSATLSKE-------I----RPVCKKFMQDPMEIYVDDEAK--LTLHGLVQHYIKLS  271 (423)
Q Consensus       218 ~-------------~~~~~~~v~~SAT~~~~-------~----~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~  271 (423)
                      .             ..+.++++++|||+...       .    ..+...+..............  .........+....
T Consensus       164 ~~~~~~~~~~~~~~~~~~~~il~lTATp~~~~~~~~~~~~~~i~~l~~~l~~~~i~~~~~~~~~l~~~~~~p~~~~~~~~  243 (699)
T 4gl2_A          164 QKLKNNRLKKENKPVIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCKKFAIAD  243 (699)
T ss_dssp             HHHHHHHHHC----CCCCCEEEEECSCCCCCSCCSHHHHHHHHHHHHHHHTCSCCCCCCTTHHHHHHHSCCCEEEEEEEC
T ss_pred             hhhcccccccccccCCCCCEEEEecccccccccccHHHHHHHHHHHHhhcCCCEEEeecCchHHHhhhcCCCceEEEEcc
Confidence            1             12567899999999863       1    111111111000000000000  00000000000000


Q ss_pred             --------------------------------------------------------------------------------
Q 014486          272 --------------------------------------------------------------------------------  271 (423)
Q Consensus       272 --------------------------------------------------------------------------------  271 (423)
                                                                                                      
T Consensus       244 ~~~~~~~~~~l~~l~~~i~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  323 (699)
T 4gl2_A          244 ATREDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKERVCAEHLRKYNEALQINDTIRMIDAY  323 (699)
T ss_dssp             -----CHHHHHHHHHHHHHHHHTCCCCSCSSSHHHHHHHHHHHHHHHHHTCTTTHHHHHHHHHHHHHHHHHHHSCHHHHH
T ss_pred             cccCChHHHHHHHHHHHHHHHhccCcchhccchHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             -------------------------------------------------------hHHHHHHHHHHHHh----hc-CCcE
Q 014486          272 -------------------------------------------------------ELEKNRKLNDLLDA----LD-FNQV  291 (423)
Q Consensus       272 -------------------------------------------------------~~~~~~~l~~ll~~----~~-~~~~  291 (423)
                                                                             ...|...+.+++..    .+ .+++
T Consensus       324 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~~L~~~~~~~~~~~~~  403 (699)
T 4gl2_A          324 THLETFYNEEKDKKFAVIEDDLKKPLKLDETDRFLMTLFFENNKMLKRLAENPEYENEKLTKLRNTIMEQYTRTEESARG  403 (699)
T ss_dssp             HHHHHHHHHHHHHHC------------CCHHHHHHHHHHHHHHHHHHHHHTCCC----CSSCSHHHHHHHHHHSSSCCCE
T ss_pred             HHHHHHHHHHHhhhccccccccccccccchhHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhcCCCCCcE
Confidence                                                                   00111112222322    13 6899


Q ss_pred             EEEEcChhhHHHHHHHHHhC------CCCeEEEcCC--------CCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCC
Q 014486          292 VIFVKSVSRAAELNKLLVEC------NFPSICIHSG--------MSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV  357 (423)
Q Consensus       292 ivf~~~~~~~~~l~~~L~~~------~~~~~~~~~~--------~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~  357 (423)
                      ||||++++.++.+++.|...      |+++..+||+        |++.+|.++++.|++|+.+|||||+++++|+|+|++
T Consensus       404 IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GIDip~v  483 (699)
T 4gl2_A          404 IIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKEC  483 (699)
T ss_dssp             EEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSCCCSC
T ss_pred             EEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCccccC
Confidence            99999999999999999987      8999999999        999999999999999999999999999999999999


Q ss_pred             CEEEEccCCCCcchhhhcccccCCCCCceEEEEEec
Q 014486          358 NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVS  393 (423)
Q Consensus       358 ~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~  393 (423)
                      ++||+|++|+|+..|+||+||+||.|  +.++++..
T Consensus       484 ~~VI~~d~p~s~~~~~Qr~GRArr~g--~~~~l~~~  517 (699)
T 4gl2_A          484 NIVIRYGLVTNEIAMVQARGRARADE--STYVLVAH  517 (699)
T ss_dssp             CCCEEESCCCCHHHHHHHHTTSCSSS--CEEEEEEE
T ss_pred             CEEEEeCCCCCHHHHHHHcCCCCCCC--ceEEEEEe
Confidence            99999999999999999999987765  34444444

>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=1.8e-43  Score=365.19  Aligned_cols=324  Identities=17%  Similarity=0.263  Sum_probs=248.7

Q ss_pred             HHHHh-CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           59 RAIVD-SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        59 ~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      +.+.+ +||. | ++|.++++.++.|+++++.+|||||||+ +.+|++..+...  ++++||++|+++|+.|+++.++++
T Consensus        48 ~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~~--~~~~lil~PtreLa~Q~~~~l~~l  122 (1054)
T 1gku_B           48 EFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLALK--GKRCYVIFPTSLLVIQAAETIRKY  122 (1054)
T ss_dssp             HHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHTT--SCCEEEEESCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhhc--CCeEEEEeccHHHHHHHHHHHHHH
Confidence            44444 6998 9 9999999999999999999999999998 777887766543  348999999999999999999999


Q ss_pred             hccCCCc----eEEEEEcCcchHHH---HHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHH
Q 014486          138 STYLPDI----KVAVFYGGVNIKIH---KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRR  210 (423)
Q Consensus       138 ~~~~~~~----~~~~~~~~~~~~~~---~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~  210 (423)
                      .... ++    ++..++|+.+...+   ...+.+  ++|+|+||++|..++..    +.++++||+||||++.+   +..
T Consensus       123 ~~~~-~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~--~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~---~~~  192 (1054)
T 1gku_B          123 AEKA-GVGTENLIGYYHGRIPKREKENFMQNLRN--FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILK---ASK  192 (1054)
T ss_dssp             HTTT-CCSGGGSEEECCSSCCSHHHHHHHHSGGG--CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHT---STH
T ss_pred             Hhhc-CCCccceEEEEeCCCChhhHHHHHhhccC--CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhh---ccc
Confidence            8765 66    89999999887664   233344  69999999999987664    66899999999999976   456


Q ss_pred             HHHHHHHhC-----------CCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHH
Q 014486          211 DVQEIFKMT-----------PHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKL  279 (423)
Q Consensus       211 ~~~~~~~~~-----------~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  279 (423)
                      .+..++..+           +...|++++|||++.. ......++..+..+.+.... .....+.+.+.   ...+...+
T Consensus       193 ~~~~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~~~-~~~~~i~~~~~---~~~k~~~L  267 (1054)
T 1gku_B          193 NVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGSSR-ITVRNVEDVAV---NDESISTL  267 (1054)
T ss_dssp             HHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSCCE-ECCCCEEEEEE---SCCCTTTT
T ss_pred             cHHHHHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccCcc-cCcCCceEEEe---chhHHHHH
Confidence            666666665           3467899999999887 43333333322222222211 12223333333   23455566


Q ss_pred             HHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEE----cCccccCCCCC
Q 014486          280 NDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVA----TDLVGRGIDIE  355 (423)
Q Consensus       280 ~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~----T~~~~~Gld~~  355 (423)
                      ..++... ++++||||++++.++.+++.|+.. +++..+||++.     .+++.|++|+.+||||    |+++++|+|+|
T Consensus       268 ~~ll~~~-~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~~-----~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip  340 (1054)
T 1gku_B          268 SSILEKL-GTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATKK-----GDYEKFVEGEIDHLIGTAHYYGTLVRGLDLP  340 (1054)
T ss_dssp             HHHHTTS-CSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSSS-----HHHHHHHHTSCSEEEEECC------CCSCCT
T ss_pred             HHHHhhc-CCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccHH-----HHHHHHHcCCCcEEEEecCCCCeeEeccccC
Confidence            6777665 478999999999999999999988 99999999983     6788999999999999    89999999999


Q ss_pred             CC-CEEEEccCC--------------------------------------------------------------------
Q 014486          356 RV-NIVINYDMP--------------------------------------------------------------------  366 (423)
Q Consensus       356 ~~-~~vi~~~~~--------------------------------------------------------------------  366 (423)
                      +| ++||+++.|                                                                    
T Consensus       341 ~VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  420 (1054)
T 1gku_B          341 ERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGE  420 (1054)
T ss_dssp             TTCCEEEEESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEEETTE
T ss_pred             CcccEEEEeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeEeecc
Confidence            96 999999999                                                                    


Q ss_pred             ---CCcchhhhcccccCCCCCce--EEEEEecCcccHHHHHHHHHHHhc
Q 014486          367 ---DSADTYLHRVGRAGRFGTKG--LAITFVSSASDSDILNQVSKFMFL  410 (423)
Q Consensus       367 ---~s~~~~~Q~~GR~~R~g~~~--~~~~~~~~~~~~~~~~~~~~~~~~  410 (423)
                         .++..|+||+||+||.|..|  .+++++.. ++...+..+++.++.
T Consensus       421 ~~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~-~d~~~~~~l~~~l~~  468 (1054)
T 1gku_B          421 VIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLE-DDSELLSAFIERAKL  468 (1054)
T ss_dssp             EEEECHHHHHHHHHTTCCEETTEECCEEEEEEC-SCHHHHHHHHHHHHT
T ss_pred             eecCcHHHHhhhhchhhhccCCCCceEEEEEEe-cCHHHHHHHHHHHhh
Confidence               78999999999999987765  36666654 467788888888874

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=100.00  E-value=2.6e-42  Score=353.39  Aligned_cols=311  Identities=19%  Similarity=0.233  Sum_probs=240.7

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      +| .|+++|.++++.++.++++++.+|||+|||++|++++......+   .++||++|+++|+.|+++.++++.   +++
T Consensus        37 ~f-~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~g---~~vlvl~PtraLa~Q~~~~l~~~~---~~~  109 (997)
T 4a4z_A           37 PF-ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNM---TKTIYTSPIKALSNQKFRDFKETF---DDV  109 (997)
T ss_dssp             SS-CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHTT---CEEEEEESCGGGHHHHHHHHHTTC-----C
T ss_pred             CC-CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhcC---CeEEEEeCCHHHHHHHHHHHHHHc---CCC
Confidence            45 58999999999999999999999999999999988887765433   389999999999999999888754   367


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCce
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQ  224 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~  224 (423)
                      ++..++|+....        +..+|+|+||++|...+......+.++++||+||||++.+ .++...+..+...+++..+
T Consensus       110 ~v~~l~G~~~~~--------~~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d-~~~g~~~e~ii~~l~~~v~  180 (997)
T 4a4z_A          110 NIGLITGDVQIN--------PDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVND-QDRGVVWEEVIIMLPQHVK  180 (997)
T ss_dssp             CEEEECSSCEEC--------TTSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCT-TCTTCCHHHHHHHSCTTCE
T ss_pred             eEEEEeCCCccC--------CCCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccc-cchHHHHHHHHHhcccCCC
Confidence            889999987543        3369999999999998887777788999999999999887 5677778888889999999


Q ss_pred             EEEEeccCCccHHHHHHHhc---cCCceeeeccccccccccce------E------------------------------
Q 014486          225 VMMFSATLSKEIRPVCKKFM---QDPMEIYVDDEAKLTLHGLV------Q------------------------------  265 (423)
Q Consensus       225 ~v~~SAT~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~------~------------------------------  265 (423)
                      ++++|||+++.. .+...+.   ..+..+........+.....      .                              
T Consensus       181 iIlLSAT~~n~~-ef~~~l~~~~~~~~~vi~~~~r~~pl~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  259 (997)
T 4a4z_A          181 FILLSATVPNTY-EFANWIGRTKQKNIYVISTPKRPVPLEINIWAKKELIPVINQNSEFLEANFRKHKEILNGESAKGAP  259 (997)
T ss_dssp             EEEEECCCTTHH-HHHHHHHHHHTCCEEEEECSSCSSCEEEEEEETTEEEEEECTTCCBCHHHHHHHHHHHC--------
T ss_pred             EEEEcCCCCChH-HHHHHHhcccCCceEEEecCCCCccceEEEecCCcchhcccchhhhhHHHHHHHHHHhhcccccccc
Confidence            999999998653 2322221   11211111110000000000      0                              


Q ss_pred             ------------------------------------------------------EEEEeChHHHHHHHHHHHHhhcCCcE
Q 014486          266 ------------------------------------------------------HYIKLSELEKNRKLNDLLDALDFNQV  291 (423)
Q Consensus       266 ------------------------------------------------------~~~~~~~~~~~~~l~~ll~~~~~~~~  291 (423)
                                                                            +........+...+...+......++
T Consensus       260 ~~~~~~~~~~~~~~~~~~~~~rg~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~l~~~~~~~~  339 (997)
T 4a4z_A          260 SKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNYLRKRELLPM  339 (997)
T ss_dssp             ---------------------------------------------------------CCCCTTHHHHHHHHHHHTTCCSE
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhHHHHHHHHHHhCCCCCE
Confidence                                                                  00000112234456667777777899


Q ss_pred             EEEEcChhhHHHHHHHHHhCCC---------------------------------------CeEEEcCCCCHHHHHHHHH
Q 014486          292 VIFVKSVSRAAELNKLLVECNF---------------------------------------PSICIHSGMSQEERLTRYK  332 (423)
Q Consensus       292 ivf~~~~~~~~~l~~~L~~~~~---------------------------------------~~~~~~~~~~~~~r~~~~~  332 (423)
                      ||||++++.++.++..|...++                                       .+..+|+++++.+|..+++
T Consensus       340 IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gi~~~H~gl~~~~R~~v~~  419 (997)
T 4a4z_A          340 VVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELIEI  419 (997)
T ss_dssp             EEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHH
T ss_pred             EEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcCeeeecCCCCHHHHHHHHH
Confidence            9999999999999999987665                                       4789999999999999999


Q ss_pred             hhhcCCccEEEEcCccccCCCCCCCCEEEEccCCC---------CcchhhhcccccCCCC--CceEEEEEec
Q 014486          333 GFKEGNKRILVATDLVGRGIDIERVNIVINYDMPD---------SADTYLHRVGRAGRFG--TKGLAITFVS  393 (423)
Q Consensus       333 ~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~---------s~~~~~Q~~GR~~R~g--~~~~~~~~~~  393 (423)
                      .|.+|.++|||||+++++|+|+|+ ..||+++.++         |+..|+||+|||||.|  ..|.+++++.
T Consensus       420 ~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~~~~G~vi~l~~  490 (997)
T 4a4z_A          420 LFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAY  490 (997)
T ss_dssp             HHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGCCTTTCSSEEEEEECC
T ss_pred             HHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHhcccccCCCCcceEEEEecC
Confidence            999999999999999999999999 6667666665         9999999999999998  4577777773

>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=1.3e-42  Score=345.03  Aligned_cols=318  Identities=22%  Similarity=0.239  Sum_probs=236.4

Q ss_pred             HHHHHHHHhCCCCCCChhhhhcccccccC------CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHH
Q 014486           55 PELLRAIVDSGFEHPSEVQHECIPQAILG------MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAY  128 (423)
Q Consensus        55 ~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~------~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~  128 (423)
                      +.+.+.+...+| .|+++|.++++.++.+      .++++++|||||||++++++++..+..+   .+++|++|+++|+.
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            444555667899 8999999999998875      5899999999999999999999876533   38999999999999


Q ss_pred             HHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc
Q 014486          129 QICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       129 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~  205 (423)
                      |+++.+.++.... ++++..++|+.......   ..+.++.++|+|+||+.+..     ...+.++++||+||+|++.. 
T Consensus       432 Q~~~~l~~~~~~~-gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l~lVVIDEaHr~g~-  504 (780)
T 1gm5_A          432 QHYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGV-  504 (780)
T ss_dssp             HHHHHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC---
T ss_pred             HHHHHHHHHhhhc-CceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-----hhhccCCceEEecccchhhH-
Confidence            9999999988665 78999999998765543   34556668999999987754     45678999999999998743 


Q ss_pred             CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHH-
Q 014486          206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLD-  284 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~-  284 (423)
                       ..+    ..+.......+++++|||+.+......  .........+... ......+....  .... +...+...+. 
T Consensus       505 -~qr----~~l~~~~~~~~vL~mSATp~p~tl~~~--~~g~~~~s~i~~~-p~~r~~i~~~~--~~~~-~~~~l~~~i~~  573 (780)
T 1gm5_A          505 -KQR----EALMNKGKMVDTLVMSATPIPRSMALA--FYGDLDVTVIDEM-PPGRKEVQTML--VPMD-RVNEVYEFVRQ  573 (780)
T ss_dssp             --------CCCCSSSSCCCEEEEESSCCCHHHHHH--HTCCSSCEEECCC-CSSCCCCEECC--CCSS-THHHHHHHHHH
T ss_pred             -HHH----HHHHHhCCCCCEEEEeCCCCHHHHHHH--HhCCcceeeeecc-CCCCcceEEEE--eccc-hHHHHHHHHHH
Confidence             111    112223346889999999877654432  2222111111111 11111111111  1121 2223333333 


Q ss_pred             hh-cCCcEEEEEcChh--------hHHHHHHHHHh---CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCC
Q 014486          285 AL-DFNQVVIFVKSVS--------RAAELNKLLVE---CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGI  352 (423)
Q Consensus       285 ~~-~~~~~ivf~~~~~--------~~~~l~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gl  352 (423)
                      .. .+++++|||+..+        .+..+++.|..   .++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+
T Consensus       574 ~l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GI  653 (780)
T 1gm5_A          574 EVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGI  653 (780)
T ss_dssp             HTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCS
T ss_pred             HHhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCCCccc
Confidence            22 4578999999664        46788888887   477889999999999999999999999999999999999999


Q ss_pred             CCCCCCEEEEccCCC-CcchhhhcccccCCCCCceEEEEEecC
Q 014486          353 DIERVNIVINYDMPD-SADTYLHRVGRAGRFGTKGLAITFVSS  394 (423)
Q Consensus       353 d~~~~~~vi~~~~~~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~  394 (423)
                      |+|++++||+++.|+ +...+.||+||+||.|++|.|++++++
T Consensus       654 DiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~  696 (780)
T 1gm5_A          654 DVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGD  696 (780)
T ss_dssp             CCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCS
T ss_pred             cCCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECC
Confidence            999999999999996 788999999999999999999999874

>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=7.7e-41  Score=347.48  Aligned_cols=323  Identities=18%  Similarity=0.171  Sum_probs=247.5

Q ss_pred             CCCCHHHHHHHHh-CCCCCCChhhhhccccccc----CC--ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           51 FLLKPELLRAIVD-SGFEHPSEVQHECIPQAIL----GM--DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        51 ~~l~~~~~~~l~~-~~~~~~~~~Q~~~i~~~~~----~~--~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      ++.++...+.+.+ .+| .+||+|.++++.++.    ++  ++++++|||+|||++++.+++.....+   .+++|++||
T Consensus       586 ~~~~~~~~~~~~~~f~~-~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~g---~~vlvlvPt  661 (1151)
T 2eyq_A          586 FKHDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNH---KQVAVLVPT  661 (1151)
T ss_dssp             CCCCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTT---CEEEEECSS
T ss_pred             CCCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHhC---CeEEEEech
Confidence            4566666666654 477 479999999999987    55  899999999999999988887765543   389999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHH---HHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcc
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH---KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECD  200 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h  200 (423)
                      ++|+.|+++.+.+..... ++++..+++..+....   ...+.++.++|+|+||+.+.     ....+.++++||+||+|
T Consensus       662 ~~La~Q~~~~~~~~~~~~-~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~-----~~~~~~~l~lvIiDEaH  735 (1151)
T 2eyq_A          662 TLLAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEH  735 (1151)
T ss_dssp             HHHHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGG
T ss_pred             HHHHHHHHHHHHHHhhcC-CCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh-----CCccccccceEEEechH
Confidence            999999999999876654 5788888876654443   33455666899999998663     34668899999999999


Q ss_pred             hhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHH
Q 014486          201 KMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLN  280 (423)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  280 (423)
                      ++..      .....++.++...+++++|||+.+............+..+...+   .....+..........   ....
T Consensus       736 ~~g~------~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~~---~~r~~i~~~~~~~~~~---~i~~  803 (1151)
T 2eyq_A          736 RFGV------RHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPP---ARRLAVKTFVREYDSM---VVRE  803 (1151)
T ss_dssp             GSCH------HHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEECCCCC---CBCBCEEEEEEECCHH---HHHH
T ss_pred             hcCh------HHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEEecCC---CCccccEEEEecCCHH---HHHH
Confidence            8632      22334444556789999999998776555444333322222111   1112222222222222   2222


Q ss_pred             HHHHhh-cCCcEEEEEcChhhHHHHHHHHHhC--CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCC
Q 014486          281 DLLDAL-DFNQVVIFVKSVSRAAELNKLLVEC--NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV  357 (423)
Q Consensus       281 ~ll~~~-~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~  357 (423)
                      .++... .+++++|||++++.++.+++.|++.  +..+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++
T Consensus       804 ~il~~l~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v  883 (1151)
T 2eyq_A          804 AILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTA  883 (1151)
T ss_dssp             HHHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTE
T ss_pred             HHHHHHhcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCC
Confidence            333332 4689999999999999999999987  7889999999999999999999999999999999999999999999


Q ss_pred             CEEEEccC-CCCcchhhhcccccCCCCCceEEEEEecCc
Q 014486          358 NIVINYDM-PDSADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       358 ~~vi~~~~-~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      ++||+++. ++++.+|.||+||+||.|+.|.|++++.+.
T Consensus       884 ~~VIi~~~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          884 NTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             EEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             cEEEEeCCCCCCHHHHHHHHhccCcCCCceEEEEEECCc
Confidence            99999988 578999999999999999999999998753

>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=5.1e-42  Score=333.01  Aligned_cols=310  Identities=16%  Similarity=0.182  Sum_probs=231.1

Q ss_pred             CCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceE
Q 014486           67 EHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKV  146 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~  146 (423)
                      ..|+|+|.++++.++.++++++++|||+|||++++.++...+...+  .++||++|+++|+.||.++++++... ++..+
T Consensus       112 ~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~--~~vlvl~P~~~L~~Q~~~~~~~~~~~-~~~~v  188 (510)
T 2oca_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYE--GKILIIVPTTALTTQMADDFVDYRLF-SHAMI  188 (510)
T ss_dssp             ECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHCS--SEEEEEESSHHHHHHHHHHHHHTTSS-CGGGE
T ss_pred             CCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCCC--CeEEEEECcHHHHHHHHHHHHHhhcC-Cccce
Confidence            3899999999999999999999999999999999888877654322  28999999999999999999887543 46788


Q ss_pred             EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEE
Q 014486          147 AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVM  226 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v  226 (423)
                      ..++++.....+    ..+..+|+|+||+.+..   .....+.++++||+||+|++..     ..+..+++.+.+..+++
T Consensus       189 ~~~~~~~~~~~~----~~~~~~I~i~T~~~l~~---~~~~~~~~~~liIiDE~H~~~~-----~~~~~il~~~~~~~~~l  256 (510)
T 2oca_A          189 KKIGGGASKDDK----YKNDAPVVVGTWQTVVK---QPKEWFSQFGMMMNDECHLATG-----KSISSIISGLNNCMFKF  256 (510)
T ss_dssp             EECGGGCCTTGG----GCTTCSEEEEEHHHHTT---SCGGGGGGEEEEEEETGGGCCH-----HHHHHHGGGCTTCCEEE
T ss_pred             EEEecCCccccc----cccCCcEEEEeHHHHhh---chhhhhhcCCEEEEECCcCCCc-----ccHHHHHHhcccCcEEE
Confidence            888888665443    23346999999997653   2334567899999999998864     45667778887888999


Q ss_pred             EEeccCCccHHHHHH--HhccCCceeeeccc-----cccccccceEEEEEeCh---------------------HHHHHH
Q 014486          227 MFSATLSKEIRPVCK--KFMQDPMEIYVDDE-----AKLTLHGLVQHYIKLSE---------------------LEKNRK  278 (423)
Q Consensus       227 ~~SAT~~~~~~~~~~--~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~---------------------~~~~~~  278 (423)
                      ++|||+++.......  .++. +..+.....     ...............+.                     ..+...
T Consensus       257 ~lSATp~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  335 (510)
T 2oca_A          257 GLSGSLRDGKANIMQYVGMFG-EIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKW  335 (510)
T ss_dssp             EEESCGGGCSSCHHHHHHHHC-SEECCCCCC---------CCEEEEEEEECCHHHHHHHTTCCHHHHHHHHHTCHHHHHH
T ss_pred             EEEeCCCCCcccHHHhHHhhC-CeEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccchHHHHHHHhccHHHHHH
Confidence            999999766422111  1111 211111111     00000011111111111                     123334


Q ss_pred             HHHHHHhh---cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEc-CccccCCCC
Q 014486          279 LNDLLDAL---DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVAT-DLVGRGIDI  354 (423)
Q Consensus       279 l~~ll~~~---~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T-~~~~~Gld~  354 (423)
                      +.+++...   ...++|||++ .+++..+++.|.+.+.++..+||+++..+|..+++.|++|+.+||||| +++++|+|+
T Consensus       336 l~~~l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDi  414 (510)
T 2oca_A          336 IAKLAIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISV  414 (510)
T ss_dssp             HHHHHHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCC
T ss_pred             HHHHHHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhccccc
Confidence            45555444   3344555555 899999999999988899999999999999999999999999999999 999999999


Q ss_pred             CCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEec
Q 014486          355 ERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVS  393 (423)
Q Consensus       355 ~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~  393 (423)
                      |++++||++++|+++..|.|++||+||.|+.+..+++++
T Consensus       415 p~v~~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          415 KNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             CSEEEEEESSCCCSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             ccCcEEEEeCCCCCHHHHHHHHhcccccCCCCceEEEEE
Confidence            999999999999999999999999999998775555554

>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=1.2e-40  Score=323.59  Aligned_cols=321  Identities=17%  Similarity=0.204  Sum_probs=226.7

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      |. +|+++|..+++.++.|+  +..++||+|||++|++|++.....+   +.++|++||++||.|.++.+..+.... ++
T Consensus        72 g~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~g---~~vlVltPTreLA~Q~~e~~~~l~~~l-gl  144 (853)
T 2fsf_A           72 GM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALTG---KGVHVVTVNDYLAQRDAENNRPLFEFL-GL  144 (853)
T ss_dssp             SC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTTS---SCCEEEESSHHHHHHHHHHHHHHHHHT-TC
T ss_pred             CC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHcC---CcEEEEcCCHHHHHHHHHHHHHHHHhc-CC
Confidence            54 89999999999999987  9999999999999999998654432   378999999999999999999998887 89


Q ss_pred             eEEEEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcCC------CCCCCccEEEEcCcchhhccC-----------
Q 014486          145 KVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDKD------LSLKNVRHFILDECDKMLESL-----------  206 (423)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~~------~~~~~~~~vVvDE~h~~~~~~-----------  206 (423)
                      ++..++||.+......  ..+ ++|+|+||+.| +++++.+.      ..+.+++++|+||||+++.+.           
T Consensus       145 ~v~~i~GG~~~~~r~~--~~~-~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~tpLIiSg~~  221 (853)
T 2fsf_A          145 TVGINLPGMPAPAKRE--AYA-ADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTPLIISGPA  221 (853)
T ss_dssp             CEEECCTTCCHHHHHH--HHH-SSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTCEEEEEEC-
T ss_pred             eEEEEeCCCCHHHHHH--hcC-CCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCcccccccCCC
Confidence            9999999987653332  223 59999999999 77776543      456889999999999998422           


Q ss_pred             ----CcHHHHHHHHHhCCC--------------------CceEE------------------------EEeccCCccHHH
Q 014486          207 ----DMRRDVQEIFKMTPH--------------------DKQVM------------------------MFSATLSKEIRP  238 (423)
Q Consensus       207 ----~~~~~~~~~~~~~~~--------------------~~~~v------------------------~~SAT~~~~~~~  238 (423)
                          ++...+..+...+++                    .+|+.                        ++|||.+.....
T Consensus       222 ~~~~~~y~~i~~iv~~L~~~~~~~~~~~~~~~dy~vdek~rqv~lte~g~~~~e~~l~~~~l~~~~~~Lfsat~~~~~~~  301 (853)
T 2fsf_A          222 EDSSEMYKRVNKIIPHLIRQEKEDSETFQGEGHFSVDEKSRQVNLTERGLVLIEELLVKEGIMDEGESLYSPANIMLMHH  301 (853)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccchhHHHHHHHHHHhchhhhccccccccccccceeccccceEEEcHHHHHHHHHHHHhCCcccccccccCcccchHHHH
Confidence                245566666666653                    34443                        788886532111


Q ss_pred             H---HH--Hhc---------------------------------cCC----ceeeecccc--------------------
Q 014486          239 V---CK--KFM---------------------------------QDP----MEIYVDDEA--------------------  256 (423)
Q Consensus       239 ~---~~--~~~---------------------------------~~~----~~~~~~~~~--------------------  256 (423)
                      +   ++  .++                                 +.+    ..+.+..+.                    
T Consensus       302 i~~al~A~~l~~~d~dYiV~d~~vviVde~tgR~m~grr~sdGLhQaieake~v~I~~e~~tla~It~qnyfr~Y~kl~G  381 (853)
T 2fsf_A          302 VTAALRAHALFTRDVDYIVKDGEVIIVDEHTGRTMQGRRWSDGLHQAVEAKEGVQIQNENQTLASITFQNYFRLYEKLAG  381 (853)
T ss_dssp             -------------------------------------------------------CCCCCEEEEEEEHHHHHTTSSEEEE
T ss_pred             HHHHHHHHHHhhcCccceeecCcEEEEecccCcccCCCccchhhhHHHHhcccceecccccccceeehHHHHhhhhhhhc
Confidence            1   00  000                                 000    001110000                    


Q ss_pred             --------------------------ccccccceEEEEEeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHH
Q 014486          257 --------------------------KLTLHGLVQHYIKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLL  308 (423)
Q Consensus       257 --------------------------~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L  308 (423)
                                                ......-....+......|...+.+.+...  .+.++||||++++.++.+++.|
T Consensus       382 mTGTa~te~~ef~~iY~l~vv~IPtn~p~~R~d~~d~v~~~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L  461 (853)
T 2fsf_A          382 MTGTADTEAFEFSSIYKLDTVVVPTNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNEL  461 (853)
T ss_dssp             EECTTCCCHHHHHHHHCCEEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHH
T ss_pred             CCCCchhHHHHHHHHhCCcEEEcCCCCCceeecCCcEEEeCHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHH
Confidence                                      000000011234567778888888877543  4678999999999999999999


Q ss_pred             HhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCC-------------------------------
Q 014486          309 VECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERV-------------------------------  357 (423)
Q Consensus       309 ~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~-------------------------------  357 (423)
                      +..|+++..+|++....++..+..+|+.|  .|+|||++++||+|++..                               
T Consensus       462 ~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  539 (853)
T 2fsf_A          462 TKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDA  539 (853)
T ss_dssp             HHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHH
T ss_pred             HHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecccccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhH
Confidence            99999999999999888888888888877  699999999999999874                               


Q ss_pred             ------CEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          358 ------NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       358 ------~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                            .+||+++.|.|...|.||+||+||.|.+|.++.|++..++
T Consensus       540 V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls~eD~  585 (853)
T 2fsf_A          540 VLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLSMEDA  585 (853)
T ss_dssp             HHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSG
T ss_pred             HHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEecccHH
Confidence                  5999999999999999999999999999999999987554

>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=8.5e-40  Score=317.91  Aligned_cols=322  Identities=21%  Similarity=0.241  Sum_probs=250.8

Q ss_pred             CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           64 SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        64 ~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      .|+ +|+++|..+++.++.|+  |..++||+|||++|++|++.....+   ..++|++||+.||.|.++++..+.... +
T Consensus       108 lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~g---~~v~VvTpTreLA~Qdae~m~~l~~~l-G  180 (922)
T 1nkt_A          108 LDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALAG---NGVHIVTVNDYLAKRDSEWMGRVHRFL-G  180 (922)
T ss_dssp             HSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTTT---SCEEEEESSHHHHHHHHHHHHHHHHHT-T
T ss_pred             cCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHhC---CCeEEEeCCHHHHHHHHHHHHHHHhhc-C
Confidence            478 99999999999999987  9999999999999999997654433   279999999999999999999998887 8


Q ss_pred             ceEEEEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcC------CCCCCCccEEEEcCcchhhcc-----------
Q 014486          144 IKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDK------DLSLKNVRHFILDECDKMLES-----------  205 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~------~~~~~~~~~vVvDE~h~~~~~-----------  205 (423)
                      +++.++.||.+........  + ++|+|+||+.| ++++..+      ...+..+.++|+||||+++.+           
T Consensus       181 Lsv~~i~gg~~~~~r~~~y--~-~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLiiSg~  257 (922)
T 1nkt_A          181 LQVGVILATMTPDERRVAY--N-ADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGP  257 (922)
T ss_dssp             CCEEECCTTCCHHHHHHHH--H-SSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEEEEEE
T ss_pred             CeEEEEeCCCCHHHHHHhc--C-CCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccceeecCC
Confidence            9999999998765443332  3 59999999999 7777654      355678999999999999842           


Q ss_pred             ----CCcHHHHHHHHHhCC---------CCceEE-----------------EEeccCCccHHH---HHHH--hcc-CCce
Q 014486          206 ----LDMRRDVQEIFKMTP---------HDKQVM-----------------MFSATLSKEIRP---VCKK--FMQ-DPME  249 (423)
Q Consensus       206 ----~~~~~~~~~~~~~~~---------~~~~~v-----------------~~SAT~~~~~~~---~~~~--~~~-~~~~  249 (423)
                          .++...+..+...++         +.+|+.                 ++|||.+.....   .++.  ++. +..+
T Consensus       258 ~~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l~~~i~~aL~A~~l~~~d~dY  337 (922)
T 1nkt_A          258 ADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLNNALKAKELFSRDKDY  337 (922)
T ss_dssp             CCCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCHHHHHHHHHHHHHHCCBTTTE
T ss_pred             CCcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchhHHHHHHHHHHHHHHhhcccce
Confidence                247788899999997         678888                 889998753222   1111  111 1100


Q ss_pred             ee-------ec-----------------------------ccc-------------------------------------
Q 014486          250 IY-------VD-----------------------------DEA-------------------------------------  256 (423)
Q Consensus       250 ~~-------~~-----------------------------~~~-------------------------------------  256 (423)
                      +.       ++                             .+.                                     
T Consensus       338 iV~dg~vviVDe~TGR~m~grr~sdGLHQaieaKe~V~I~~e~~TlatIt~Qnyfr~Y~kL~GMTGTa~te~~Ef~~iY~  417 (922)
T 1nkt_A          338 IVRDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAAELHEIYK  417 (922)
T ss_dssp             EECSSCEEEBCSSSCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEECHHHHHTTSSEEEEEESCCGGGHHHHHHHHC
T ss_pred             eeecCceEEEecccCcccCCccccchhhHHHhccccccccccccccceeehHHHHHhhhhhhccccCchhHHHHHHHHhC
Confidence            00       00                             000                                     


Q ss_pred             --------ccccccc-eEEEEEeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHH
Q 014486          257 --------KLTLHGL-VQHYIKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQE  325 (423)
Q Consensus       257 --------~~~~~~~-~~~~~~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~  325 (423)
                              ..+.... ....+......|...+...+...  .+.++||||++++.++.+++.|+..|+++..+|++....
T Consensus       418 l~vv~IPtn~p~~R~d~~d~v~~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~r  497 (922)
T 1nkt_A          418 LGVVSIPTNMPMIREDQSDLIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQ  497 (922)
T ss_dssp             CEEEECCCSSCCCCEECCCEEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHH
T ss_pred             CCeEEeCCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHH
Confidence                    0000000 01234556677887777777543  457899999999999999999999999999999998877


Q ss_pred             HHHHHHHhhhcCCccEEEEcCccccCCCCCCC------------------------------------------------
Q 014486          326 ERLTRYKGFKEGNKRILVATDLVGRGIDIERV------------------------------------------------  357 (423)
Q Consensus       326 ~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~------------------------------------------------  357 (423)
                      ++..+.+.|+.|  .|+|||++++||+|++..                                                
T Consensus       498 Ea~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~  575 (922)
T 1nkt_A          498 EATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVI  575 (922)
T ss_dssp             HHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHH
T ss_pred             HHHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHH
Confidence            777777777776  699999999999999975                                                


Q ss_pred             ----CEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          358 ----NIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       358 ----~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                          .+||+++.|.|...|.|++||+||.|.+|.++.|++..++
T Consensus       576 ~~GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD~  619 (922)
T 1nkt_A          576 EAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDE  619 (922)
T ss_dssp             HTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             hcCCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhHH
Confidence                4999999999999999999999999999999999987544

>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=9.4e-41  Score=356.07  Aligned_cols=338  Identities=17%  Similarity=0.186  Sum_probs=246.8

Q ss_pred             CCHHHHHHHHhCCCCCCChhhhhccccccc-CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHH
Q 014486           53 LKPELLRAIVDSGFEHPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQIC  131 (423)
Q Consensus        53 l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~-~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  131 (423)
                      +.+...+++...+|..++|+|.++++.++. +++++++||||||||+++.++++..+...+++ +++|++|+++|+.|.+
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~~~-kavyi~P~raLa~q~~  989 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEG-RCVYITPMEALAEQVY  989 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCTTC-CEEEECSCHHHHHHHH
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCCCC-EEEEEcChHHHHHHHH
Confidence            445677888888999999999999999976 56799999999999999999999887654433 8999999999999999


Q ss_pred             HHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCC--CCCCccEEEEcCcchhhccCCcH
Q 014486          132 HEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDL--SLKNVRHFILDECDKMLESLDMR  209 (423)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~--~~~~~~~vVvDE~h~~~~~~~~~  209 (423)
                      +.+.+......++++..++|+......  ...+  ++|+||||+++..++++...  .+.++++||+||+|.+.+.  ..
T Consensus       990 ~~~~~~f~~~~g~~V~~ltGd~~~~~~--~~~~--~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~--rg 1063 (1724)
T 4f92_B          990 MDWYEKFQDRLNKKVVLLTGETSTDLK--LLGK--GNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGE--NG 1063 (1724)
T ss_dssp             HHHHHHHTTTSCCCEEECCSCHHHHHH--HHHH--CSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGST--TH
T ss_pred             HHHHHHhchhcCCEEEEEECCCCcchh--hcCC--CCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCC--CC
Confidence            998765443337899999987654322  2223  59999999999887765432  3678999999999988752  33


Q ss_pred             HH-------HHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeC---hHHHH---
Q 014486          210 RD-------VQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLS---ELEKN---  276 (423)
Q Consensus       210 ~~-------~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~---  276 (423)
                      ..       +..+....++..|+|++|||+++. ..+.+.....+..+........+ ..+..+.....   ...+.   
T Consensus      1064 ~~le~il~rl~~i~~~~~~~~riI~lSATl~N~-~dla~WL~~~~~~~~~~~~~~RP-vpL~~~i~~~~~~~~~~~~~~~ 1141 (1724)
T 4f92_B         1064 PVLEVICSRMRYISSQIERPIRIVALSSSLSNA-KDVAHWLGCSATSTFNFHPNVRP-VPLELHIQGFNISHTQTRLLSM 1141 (1724)
T ss_dssp             HHHHHHHHHHHHHHHTTSSCCEEEEEESCBTTH-HHHHHHHTCCSTTEEECCGGGCS-SCEEEEEEEECCCSHHHHHHTT
T ss_pred             ccHHHHHHHHHHHHhhcCCCceEEEEeCCCCCH-HHHHHHhCCCCCCeEEeCCCCCC-CCeEEEEEeccCCCchhhhhhh
Confidence            32       333344567789999999999863 44555444333322222211111 11222222221   11111   


Q ss_pred             -HHHHHHH-HhhcCCcEEEEEcChhhHHHHHHHHHhC----------------------------------CCCeEEEcC
Q 014486          277 -RKLNDLL-DALDFNQVVIFVKSVSRAAELNKLLVEC----------------------------------NFPSICIHS  320 (423)
Q Consensus       277 -~~l~~ll-~~~~~~~~ivf~~~~~~~~~l~~~L~~~----------------------------------~~~~~~~~~  320 (423)
                       ..+...+ ...+.+++||||+++..+..++..|...                                  ...+..+|+
T Consensus      1142 ~~~~~~~i~~~~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHa 1221 (1724)
T 4f92_B         1142 AKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHE 1221 (1724)
T ss_dssp             HHHHHHHHHHHCSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECT
T ss_pred             cchHHHHHHHhcCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECC
Confidence             1222223 3345689999999999988877665321                                  235788999


Q ss_pred             CCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE----c------cCCCCcchhhhcccccCCCCC--ceEE
Q 014486          321 GMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN----Y------DMPDSADTYLHRVGRAGRFGT--KGLA  388 (423)
Q Consensus       321 ~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~----~------~~~~s~~~~~Q~~GR~~R~g~--~~~~  388 (423)
                      ++++.+|..+.+.|++|.++|||||+++++|+|+|..++||.    |      ..|.++.+|.||+|||||.|.  .|.+
T Consensus      1222 gL~~~~R~~VE~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~a 1301 (1724)
T 4f92_B         1222 GLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRC 1301 (1724)
T ss_dssp             TSCHHHHHHHHHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEE
T ss_pred             CCCHHHHHHHHHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEE
Confidence            999999999999999999999999999999999999888883    2      235688999999999999986  6889


Q ss_pred             EEEecCcccHH
Q 014486          389 ITFVSSASDSD  399 (423)
Q Consensus       389 ~~~~~~~~~~~  399 (423)
                      ++++.+.....
T Consensus      1302 vll~~~~~~~~ 1312 (1724)
T 4f92_B         1302 VIMCQGSKKDF 1312 (1724)
T ss_dssp             EEEEEGGGHHH
T ss_pred             EEEecchHHHH
Confidence            98887654443

>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=2.5e-41  Score=324.98  Aligned_cols=296  Identities=20%  Similarity=0.258  Sum_probs=221.2

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCce-E
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIK-V  146 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~-~  146 (423)
                      .|+|+|.++++.++.++++++++|||+|||++++.++...      +.++||++|+++|+.||.+++.++     +++ +
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~------~~~~Lvl~P~~~L~~Q~~~~~~~~-----~~~~v  161 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF-----GEEYV  161 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH------CSCEEEEESSHHHHHHHHHHGGGG-----CGGGE
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEECCHHHHHHHHHHHHhC-----CCcce
Confidence            7999999999999999999999999999999999888765      228999999999999999998884     567 8


Q ss_pred             EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEE
Q 014486          147 AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVM  226 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v  226 (423)
                      ..++|+...          ..+|+|+||+.+.......   ..++++||+||+|.+.+ ..+..    +...+ +..+++
T Consensus       162 ~~~~g~~~~----------~~~Ivv~T~~~l~~~~~~~---~~~~~liIvDEaH~~~~-~~~~~----~~~~~-~~~~~l  222 (472)
T 2fwr_A          162 GEFSGRIKE----------LKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPA-ESYVQ----IAQMS-IAPFRL  222 (472)
T ss_dssp             EEBSSSCBC----------CCSEEEEEHHHHHHTHHHH---TTTCSEEEEETGGGTTS-TTTHH----HHHTC-CCSEEE
T ss_pred             EEECCCcCC----------cCCEEEEEcHHHHHHHHHh---cCCCCEEEEECCcCCCC-hHHHH----HHHhc-CCCeEE
Confidence            888887642          2599999999998765421   24589999999999987 45543    44444 357899


Q ss_pred             EEeccCCcc-------------------HHHHHHHhccCCcee--eeccccc--cc---------------------ccc
Q 014486          227 MFSATLSKE-------------------IRPVCKKFMQDPMEI--YVDDEAK--LT---------------------LHG  262 (423)
Q Consensus       227 ~~SAT~~~~-------------------~~~~~~~~~~~~~~~--~~~~~~~--~~---------------------~~~  262 (423)
                      ++||||.+.                   ...+...++..+...  .+.....  ..                     ...
T Consensus       223 ~lSATp~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  302 (472)
T 2fwr_A          223 GLTATFEREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAED  302 (472)
T ss_dssp             EEESCCCCTTSGGGSHHHHTCCEEEECCHHHHTSCCCCSEEECCEEECCCHHHHHHTTTTTHHHHSCSSSCCCTTTCCSS
T ss_pred             EEecCccCCCCHHHHHHHHhCCeEeecCHHHHhcCcCCCeEEEEEEcCCCHHHHHHHHHHHHHHHHHHHhcCccccchhh
Confidence            999999732                   222211111111110  0000000  00                     000


Q ss_pred             ceEE---------------------EEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCC
Q 014486          263 LVQH---------------------YIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSG  321 (423)
Q Consensus       263 ~~~~---------------------~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~  321 (423)
                      +...                     ........|...+.+++....++++||||++.+.++.+++.|.     +..+||+
T Consensus       303 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~  377 (472)
T 2fwr_A          303 FNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHR  377 (472)
T ss_dssp             STTTTTTTCCSSSSSTTTHHHHHHHHHHHSCSHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSS
T ss_pred             HHHHHHHhccCHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHhC-----cceeeCC
Confidence            0000                     0001223456778888888788999999999999999999884     4568999


Q ss_pred             CCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCc-e--EEEEEecCcccH
Q 014486          322 MSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTK-G--LAITFVSSASDS  398 (423)
Q Consensus       322 ~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~-~--~~~~~~~~~~~~  398 (423)
                      ++..+|.++++.|++|+.+|||+|+++++|+|+|++++||++++|+++..|.||+||+||.|+. +  .++.+++....+
T Consensus       378 ~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~t~e  457 (472)
T 2fwr_A          378 TSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRGTGE  457 (472)
T ss_dssp             SCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECSCC-
T ss_pred             CCHHHHHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCCCch
Confidence            9999999999999999999999999999999999999999999999999999999999999854 3  444456544333

>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=1.6e-40  Score=354.20  Aligned_cols=331  Identities=23%  Similarity=0.323  Sum_probs=239.3

Q ss_pred             CCCCCChhhhhccccccc-CCceEEEccCCCcchhHHHHHHhhccCC--------CCCCeEEEEEecChHHHHHHHHHHH
Q 014486           65 GFEHPSEVQHECIPQAIL-GMDVICQAKSGMGKTAVFVLSTLQQTEP--------NPGQVTALVLCHTRELAYQICHEFE  135 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~-~~~~ii~~~tGsGKT~~~~~~~~~~~~~--------~~~~~~~lil~P~~~L~~q~~~~~~  135 (423)
                      ||++++++|.++++.++. ++|++++||||||||+++.++++..+..        ...+.++||++|+++|+.|.++.++
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            789999999999998875 7889999999999999999999976542        1234589999999999999999998


Q ss_pred             HHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCC--CCCCccEEEEcCcchhhccCCcHHHHH
Q 014486          136 RFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDL--SLKNVRHFILDECDKMLESLDMRRDVQ  213 (423)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~--~~~~~~~vVvDE~h~~~~~~~~~~~~~  213 (423)
                      +..... ++++..++|+.......  . . .++|+|+||+++..++++...  .+.++++||+||+|.+.+  +....+.
T Consensus       156 ~~~~~~-gi~V~~~tGd~~~~~~~--~-~-~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d--~RG~~lE  228 (1724)
T 4f92_B          156 KRLATY-GITVAELTGDHQLCKEE--I-S-ATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD--DRGPVLE  228 (1724)
T ss_dssp             HHHTTT-TCCEEECCSSCSSCCTT--G-G-GCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGS--TTHHHHH
T ss_pred             HHHhhC-CCEEEEEECCCCCCccc--c-C-CCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCC--ccHHHHH
Confidence            877665 88999999987654321  1 1 269999999998776665432  267899999999998865  2332222


Q ss_pred             -------HHHHhCCCCceEEEEeccCCccHHHHHHHhccCCc-e-eeeccccccccccceEEEEEeCh---HHHHHH---
Q 014486          214 -------EIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPM-E-IYVDDEAKLTLHGLVQHYIKLSE---LEKNRK---  278 (423)
Q Consensus       214 -------~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~---  278 (423)
                             +.....++..|+|++|||+|+. ..+.+.....+. . ..+.... . +..+.+.+.....   ..+...   
T Consensus       229 ~~l~rl~~~~~~~~~~~riI~LSATl~N~-~dvA~wL~~~~~~~~~~~~~~~-R-PvpL~~~~~~~~~~~~~~~~~~~~~  305 (1724)
T 4f92_B          229 ALVARAIRNIEMTQEDVRLIGLSATLPNY-EDVATFLRVDPAKGLFYFDNSF-R-PVPLEQTYVGITEKKAIKRFQIMNE  305 (1724)
T ss_dssp             HHHHHHHHHHHHHTCCCEEEEEECSCTTH-HHHHHHTTCCHHHHEEECCGGG-C-SSCEEEECCEECCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCcEEEEecccCCH-HHHHHHhCCCCCCCeEEECCCC-c-cCccEEEEeccCCcchhhhhHHHHH
Confidence                   2234457788999999999863 344443322221 1 1111111 1 1112222222221   112122   


Q ss_pred             -HHHHH-HhhcCCcEEEEEcChhhHHHHHHHHHhC-------------------------------------CCCeEEEc
Q 014486          279 -LNDLL-DALDFNQVVIFVKSVSRAAELNKLLVEC-------------------------------------NFPSICIH  319 (423)
Q Consensus       279 -l~~ll-~~~~~~~~ivf~~~~~~~~~l~~~L~~~-------------------------------------~~~~~~~~  319 (423)
                       +...+ +...++++||||++++.+..+++.|.+.                                     ...+..+|
T Consensus       306 ~~~~~v~~~~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HH  385 (1724)
T 4f92_B          306 IVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHH  385 (1724)
T ss_dssp             HHHHHHTTCCSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEEC
T ss_pred             HHHHHHHHHhcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEc
Confidence             22222 2235678999999999888877776531                                     23477899


Q ss_pred             CCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE----ccC------CCCcchhhhcccccCCCCC--ceE
Q 014486          320 SGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN----YDM------PDSADTYLHRVGRAGRFGT--KGL  387 (423)
Q Consensus       320 ~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~----~~~------~~s~~~~~Q~~GR~~R~g~--~~~  387 (423)
                      ++|++.+|..+.+.|++|.++|||||+++++|+|+|..++||.    |++      |.++.+|.||+|||||.|.  .|.
T Consensus       386 agL~~~~R~~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~  465 (1724)
T 4f92_B          386 AGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGE  465 (1724)
T ss_dssp             SSSCTHHHHHHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEE
T ss_pred             CCCCHHHHHHHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccE
Confidence            9999999999999999999999999999999999999998885    443      4588999999999999874  689


Q ss_pred             EEEEecCcccHHHHHHHH
Q 014486          388 AITFVSSASDSDILNQVS  405 (423)
Q Consensus       388 ~~~~~~~~~~~~~~~~~~  405 (423)
                      ++++.+..+...+...+.
T Consensus       466 ~ii~~~~~~~~~~~~ll~  483 (1724)
T 4f92_B          466 GILITSHGELQYYLSLLN  483 (1724)
T ss_dssp             EEEEEESTTCCHHHHHTT
T ss_pred             EEEEecchhHHHHHHHHc
Confidence            998888766555554443

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=100.00  E-value=2.9e-41  Score=329.67  Aligned_cols=316  Identities=15%  Similarity=0.114  Sum_probs=228.1

Q ss_pred             CCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHH
Q 014486           51 FLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        51 ~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~  130 (423)
                      +++++.+.++|... ...++|+|+.+++.++.++++++.+|||||||++|++|++..+...  ++++||++|+++||.|+
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~--~~~vLvl~PtreLa~Qi  231 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKR--RLRTLILAPTRVVAAEM  231 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHH
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhC--CCeEEEEcChHHHHHHH
Confidence            44566655555543 4678999998999999999999999999999999999999776543  34899999999999999


Q ss_pred             HHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHH
Q 014486          131 CHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRR  210 (423)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~  210 (423)
                      .+.++       +..+. +.+.. ..    ........+.++|.+.+...+... ..+.++++||+||||++ + ..+..
T Consensus       232 ~~~l~-------~~~v~-~~~~~-l~----~~~tp~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~-~~~~~  295 (618)
T 2whx_A          232 EEALR-------GLPIR-YQTPA-VK----SDHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-D-PCSVA  295 (618)
T ss_dssp             HHHTT-------TSCEE-ECCTT-SS----CCCCSSSCEEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-S-HHHHH
T ss_pred             HHHhc-------CCcee-Eeccc-ce----eccCCCceEEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-C-ccHHH
Confidence            97775       22333 22211 00    011222367788888887655443 45788999999999998 2 46666


Q ss_pred             HHHHHHHhCC-CCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCC
Q 014486          211 DVQEIFKMTP-HDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFN  289 (423)
Q Consensus       211 ~~~~~~~~~~-~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~  289 (423)
                      .+..+...++ +..|++++|||++.....+..   ..+..+.+....              +. .+...+...+.. ..+
T Consensus       296 ~~~~i~~~l~~~~~q~il~SAT~~~~~~~~~~---~~~~~~~v~~~~--------------~~-~~~~~ll~~l~~-~~~  356 (618)
T 2whx_A          296 ARGYISTRVEMGEAAAIFMTATPPGSTDPFPQ---SNSPIEDIEREI--------------PE-RSWNTGFDWITD-YQG  356 (618)
T ss_dssp             HHHHHHHHHHHTSCEEEEECSSCTTCCCSSCC---CSSCEEEEECCC--------------CS-SCCSSSCHHHHH-CCS
T ss_pred             HHHHHHHHhcccCccEEEEECCCchhhhhhhc---cCCceeeecccC--------------CH-HHHHHHHHHHHh-CCC
Confidence            6666666654 678999999999876442211   122222221110              00 000111222222 357


Q ss_pred             cEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEE---------
Q 014486          290 QVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIV---------  360 (423)
Q Consensus       290 ~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~v---------  360 (423)
                      ++||||++++.++.+++.|+..++++..+|+.    +|.++++.|++|+.+|||||+++++|+|++ +++|         
T Consensus       357 ~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P  431 (618)
T 2whx_A          357 KTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKP  431 (618)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEE
T ss_pred             CEEEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcceecc
Confidence            99999999999999999999999999999984    688899999999999999999999999997 8888         


Q ss_pred             -----------EEccCCCCcchhhhcccccCCCCC-ceEEEEEec--CcccHHHHHHHHHHHh
Q 014486          361 -----------INYDMPDSADTYLHRVGRAGRFGT-KGLAITFVS--SASDSDILNQVSKFMF  409 (423)
Q Consensus       361 -----------i~~~~~~s~~~~~Q~~GR~~R~g~-~~~~~~~~~--~~~~~~~~~~~~~~~~  409 (423)
                                 |+++.|.+..+|+||+||+||.|. +|.+++|++  ...+...+..+++.+.
T Consensus       432 ~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~~le~~i~  494 (618)
T 2whx_A          432 VILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKML  494 (618)
T ss_dssp             EEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHHHHHHHH
T ss_pred             eecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHHHHHHHhHhc
Confidence                       677779999999999999999965 899999986  2455566677777654

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=100.00  E-value=1.7e-40  Score=315.29  Aligned_cols=287  Identities=15%  Similarity=0.118  Sum_probs=209.7

Q ss_pred             CCCCCChhhhhcccccccCCce-EEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           65 GFEHPSEVQHECIPQAILGMDV-ICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~-ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      |+.+|+|+|+ +++.++.+++. ++++|||||||++|+++++......+  +++||++|+++|+.|+++.+.       +
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~--~~~lvl~Ptr~La~Q~~~~l~-------g   70 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLRR--LRTLILAPTRVVAAEMEEALR-------G   70 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHTT--CCEEEEESSHHHHHHHHHHTT-------T
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhcC--CcEEEECCCHHHHHHHHHHhc-------C
Confidence            6778999986 79999998886 99999999999999999987654332  489999999999999998774       3


Q ss_pred             ceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHH-HhCCCC
Q 014486          144 IKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIF-KMTPHD  222 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~-~~~~~~  222 (423)
                      ..+.........      .......|.++|++.+.+.+... ..+.++++||+||||++.  ..+......+. ....+.
T Consensus        71 ~~v~~~~~~~~~------~~~~~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~~--~~~~~~~~~~~~~~~~~~  141 (451)
T 2jlq_A           71 LPIRYQTPAVKS------DHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFTD--PCSVAARGYISTRVEMGE  141 (451)
T ss_dssp             SCEEECCTTCSC------CCCSSCCEEEEEHHHHHHHHHHC-SCCCCCSEEEEETTTCCS--HHHHHHHHHHHHHHHTTS
T ss_pred             ceeeeeeccccc------cCCCCceEEEEChHHHHHHhhCc-ccccCCCEEEEeCCccCC--cchHHHHHHHHHhhcCCC
Confidence            333322211110      11222479999999988766543 457899999999999772  22222222222 223457


Q ss_pred             ceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHH
Q 014486          223 KQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAA  302 (423)
Q Consensus       223 ~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~  302 (423)
                      .|++++|||++......   +...+..+.......  ....             ..+...+.. ..+++||||++++.++
T Consensus       142 ~~~i~~SAT~~~~~~~~---~~~~~~~~~~~~~~p--~~~~-------------~~~~~~l~~-~~~~~lVF~~s~~~a~  202 (451)
T 2jlq_A          142 AAAIFMTATPPGSTDPF---PQSNSPIEDIEREIP--ERSW-------------NTGFDWITD-YQGKTVWFVPSIKAGN  202 (451)
T ss_dssp             CEEEEECSSCTTCCCSS---CCCSSCEEEEECCCC--SSCC-------------SSSCHHHHH-CCSCEEEECSSHHHHH
T ss_pred             ceEEEEccCCCccchhh---hcCCCceEecCccCC--chhh-------------HHHHHHHHh-CCCCEEEEcCCHHHHH
Confidence            89999999998754322   122222222111000  0000             001222333 3579999999999999


Q ss_pred             HHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEcc------------------
Q 014486          303 ELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYD------------------  364 (423)
Q Consensus       303 ~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~------------------  364 (423)
                      .+++.|+..++.+..+|+.+.    ..+++.|++|+.+|||||+++++|+|+|+ ++||+++                  
T Consensus       203 ~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~  277 (451)
T 2jlq_A          203 DIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRCLKPVILTDGPERVILA  277 (451)
T ss_dssp             HHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEE
T ss_pred             HHHHHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCcccccccccccceeeec
Confidence            999999999999999999754    56899999999999999999999999999 9999998                  


Q ss_pred             --CCCCcchhhhcccccCCCCC-ceEEEEEecC
Q 014486          365 --MPDSADTYLHRVGRAGRFGT-KGLAITFVSS  394 (423)
Q Consensus       365 --~~~s~~~~~Q~~GR~~R~g~-~~~~~~~~~~  394 (423)
                        .|.+..+|+||+||+||.|. +|.+++++..
T Consensus       278 ~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          278 GPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             EEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             ccccCCHHHHHHhccccCCCCCCCccEEEEeCC
Confidence              99999999999999999998 7888877643

>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-39  Score=314.57  Aligned_cols=277  Identities=19%  Similarity=0.200  Sum_probs=211.1

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .++++|+.+++.+..++++++.+|||||||+++++++++.      +.++||++|+++||.|+++.+.+..    +..+.
T Consensus       217 P~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~------g~~vLVl~PTReLA~Qia~~l~~~~----g~~vg  286 (666)
T 3o8b_A          217 PVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAH----GIDPN  286 (666)
T ss_dssp             CSCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHT------TCCEEEEESCHHHHHHHHHHHHHHH----SCCCE
T ss_pred             CcHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHC------CCeEEEEcchHHHHHHHHHHHHHHh----CCCee
Confidence            5667777777777788899999999999999999988873      2289999999999999999887665    34555


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCce--E
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQ--V  225 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~--~  225 (423)
                      ...|+..        .....+|+|+||++|+   ....+.+.++++||+||||.+.  .++...+..+.+.++...+  +
T Consensus       287 ~~vG~~~--------~~~~~~IlV~TPGrLl---~~~~l~l~~l~~lVlDEAH~l~--~~~~~~l~~Il~~l~~~~~~ll  353 (666)
T 3o8b_A          287 IRTGVRT--------ITTGAPVTYSTYGKFL---ADGGCSGGAYDIIICDECHSTD--STTILGIGTVLDQAETAGARLV  353 (666)
T ss_dssp             EECSSCE--------ECCCCSEEEEEHHHHH---HTTSCCTTSCSEEEETTTTCCS--HHHHHHHHHHHHHTTTTTCSEE
T ss_pred             EEECcEe--------ccCCCCEEEECcHHHH---hCCCcccCcccEEEEccchhcC--ccHHHHHHHHHHhhhhcCCceE
Confidence            6666643        2334699999999973   5666778899999999998764  4777778888888887666  7


Q ss_pred             EEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHH
Q 014486          226 MMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELN  305 (423)
Q Consensus       226 v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~  305 (423)
                      +++|||++..+.      ...+....+....    ............          +.....+++||||++++.++.++
T Consensus       354 il~SAT~~~~i~------~~~p~i~~v~~~~----~~~i~~~~~~~~----------l~~~~~~~vLVFv~Tr~~ae~la  413 (666)
T 3o8b_A          354 VLATATPPGSVT------VPHPNIEEVALSN----TGEIPFYGKAIP----------IEAIRGGRHLIFCHSKKKCDELA  413 (666)
T ss_dssp             EEEESSCTTCCC------CCCTTEEEEECBS----CSSEEETTEEEC----------GGGSSSSEEEEECSCHHHHHHHH
T ss_pred             EEECCCCCcccc------cCCcceEEEeecc----cchhHHHHhhhh----------hhhccCCcEEEEeCCHHHHHHHH
Confidence            888999997421      1111111110000    000110000000          22336789999999999999999


Q ss_pred             HHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEE----------Ecc-----------
Q 014486          306 KLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVI----------NYD-----------  364 (423)
Q Consensus       306 ~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi----------~~~-----------  364 (423)
                      +.|++.++++..+||++++.+       |.++..+|||||+++++|||++ +++||          +||           
T Consensus       414 ~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl~~~~  485 (666)
T 3o8b_A          414 AKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTIETTT  485 (666)
T ss_dssp             HHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEEEEEE
T ss_pred             HHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCccccccccccccccccccccc
Confidence            999999999999999999764       5556679999999999999997 99998          566           


Q ss_pred             CCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          365 MPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       365 ~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      .|.+..+|+||+||+|| |++|. +.|+++.+.
T Consensus       486 ~P~s~~syiQRiGRtGR-g~~G~-i~lvt~~e~  516 (666)
T 3o8b_A          486 VPQDAVSRSQRRGRTGR-GRRGI-YRFVTPGER  516 (666)
T ss_dssp             EECBHHHHHHHHTTBCS-SSCEE-EEESCCCCB
T ss_pred             CcCCHHHHHHHhccCCC-CCCCE-EEEEecchh
Confidence            89999999999999999 99999 888886544

>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=1.2e-39  Score=326.07  Aligned_cols=333  Identities=15%  Similarity=0.178  Sum_probs=238.9

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccC-CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~-~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      ..+|.++++++.+.+.+...+ ..|++.|+++++.++.+ +++++.||||||||++..+.++......+.+.++++++|+
T Consensus        71 ~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtllp~ll~~~~~~~~~g~~ilvl~P~  149 (773)
T 2xau_A           71 INPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPR  149 (773)
T ss_dssp             BCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHCGGGGTCEEEEEESC
T ss_pred             CCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHhccccCCCceEEecCch
Confidence            346999999999999999887 68999999999888874 5799999999999994333333322222223479999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcch-h
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDK-M  202 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~-~  202 (423)
                      ++|+.|+++.+........+..+..-.....       ......+|+++||+.+.+.+... ..+.++++||+||+|. .
T Consensus       150 r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~-------~~~~~~~I~v~T~G~l~r~l~~~-~~l~~~~~lIlDEah~R~  221 (773)
T 2xau_A          150 RVAAMSVAQRVAEEMDVKLGEEVGYSIRFEN-------KTSNKTILKYMTDGMLLREAMED-HDLSRYSCIILDEAHERT  221 (773)
T ss_dssp             HHHHHHHHHHHHHHTTCCBTTTEEEEETTEE-------ECCTTCSEEEEEHHHHHHHHHHS-TTCTTEEEEEECSGGGCC
T ss_pred             HHHHHHHHHHHHHHhCCchhheecceecccc-------ccCCCCCEEEECHHHHHHHHhhC-ccccCCCEEEecCccccc
Confidence            9999999987766542211222221111111       01123699999999999866553 4578999999999995 3


Q ss_pred             hccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHH----HHH
Q 014486          203 LESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEK----NRK  278 (423)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~  278 (423)
                      ++.......+..+... .+..+++++|||++..  .+ ..++.....+.+....    ..+...+......+.    ...
T Consensus       222 ld~d~~~~~l~~l~~~-~~~~~iIl~SAT~~~~--~l-~~~~~~~~vi~v~gr~----~pv~~~~~~~~~~~~~~~~l~~  293 (773)
T 2xau_A          222 LATDILMGLLKQVVKR-RPDLKIIIMSATLDAE--KF-QRYFNDAPLLAVPGRT----YPVELYYTPEFQRDYLDSAIRT  293 (773)
T ss_dssp             HHHHHHHHHHHHHHHH-CTTCEEEEEESCSCCH--HH-HHHTTSCCEEECCCCC----CCEEEECCSSCCSCHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHh-CCCceEEEEeccccHH--HH-HHHhcCCCcccccCcc----cceEEEEecCCchhHHHHHHHH
Confidence            3311223334444443 3578999999999643  23 3344433333332221    112222222222222    233


Q ss_pred             HHHHHHhhcCCcEEEEEcChhhHHHHHHHHHh-----------CCCCeEEEcCCCCHHHHHHHHHhhh-----cCCccEE
Q 014486          279 LNDLLDALDFNQVVIFVKSVSRAAELNKLLVE-----------CNFPSICIHSGMSQEERLTRYKGFK-----EGNKRIL  342 (423)
Q Consensus       279 l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~-----------~~~~~~~~~~~~~~~~r~~~~~~f~-----~~~~~il  342 (423)
                      +..++.....+++||||++++.++.+++.|.+           .++.+..+||++++.+|..+++.|.     +|..+||
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------------------CCCcchhhhcccccCCCCCceEEEEEecCc
Q 014486          343 VATDLVGRGIDIERVNIVINYDM------------------PDSADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       343 i~T~~~~~Gld~~~~~~vi~~~~------------------~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      |||+++++|+|+|++++||+++.                  |.|...|.||+||+||. .+|.|+.|+++.
T Consensus       374 VAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~  443 (773)
T 2xau_A          374 ISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEE  443 (773)
T ss_dssp             EECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHH
T ss_pred             EeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHH
Confidence            99999999999999999999887                  88999999999999999 789999999753

>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=2.2e-41  Score=319.84  Aligned_cols=289  Identities=17%  Similarity=0.155  Sum_probs=190.9

Q ss_pred             ccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHH
Q 014486           79 QAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH  158 (423)
Q Consensus        79 ~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (423)
                      .++.++++++++|||||||++|+++++..+...+  ++++|++||++||.|+++.++.+       .+....+...    
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~~--~~~lil~Ptr~La~Q~~~~l~~~-------~v~~~~~~~~----   70 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARRR--LRTLVLAPTRVVLSEMKEAFHGL-------DVKFHTQAFS----   70 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTT--CCEEEEESSHHHHHHHHHHTTTS-------CEEEESSCCC----
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhcC--CeEEEEcchHHHHHHHHHHHhcC-------CeEEecccce----
Confidence            4677999999999999999999999988655432  48999999999999999877633       3322111100    


Q ss_pred             HHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhC-CCCceEEEEeccCCccHH
Q 014486          159 KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMT-PHDKQVMMFSATLSKEIR  237 (423)
Q Consensus       159 ~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-~~~~~~v~~SAT~~~~~~  237 (423)
                        .......-+-..+.+.+...+. ....+.++++||+||+|++.  ..+...+..+.... +...|++++|||+++...
T Consensus        71 --~v~Tp~~l~~~l~~~~l~~~~~-~~~~~~~l~~vViDEah~~~--~~~~~~~~~~~~~~~~~~~~~l~~SAT~~~~~~  145 (440)
T 1yks_A           71 --AHGSGREVIDAMCHATLTYRML-EPTRVVNWEVIIMDEAHFLD--PASIAARGWAAHRARANESATILMTATPPGTSD  145 (440)
T ss_dssp             --CCCCSSCCEEEEEHHHHHHHHT-SSSCCCCCSEEEETTTTCCS--HHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCC
T ss_pred             --eccCCccceeeecccchhHhhh-CcccccCccEEEEECccccC--cchHHHHHHHHHHhccCCceEEEEeCCCCchhh
Confidence              0001100112222233332222 23457899999999999982  23333332232222 357899999999987643


Q ss_pred             HHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEE
Q 014486          238 PVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSIC  317 (423)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~  317 (423)
                      .+..    ....+...             ....+.......+ ..+.. .++++||||++++.++.+++.|+..++++..
T Consensus       146 ~~~~----~~~~~~~~-------------~~~~~~~~~~~~~-~~l~~-~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~  206 (440)
T 1yks_A          146 EFPH----SNGEIEDV-------------QTDIPSEPWNTGH-DWILA-DKRPTAWFLPSIRAANVMAASLRKAGKSVVV  206 (440)
T ss_dssp             SSCC----CSSCEEEE-------------ECCCCSSCCSSSC-HHHHH-CCSCEEEECSCHHHHHHHHHHHHHTTCCEEE
T ss_pred             hhhh----cCCCeeEe-------------eeccChHHHHHHH-HHHHh-cCCCEEEEeCCHHHHHHHHHHHHHcCCCEEE
Confidence            2211    11111000             0000111111111 22222 2579999999999999999999999999999


Q ss_pred             EcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE-------------------ccCCCCcchhhhcccc
Q 014486          318 IHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN-------------------YDMPDSADTYLHRVGR  378 (423)
Q Consensus       318 ~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~-------------------~~~~~s~~~~~Q~~GR  378 (423)
                      +||    .+|..+++.|++|+.+|||||+++++|+|+| +++||+                   ++.|.++.+|.||+||
T Consensus       207 lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR  281 (440)
T 1yks_A          207 LNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGR  281 (440)
T ss_dssp             CCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTT
T ss_pred             ecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccceeeecccccceeeccccccCHHHHHHhccc
Confidence            999    3688889999999999999999999999999 999986                   8889999999999999


Q ss_pred             cCCC-CCceEEEEEec--CcccHHHHHHHHHHHh
Q 014486          379 AGRF-GTKGLAITFVS--SASDSDILNQVSKFMF  409 (423)
Q Consensus       379 ~~R~-g~~~~~~~~~~--~~~~~~~~~~~~~~~~  409 (423)
                      +||. |++|.+++|+.  ...+...+..+++.+.
T Consensus       282 ~GR~g~~~g~~~~l~~~~~~~~~~~l~~l~~~~~  315 (440)
T 1yks_A          282 IGRNPNRDGDSYYYSEPTSENNAHHVCWLEASML  315 (440)
T ss_dssp             SSCCTTCCCEEEEECSCCCCCCTTBHHHHHHHHH
T ss_pred             cCCCCCCCceEEEEeccCChhhhhhhhhhhHHhc
Confidence            9997 68999999973  3455566777777653

>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=5.9e-40  Score=322.21  Aligned_cols=307  Identities=17%  Similarity=0.195  Sum_probs=214.3

Q ss_pred             HHHhCCCC-----CCChhhh-----hcccccc------cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           60 AIVDSGFE-----HPSEVQH-----ECIPQAI------LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        60 ~l~~~~~~-----~~~~~Q~-----~~i~~~~------~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      +|...||.     .|+++|+     ++|+.++      .++++++++|||||||++|+++++..+...+  ++++|++||
T Consensus       202 ~l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~~--~~~lilaPT  279 (673)
T 2wv9_A          202 GLYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQKR--LRTAVLAPT  279 (673)
T ss_dssp             EEEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHTT--CCEEEEESS
T ss_pred             EeeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhCC--CcEEEEccH
Confidence            45556766     8999999     9999988      8999999999999999999999997754332  489999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                      ++||.|+++.++.+     ++.  ...+.  .    ........-+-+.+.+.+...+... ..+.++++||+||+|++.
T Consensus       280 r~La~Q~~~~l~~~-----~i~--~~~~~--l----~~v~tp~~ll~~l~~~~l~~~l~~~-~~l~~l~lvViDEaH~~~  345 (673)
T 2wv9_A          280 RVVAAEMAEALRGL-----PVR--YLTPA--V----QREHSGNEIVDVMCHATLTHRLMSP-LRVPNYNLFVMDEAHFTD  345 (673)
T ss_dssp             HHHHHHHHHHTTTS-----CCE--ECCC---------CCCCSCCCEEEEEHHHHHHHHHSS-SCCCCCSEEEEESTTCCC
T ss_pred             HHHHHHHHHHHhcC-----Cee--eeccc--c----cccCCHHHHHHHHHhhhhHHHHhcc-cccccceEEEEeCCcccC
Confidence            99999999877643     121  11110  0    0011111234455556665544432 567899999999999882


Q ss_pred             ccCCcHHHHHHHHHhC-CCCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHH
Q 014486          204 ESLDMRRDVQEIFKMT-PHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDL  282 (423)
Q Consensus       204 ~~~~~~~~~~~~~~~~-~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l  282 (423)
                        ..+...+..+...+ +...|+++||||+++.+..+...  ..+. ..+..              ..+.......+ ..
T Consensus       346 --~~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~~~--~~~i-~~v~~--------------~~~~~~~~~~l-~~  405 (673)
T 2wv9_A          346 --PASIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPDT--NSPV-HDVSS--------------EIPDRAWSSGF-EW  405 (673)
T ss_dssp             --HHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCC--SSCE-EEEEC--------------CCCSSCCSSCC-HH
T ss_pred             --ccHHHHHHHHHHhccccCCcEEEEcCCCChhhhhhccc--CCce-EEEee--------------ecCHHHHHHHH-HH
Confidence              22222333333333 25789999999998764322110  0111 00000              00000001111 22


Q ss_pred             HHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE
Q 014486          283 LDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN  362 (423)
Q Consensus       283 l~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~  362 (423)
                      +.. ..+++||||++++.++.+++.|+..++++..+||.    +|..+++.|++|+.+|||||+++++|+|+| +++||+
T Consensus       406 l~~-~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~  479 (673)
T 2wv9_A          406 ITD-YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVID  479 (673)
T ss_dssp             HHS-CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEE
T ss_pred             HHh-CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEE
Confidence            222 46899999999999999999999999999999994    788999999999999999999999999999 999998


Q ss_pred             --------------------ccCCCCcchhhhcccccCCC-CCceEEEEEec--CcccHHHHHHHHHHH
Q 014486          363 --------------------YDMPDSADTYLHRVGRAGRF-GTKGLAITFVS--SASDSDILNQVSKFM  408 (423)
Q Consensus       363 --------------------~~~~~s~~~~~Q~~GR~~R~-g~~~~~~~~~~--~~~~~~~~~~~~~~~  408 (423)
                                          ++.|.++.+|.||+||+||. |+.|.+++|+.  ...+...+..++..+
T Consensus       480 ~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~~~l~~ie~~~  548 (673)
T 2wv9_A          480 CRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDDTMLAHWTEAKI  548 (673)
T ss_dssp             CCEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCCCCTTBHHHHHHHH
T ss_pred             CCCcccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCChhHHHHHHHHHHHH
Confidence                                56889999999999999998 78999999973  345555566666655

>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=3.6e-38  Score=310.79  Aligned_cols=309  Identities=18%  Similarity=0.212  Sum_probs=189.7

Q ss_pred             CCChhhhhccccccc----C-CceEEEccCCCcchhHHHHHHhhccCCC------CCCeEEEEEecChHHHHHHH-HHHH
Q 014486           68 HPSEVQHECIPQAIL----G-MDVICQAKSGMGKTAVFVLSTLQQTEPN------PGQVTALVLCHTRELAYQIC-HEFE  135 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~-~~~ii~~~tGsGKT~~~~~~~~~~~~~~------~~~~~~lil~P~~~L~~q~~-~~~~  135 (423)
                      .|+++|.++++.++.    + +++++++|||+|||++++..+...+...      ...+++||++|+++|+.|+. +.++
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            799999999998876    4 5689999999999999765544433322      13458999999999999998 6666


Q ss_pred             HHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhc----CCCCCCCccEEEEcCcchhhccCCcHHH
Q 014486          136 RFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARD----KDLSLKNVRHFILDECDKMLESLDMRRD  211 (423)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~----~~~~~~~~~~vVvDE~h~~~~~~~~~~~  211 (423)
                      .+.     ..+..+.++.         .....+|+|+||++|......    ..+....+++||+||||++...  ....
T Consensus       258 ~~~-----~~~~~~~~~~---------~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~--~~~~  321 (590)
T 3h1t_A          258 PFG-----DARHKIEGGK---------VVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSAR--DNSN  321 (590)
T ss_dssp             TTC-----SSEEECCC-----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC-----------
T ss_pred             hcc-----hhhhhhhccC---------CCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCcccccc--chHH
Confidence            542     2333333221         122369999999999876542    2344567899999999998652  2244


Q ss_pred             HHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeeccc-----cccccc-------------------------
Q 014486          212 VQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDE-----AKLTLH-------------------------  261 (423)
Q Consensus       212 ~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~-------------------------  261 (423)
                      +..++..++ ..+++++||||..........++..+...+....     ......                         
T Consensus       322 ~~~il~~~~-~~~~l~lTATP~~~~~~~~~~~f~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  400 (590)
T 3h1t_A          322 WREILEYFE-PAFQIGMTATPLREDNRDTYRYFGNPIYTYSLRQGIDDGFLAPYRVHRVISEVDAAGWRPSKGDVDRFGR  400 (590)
T ss_dssp             CHHHHHHST-TSEEEEEESSCSCTTTHHHHHHSCSCSEEECHHHHHHHTSSCCEEEEEEEETTCC---------------
T ss_pred             HHHHHHhCC-cceEEEeccccccccchhHHHHcCCceEecCHHHHhhCCccCCcEEEEeeeeeecccccccccccccccc
Confidence            556666665 4679999999886543333333333221110000     000000                         


Q ss_pred             cceEEEEEeChH-------HHHH----HHHHHHHhh-cCCcEEEEEcChhhHHHHHHHHHhCCC--------CeEEEcCC
Q 014486          262 GLVQHYIKLSEL-------EKNR----KLNDLLDAL-DFNQVVIFVKSVSRAAELNKLLVECNF--------PSICIHSG  321 (423)
Q Consensus       262 ~~~~~~~~~~~~-------~~~~----~l~~ll~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~--------~~~~~~~~  321 (423)
                      .+..........       .+..    .+..++... +.+++||||+++++++.+++.|...+.        .+..+||.
T Consensus       401 ~~~~~~~~~~~~~~~~~~~~r~~~i~~~l~~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~  480 (590)
T 3h1t_A          401 EIPDGEYQTKDFERVIALKARTDAFAKHLTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSE  480 (590)
T ss_dssp             --------CCSHHHHHHHHHTHHHHHHHHHHHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSST
T ss_pred             ccccccCCHHHhhhHhcChHHHHHHHHHHHHHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCC
Confidence            000000000010       1111    233333333 447999999999999999999987543        26778888


Q ss_pred             CCHHHHHHHHHhhhcCCcc---EEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCC--ceEEEEEecC
Q 014486          322 MSQEERLTRYKGFKEGNKR---ILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGT--KGLAITFVSS  394 (423)
Q Consensus       322 ~~~~~r~~~~~~f~~~~~~---ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~--~~~~~~~~~~  394 (423)
                      ++. +|.++++.|++++.+   |||+|+++++|+|+|++++||++++|+|+..|.||+||++|.+.  .+..+++++.
T Consensus       481 ~~~-~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~~~~k~~~~I~D~  557 (590)
T 3h1t_A          481 EGK-IGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLREDYGKLWFNIIDY  557 (590)
T ss_dssp             THH-HHHHHHHHHHCTTCCCCCEEEESSTTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBGGGTBSCEEEEEC
T ss_pred             ChH-HHHHHHHHHhCCCCCCCEEEEECChhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCccCCCCEEEEEec
Confidence            764 799999999998766   88899999999999999999999999999999999999999875  3444444443

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=100.00  E-value=2.9e-37  Score=265.93  Aligned_cols=215  Identities=80%  Similarity=1.311  Sum_probs=187.7

Q ss_pred             ccCCcccccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCe
Q 014486           36 AKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQV  115 (423)
Q Consensus        36 ~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~  115 (423)
                      .+.++.+.+..+|+++++++.+.++|.+.|+..|+++|.++++.++.++++++.+|||+|||++++++++..+.....++
T Consensus         4 ~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~   83 (220)
T 1t6n_A            4 VKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQV   83 (220)
T ss_dssp             ----------CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCC
T ss_pred             CCCCcccccCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCE
Confidence            34566777788899999999999999999999999999999999999999999999999999999999999887666666


Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEE
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFI  195 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vV  195 (423)
                      ++||++|+++|+.|+++.++++....+++++..++|+.....+...+.++.++|+|+||+++..++......+.+++++|
T Consensus        84 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lV  163 (220)
T 1t6n_A           84 SVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFI  163 (220)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             EEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEE
Confidence            89999999999999999999998777788999999999888877777776679999999999999888888889999999


Q ss_pred             EcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCcee
Q 014486          196 LDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEI  250 (423)
Q Consensus       196 vDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~  250 (423)
                      +||||++.++.++...+..+...+++..|++++|||+++.+..+++.++.+|..+
T Consensus       164 iDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i  218 (220)
T 1t6n_A          164 LDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEI  218 (220)
T ss_dssp             EESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEE
T ss_pred             EcCHHHHhcccCcHHHHHHHHHhCCCcCeEEEEEeecCHHHHHHHHHHcCCCeEE
Confidence            9999999875578888999999998899999999999999999999998888655

>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=1e-37  Score=320.17  Aligned_cols=318  Identities=18%  Similarity=0.180  Sum_probs=222.7

Q ss_pred             CCChhhhhcccccccC--CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCce
Q 014486           68 HPSEVQHECIPQAILG--MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIK  145 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~--~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  145 (423)
                      .|+|||.+++..++..  .+++++++||+|||++++..+......+..+ ++|||||+ .|+.||..++.+..    +++
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~~-rvLIVvP~-sLl~Qw~~E~~~~f----~l~  226 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAE-RVLIIVPE-TLQHQWLVEMLRRF----NLR  226 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTSSCC-CEEEECCT-TTHHHHHHHHHHHS----CCC
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhCCCC-eEEEEeCH-HHHHHHHHHHHHHh----CCC
Confidence            7999999999988874  4799999999999999887776655444333 79999999 99999999997765    456


Q ss_pred             EEEEEcCcchHHHHHH-HhcCCCcEEEechHHHHHHHhc-CCCCCCCccEEEEcCcchhhccCCcH-HHHHHHHHhCCCC
Q 014486          146 VAVFYGGVNIKIHKDL-LKNECPQIVVGTPGRILALARD-KDLSLKNVRHFILDECDKMLESLDMR-RDVQEIFKMTPHD  222 (423)
Q Consensus       146 ~~~~~~~~~~~~~~~~-~~~~~~~ilv~T~~~l~~~~~~-~~~~~~~~~~vVvDE~h~~~~~~~~~-~~~~~~~~~~~~~  222 (423)
                      +..++++......... ......+|+|+|++.+...... ..+...++++||+||||++.+..... .....+.......
T Consensus       227 v~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~~L~~~~  306 (968)
T 3dmq_A          227 FALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHV  306 (968)
T ss_dssp             CEECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHHHHHTTC
T ss_pred             EEEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHHHHhhcC
Confidence            6666554322211110 0012358999999988642111 11234578999999999997643221 2222333333345


Q ss_pred             ceEEEEeccCCc----cHHHHHHHhccCCc---------------------------e----------------------
Q 014486          223 KQVMMFSATLSK----EIRPVCKKFMQDPM---------------------------E----------------------  249 (423)
Q Consensus       223 ~~~v~~SAT~~~----~~~~~~~~~~~~~~---------------------------~----------------------  249 (423)
                      .+++++||||..    ++...+........                           .                      
T Consensus       307 ~~~L~LTATPi~n~~~el~sll~~L~p~~~~~~~~f~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~L~~~l~~~~~~~l~  386 (968)
T 3dmq_A          307 PGVLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEEQKNYCPVADAVAMLLAGNKLSNDELNMLGEMIGEQDIEPLL  386 (968)
T ss_dssp             SSEEESCSSCSSSCSSCTHHHHHHHCTTTCSSTHHHHHHHHHHHHHHHHHHTTTTSCCCCGGGTTSSTTTTCTTCSSTTG
T ss_pred             CcEEEEEcCCccCCHHHHHHHHHhcCccccCCHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHhcchhhHHHH
Confidence            679999999843    11111110000000                           0                      


Q ss_pred             -----------------------------eeec----cccccccccceEEEE----------------------------
Q 014486          250 -----------------------------IYVD----DEAKLTLHGLVQHYI----------------------------  268 (423)
Q Consensus       250 -----------------------------~~~~----~~~~~~~~~~~~~~~----------------------------  268 (423)
                                                   +...    ...............                            
T Consensus       387 ~~~~~~~~~~~~~~~~~i~~lld~~g~~~~l~r~~r~~i~~~p~r~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  466 (968)
T 3dmq_A          387 QAANSDSEDAQSARQELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQTAIKVSGIMGARKSAEDRARD  466 (968)
T ss_dssp             GGTCCCSSCSTTTHHHHHHHHGGGCTTTTTEECCCTTTCCCCCCCCCCEEEECCCHHHHHHHHHHHHTTCCSSGGGGTHH
T ss_pred             hcccchhhhhHHHHHHHHHHHHHhhCcchhhhhhhhhhhcccChhheEeeecCCCHHHHHHHHHHhhhhhhhhhHHHHhh
Confidence                                         0000    000000000000000                            


Q ss_pred             -----------------EeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHh-CCCCeEEEcCCCCHHHHHHH
Q 014486          269 -----------------KLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVE-CNFPSICIHSGMSQEERLTR  330 (423)
Q Consensus       269 -----------------~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~-~~~~~~~~~~~~~~~~r~~~  330 (423)
                                       ......|...+.+++...+++++||||++...++.+.+.|.. .|+++..+||++++.+|..+
T Consensus       467 ~l~pe~~~~~l~~~~~~~~~~~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~  546 (968)
T 3dmq_A          467 MLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRA  546 (968)
T ss_dssp             HHCSGGGTTTTTSSSCCTTTTSHHHHHHHHHHHHTSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHH
T ss_pred             hcChHHHHHHhhhhhhcccCccHHHHHHHHHHHhCCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHH
Confidence                             112334677788888887889999999999999999999995 59999999999999999999


Q ss_pred             HHhhhcCC--ccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEE
Q 014486          331 YKGFKEGN--KRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITF  391 (423)
Q Consensus       331 ~~~f~~~~--~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~  391 (423)
                      ++.|++|+  ++|||||+++++|+|+|++++||++++|+++..|.|++||+||.|+.+.++++
T Consensus       547 l~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~  609 (968)
T 3dmq_A          547 AAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIH  609 (968)
T ss_dssp             HHHHHSTTSSCEEEECSCCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEE
T ss_pred             HHHHhCCCCcccEEEecchhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEE
Confidence            99999998  99999999999999999999999999999999999999999999998865554

>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=2.6e-37  Score=299.18  Aligned_cols=309  Identities=17%  Similarity=0.211  Sum_probs=211.5

Q ss_pred             CCChhhhhcccccc----cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           68 HPSEVQHECIPQAI----LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~----~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      .|+|||.++++.+.    .+++++++++||+|||++++..+........ ..++|||||+ .|+.||.++++++.   ++
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~~~~~-~~~~LIv~P~-~l~~qw~~e~~~~~---~~  111 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENE-LTPSLVICPL-SVLKNWEEELSKFA---PH  111 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTTC-CSSEEEEECS-TTHHHHHHHHHHHC---TT
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHHhcCC-CCCEEEEccH-HHHHHHHHHHHHHC---CC
Confidence            79999999998774    4678999999999999997665544433222 2379999995 68999999999886   46


Q ss_pred             ceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCc
Q 014486          144 IKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK  223 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~  223 (423)
                      +++..++|+...      .....++|+|+||+.+.....   +....+++||+||||++.+. .  ....+....++ ..
T Consensus       112 ~~v~~~~g~~~~------~~~~~~~ivi~t~~~l~~~~~---l~~~~~~~vIvDEaH~~kn~-~--~~~~~~l~~l~-~~  178 (500)
T 1z63_A          112 LRFAVFHEDRSK------IKLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNP-Q--TKIFKAVKELK-SK  178 (500)
T ss_dssp             SCEEECSSSTTS------CCGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCT-T--SHHHHHHHTSC-EE
T ss_pred             ceEEEEecCchh------ccccCCcEEEeeHHHHhccch---hcCCCcCEEEEeCccccCCH-h--HHHHHHHHhhc-cC
Confidence            677777776532      111236999999999875432   23356889999999999762 2  12233334443 46


Q ss_pred             eEEEEeccCCcc-HHH---HHHHhc--------------------------------cCCceeeecccc---ccccccce
Q 014486          224 QVMMFSATLSKE-IRP---VCKKFM--------------------------------QDPMEIYVDDEA---KLTLHGLV  264 (423)
Q Consensus       224 ~~v~~SAT~~~~-~~~---~~~~~~--------------------------------~~~~~~~~~~~~---~~~~~~~~  264 (423)
                      +++++||||... ..+   .+....                                ..+..+......   ....+...
T Consensus       179 ~~l~LTaTP~~n~~~el~~ll~~l~p~~~~~~~~f~~~~~~~~~~~~~~~~~~l~~~l~~~~lrr~k~~~~~~~~lp~~~  258 (500)
T 1z63_A          179 YRIALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAIISPFILRRTKYDKAIINDLPDKI  258 (500)
T ss_dssp             EEEEECSSCSTTCHHHHHHHHHHHSTTTTCCHHHHHTTTHHHHHTTCHHHHHHHHHHHTTTEECCCTTCHHHHTTSCSEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHhCCCcCCCHHHHHHHhccccccccHHHHHHHHHHHhhHeeeecccccchhhcCCCCe
Confidence            789999998542 111   111000                                011111000000   00011111


Q ss_pred             EEEEEeC--h-------------------------------------------------------HHHHHHHHHHHHhh-
Q 014486          265 QHYIKLS--E-------------------------------------------------------LEKNRKLNDLLDAL-  286 (423)
Q Consensus       265 ~~~~~~~--~-------------------------------------------------------~~~~~~l~~ll~~~-  286 (423)
                      ...+.+.  .                                                       ..|...+.+++... 
T Consensus       259 ~~~v~~~l~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lr~~~~~p~l~~~~~~~~~~s~K~~~l~~~l~~~~  338 (500)
T 1z63_A          259 ETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPALLKGGEQSVRRSGKMIRTMEIIEEAL  338 (500)
T ss_dssp             EEEEEECCCHHHHHHHHHHHHHHTTTTTTCCTHHHHHHHHHHHHHHHHHTTCTHHHHCSCCCSTTCHHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhCCHHHhcCccchhhcchhHHHHHHHHHHHH
Confidence            1111111  1                                                       12333444555443 


Q ss_pred             -cCCcEEEEEcChhhHHHHHHHHHhC-CCCeEEEcCCCCHHHHHHHHHhhhcC-Ccc-EEEEcCccccCCCCCCCCEEEE
Q 014486          287 -DFNQVVIFVKSVSRAAELNKLLVEC-NFPSICIHSGMSQEERLTRYKGFKEG-NKR-ILVATDLVGRGIDIERVNIVIN  362 (423)
Q Consensus       287 -~~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~-ili~T~~~~~Gld~~~~~~vi~  362 (423)
                       .+.++||||++...++.+.+.|... |+.+..+||+++..+|.++++.|+++ ..+ +|++|+++++|+|++.+++||+
T Consensus       339 ~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Glnl~~~~~vi~  418 (500)
T 1z63_A          339 DEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIH  418 (500)
T ss_dssp             TTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCCCCTTCSEEEE
T ss_pred             ccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCCchhhCCEEEE
Confidence             5679999999999999999999885 99999999999999999999999998 455 7889999999999999999999


Q ss_pred             ccCCCCcchhhhcccccCCCCCceEE--EEEecC
Q 014486          363 YDMPDSADTYLHRVGRAGRFGTKGLA--ITFVSS  394 (423)
Q Consensus       363 ~~~~~s~~~~~Q~~GR~~R~g~~~~~--~~~~~~  394 (423)
                      +++||++..+.|++||++|.|+.+.+  +.++..
T Consensus       419 ~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~  452 (500)
T 1z63_A          419 FDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISV  452 (500)
T ss_dssp             SSCCSCC---CHHHHTTTTTTTTSCEEEEEEEET
T ss_pred             eCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeC
Confidence            99999999999999999999987655  444544

>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=5.7e-38  Score=298.34  Aligned_cols=278  Identities=17%  Similarity=0.168  Sum_probs=192.1

Q ss_pred             ccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchH
Q 014486           77 IPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIK  156 (423)
Q Consensus        77 i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (423)
                      ...+..++++++++|||||||++|++|++..+...+  +++||++|+++|+.|+++.++       +..+....+.... 
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~~--~~~lvl~Ptr~La~Q~~~~l~-------g~~v~~~~~~~~~-   84 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQR--LRTAVLAPTRVVAAEMAEALR-------GLPVRYQTSAVQR-   84 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHTT--CCEEEEECSHHHHHHHHHHTT-------TSCEEECC------
T ss_pred             HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhCC--CcEEEECchHHHHHHHHHHhc-------CceEeEEeccccc-
Confidence            344566888999999999999999999998765322  389999999999999998775       2233222111110 


Q ss_pred             HHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccH
Q 014486          157 IHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEI  236 (423)
Q Consensus       157 ~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~  236 (423)
                          . ..+...+.++|.+.+...+... ..+.++++||+||||.+.........+.... ...+..|++++|||++..+
T Consensus        85 ----~-~t~~~~i~~~~~~~l~~~l~~~-~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~-~~~~~~~~il~SAT~~~~~  157 (459)
T 2z83_A           85 ----E-HQGNEIVDVMCHATLTHRLMSP-NRVPNYNLFVMDEAHFTDPASIAARGYIATK-VELGEAAAIFMTATPPGTT  157 (459)
T ss_dssp             --------CCCSEEEEEHHHHHHHHHSC-C-CCCCSEEEESSTTCCSHHHHHHHHHHHHH-HHTTSCEEEEECSSCTTCC
T ss_pred             ----C-CCCCcEEEEEchHHHHHHhhcc-ccccCCcEEEEECCccCCchhhHHHHHHHHH-hccCCccEEEEEcCCCcch
Confidence                0 1222367788888887655443 4578999999999997421001111111111 1235789999999999764


Q ss_pred             HHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeE
Q 014486          237 RPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSI  316 (423)
Q Consensus       237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~  316 (423)
                      ..+...  ..+.......               .+. .....+..++... .+++||||++++.++.+++.|+..++.+.
T Consensus       158 ~~~~~~--~~pi~~~~~~---------------~~~-~~~~~~~~~l~~~-~~~~LVF~~s~~~~~~l~~~L~~~g~~v~  218 (459)
T 2z83_A          158 DPFPDS--NAPIHDLQDE---------------IPD-RAWSSGYEWITEY-AGKTVWFVASVKMGNEIAMCLQRAGKKVI  218 (459)
T ss_dssp             CSSCCC--SSCEEEEECC---------------CCS-SCCSSCCHHHHHC-CSCEEEECSCHHHHHHHHHHHHHTTCCEE
T ss_pred             hhhccC--CCCeEEeccc---------------CCc-chhHHHHHHHHhc-CCCEEEEeCChHHHHHHHHHHHhcCCcEE
Confidence            322111  1111111000               000 0000111223333 57999999999999999999999999999


Q ss_pred             EEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE--------------------ccCCCCcchhhhcc
Q 014486          317 CIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN--------------------YDMPDSADTYLHRV  376 (423)
Q Consensus       317 ~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~--------------------~~~~~s~~~~~Q~~  376 (423)
                      .+|+.    +|..+++.|++|+.+|||||+++++|+|+|+ ++||+                    |+.|.|+.+|+||+
T Consensus       219 ~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~  293 (459)
T 2z83_A          219 QLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRR  293 (459)
T ss_dssp             EESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHHHHH
T ss_pred             ecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHHHHHhc
Confidence            99995    6778899999999999999999999999999 99998                    67999999999999


Q ss_pred             cccCCCCC-ceEEEEEecCc
Q 014486          377 GRAGRFGT-KGLAITFVSSA  395 (423)
Q Consensus       377 GR~~R~g~-~~~~~~~~~~~  395 (423)
                      ||+||.|. +|.+++|+.+.
T Consensus       294 GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          294 GRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             TTSSCCTTCCCEEEEECSCC
T ss_pred             cccCCCCCCCCeEEEEEccc
Confidence            99999997 89999999864

>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=2.9e-37  Score=291.13  Aligned_cols=268  Identities=14%  Similarity=0.149  Sum_probs=188.0

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL  162 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (423)
                      ++++++++|||||||++|++++++.+...+  .+++|++||++|+.|+++.+.       ++.+....++..      ..
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~~~~g--~~~lvl~Pt~~La~Q~~~~~~-------~~~v~~~~~~~~------~~   66 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREAVKKR--LRTVILAPTRVVASEMYEALR-------GEPIRYMTPAVQ------SE   66 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHHHHTT--CCEEEEESSHHHHHHHHHHTT-------TSCEEEC-------------
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHhCC--CCEEEECcHHHHHHHHHHHhC-------CCeEEEEecCcc------cc
Confidence            678999999999999999998885544332  389999999999999887664       445555444321      12


Q ss_pred             hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHh-CCCCceEEEEeccCCccHHHHHH
Q 014486          163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKM-TPHDKQVMMFSATLSKEIRPVCK  241 (423)
Q Consensus       163 ~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~-~~~~~~~v~~SAT~~~~~~~~~~  241 (423)
                      .....-+.+.|.+.+.+.+.. ...+.++++||+||+|++.  ..+......+... .+...+++++|||+++.+..+..
T Consensus        67 ~~~~~~~~~~~~~~l~~~l~~-~~~~~~l~~vViDEaH~~~--~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~~~~~  143 (431)
T 2v6i_A           67 RTGNEIVDFMCHSTFTMKLLQ-GVRVPNYNLYIMDEAHFLD--PASVAARGYIETRVSMGDAGAIFMTATPPGTTEAFPP  143 (431)
T ss_dssp             --CCCSEEEEEHHHHHHHHHH-TCCCCCCSEEEEESTTCCS--HHHHHHHHHHHHHHHTTSCEEEEEESSCTTCCCSSCC
T ss_pred             CCCCceEEEEchHHHHHHHhc-CccccCCCEEEEeCCccCC--ccHHHHHHHHHHHhhCCCCcEEEEeCCCCcchhhhcC
Confidence            222236777888888765554 4568899999999999873  2222333333322 24678999999999975322111


Q ss_pred             HhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCC
Q 014486          242 KFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSG  321 (423)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~  321 (423)
                      .   .+........              .+. .+...+..++... .+++||||++++.++.+++.|+..++++..+||+
T Consensus       144 ~---~~~i~~~~~~--------------~~~-~~~~~~~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~  204 (431)
T 2v6i_A          144 S---NSPIIDEETR--------------IPD-KAWNSGYEWITEF-DGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK  204 (431)
T ss_dssp             C---SSCCEEEECC--------------CCS-SCCSSCCHHHHSC-SSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT
T ss_pred             C---CCceeecccc--------------CCH-HHHHHHHHHHHcC-CCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc
Confidence            0   0100110000              000 0011122333333 5789999999999999999999999999999997


Q ss_pred             CCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCE-----------------EEEccCCCCcchhhhcccccCCCCC
Q 014486          322 MSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNI-----------------VINYDMPDSADTYLHRVGRAGRFGT  384 (423)
Q Consensus       322 ~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~-----------------vi~~~~~~s~~~~~Q~~GR~~R~g~  384 (423)
                          +|.++++.|++|+.+|||||+++++|+|+| +.+                 ||+++.|.+..+|.||+||+||.|.
T Consensus       205 ----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~  279 (431)
T 2v6i_A          205 ----TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPE  279 (431)
T ss_dssp             ----THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTT
T ss_pred             ----cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHHHhhhccCCCCC
Confidence                577889999999999999999999999999 555                 5778899999999999999999985


Q ss_pred             c-eEEEEEe
Q 014486          385 K-GLAITFV  392 (423)
Q Consensus       385 ~-~~~~~~~  392 (423)
                      . +.++++.
T Consensus       280 ~~~~~~~~~  288 (431)
T 2v6i_A          280 KLGDIYAYS  288 (431)
T ss_dssp             CCCCEEEEC
T ss_pred             CCCeEEEEc
Confidence            4 4555554

>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=6.9e-36  Score=254.73  Aligned_cols=203  Identities=32%  Similarity=0.565  Sum_probs=184.8

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      .+|+++++++.++++|.+.||..|+++|.++++.++.++++++.+|||+|||++|++|++..+.....++++||++|+++
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            46999999999999999999999999999999999999999999999999999999999998876666668999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~  205 (423)
                      |+.|+.+.++++....+++++..++|+.........+..+ ++|+|+||+++...+......+.+++++|+||||++.+ 
T Consensus        83 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~-  160 (206)
T 1vec_A           83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT-VHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLS-  160 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSC-CSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTS-
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCC-CCEEEeCHHHHHHHHHcCCcCcccCCEEEEEChHHhHh-
Confidence            9999999999998777688999999998887776666555 69999999999999988888889999999999999987 


Q ss_pred             CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCcee
Q 014486          206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEI  250 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~  250 (423)
                      .++...+..+...+++..|++++|||+++.+..+++.++.+|..+
T Consensus       161 ~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          161 QDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             TTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             hCcHHHHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            689999999999999899999999999999999999998887654

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=100.00  E-value=3.6e-36  Score=269.86  Aligned_cols=205  Identities=33%  Similarity=0.546  Sum_probs=183.3

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccC--CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG--MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~--~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      ..+|+++++++.++++|.++||..|+++|.++++.++.+  +++++++|||||||++|++|++..+.....++++||++|
T Consensus        91 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~P  170 (300)
T 3fmo_B           91 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP  170 (300)
T ss_dssp             CCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             cCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcC
Confidence            357999999999999999999999999999999999997  899999999999999999999999887777779999999


Q ss_pred             ChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhc-CCCCCCCccEEEEcCcch
Q 014486          123 TRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARD-KDLSLKNVRHFILDECDK  201 (423)
Q Consensus       123 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~-~~~~~~~~~~vVvDE~h~  201 (423)
                      +++||.|+++.++.+....+++.+....|+.......    ...++|+|+||++|..++.+ ..+.+.++++||+||||+
T Consensus       171 treLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~  246 (300)
T 3fmo_B          171 TYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ----KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV  246 (300)
T ss_dssp             SHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC----CCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETTHHH
T ss_pred             cHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh----cCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeCHHH
Confidence            9999999999999998877788999888887653322    23369999999999998865 556789999999999999


Q ss_pred             hhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeec
Q 014486          202 MLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVD  253 (423)
Q Consensus       202 ~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~  253 (423)
                      +.+..++...+..+...+++..|++++|||++..+..++..++.+|..+.+.
T Consensus       247 l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~  298 (300)
T 3fmo_B          247 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLK  298 (300)
T ss_dssp             HHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEEC
T ss_pred             HhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEec
Confidence            9875689999999999999999999999999999999999999998877653

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=7e-36  Score=302.47  Aligned_cols=334  Identities=18%  Similarity=0.219  Sum_probs=232.9

Q ss_pred             CCChhhhhcccccc----cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           68 HPSEVQHECIPQAI----LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~----~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      .|+|||.+++..++    .++++|++.+||+|||++++..+............+||||| ..|+.||.+++.++.   |+
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~---p~  311 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWA---PD  311 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHS---TT
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHC---CC
Confidence            78999999998776    67889999999999999877665544322222226899999 678999999998886   57


Q ss_pred             ceEEEEEcCcchHHHHHHH-----------hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHH
Q 014486          144 IKVAVFYGGVNIKIHKDLL-----------KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDV  212 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~-----------~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~  212 (423)
                      +++..++|+..........           ....++|+|+|++.+......  +....+++||+||||++.+. .  ...
T Consensus       312 ~~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~--l~~~~w~~vIvDEaH~lkn~-~--s~~  386 (800)
T 3mwy_W          312 LNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE--LGSIKWQFMAVDEAHRLKNA-E--SSL  386 (800)
T ss_dssp             CCEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH--HHTSEEEEEEETTGGGGCCS-S--SHH
T ss_pred             ceEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH--HhcCCcceeehhhhhhhcCc-h--hHH
Confidence            7888888876655443322           223468999999999763321  22246789999999999752 2  223


Q ss_pred             HHHHHhCCCCceEEEEeccCCc----cHHHHHHHhccC-----------------------------Cceeeeccc-ccc
Q 014486          213 QEIFKMTPHDKQVMMFSATLSK----EIRPVCKKFMQD-----------------------------PMEIYVDDE-AKL  258 (423)
Q Consensus       213 ~~~~~~~~~~~~~v~~SAT~~~----~~~~~~~~~~~~-----------------------------~~~~~~~~~-~~~  258 (423)
                      ...+..+ +....+++||||-.    ++..++......                             +..+..... ...
T Consensus       387 ~~~l~~l-~~~~rl~LTgTPiqN~l~el~~ll~fL~p~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~p~~lRR~k~dv~~  465 (800)
T 3mwy_W          387 YESLNSF-KVANRMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDVEK  465 (800)
T ss_dssp             HHHHTTS-EEEEEEEECSCCCSSCSHHHHHHHHHHCSCCC---------CCTTHHHHHHHHHHHTTGGGEEECCGGGGTT
T ss_pred             HHHHHHh-hhccEEEeeCCcCCCCHHHHHHHHHHhCccccCchhhhcccccchhHHHHHHHHHHHHhHHHhhhhHHhhhh
Confidence            3334444 34557999999832    122222111110                             000000000 000


Q ss_pred             ccccceEEEEEeC-------------------------------------------------------------------
Q 014486          259 TLHGLVQHYIKLS-------------------------------------------------------------------  271 (423)
Q Consensus       259 ~~~~~~~~~~~~~-------------------------------------------------------------------  271 (423)
                      ..+......+.+.                                                                   
T Consensus       466 ~LP~k~~~~v~v~ls~~q~~~Y~~i~~~~~~~l~~~~~~~~~~~l~~l~~Lrk~~~hp~l~~~~~~~~~~~~~~~~~~~~  545 (800)
T 3mwy_W          466 SLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTRE  545 (800)
T ss_dssp             TSCCEEEEEEEECCCHHHHHHHHHHHHHCCC----------CTHHHHHHHHHHHHHCGGGSSSHHHHHCCCC----CCSH
T ss_pred             ccCCcEEEEEEeCCCHHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHhcChhhhcchHHHHHHhcccccccHH
Confidence            0000001111110                                                                   


Q ss_pred             --------hHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCcc-
Q 014486          272 --------ELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKR-  340 (423)
Q Consensus       272 --------~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~-  340 (423)
                              ...|...+..++..+  .+.++||||+....++.+.+.|...|+++..+||+++..+|..+++.|+++... 
T Consensus       546 ~~~~~l~~~s~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~  625 (800)
T 3mwy_W          546 NVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSND  625 (800)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSC
T ss_pred             HHHHHhhhcChHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCc
Confidence                    122444556666554  457999999999999999999999999999999999999999999999986654 


Q ss_pred             --EEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEE--EEecC-cccHHHHHHHHHHHhcc
Q 014486          341 --ILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAI--TFVSS-ASDSDILNQVSKFMFLL  411 (423)
Q Consensus       341 --ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~--~~~~~-~~~~~~~~~~~~~~~~~  411 (423)
                        +|++|.++++|+|++.+++||++++|||+..+.||+||++|.||+..|.  .|++. ..+..+++...+++.+.
T Consensus       626 ~v~LlSt~agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~TiEe~i~~~~~~K~~l~  701 (800)
T 3mwy_W          626 FVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILE  701 (800)
T ss_dssp             CCEEEEHHHHTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSHHHHHHHHHHHHTTSC
T ss_pred             eEEEEecccccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCCHHHHHHHHHHHHHHHH
Confidence              8999999999999999999999999999999999999999999876544  34543 45667777777777543

>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=5.4e-36  Score=261.51  Aligned_cols=210  Identities=26%  Similarity=0.446  Sum_probs=189.3

Q ss_pred             cccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC-----CCCeE
Q 014486           42 GIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN-----PGQVT  116 (423)
Q Consensus        42 ~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~-----~~~~~  116 (423)
                      +....+|.++++++.+.+++.+.||..|+++|.++++.++.|+++++.+|||+|||++|++|++..+...     ..+++
T Consensus        25 p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~  104 (242)
T 3fe2_A           25 PKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPI  104 (242)
T ss_dssp             CCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCS
T ss_pred             CCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCE
Confidence            3445679999999999999999999999999999999999999999999999999999999999875432     34558


Q ss_pred             EEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEE
Q 014486          117 ALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFIL  196 (423)
Q Consensus       117 ~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVv  196 (423)
                      +||++|+++|+.|+.+.++++.... ++++..++|+.........+.++ ++|+|+||+++..++......+.+++++|+
T Consensus       105 ~lil~Pt~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~I~v~Tp~~l~~~l~~~~~~~~~~~~lVi  182 (242)
T 3fe2_A          105 CLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLERG-VEICIATPGRLIDFLECGKTNLRRTTYLVL  182 (242)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEECTTSCHHHHHHHHHHC-CSEEEECHHHHHHHHHHTSCCCTTCCEEEE
T ss_pred             EEEEeCcHHHHHHHHHHHHHHHhhc-CceEEEEECCCChHHHHHHhcCC-CCEEEECHHHHHHHHHcCCCCcccccEEEE
Confidence            9999999999999999999988776 78999999999888887777776 699999999999999888888999999999


Q ss_pred             cCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeecc
Q 014486          197 DECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDD  254 (423)
Q Consensus       197 DE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~  254 (423)
                      ||||++.+ .+|...+..+...+++..|++++|||+++.+..+++.++.++..+.+..
T Consensus       183 DEah~l~~-~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~  239 (242)
T 3fe2_A          183 DEADRMLD-MGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGA  239 (242)
T ss_dssp             TTHHHHHH-TTCHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEECC
T ss_pred             eCHHHHhh-hCcHHHHHHHHHhCCccceEEEEEeecCHHHHHHHHHHCCCCEEEEecC
Confidence            99999988 7899999999999999999999999999999999999999888776654

>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=9.9e-36  Score=257.78  Aligned_cols=207  Identities=35%  Similarity=0.509  Sum_probs=183.1

Q ss_pred             ccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           43 IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        43 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      ....+|+++++++.+.++|.+.||..|+++|.++++.++.++++++.+|||+|||++|+++++..+.....++++||++|
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            34567999999999999999999999999999999999999999999999999999999999988776555669999999


Q ss_pred             ChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchh
Q 014486          123 TRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM  202 (423)
Q Consensus       123 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~  202 (423)
                      +++|+.|+++.++++....+++++..+.|+.....+...+..  ++|+|+||+++..++......+.+++++|+||||++
T Consensus       101 t~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~--~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~  178 (230)
T 2oxc_A          101 TREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKK--CHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKL  178 (230)
T ss_dssp             SHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTTS--CSEEEECHHHHHHHHHTTSSCGGGCCEEEESSHHHH
T ss_pred             CHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhccC--CCEEEECHHHHHHHHhcCCcccccCCEEEeCCchHh
Confidence            999999999999999876668899999999887776665543  599999999999998887788889999999999999


Q ss_pred             hccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceee
Q 014486          203 LESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIY  251 (423)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~  251 (423)
                      .++..+...+..+...++...|++++|||+++.+...+..++.+|..+.
T Consensus       179 ~~~~~~~~~~~~i~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~p~~i~  227 (230)
T 2oxc_A          179 LEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVR  227 (230)
T ss_dssp             HSTTSSHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHTTTCSSCEEEC
T ss_pred             hcCcchHHHHHHHHHhCCCCCeEEEEEeccCHHHHHHHHHHcCCCeEEE
Confidence            8833499999999999998999999999999999888888888876654

>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=8.6e-36  Score=259.27  Aligned_cols=206  Identities=42%  Similarity=0.628  Sum_probs=175.4

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ..+|+++++++.+.++|.+.||..|+++|.++++.++.++++++.+|||+|||++|+++++..+.....++++||++|++
T Consensus        29 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~  108 (237)
T 3bor_A           29 VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTR  108 (237)
T ss_dssp             CCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             cCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECcH
Confidence            45699999999999999999999999999999999999999999999999999999999999887655566999999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      +|+.|+.+.++++.... ++.+..+.|+.....+...+..+.++|+|+||+++...+......+.++++||+||||++.+
T Consensus       109 ~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~  187 (237)
T 3bor_A          109 ELAQQIQKVILALGDYM-GATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLS  187 (237)
T ss_dssp             HHHHHHHHHHHHHTTTT-TCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhc-CceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEECCchHhhc
Confidence            99999999999987654 67888888888777666666666579999999999999988778889999999999999987


Q ss_pred             cCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeee
Q 014486          205 SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV  252 (423)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  252 (423)
                       .++...+..+...++...|++++|||+++.+..+++.++.+|..+.+
T Consensus       188 -~~~~~~l~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v  234 (237)
T 3bor_A          188 -RGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILV  234 (237)
T ss_dssp             -TTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCSSCEEEC-
T ss_pred             -cCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHCCCCEEEEe
Confidence             68899999999999999999999999999999999999988876654

>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=1.5e-35  Score=259.24  Aligned_cols=205  Identities=32%  Similarity=0.613  Sum_probs=183.6

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ..+|+++++++.+.++|.++|+..|+++|.++++.++.++++++.+|||+|||++|+++++..+...+.++++||++|++
T Consensus        42 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~Ptr  121 (249)
T 3ber_A           42 TKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTR  121 (249)
T ss_dssp             HCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECSSH
T ss_pred             cCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeCCH
Confidence            45699999999999999999999999999999999999999999999999999999999998776655556899999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhc-CCCCCCCccEEEEcCcchhh
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARD-KDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~-~~~~~~~~~~vVvDE~h~~~  203 (423)
                      +|+.|+++.++++.... ++++..+.|+.....+...+..+ ++|+|+||+++...+.. ....+.++++||+||||++.
T Consensus       122 ~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l~  199 (249)
T 3ber_A          122 ELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSLALAKK-PHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRIL  199 (249)
T ss_dssp             HHHHHHHHHHHHHHGGG-TCCEEEECTTSCHHHHHHHHHTC-CSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHHH
T ss_pred             HHHHHHHHHHHHHhccC-CeeEEEEECCCChHHHHHHhcCC-CCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhhh
Confidence            99999999999987765 78899999998877666666655 69999999999998775 45678899999999999998


Q ss_pred             ccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeee
Q 014486          204 ESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV  252 (423)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  252 (423)
                      + .++...+..+...+++..|++++|||+++.+..+++.++.+|..+.+
T Consensus       200 ~-~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v  247 (249)
T 3ber_A          200 N-MDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAV  247 (249)
T ss_dssp             H-TTCHHHHHHHHHSSCSSSEEEEEESSCCHHHHHHHHHHCSSCEEEEC
T ss_pred             c-cChHHHHHHHHHhCCCCCeEEEEeccCCHHHHHHHHHHCCCCEEEEe
Confidence            8 68999999999999999999999999999999999999998876644

>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=7.9e-34  Score=280.57  Aligned_cols=333  Identities=15%  Similarity=0.122  Sum_probs=223.6

Q ss_pred             CCChhhhhcccccc---------cCCceEEEccCCCcchhHHHHHHhhccCCCC----CCeEEEEEecChHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAI---------LGMDVICQAKSGMGKTAVFVLSTLQQTEPNP----GQVTALVLCHTRELAYQICHEF  134 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~---------~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~----~~~~~lil~P~~~L~~q~~~~~  134 (423)
                      .|+|||.+++..+.         .+.++|++.+||+|||++++..+...+...+    ...++|||+|+ +|+.||.+++
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            68999999998874         3456999999999999988776655433221    22368999996 8999999999


Q ss_pred             HHHhccCCCceEEEEEcCcchHHHH--HHHhc-----CCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCC
Q 014486          135 ERFSTYLPDIKVAVFYGGVNIKIHK--DLLKN-----ECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLD  207 (423)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~-----~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~  207 (423)
                      .++...  .+.+..++++.......  ..+..     ...+|+|+|++.+.....  .+....+++||+||||++.+.  
T Consensus       134 ~~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~--~l~~~~~~~vI~DEaH~ikn~--  207 (644)
T 1z3i_X          134 GKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKNS--  207 (644)
T ss_dssp             HHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCTT--
T ss_pred             HHHcCC--CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHH--HhhcCCccEEEEECceecCCh--
Confidence            998754  35666666665432211  12211     136899999999876432  334467889999999999762  


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeccCCccH----HHHH---------------HHhcc-----------------------
Q 014486          208 MRRDVQEIFKMTPHDKQVMMFSATLSKEI----RPVC---------------KKFMQ-----------------------  245 (423)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~v~~SAT~~~~~----~~~~---------------~~~~~-----------------------  245 (423)
                      .......+. .+. ....+++||||-..-    ..++               +.+..                       
T Consensus       208 ~~~~~~al~-~l~-~~~rl~LTgTPiqN~l~El~sll~fl~p~~l~~~~~F~~~f~~pi~~~~~~~~~~~~~~~~~~~~~  285 (644)
T 1z3i_X          208 DNQTYLALN-SMN-AQRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQKLQ  285 (644)
T ss_dssp             CHHHHHHHH-HHC-CSEEEEECSSCSGGGGGGCHHHHHHHHHHHHCCHHHHHHHTHHHHHHHHSTTCCSHHHHHHHHHHH
T ss_pred             hhHHHHHHH-hcc-cCcEEEEecCcccCCHHHHHHHHHhhCCCcCCCHHHHHHhhcchhhhcCCcCCCHHHHHHHHHHHH
Confidence            222233332 232 456899999984321    1100               00000                       


Q ss_pred             ------CCceeeec-cccccccccceEEEEEe------------------------------------------------
Q 014486          246 ------DPMEIYVD-DEAKLTLHGLVQHYIKL------------------------------------------------  270 (423)
Q Consensus       246 ------~~~~~~~~-~~~~~~~~~~~~~~~~~------------------------------------------------  270 (423)
                            .+..+... .......+......+.+                                                
T Consensus       286 ~L~~~l~~~~lRR~k~~v~~~LP~k~~~~v~~~ls~~q~~lY~~~~~~~~~~~~~~~g~~~~~~l~~l~~Lrk~c~hp~l  365 (644)
T 1z3i_X          286 ELISIVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVESLQTGKISVSSLSSITSLKKLCNHPAL  365 (644)
T ss_dssp             HHHHHHHHHEECCCGGGGGGTSCCEEEEEEEECCCHHHHHHHHHHHHHHCGGGSSCTTCCCHHHHHHHHHHHHHHHCTHH
T ss_pred             HHHHHHHHHHHHhhHHhHhhhCCCceEEEEEeCCCHHHHHHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHhCCHHH
Confidence                  00000000 00000000000011100                                                


Q ss_pred             ------------------------------ChHHHHHHHHHHHHh---hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEE
Q 014486          271 ------------------------------SELEKNRKLNDLLDA---LDFNQVVIFVKSVSRAAELNKLLVECNFPSIC  317 (423)
Q Consensus       271 ------------------------------~~~~~~~~l~~ll~~---~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~  317 (423)
                                                    ....|...+..++..   ..+.++||||+....++.+.+.|...|+.+..
T Consensus       366 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~  445 (644)
T 1z3i_X          366 IYEKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVR  445 (644)
T ss_dssp             HHHHHHHTCTTCTTGGGTSCSSCCSSSCCGGGSHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEE
T ss_pred             HHHHHhcccchhhhHHhhccccccccccCcccChHHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHCCCCEEE
Confidence                                          012233334444433   24689999999999999999999999999999


Q ss_pred             EcCCCCHHHHHHHHHhhhcCCcc---EEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEE--EEe
Q 014486          318 IHSGMSQEERLTRYKGFKEGNKR---ILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAI--TFV  392 (423)
Q Consensus       318 ~~~~~~~~~r~~~~~~f~~~~~~---ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~--~~~  392 (423)
                      +||+++..+|.++++.|+++...   +|++|.++++|+|++++++||++++||++..+.|++||++|.||++.|.  .++
T Consensus       446 l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv  525 (644)
T 1z3i_X          446 LDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLL  525 (644)
T ss_dssp             ECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEE
T ss_pred             EeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEEEEE
Confidence            99999999999999999998764   8889999999999999999999999999999999999999999876544  345


Q ss_pred             cCc-ccHHHHHHHHHHHh
Q 014486          393 SSA-SDSDILNQVSKFMF  409 (423)
Q Consensus       393 ~~~-~~~~~~~~~~~~~~  409 (423)
                      ... .+..++....++..
T Consensus       526 ~~~tiEe~i~~~~~~K~~  543 (644)
T 1z3i_X          526 STGTIEEKILQRQAHKKA  543 (644)
T ss_dssp             ETTSHHHHHHHHHHHHHH
T ss_pred             ECCCHHHHHHHHHHHHHH
Confidence            443 34555666555554

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=1.5e-35  Score=254.83  Aligned_cols=207  Identities=33%  Similarity=0.596  Sum_probs=182.9

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      .+|+++++++.+.++|.+.|+..|+++|.++++.++.++++++.+|||+|||++|+++++..+.....++++||++|+++
T Consensus         4 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   83 (219)
T 1q0u_A            4 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRE   83 (219)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcHH
Confidence            46999999999999999999999999999999999999999999999999999999999998877666669999999999


Q ss_pred             HHHHHHHHHHHHhccCC---CceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchh
Q 014486          126 LAYQICHEFERFSTYLP---DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM  202 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~  202 (423)
                      |+.|+.+.++++....+   ++.+..+.|+.........+..+ ++|+|+||+++...+......+.+++++|+||||++
T Consensus        84 L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~-~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~  162 (219)
T 1q0u_A           84 LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQ-PHIVIGTPGRINDFIREQALDVHTAHILVVDEADLM  162 (219)
T ss_dssp             HHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSC-CSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHH
T ss_pred             HHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCC-CCEEEeCHHHHHHHHHcCCCCcCcceEEEEcCchHH
Confidence            99999999999876543   57888888887665544444333 699999999999999888788899999999999999


Q ss_pred             hccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeecc
Q 014486          203 LESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDD  254 (423)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~  254 (423)
                      .+ .++...+..+...+++..|++++|||+++++..+++.++.+|..+....
T Consensus       163 ~~-~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~~  213 (219)
T 1q0u_A          163 LD-MGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLE  213 (219)
T ss_dssp             HH-TTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEECC-
T ss_pred             hh-hChHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHcCCCeEEEeec
Confidence            87 6889999999999998999999999999999999999999987765543

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=100.00  E-value=1.9e-35  Score=255.93  Aligned_cols=207  Identities=29%  Similarity=0.540  Sum_probs=177.9

Q ss_pred             ccccCCCCcC-CCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC------CC
Q 014486           41 VGIHSSGFRD-FLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN------PG  113 (423)
Q Consensus        41 ~~~~~~~~~~-~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~------~~  113 (423)
                      .+....+|++ +++++.+.++|.+.||..|+++|.++++.++.++++++.+|||+|||++|++|++..+...      ..
T Consensus        14 ~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~   93 (228)
T 3iuy_A           14 IPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRN   93 (228)
T ss_dssp             CCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------C
T ss_pred             CCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccC
Confidence            3444567888 8999999999999999999999999999999999999999999999999999998866532      24


Q ss_pred             CeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccE
Q 014486          114 QVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRH  193 (423)
Q Consensus       114 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~  193 (423)
                      ++++||++|+++|+.|+.+.++++..  .++++..++|+.....+...+.++ ++|+|+||+++..++......+.++++
T Consensus        94 ~~~~lil~Pt~~L~~q~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~-~~iiv~Tp~~l~~~~~~~~~~~~~~~~  170 (228)
T 3iuy_A           94 GPGMLVLTPTRELALHVEAECSKYSY--KGLKSICIYGGRNRNGQIEDISKG-VDIIIATPGRLNDLQMNNSVNLRSITY  170 (228)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHCC--TTCCEEEECC------CHHHHHSC-CSEEEECHHHHHHHHHTTCCCCTTCCE
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHhcc--cCceEEEEECCCChHHHHHHhcCC-CCEEEECHHHHHHHHHcCCcCcccceE
Confidence            45899999999999999999999863  378899999998877777777666 699999999999998888888999999


Q ss_pred             EEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceee
Q 014486          194 FILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIY  251 (423)
Q Consensus       194 vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~  251 (423)
                      ||+||||++.+ .++...+..+...+++..|++++|||+++.+..++..++.+|..+.
T Consensus       171 lViDEah~~~~-~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~  227 (228)
T 3iuy_A          171 LVIDEADKMLD-MEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVY  227 (228)
T ss_dssp             EEECCHHHHHH-TTCHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEE
T ss_pred             EEEECHHHHhc-cchHHHHHHHHHhCCcCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence            99999999988 6899999999999999999999999999999999999998887654

>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=3.8e-35  Score=253.51  Aligned_cols=207  Identities=37%  Similarity=0.590  Sum_probs=177.1

Q ss_pred             cCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           44 HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      ...+|+++++++.+.+.|.+.|+..|+++|.++++.++.++++++.+|||+|||++|+++++..+.....++++||++|+
T Consensus        12 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (224)
T 1qde_A           12 VVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPT   91 (224)
T ss_dssp             CCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSS
T ss_pred             ccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECC
Confidence            34569999999999999999999999999999999999999999999999999999999999988776666799999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                      ++|+.|+++.++++.... ++++..+.|+.........+.+  ++|+|+||+++...+......+.++++||+||||++.
T Consensus        92 ~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~--~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEah~~~  168 (224)
T 1qde_A           92 RELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEML  168 (224)
T ss_dssp             HHHHHHHHHHHHHHTTTS-CCCEEEECC----------CTT--CSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHH
T ss_pred             HHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHhcCCC--CCEEEECHHHHHHHHHhCCcchhhCcEEEEcChhHHh
Confidence            999999999999987665 7888899998876666555544  6999999999999988888888999999999999998


Q ss_pred             ccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeecc
Q 014486          204 ESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDD  254 (423)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~  254 (423)
                      + .++...+..+...+++..|++++|||+++.+..+++.++.+|..+.+..
T Consensus       169 ~-~~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~  218 (224)
T 1qde_A          169 S-SGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKK  218 (224)
T ss_dssp             H-TTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC---
T ss_pred             h-hhhHHHHHHHHHhCCccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecC
Confidence            7 6899999999999999999999999999999999999999887765543

>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=1.1e-34  Score=284.07  Aligned_cols=294  Identities=17%  Similarity=0.163  Sum_probs=212.0

Q ss_pred             CHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHH
Q 014486           54 KPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHE  133 (423)
Q Consensus        54 ~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~  133 (423)
                      +...++++.+...    |.|.......+.+++++++||||||||+.++..+...    +   .++|++|+++||.|+++.
T Consensus       130 ~~d~l~~i~dl~~----p~~~~p~ar~l~rk~vlv~apTGSGKT~~al~~l~~~----~---~gl~l~PtR~LA~Qi~~~  198 (677)
T 3rc3_A          130 CKDDLRKISDLRI----PPNWYPDARAMQRKIIFHSGPTNSGKTYHAIQKYFSA----K---SGVYCGPLKLLAHEIFEK  198 (677)
T ss_dssp             CHHHHHHHTBCCC----GGGGCHHHHTSCCEEEEEECCTTSSHHHHHHHHHHHS----S---SEEEEESSHHHHHHHHHH
T ss_pred             CHHHHHHHhhccC----hhhhCHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhc----C---CeEEEeCHHHHHHHHHHH
Confidence            3444555544322    5566566667889999999999999998544444332    2   459999999999999999


Q ss_pred             HHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHH
Q 014486          134 FERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQ  213 (423)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~  213 (423)
                      +++.     ++++..++|+......   -.....+++++|++.+.        ....+++||+||+|++.+ .++...+.
T Consensus       199 l~~~-----g~~v~lltG~~~~iv~---TpGr~~~il~~T~e~~~--------l~~~v~lvVIDEaH~l~d-~~~g~~~~  261 (677)
T 3rc3_A          199 SNAA-----GVPCDLVTGEERVTVQ---PNGKQASHVSCTVEMCS--------VTTPYEVAVIDEIQMIRD-PARGWAWT  261 (677)
T ss_dssp             HHHT-----TCCEEEECSSCEECCS---TTCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGC-TTTHHHHH
T ss_pred             HHhc-----CCcEEEEECCeeEEec---CCCcccceeEecHhHhh--------hcccCCEEEEecceecCC-ccchHHHH
Confidence            8775     6788888888654110   00112578888886542        246779999999999976 67888888


Q ss_pred             HHHHhCC-CCceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEE
Q 014486          214 EIFKMTP-HDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVV  292 (423)
Q Consensus       214 ~~~~~~~-~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~i  292 (423)
                      .++..++ ...+++++|||.+ .+..+.... .....+.....  .     .........      + ..+... ....+
T Consensus       262 ~~l~~l~~~~i~il~~SAT~~-~i~~l~~~~-~~~~~v~~~~r--~-----~~l~~~~~~------l-~~l~~~-~~g~i  324 (677)
T 3rc3_A          262 RALLGLCAEEVHLCGEPAAID-LVMELMYTT-GEEVEVRDYKR--L-----TPISVLDHA------L-ESLDNL-RPGDC  324 (677)
T ss_dssp             HHHHHCCEEEEEEEECGGGHH-HHHHHHHHH-TCCEEEEECCC--S-----SCEEECSSC------C-CSGGGC-CTTEE
T ss_pred             HHHHccCccceEEEeccchHH-HHHHHHHhc-CCceEEEEeee--c-----chHHHHHHH------H-HHHHhc-CCCCE
Confidence            8888777 6789999999943 222222222 22222211100  0     000000000      0 011122 24568


Q ss_pred             EEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhc--CCccEEEEcCccccCCCCCCCCEEEEccC-----
Q 014486          293 IFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKE--GNKRILVATDLVGRGIDIERVNIVINYDM-----  365 (423)
Q Consensus       293 vf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~--~~~~ili~T~~~~~Gld~~~~~~vi~~~~-----  365 (423)
                      |||++++.++.+++.|.+.++.+..+||++++.+|..+++.|++  |..+|||||+++++|+|+ ++++||+++.     
T Consensus       325 If~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~k~~~  403 (677)
T 3rc3_A          325 IVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLIKPSI  403 (677)
T ss_dssp             EECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSBC---
T ss_pred             EEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCcccccc
Confidence            99999999999999999999999999999999999999999999  889999999999999999 8999999998     


Q ss_pred             ---------CCCcchhhhcccccCCCCCc---eEEEEEec
Q 014486          366 ---------PDSADTYLHRVGRAGRFGTK---GLAITFVS  393 (423)
Q Consensus       366 ---------~~s~~~~~Q~~GR~~R~g~~---~~~~~~~~  393 (423)
                               |.+..+|.||+||+||.|+.   |.++.++.
T Consensus       404 ~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l~~  443 (677)
T 3rc3_A          404 NEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNH  443 (677)
T ss_dssp             --------CBCCHHHHHHHHTTBTCTTSSCSSEEEEESST
T ss_pred             ccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEEec
Confidence                     77899999999999999965   56555543

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=100.00  E-value=3.5e-34  Score=244.40  Aligned_cols=201  Identities=37%  Similarity=0.614  Sum_probs=179.0

Q ss_pred             CCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC---CCCeEEEEEecC
Q 014486           47 GFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN---PGQVTALVLCHT  123 (423)
Q Consensus        47 ~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~  123 (423)
                      +|+++++++.+.+.|.+.|+..|+++|.++++.++.++++++.+|||+|||++++++++..+...   ..++++||++|+
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            58999999999999999999999999999999999999999999999999999999999877542   334589999999


Q ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          124 RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       124 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                      ++|+.|+.+.++++..   .+++..++|+.....+...+..+ ++|+|+||+++..++......+.++++||+||||++.
T Consensus        82 ~~L~~q~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~  157 (207)
T 2gxq_A           82 RELALQVASELTAVAP---HLKVVAVYGGTGYGKQKEALLRG-ADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEML  157 (207)
T ss_dssp             HHHHHHHHHHHHHHCT---TSCEEEECSSSCSHHHHHHHHHC-CSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHH
T ss_pred             HHHHHHHHHHHHHHhh---cceEEEEECCCChHHHHHHhhCC-CCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhh
Confidence            9999999999998864   46888899988877766666665 6999999999999988888888999999999999998


Q ss_pred             ccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeee
Q 014486          204 ESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV  252 (423)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  252 (423)
                      + .++...+..+...+++..|++++|||+++.+..+.+.++.+|..+.+
T Consensus       158 ~-~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~~  205 (207)
T 2gxq_A          158 S-MGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV  205 (207)
T ss_dssp             H-TTCHHHHHHHHHTSCTTSEEEEECSSCCHHHHHHHHHHCSSCEEEEC
T ss_pred             c-cchHHHHHHHHHhCCccCeEEEEEEecCHHHHHHHHHHcCCCeEEEc
Confidence            7 68999999999999999999999999999999999999888876543

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=100.00  E-value=2.4e-34  Score=253.49  Aligned_cols=202  Identities=27%  Similarity=0.476  Sum_probs=174.2

Q ss_pred             cCCCCcCCC--CCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC----CCCeEE
Q 014486           44 HSSGFRDFL--LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN----PGQVTA  117 (423)
Q Consensus        44 ~~~~~~~~~--l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~----~~~~~~  117 (423)
                      ....|.+++  +++.++++|.++||..|+++|.++++.++.++++++++|||+|||++|++|++..+...    ..+.++
T Consensus        50 ~~~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~  129 (262)
T 3ly5_A           50 EDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGV  129 (262)
T ss_dssp             GGGCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCE
T ss_pred             ccCChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceE
Confidence            345677777  99999999999999999999999999999999999999999999999999999765431    134489


Q ss_pred             EEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC-CCCCCCccEEEE
Q 014486          118 LVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK-DLSLKNVRHFIL  196 (423)
Q Consensus       118 lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~-~~~~~~~~~vVv  196 (423)
                      ||++|+++|+.|+++.++++.... +..+..+.|+.........+..+ ++|+|+||+++..++... ...+.++++||+
T Consensus       130 lil~Pt~~La~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lVi  207 (262)
T 3ly5_A          130 LILSPTRELAMQTFGVLKELMTHH-VHTYGLIMGGSNRSAEAQKLGNG-INIIVATPGRLLDHMQNTPGFMYKNLQCLVI  207 (262)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTC-CSCEEEECSSSCHHHHHHHHHHC-CSEEEECHHHHHHHHHHCTTCCCTTCCEEEE
T ss_pred             EEEeCCHHHHHHHHHHHHHHHhhc-CceEEEEECCCCHHHHHHHhcCC-CCEEEEcHHHHHHHHHccCCcccccCCEEEE
Confidence            999999999999999999988765 77888999998888777777776 699999999999877654 467889999999


Q ss_pred             cCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCc
Q 014486          197 DECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPM  248 (423)
Q Consensus       197 DE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~  248 (423)
                      ||||++.+ .++...+..+...++...|++++|||+++.+..+.+.++..+.
T Consensus       208 DEah~l~~-~~~~~~l~~i~~~~~~~~q~l~~SAT~~~~v~~~~~~~l~~~~  258 (262)
T 3ly5_A          208 DEADRILD-VGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEP  258 (262)
T ss_dssp             CSHHHHHH-TTCHHHHHHHHHHSCSSSEEEEECSSCCHHHHHHHHHHCSSCC
T ss_pred             cChHHHhh-hhHHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHcCCCC
Confidence            99999988 6899999999999999999999999999999999888776543

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=100.00  E-value=1.4e-32  Score=261.80  Aligned_cols=318  Identities=19%  Similarity=0.194  Sum_probs=231.5

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDI  144 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~  144 (423)
                      |+ +|++.|.-+.-.+..|+  |..+.||+|||+++.+|++.....+.   .+.|++|+..||.|-++++..+...+ ++
T Consensus        73 g~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~G~---~vhVvT~ndyLA~rdae~m~~l~~~L-gl  145 (822)
T 3jux_A           73 GM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALIGK---GVHLVTVNDYLARRDALWMGPVYLFL-GL  145 (822)
T ss_dssp             SC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTTSS---CEEEEESSHHHHHHHHHHHHHHHHHT-TC
T ss_pred             CC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhcCC---ceEEEeccHHHHHhHHHHHHHHHHHh-CC
Confidence            44 78899988877777665  99999999999999999986665543   68999999999999999999998887 89


Q ss_pred             eEEEEEcC--------------------------------------------------cchHHHHHHHhcCCCcEEEech
Q 014486          145 KVAVFYGG--------------------------------------------------VNIKIHKDLLKNECPQIVVGTP  174 (423)
Q Consensus       145 ~~~~~~~~--------------------------------------------------~~~~~~~~~~~~~~~~ilv~T~  174 (423)
                      ++.++...                                                  .+.. +.+..+.  .+|+++|.
T Consensus       146 svg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~-err~aY~--~DItYgTn  222 (822)
T 3jux_A          146 RVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEI-TRKEAYL--CDVTYGTN  222 (822)
T ss_dssp             CEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBC-CHHHHHH--SSEEEEEH
T ss_pred             EEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHH-HHHHHhc--CCCEEccC
Confidence            99998872                                                  1111 1222222  39999999


Q ss_pred             HHHH-HHHhcCC------CCCCCccEEEEcCcchhhcc------------CCcHH---HHHHHHHhC-------------
Q 014486          175 GRIL-ALARDKD------LSLKNVRHFILDECDKMLES------------LDMRR---DVQEIFKMT-------------  219 (423)
Q Consensus       175 ~~l~-~~~~~~~------~~~~~~~~vVvDE~h~~~~~------------~~~~~---~~~~~~~~~-------------  219 (423)
                      .-|- ++++.+.      .-...+.+.||||+|.++-+            .....   .+..+...+             
T Consensus       223 ~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiLIDeArtPLiISg~~~~~~~~y~~~~~~v~~l~~~~dy~vdek~~  302 (822)
T 3jux_A          223 NEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEKAR  302 (822)
T ss_dssp             HHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHHTTGGGSCEEEECCCCSCHHHHHHHHHHTTSSCBTTTEEECCSSS
T ss_pred             cchhhHhHHhhccCCHHHhccCCCCeEEEecccceeecCCCCCceeeCCCCCccHHHHHHHHHHHhcCcCCcEEEEcccC
Confidence            8763 4555332      22466889999999987621            00000   111111111             


Q ss_pred             -------------------------------------------CCC----------------------------------
Q 014486          220 -------------------------------------------PHD----------------------------------  222 (423)
Q Consensus       220 -------------------------------------------~~~----------------------------------  222 (423)
                                                                 .++                                  
T Consensus       303 ~v~lTe~G~~~~E~~l~i~nly~~~n~~l~~~i~~AL~A~~l~~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQai  382 (822)
T 3jux_A          303 TIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIVDEFTGRLLPGRRYSGGLHQAI  382 (822)
T ss_dssp             CEEECHHHHHHHHHHHTCSCTTSGGGHHHHHHHHHHHHHHHHSTTTSSEEEETTEEEECSSSSCSCCCSCCCGGGHHHHH
T ss_pred             eEEECHHHHHHHHHHhCCccccchhhhHHHHHHHHHHHHHHHHcCCCcEEEECCEEEEEECCCCcCCCCCcCchHHHHHH
Confidence                                                       000                                  


Q ss_pred             ---------------------------ceEEEEeccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHH
Q 014486          223 ---------------------------KQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEK  275 (423)
Q Consensus       223 ---------------------------~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  275 (423)
                                                 .++.+||||+..+...+.+.+....  +.+....+.. .......+.....+|
T Consensus       383 EaKEgv~i~~e~~tla~IT~Qn~Fr~Y~kL~GMTGTa~te~~Ef~~iY~l~v--v~IPtnkp~~-R~d~~d~vy~t~~eK  459 (822)
T 3jux_A          383 EAKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESEFVQVYGMEV--VVIPTHKPMI-RKDHDDLVFRTQKEK  459 (822)
T ss_dssp             HHHHSSCCCCCCCEEEEECHHHHHTTSSEEEEEESSCGGGHHHHHHHSCCCE--EECCCSSCCC-CEECCCEEESSHHHH
T ss_pred             HHHcCCCCCCCcchhHHHHHHHHHHHhhHHeEECCCCchHHHHHHHHhCCeE--EEECCCCCcc-eeecCcEEEecHHHH
Confidence                                       0689999999988776665554332  2222221111 111122455677778


Q ss_pred             HHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCC
Q 014486          276 NRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGID  353 (423)
Q Consensus       276 ~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld  353 (423)
                      ...+...+...  .+.++||||++++.++.+++.|.+.|+++..+|++....++..+...++.|  .|+|||++++||+|
T Consensus       460 ~~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgRGtD  537 (822)
T 3jux_A          460 YEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGRGTD  537 (822)
T ss_dssp             HHHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTTTCC
T ss_pred             HHHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhCCcC
Confidence            88888877653  568999999999999999999999999999999996555555455555544  69999999999999


Q ss_pred             CC--------CCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          354 IE--------RVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       354 ~~--------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      ++        +..+||+++.|.|...|.||+||+||.|.+|.++.|++..++
T Consensus       538 I~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD~  589 (822)
T 3jux_A          538 IKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDD  589 (822)
T ss_dssp             CCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTSH
T ss_pred             ccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhHH
Confidence            98        667999999999999999999999999999999999987553

>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=8.7e-34  Score=246.84  Aligned_cols=205  Identities=26%  Similarity=0.499  Sum_probs=177.1

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC----CCCCeEEEEE
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP----NPGQVTALVL  120 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~----~~~~~~~lil  120 (423)
                      ..+|+++++++.+.++|.+.|+..|+++|.++++.++.++++++.+|||+|||++|++|++..+..    ...++++||+
T Consensus        24 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil  103 (236)
T 2pl3_A           24 ITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLII  103 (236)
T ss_dssp             CSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEE
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEE
Confidence            456999999999999999999999999999999999999999999999999999999999876532    1234489999


Q ss_pred             ecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC-CCCCCCccEEEEcCc
Q 014486          121 CHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK-DLSLKNVRHFILDEC  199 (423)
Q Consensus       121 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~-~~~~~~~~~vVvDE~  199 (423)
                      +|+++|+.|+.+.++++.... ++++..++|+.....+...+.  .++|+|+||+++...+... ...+.++++||+|||
T Consensus       104 ~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~--~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEa  180 (236)
T 2pl3_A          104 SPTRELAYQTFEVLRKVGKNH-DFSAGLIIGGKDLKHEAERIN--NINILVCTPGRLLQHMDETVSFHATDLQMLVLDEA  180 (236)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTS-SCCEEEECCC--CHHHHHHHT--TCSEEEECHHHHHHHHHHCSSCCCTTCCEEEETTH
T ss_pred             eCCHHHHHHHHHHHHHHhCCC-CeeEEEEECCCCHHHHHHhCC--CCCEEEECHHHHHHHHHhcCCcccccccEEEEeCh
Confidence            999999999999999987654 688999999887766665553  3699999999999877654 466789999999999


Q ss_pred             chhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeeec
Q 014486          200 DKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVD  253 (423)
Q Consensus       200 h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~  253 (423)
                      |++.+ .++...+..+...+++..|++++|||+++.+..+.+.++.+|..+.+.
T Consensus       181 h~~~~-~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~  233 (236)
T 2pl3_A          181 DRILD-MGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVH  233 (236)
T ss_dssp             HHHHH-TTTHHHHHHHHHTSCTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECC
T ss_pred             HHHhc-CCcHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeC
Confidence            99987 688999999999999999999999999999999999999888776553

>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=4.2e-34  Score=251.48  Aligned_cols=208  Identities=28%  Similarity=0.511  Sum_probs=180.9

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC---------CCCe
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN---------PGQV  115 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~---------~~~~  115 (423)
                      ..+|+++++++.+.++|.+.||..|+++|.++++.++.++++++.+|||+|||++|++|++..+...         ..++
T Consensus        22 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~  101 (253)
T 1wrb_A           22 IENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYP  101 (253)
T ss_dssp             CCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCC
T ss_pred             cCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCc
Confidence            3569999999999999999999999999999999999999999999999999999999999875432         2235


Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEE
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFI  195 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vV  195 (423)
                      ++||++|+++|+.|+.+.++++.... ++.+..++|+.....+...+..+ ++|+|+||+++..++......+.++++||
T Consensus       102 ~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lV  179 (253)
T 1wrb_A          102 KCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREVQMG-CHLLVATPGRLVDFIEKNKISLEFCKYIV  179 (253)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHHSSC-CSEEEECHHHHHHHHHTTSBCCTTCCEEE
T ss_pred             eEEEEECCHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhCCC-CCEEEECHHHHHHHHHcCCCChhhCCEEE
Confidence            89999999999999999999987664 67888999998887777766665 69999999999999988888889999999


Q ss_pred             EcCcchhhccCCcHHHHHHHHHh--CCC--CceEEEEeccCCccHHHHHHHhccCCceeeeccc
Q 014486          196 LDECDKMLESLDMRRDVQEIFKM--TPH--DKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDE  255 (423)
Q Consensus       196 vDE~h~~~~~~~~~~~~~~~~~~--~~~--~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  255 (423)
                      +||||++.+ .++...+..+...  .+.  ..|++++|||+++.+..+++.++.++..+.+...
T Consensus       180 iDEah~~~~-~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  242 (253)
T 1wrb_A          180 LDEADRMLD-MGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRV  242 (253)
T ss_dssp             EETHHHHHH-TTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC--
T ss_pred             EeCHHHHHh-CchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCC
Confidence            999999988 6899999999885  343  6799999999999999999999988877765543

>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=2.4e-33  Score=285.59  Aligned_cols=325  Identities=14%  Similarity=0.134  Sum_probs=216.0

Q ss_pred             CCChhhhhccccccc--------------CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAIL--------------GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHE  133 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~--------------~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~  133 (423)
                      .|||+|..+++.++.              +++++++++||||||+++ ++++..+...+...++|||+|+++|+.|+.+.
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            699999999998875              367999999999999997 55555554434445999999999999999999


Q ss_pred             HHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC--CCCCCccEEEEcCcchhhccCCcHHH
Q 014486          134 FERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD--LSLKNVRHFILDECDKMLESLDMRRD  211 (423)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~--~~~~~~~~vVvDE~h~~~~~~~~~~~  211 (423)
                      +..+...       .+.++.+.......+....++|+|+|+++|..++....  ..+..+.+||+||||++..    ...
T Consensus       350 f~~f~~~-------~v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~----~~~  418 (1038)
T 2w00_A          350 YQRFSPD-------SVNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQF----GEA  418 (1038)
T ss_dssp             HHTTSTT-------CSSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHH----HHH
T ss_pred             HHHhccc-------ccccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcc----hHH
Confidence            9887532       12244444555555554447999999999998776432  2356788999999998753    233


Q ss_pred             HHHHHHhCCCCceEEEEeccCCccHH----HHHHHhccC-----------------Cceeeeccc-ccc----------c
Q 014486          212 VQEIFKMTPHDKQVMMFSATLSKEIR----PVCKKFMQD-----------------PMEIYVDDE-AKL----------T  259 (423)
Q Consensus       212 ~~~~~~~~~~~~~~v~~SAT~~~~~~----~~~~~~~~~-----------------~~~~~~~~~-~~~----------~  259 (423)
                      ...+...++ ..+++++||||.....    .....+++.                 |..+..... ...          .
T Consensus       419 ~~~I~~~~p-~a~~lgfTATP~~~~~~~~~~~t~~~FG~~i~~Y~l~~AI~dg~l~p~~v~y~~v~~~~~~~~~e~d~~~  497 (1038)
T 2w00_A          419 QKNLKKKFK-RYYQFGFTGTPIFPENALGSETTASVFGRELHSYVITDAIRDEKVLKFKVDYNDVRPQFKSLETETDEKK  497 (1038)
T ss_dssp             HHHHHHHCS-SEEEEEEESSCCCSTTCTTSCCHHHHHCSEEEEECHHHHHHHTSSCCEEEEECCCCGGGHHHHTCCCHHH
T ss_pred             HHHHHHhCC-cccEEEEeCCccccccchhhhHHHHHhCCeeEeecHHHHHhCCCcCCeEEEEEeccchhhhccccccHHH
Confidence            455666665 4789999999975321    011111111                 111111000 000          0


Q ss_pred             cccceEEEEEeChHHHHHHHH-HHHHhh-----------cCCcEEEEEcChhhHHHHHHHHHhCC------------CCe
Q 014486          260 LHGLVQHYIKLSELEKNRKLN-DLLDAL-----------DFNQVVIFVKSVSRAAELNKLLVECN------------FPS  315 (423)
Q Consensus       260 ~~~~~~~~~~~~~~~~~~~l~-~ll~~~-----------~~~~~ivf~~~~~~~~~l~~~L~~~~------------~~~  315 (423)
                      ........ ......+...+. .++...           .+.++||||+++..|..+++.|.+.+            +++
T Consensus       498 ~~~i~~~~-~l~~~~ri~~I~~~Il~~~~~~~~~~~~~~~g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~  576 (1038)
T 2w00_A          498 LSAAENQQ-AFLHPMRIQEITQYILNNFRQKTHRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRI  576 (1038)
T ss_dssp             HHHTCSTT-TTTCHHHHHHHHHHHHHHHHHHTTCSSSSCCCCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCE
T ss_pred             HHHHHHHH-HhcCHHHHHHHHHHHHHHHHHhhhhhcccCCCCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcE
Confidence            00000000 001122222322 233321           23579999999999999999997754            455


Q ss_pred             E-EEcCC----------C----------CH-----------------------------HHHHHHHHhhhcCCccEEEEc
Q 014486          316 I-CIHSG----------M----------SQ-----------------------------EERLTRYKGFKEGNKRILVAT  345 (423)
Q Consensus       316 ~-~~~~~----------~----------~~-----------------------------~~r~~~~~~f~~~~~~ili~T  345 (423)
                      . .+|+.          +          ++                             ..|..++++|++|+++|||+|
T Consensus       577 avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvv  656 (1038)
T 2w00_A          577 ATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAIREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVV  656 (1038)
T ss_dssp             EEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHHHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEES
T ss_pred             EEEEeCCCccccccccccccccccccccchhHHHHHHHHHHHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEc
Confidence            4 44542          2          22                             137788999999999999999


Q ss_pred             CccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCc----eEEEEEecCcccHHHHHHHHHHHh
Q 014486          346 DLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTK----GLAITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       346 ~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~----~~~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                      +++.+|+|+|.+ +++.++.|.+...|+|++||++|.+..    |.++.|+.  ....+.+++..+.+
T Consensus       657 d~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~--~~~~l~~Al~~y~~  721 (1038)
T 2w00_A          657 GMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRD--LERSTIDAITLFGD  721 (1038)
T ss_dssp             STTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSC--CHHHHHHHHHHTSC
T ss_pred             chHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEccc--cHHHHHHHHHHHhC
Confidence            999999999999 678899999999999999999998653    66776665  34444555554443

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=100.00  E-value=1.4e-33  Score=247.04  Aligned_cols=209  Identities=26%  Similarity=0.448  Sum_probs=173.3

Q ss_pred             CCCCcCC----CCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC-CCCCeEEEE
Q 014486           45 SSGFRDF----LLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP-NPGQVTALV  119 (423)
Q Consensus        45 ~~~~~~~----~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~li  119 (423)
                      ..+|+++    ++++.++++|.+.||..|+++|.++++.++.++++++.+|||+|||++|++|++..+.. ...++++||
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            3456665    89999999999999999999999999999999999999999999999999999987764 234458999


Q ss_pred             EecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcC--CCCCCCccEEEEc
Q 014486          120 LCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDK--DLSLKNVRHFILD  197 (423)
Q Consensus       120 l~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~--~~~~~~~~~vVvD  197 (423)
                      ++|+++|+.|+++.++++.... ++++..++|+..............++|+|+||+++..++...  ...+.++++||+|
T Consensus       104 l~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViD  182 (245)
T 3dkp_A          104 ISPTRELASQIHRELIKISEGT-GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVD  182 (245)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTS-CCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEES
T ss_pred             EeCCHHHHHHHHHHHHHHhccc-CceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEe
Confidence            9999999999999999987664 677777766544333322223345799999999999988776  4678899999999


Q ss_pred             Ccchhhcc--CCcHHHHHHHHHhC-CCCceEEEEeccCCccHHHHHHHhccCCceeeecc
Q 014486          198 ECDKMLES--LDMRRDVQEIFKMT-PHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDD  254 (423)
Q Consensus       198 E~h~~~~~--~~~~~~~~~~~~~~-~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~~  254 (423)
                      |||++.++  .++...+..++..+ +...|++++|||+++++..+++.++.+|..+.+..
T Consensus       183 Eah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~  242 (245)
T 3dkp_A          183 ESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGA  242 (245)
T ss_dssp             SHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC
T ss_pred             ChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCC
Confidence            99999864  47888888887665 45789999999999999999999999888776654

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.97  E-value=6.7e-28  Score=233.98  Aligned_cols=318  Identities=20%  Similarity=0.196  Sum_probs=231.4

Q ss_pred             CCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           64 SGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        64 ~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      .|+ +|+++|..+++.+++|+  +..+.||+|||+++++|++.....+.   .++|++||+.||.|.++.+..+.... +
T Consensus        76 lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~G~---qv~VvTPTreLA~Qdae~m~~l~~~l-G  148 (997)
T 2ipc_A           76 LGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALTGK---GVHVVTVNDYLARRDAEWMGPVYRGL-G  148 (997)
T ss_dssp             TCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTTCS---CCEEEESSHHHHHHHHHHHHHHHHTT-T
T ss_pred             hCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHhCC---CEEEEeCCHHHHHHHHHHHHHHHHhc-C
Confidence            488 99999999999999998  99999999999999999965444332   78999999999999999999998887 8


Q ss_pred             ceEEEEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcCC------CCCC---CccEEEEcCcchhhccCC------
Q 014486          144 IKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDKD------LSLK---NVRHFILDECDKMLESLD------  207 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~~------~~~~---~~~~vVvDE~h~~~~~~~------  207 (423)
                      +++..+.||.+.......  .+ ++|+|+||+.| +++++.+.      ..+.   +++++|+||+|.++.+..      
T Consensus       149 Lsv~~i~Gg~~~~~r~~a--y~-~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmLiDeartPLII  225 (997)
T 2ipc_A          149 LSVGVIQHASTPAERRKA--YL-ADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSILIDEARTPLII  225 (997)
T ss_dssp             CCEEECCTTCCHHHHHHH--HT-SSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHTTSSTTSCEEE
T ss_pred             CeEEEEeCCCCHHHHHHH--cC-CCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHHHhCCCCCeee
Confidence            999999999875433333  23 59999999999 78777653      4567   899999999999873211      


Q ss_pred             ---------cHHHHHHHHHhCCCC--------------------------------------------------------
Q 014486          208 ---------MRRDVQEIFKMTPHD--------------------------------------------------------  222 (423)
Q Consensus       208 ---------~~~~~~~~~~~~~~~--------------------------------------------------------  222 (423)
                               ....+..+...++..                                                        
T Consensus       226 Sgp~~~~~~lY~~~~~~i~~L~~~~~~~~~~~~~~~~dy~vdek~r~v~LTe~G~~~~E~~l~i~~Ly~~~n~~l~~~i~  305 (997)
T 2ipc_A          226 SGPAEKATDLYYKMAEIAKKLERGLPAEPGVRKEPTGDYTVEEKNRSVHLTLQGIAKAEKLLGIEGLFSPENMELAHMLI  305 (997)
T ss_dssp             EESCSSCHHHHHHHHHHHHHSCCCCCCCSSSCCCSSCCCCCTTSCCCCCCCHHHHHHHHHHHSCHHHHTTTCHHHHHHHH
T ss_pred             eCCCccchHHHHHHHHHHHHhhhccccccccccCCCCCeEEecCcceEEEchHHHHHHHHHcCCccccCchhHHHHHHHH
Confidence                     111222222222210                                                        


Q ss_pred             -------------------------------------------------------------------------ceEEEEe
Q 014486          223 -------------------------------------------------------------------------KQVMMFS  229 (423)
Q Consensus       223 -------------------------------------------------------------------------~~~v~~S  229 (423)
                                                                                               .++.+||
T Consensus       306 ~ALrA~~lf~rd~dYiV~dgeV~IVDe~TGR~m~grrwsdGLHQAiEAKEgv~I~~e~~TlAsIT~QnyFr~Y~kLsGMT  385 (997)
T 2ipc_A          306 QAIRAKELYHRDRDYIVQDGQVIIVDEFTGRLMPGRRYGEGLHQAIEAKEGVRIERENQTLATITYQNFFRLYEKRAGMT  385 (997)
T ss_dssp             HHHHHHHSSCHHHHEEECSSCEEEEETTTTEECTTCCCGGGHHHHHHHHTTCCCCCSCEEEEEECHHHHHTTSSEEEEEE
T ss_pred             HHHHHHHHHhcCCCeEEECCEEEEEECCCCeeCCCCcccHHHHHHHHHHhCCCCCCCceeeeeeeHHHHHHhChHheecC
Confidence                                                                                     0688899


Q ss_pred             ccCCccHHHHHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHH-hh-cCCcEEEEEcChhhHHHHHHH
Q 014486          230 ATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLD-AL-DFNQVVIFVKSVSRAAELNKL  307 (423)
Q Consensus       230 AT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~-~~-~~~~~ivf~~~~~~~~~l~~~  307 (423)
                      +|...+...+.+.+......+  +...+..... ....+......|...+.+-+. .+ .+.++||.|.+++.++.+++.
T Consensus       386 GTA~tE~~Ef~~iY~l~Vv~I--PTn~p~~R~D-~~d~vy~t~~~K~~AIv~eI~~~~~~GqPVLVgT~SIe~SE~LS~~  462 (997)
T 2ipc_A          386 GTAKTEEKEFQEIYGMDVVVV--PTNRPVIRKD-FPDVVYRTEKGKFYAVVEEIAEKYERGQPVLVGTISIEKSERLSQM  462 (997)
T ss_dssp             SSCGGGHHHHHHHHCCCEEEC--CCSSCCCCEE-EEEEEESSHHHHHHHHHHHHHHHHHHTCCEEEECSSHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHhCCCEEEc--CCCCCccccc-CCCeEEcCHHHHHHHHHHHHHHHHHCCCCEEEEeCCHHHHHHHHHH
Confidence            999887776666555543322  2222222222 223344555666665554443 22 568999999999999999999


Q ss_pred             HH----------------------------------------------------------------------------hC
Q 014486          308 LV----------------------------------------------------------------------------EC  311 (423)
Q Consensus       308 L~----------------------------------------------------------------------------~~  311 (423)
                      |+                                                                            +.
T Consensus       463 L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  542 (997)
T 2ipc_A          463 LKEPRLYLPRLEMRLELFKKASQKQQGPEWERLRKLLERPAQLKDEDLAPFEGLIPPKGNLRTAWEGLKRAVHTLAVLRQ  542 (997)
T ss_dssp             HHCGGGGHHHHHHHHHHHHHHHTTCCSHHHHHHHHHTSSSTTCSHHHHSGGGGGCCSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhccccchhhhhhhhhhhhhhhhccccchhhhhhhhhccccccccccccccccccccccccccccccchhhhhhHHHHc
Confidence            98                                                                            56


Q ss_pred             CCCeEEEcCCCCHHHHHHHHHhhhcCC-ccEEEEcCccccCCCCCCC-------------------C-------------
Q 014486          312 NFPSICIHSGMSQEERLTRYKGFKEGN-KRILVATDLVGRGIDIERV-------------------N-------------  358 (423)
Q Consensus       312 ~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~ili~T~~~~~Gld~~~~-------------------~-------------  358 (423)
                      |++.-+++......+ .+++..  .|. ..|-|||++++||.|+.--                   .             
T Consensus       543 gI~H~VLNAK~he~E-AeIIAq--AG~~GaVTIATNMAGRGTDIkLggn~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  619 (997)
T 2ipc_A          543 GIPHQVLNAKHHARE-AEIVAQ--AGRSKTVTIATNMAGRGTDIKLGGNPEYLAAALLEKEGFDRYEWKVELFIKKMVAG  619 (997)
T ss_dssp             CCCCCEECSSSHHHH-HHHHHT--TTSTTCEEEECSSTTTTSCCCSSCCHHHHHHHTTSSSCSSTTHHHHHHHHHHHHHT
T ss_pred             CCCeeeccccchHHH-HHHHHh--cCCCCeEEEEecccCCCcCeecCCCHHHHHHHHHHhhccccccccccccccccccc
Confidence            777778887654333 233332  333 4599999999999998532                   1             


Q ss_pred             ------------------------------------------EEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcc
Q 014486          359 ------------------------------------------IVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSAS  396 (423)
Q Consensus       359 ------------------------------------------~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  396 (423)
                                                                +||-...+.|..--.|-.||+||.|.+|....|++-.+
T Consensus       620 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~V~e~GGLhVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLeD  699 (997)
T 2ipc_A          620 KEEEARALAQELGIREELLERIREIREECKQDEERVRALGGLFIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDD  699 (997)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTTCCCCEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESSS
T ss_pred             chhhccccchhhhhhhhHHHHHHHhhhhhhhhhhHHHhcCCeEEEeccCCchHHHHHHHhcccccCCCCCCeEEEEECCh
Confidence                                                      78888888898889999999999999999999988644


Q ss_pred             c
Q 014486          397 D  397 (423)
Q Consensus       397 ~  397 (423)
                      +
T Consensus       700 d  700 (997)
T 2ipc_A          700 D  700 (997)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.96  E-value=2.8e-28  Score=200.17  Aligned_cols=155  Identities=66%  Similarity=1.009  Sum_probs=145.1

Q ss_pred             ccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCcc
Q 014486          261 HGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKR  340 (423)
Q Consensus       261 ~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  340 (423)
                      ..+.+.+..++...|...+..+++..+.+++||||++.+.++.+++.|...++++..+||++++.+|..+++.|++|+.+
T Consensus         4 ~~i~q~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~   83 (172)
T 1t5i_A            4 HGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRR   83 (172)
T ss_dssp             -CCEEEEEECCGGGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCS
T ss_pred             CCeEEEEEECChHHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCCc
Confidence            45677888888899999999999998889999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhhh
Q 014486          341 ILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGSF  415 (423)
Q Consensus       341 ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (423)
                      |||||+++++|+|+|++++||++++|+++..|.||+||+||.|+.|.+++|+++.++...++.+++.++..+...
T Consensus        84 vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  158 (172)
T 1t5i_A           84 ILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISEL  158 (172)
T ss_dssp             EEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEEC
T ss_pred             EEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHhcchhhC
Confidence            999999999999999999999999999999999999999999999999999998777888999999998776543

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.96  E-value=1.5e-27  Score=194.30  Aligned_cols=154  Identities=36%  Similarity=0.607  Sum_probs=143.7

Q ss_pred             cccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCc
Q 014486          260 LHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNK  339 (423)
Q Consensus       260 ~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~  339 (423)
                      ...+.+.+..++...|...+.+++....++++||||++.+.+..+++.|...|+.+..+||++++.+|..+++.|++|+.
T Consensus         7 ~~~i~~~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~   86 (163)
T 2hjv_A            7 TRNIEHAVIQVREENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEY   86 (163)
T ss_dssp             CCCEEEEEEECCGGGHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             cccceEEEEECChHHHHHHHHHHHHhcCCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCC
Confidence            35567788888889999999999999888999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhh
Q 014486          340 RILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGS  414 (423)
Q Consensus       340 ~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  414 (423)
                      +|||+|+++++|+|+|++++||++++|+++..|.||+||+||.|++|.+++|+.+ .+...+..+++.++..+..
T Consensus        87 ~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~-~~~~~~~~i~~~~~~~~~~  160 (163)
T 2hjv_A           87 RYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTA-FEKRFLADIEEYIGFEIQK  160 (163)
T ss_dssp             SEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECG-GGHHHHHHHHHHHTSCCEE
T ss_pred             eEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecH-HHHHHHHHHHHHHCCCcCc
Confidence            9999999999999999999999999999999999999999999999999999975 5778889999999877643

>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=2.2e-26  Score=227.16  Aligned_cols=117  Identities=22%  Similarity=0.355  Sum_probs=106.4

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccC-
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDM-  365 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~-  365 (423)
                      .+.++||||++...++.+.+.|.+.|+++..+|+++++.+|..+++.|++|+++|||||+++++|+|+|++++||+++. 
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            4679999999999999999999999999999999999999999999999999999999999999999999999999997 


Q ss_pred             ----CCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHH
Q 014486          366 ----PDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVS  405 (423)
Q Consensus       366 ----~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~  405 (423)
                          |.|...|+||+||+||.+ .|.+++++++. +..+...+.
T Consensus       518 ~~G~p~s~~~~iQr~GRagR~~-~G~~i~~~~~~-~~~~~~~i~  559 (664)
T 1c4o_A          518 KEGFLRSERSLIQTIGRAARNA-RGEVWLYADRV-SEAMQRAIE  559 (664)
T ss_dssp             SCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSC-CHHHHHHHH
T ss_pred             ccCCCCCHHHHHHHHCccCcCC-CCEEEEEEcCC-CHHHHHHHH
Confidence                899999999999999985 79999888754 444444443

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.95  E-value=2.4e-27  Score=197.64  Aligned_cols=169  Identities=29%  Similarity=0.497  Sum_probs=137.9

Q ss_pred             hccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCC
Q 014486          243 FMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGM  322 (423)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~  322 (423)
                      ++.+|..+.+.... .....+.+.+..+....|...+.+++.... +++||||+++..++.+++.|...++++..+||++
T Consensus        11 ~~~~p~~i~v~~~~-~~~~~i~q~~~~~~~~~K~~~L~~~l~~~~-~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~   88 (191)
T 2p6n_A           11 VDLGTENLYFQSMG-AASLDVIQEVEYVKEEAKMVYLLECLQKTP-PPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGK   88 (191)
T ss_dssp             ------------------CCSEEEEEECCGGGHHHHHHHHHTTSC-SCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTS
T ss_pred             ccCCCEEEEECCCC-CCCcCceEEEEEcChHHHHHHHHHHHHhCC-CCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCC
Confidence            45556666554433 344667788888888899999999987754 6899999999999999999999999999999999


Q ss_pred             CHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHH
Q 014486          323 SQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILN  402 (423)
Q Consensus       323 ~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~  402 (423)
                      ++.+|..+++.|++|+.+|||||+++++|+|+|++++||+|++|+++..|+||+||+||.|++|.+++|+++..+.....
T Consensus        89 ~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~  168 (191)
T 2p6n_A           89 DQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLM  168 (191)
T ss_dssp             CHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCHHHHH
T ss_pred             CHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999877888888


Q ss_pred             HHHHHHhcchh
Q 014486          403 QVSKFMFLLIG  413 (423)
Q Consensus       403 ~~~~~~~~~~~  413 (423)
                      .+++.++....
T Consensus       169 ~l~~~l~~~~~  179 (191)
T 2p6n_A          169 DLKALLLEAKQ  179 (191)
T ss_dssp             HHHHHHHHTTC
T ss_pred             HHHHHHHHccC
Confidence            88888865443

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.95  E-value=1.1e-26  Score=189.85  Aligned_cols=152  Identities=41%  Similarity=0.722  Sum_probs=133.6

Q ss_pred             cceEEEEEeChHH-HHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCcc
Q 014486          262 GLVQHYIKLSELE-KNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKR  340 (423)
Q Consensus       262 ~~~~~~~~~~~~~-~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  340 (423)
                      .+.+.+..++... |...+.++++..+.+++||||++.+.++.+++.|...++.+..+||++++.+|..+++.|++|+.+
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            3456667777666 999999999998889999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhh
Q 014486          341 ILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGS  414 (423)
Q Consensus       341 ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  414 (423)
                      |||||+++++|+|+|++++||++++|+++..|.||+||+||.|++|.+++++++ .+...+..+++.++..+..
T Consensus        83 vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~-~~~~~~~~~~~~~~~~~~~  155 (165)
T 1fuk_A           83 ILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTN-EDVGAMRELEKFYSTQIEE  155 (165)
T ss_dssp             EEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEET-TTHHHHHHHHHHSSCCCEE
T ss_pred             EEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcc-hHHHHHHHHHHHHccCccc
Confidence            999999999999999999999999999999999999999999999999999985 5666788888888766543

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=99.95  E-value=6.8e-26  Score=223.49  Aligned_cols=117  Identities=21%  Similarity=0.358  Sum_probs=106.6

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccC-
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDM-  365 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~-  365 (423)
                      .+.++||||++...++.+.+.|.+.|+++..+||++++.+|..+++.|++|+++|||||+++++|+|+|++++||+++. 
T Consensus       444 ~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d  523 (661)
T 2d7d_A          444 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDAD  523 (661)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTT
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcc
Confidence            4579999999999999999999999999999999999999999999999999999999999999999999999999997 


Q ss_pred             ----CCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHH
Q 014486          366 ----PDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVS  405 (423)
Q Consensus       366 ----~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~  405 (423)
                          |.+...|+||+||+||. ..|.+++++++. +..+...++
T Consensus       524 ~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~-~~~~~~~i~  565 (661)
T 2d7d_A          524 KEGFLRSERSLIQTIGRAARN-AEGRVIMYADKI-TKSMEIAIN  565 (661)
T ss_dssp             CCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSC-CHHHHHHHH
T ss_pred             cccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCC-CHHHHHHHH
Confidence                99999999999999998 689999998764 343444333

>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=9.9e-27  Score=191.98  Aligned_cols=154  Identities=28%  Similarity=0.549  Sum_probs=137.0

Q ss_pred             cccceEEEEEeChHH-HHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCC
Q 014486          260 LHGLVQHYIKLSELE-KNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN  338 (423)
Q Consensus       260 ~~~~~~~~~~~~~~~-~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~  338 (423)
                      ...+.+.+..++... |...+..++...+.+++||||+++..+..++..|...|+.+..+||++++.+|..+++.|++|+
T Consensus         5 ~~~i~q~~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g~   84 (175)
T 2rb4_A            5 LNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGK   84 (175)
T ss_dssp             BCCEEEEEEECSSHHHHHHHHHHHHTTSCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTTS
T ss_pred             cCCceEEEEEcCChHhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCC
Confidence            355677788887655 9999999999888899999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEEcCccccCCCCCCCCEEEEccCC------CCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcch
Q 014486          339 KRILVATDLVGRGIDIERVNIVINYDMP------DSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLI  412 (423)
Q Consensus       339 ~~ili~T~~~~~Gld~~~~~~vi~~~~~------~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (423)
                      .+|||||+++++|+|+|++++||++++|      .++..|+||+||+||.|+.|.+++++.+ .+...+..+++.++..+
T Consensus        85 ~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~-~~~~~~~~i~~~~~~~~  163 (175)
T 2rb4_A           85 EKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEV-DELPSLMKIQDHFNSSI  163 (175)
T ss_dssp             CSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECG-GGHHHHHHHHHHHTCCC
T ss_pred             CeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEcc-chHHHHHHHHHHhcCcc
Confidence            9999999999999999999999999999      8999999999999999999999999975 45778899999988765


Q ss_pred             hh
Q 014486          413 GS  414 (423)
Q Consensus       413 ~~  414 (423)
                      ..
T Consensus       164 ~~  165 (175)
T 2rb4_A          164 KQ  165 (175)
T ss_dssp             EE
T ss_pred             cc
Confidence            43

>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=2.7e-26  Score=194.97  Aligned_cols=148  Identities=27%  Similarity=0.491  Sum_probs=135.5

Q ss_pred             EEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEE
Q 014486          265 QHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVA  344 (423)
Q Consensus       265 ~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~  344 (423)
                      ......+...|...+.+++....++++||||+++..++.+++.|...++.+..+||++++.+|..+++.|++|+.+||||
T Consensus         8 ~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlva   87 (212)
T 3eaq_A            8 EEAVPAPVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVA   87 (212)
T ss_dssp             CEEEECCTTSHHHHHHHHHHHHCCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEE
T ss_pred             eeEEeCCHHHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEe
Confidence            44556777889999999999988999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchh
Q 014486          345 TDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIG  413 (423)
Q Consensus       345 T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  413 (423)
                      |+++++|+|+|++++||++++|+++..|.||+||+||.|+.|.+++|+++ .+...+..+++.++..+.
T Consensus        88 T~~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~-~~~~~~~~i~~~~~~~~~  155 (212)
T 3eaq_A           88 TDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGP-RERRDVEALERAVGRRFK  155 (212)
T ss_dssp             CTTTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECG-GGHHHHHHHHHHHSSCCE
T ss_pred             cChhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEch-hHHHHHHHHHHHhcCcCe
Confidence            99999999999999999999999999999999999999999999999985 567788888888876554

>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=99.94  E-value=2.2e-26  Score=190.96  Aligned_cols=153  Identities=32%  Similarity=0.538  Sum_probs=125.6

Q ss_pred             ccccceEEEEEeChHHHHHHHHHHHHhh-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcC
Q 014486          259 TLHGLVQHYIKLSELEKNRKLNDLLDAL-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEG  337 (423)
Q Consensus       259 ~~~~~~~~~~~~~~~~~~~~l~~ll~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~  337 (423)
                      ....+.+.+..++...|...+.++++.. +.+++||||++...++.+++.|...|+.+..+||++++.+|..+++.|++|
T Consensus        16 ~~~~i~q~~~~v~~~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~g   95 (185)
T 2jgn_A           16 TSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSG   95 (185)
T ss_dssp             CCTTEEEEEEECCGGGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHHT
T ss_pred             CCCCceEEEEEeCcHHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHcC
Confidence            3456778888888899999999999887 468999999999999999999999999999999999999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcch
Q 014486          338 NKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLI  412 (423)
Q Consensus       338 ~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (423)
                      +.+|||||+++++|+|+|++++||++++|+++..|.||+||+||.|++|.+++|+++ .+...+..+.+.++...
T Consensus        96 ~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~-~~~~~~~~l~~~l~~~~  169 (185)
T 2jgn_A           96 KSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNE-RNINITKDLLDLLVEAK  169 (185)
T ss_dssp             SSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECG-GGGGGHHHHHHHHHHTT
T ss_pred             CCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEch-hhHHHHHHHHHHHHhcc
Confidence            999999999999999999999999999999999999999999999999999999985 45566777777776443

>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=2.3e-25  Score=197.81  Aligned_cols=150  Identities=28%  Similarity=0.486  Sum_probs=134.5

Q ss_pred             ceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEE
Q 014486          263 LVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRIL  342 (423)
Q Consensus       263 ~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~il  342 (423)
                      +.+.++.++...|...+.++++...++++||||+++..++.+++.|...++.+..+||++++.+|..+++.|++|+.+||
T Consensus         3 v~~~~i~~~~~~K~~~L~~ll~~~~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vL   82 (300)
T 3i32_A            3 YEEEAVPAPVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVL   82 (300)
T ss_dssp             SEEEEEECCSSSHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCEE
T ss_pred             eEEEEEECCHHHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceEE
Confidence            34567778888899999999998889999999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchh
Q 014486          343 VATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIG  413 (423)
Q Consensus       343 i~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  413 (423)
                      |||+++++|+|+|++++||++++|+++..|.||+||+||.|++|.+++|+++ .+...+..+++.++..+.
T Consensus        83 VaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~-~e~~~~~~ie~~~~~~~~  152 (300)
T 3i32_A           83 VATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGP-RERRDVEALERAVGRRFK  152 (300)
T ss_dssp             EECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECS-STHHHHHHHHHHHTCCCE
T ss_pred             EEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeCh-HHHHHHHHHHHHhCCcce
Confidence            9999999999999999999999999999999999999999999999999985 567778888888886654

>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=7e-27  Score=191.79  Aligned_cols=149  Identities=37%  Similarity=0.564  Sum_probs=134.5

Q ss_pred             eEEEEEeCh-HHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEE
Q 014486          264 VQHYIKLSE-LEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRIL  342 (423)
Q Consensus       264 ~~~~~~~~~-~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~il  342 (423)
                      .+.+..++. ..|...+..+++..+.+++||||++...++.+++.|...++.+..+||++++.+|..+++.|++|+.+||
T Consensus         5 ~~~~~~~~~~~~k~~~l~~ll~~~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vL   84 (170)
T 2yjt_D            5 HQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVL   84 (170)
Confidence            344555555 6778888888888777899999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchh
Q 014486          343 VATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIG  413 (423)
Q Consensus       343 i~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  413 (423)
                      |||+++++|+|+|++++||++++|+++..|.||+||+||.|+.|.+++++.+ .+...+..+++.++..+.
T Consensus        85 vaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~-~~~~~~~~~~~~~~~~~~  154 (170)
T 2yjt_D           85 VATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEA-HDHLLLGKVGRYIEEPIK  154 (170)
Confidence            9999999999999999999999999999999999999999999999999975 466678888888877664

>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=1.2e-24  Score=186.60  Aligned_cols=164  Identities=19%  Similarity=0.190  Sum_probs=116.8

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCC---CCCeEEEEEecChHHHHH-HHHHHHHHhcc
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPN---PGQVTALVLCHTRELAYQ-ICHEFERFSTY  140 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~~~L~~q-~~~~~~~~~~~  140 (423)
                      ....|+++|.++++.++.++++++.+|||+|||++++++++..+...   ....++||++|+++|+.| +.+.+..+...
T Consensus        30 ~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~~  109 (216)
T 3b6e_A           30 PELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK  109 (216)
T ss_dssp             CCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHTT
T ss_pred             CCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhcc
Confidence            44589999999999999999999999999999999999888654321   123489999999999999 88888888654


Q ss_pred             CCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCC------CCCCCccEEEEcCcchhhccCCcHHHHHH
Q 014486          141 LPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKD------LSLKNVRHFILDECDKMLESLDMRRDVQE  214 (423)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~------~~~~~~~~vVvDE~h~~~~~~~~~~~~~~  214 (423)
                        ++++..+.|+.........+... ++|+|+||+.+...+....      ..+.++++||+||||++.....+...+..
T Consensus       110 --~~~v~~~~g~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~  186 (216)
T 3b6e_A          110 --WYRVIGLSGDTQLKISFPEVVKS-CDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRH  186 (216)
T ss_dssp             --TSCEEECCC---CCCCHHHHHHH-CSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CHHHHHHH
T ss_pred             --CceEEEEeCCcccchhHHhhccC-CCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcHHHHHHH
Confidence              57888888876554443333333 5999999999998877643      55788999999999999763233333333


Q ss_pred             HHHhC-------------CCCceEEEEecc
Q 014486          215 IFKMT-------------PHDKQVMMFSAT  231 (423)
Q Consensus       215 ~~~~~-------------~~~~~~v~~SAT  231 (423)
                      +....             .+..+++++|||
T Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          187 YLMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHHhcccccccccccCCCCcceEEEeecC
Confidence            32211             257899999998

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.90  E-value=1.4e-23  Score=203.25  Aligned_cols=103  Identities=15%  Similarity=0.177  Sum_probs=69.0

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEE--EcCccccCCCCCC----CCEE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILV--ATDLVGRGIDIER----VNIV  360 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili--~T~~~~~Gld~~~----~~~v  360 (423)
                      .++.+|||+++...++.+.+.+..  .+ +..++..  .++.++++.|+++. .||+  +|..+++|+|+|+    +++|
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            457899999999999999988865  23 4455543  46788899998865 5777  7899999999997    8899


Q ss_pred             EEccCCCCc------------------------------chhhhcccccCCCCCceEEEEEecCc
Q 014486          361 INYDMPDSA------------------------------DTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       361 i~~~~~~s~------------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      |++++|...                              ..+.|.+||+.|..++..++++.++.
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            999988522                              23469999999987776677777654

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.89  E-value=1.2e-20  Score=183.29  Aligned_cols=313  Identities=15%  Similarity=0.155  Sum_probs=196.3

Q ss_pred             CCChhhhhcccc----cccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           68 HPSEVQHECIPQ----AILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        68 ~~~~~Q~~~i~~----~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      .+||+|.+.+..    +..++++++.+|||+|||++|++|++..      +++++|++||++|+.|+.+++..+.... +
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~------~~~v~i~~pt~~l~~q~~~~~~~l~~~~-~   75 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV------KPKVLFVVRTHNEFYPIYRDLTKIREKR-N   75 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHHH------CSEEEEEESSGGGHHHHHHHHTTCCCSS-C
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHhC------CCeEEEEcCCHHHHHHHHHHHHHHhhhc-C
Confidence            689999987664    4468899999999999999999999982      2399999999999999999888776554 6


Q ss_pred             ceEEEEEcCcch---------------------------------HHHH------------------HHHhcCCCcEEEe
Q 014486          144 IKVAVFYGGVNI---------------------------------KIHK------------------DLLKNECPQIVVG  172 (423)
Q Consensus       144 ~~~~~~~~~~~~---------------------------------~~~~------------------~~~~~~~~~ilv~  172 (423)
                      +++..+.|..+.                                 ....                  +..... .+|+|+
T Consensus        76 ~~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~~-adIVV~  154 (551)
T 3crv_A           76 ITFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYK-ADVIAL  154 (551)
T ss_dssp             CCEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGGG-CSEEEE
T ss_pred             ccEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhhc-CCEEEe
Confidence            777777664321                                 0000                  111122 599999


Q ss_pred             chHHHHHHHhcCCCCC-CCccEEEEcCcchhhccCC--------------------------------------------
Q 014486          173 TPGRILALARDKDLSL-KNVRHFILDECDKMLESLD--------------------------------------------  207 (423)
Q Consensus       173 T~~~l~~~~~~~~~~~-~~~~~vVvDE~h~~~~~~~--------------------------------------------  207 (423)
                      |+..|+.........+ ....++|+||||.+.+ ..                                            
T Consensus       155 ~~~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d-~~~~~s~~ls~~~l~~~~~~l~~~~~~~~l~~l~~~l~~~~~~~~~  233 (551)
T 3crv_A          155 TYPYFFIDRYREFIDIDLREYMIVIDEAHNLDK-VNELEERSLSEITIQMAIKQSKSEESRRILSKLLNQLREVVLPDEK  233 (551)
T ss_dssp             ETHHHHCHHHHTTSCCCSTTEEEEETTGGGGGG-GGGGGCEEEEHHHHHHHHHHCSCHHHHHHHHHHHHHHTTSCCSCSS
T ss_pred             CchHhcCHHHHHhcCCCcCCeEEEEecccchHH-HHHhhceecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence            9999988543333332 4677899999998754 00                                            


Q ss_pred             ----------cHHH----------------------------HHHHH----------------------------HhCCC
Q 014486          208 ----------MRRD----------------------------VQEIF----------------------------KMTPH  221 (423)
Q Consensus       208 ----------~~~~----------------------------~~~~~----------------------------~~~~~  221 (423)
                                +...                            +..++                            ..+..
T Consensus       234 ~~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~~~~~l~~~pl~~~~~l~~~~~  313 (551)
T 3crv_A          234 YIKVENVPKLSKEELEILADDYEDIRKDSLKQGKVNKIHIGSILRFFSLLSIGSFIPFSYSKRLVIKNPEISYYLNLLND  313 (551)
T ss_dssp             CEECSCCCCCCHHHHHHHHHHHHHHHHHHHHTTCBCCCHHHHHHHHHHHHHHSSCEEEEETTEEEEECCCTHHHHGGGGC
T ss_pred             ccccccChHHHHHHHHHHHHHHHHHHHhhhhcCCcccchHHHHHHHHHHHhccCCeEeccCCEEEEEECCHHHHHHHHhc
Confidence                      0000                            00000                            01112


Q ss_pred             C-ceEEEEeccCCccHHHHHHHhccC-Ccee---eeccccccccccceEEEEE--eCh------HHHHHHHHHHHH---h
Q 014486          222 D-KQVMMFSATLSKEIRPVCKKFMQD-PMEI---YVDDEAKLTLHGLVQHYIK--LSE------LEKNRKLNDLLD---A  285 (423)
Q Consensus       222 ~-~~~v~~SAT~~~~~~~~~~~~~~~-~~~~---~~~~~~~~~~~~~~~~~~~--~~~------~~~~~~l~~ll~---~  285 (423)
                      . ..+|++|||+.+ ...+...+... +...   ...... .. ......++.  .+.      ......+.+.+.   .
T Consensus       314 ~~~svIltSaTL~~-~~~~~~~lGl~~~~~~~~~~~~~~s-pf-~~~~~l~v~~~~~~~~~~r~~~~~~~l~~~i~~l~~  390 (551)
T 3crv_A          314 NELSIILMSGTLPP-REYMEKVWGIKRNMLYLDVEREIQK-RV-SGSYECYIGVDVTSKYDMRSDNMWKRYADYLLKIYF  390 (551)
T ss_dssp             TTCEEEEEESSCCC-HHHHHHTSCCCSCEEEEEHHHHTTS-CC-SCEEEEEEECSCCCCTTTCCHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEeeCCCc-HHHHHHHhCCCCccccccceeecCC-cC-CCceEEEEeCCCCCccccCCHHHHHHHHHHHHHHHH
Confidence            3 689999999987 33333333222 1210   000111 11 111111211  110      111222333222   2


Q ss_pred             hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEc--CccccCCCCC-----CCC
Q 014486          286 LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVAT--DLVGRGIDIE-----RVN  358 (423)
Q Consensus       286 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T--~~~~~Gld~~-----~~~  358 (423)
                      ..++.++||+++....+.+++.   .+.++..-..+++.   .+.++.|+.+...||+++  ..+.+|+|+|     .++
T Consensus       391 ~~~g~~lvlF~Sy~~l~~v~~~---~~~~v~~q~~~~~~---~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~  464 (551)
T 3crv_A          391 QAKANVLVVFPSYEIMDRVMSR---ISLPKYVESEDSSV---EDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLIS  464 (551)
T ss_dssp             HCSSEEEEEESCHHHHHHHHTT---CCSSEEECCSSCCH---HHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEE
T ss_pred             hCCCCEEEEecCHHHHHHHHHh---cCCcEEEcCCCCCH---HHHHHHHHhcCCeEEEEEecceecccccccccCCccee
Confidence            2457899999999999998862   34444443344553   446677754444799998  6999999999     378


Q ss_pred             EEEEccCCCC--------------------cc----------hhhhcccccCCCCCceEEEEEecCcccH
Q 014486          359 IVINYDMPDS--------------------AD----------TYLHRVGRAGRFGTKGLAITFVSSASDS  398 (423)
Q Consensus       359 ~vi~~~~~~s--------------------~~----------~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  398 (423)
                      +||..++|..                    .-          .+.|.+||+-|..++..+++++++....
T Consensus       465 ~viI~~lPfp~~dp~~~ar~~~~~~~~g~~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~R~~~  534 (551)
T 3crv_A          465 DVVIVGIPYPPPDDYLKILAQRVSLKMNRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLLDKRFES  534 (551)
T ss_dssp             EEEEESCCCCCCSHHHHHHHHHTTCCSSTTTHHHHTHHHHHHHHHHHHHTTCCSTTCEEEEEEESGGGGS
T ss_pred             EEEEEcCCCCCCCHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHhccCccCCCccEEEEEeehhccc
Confidence            8999887751                    10          1249999999998888888888876554

>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=99.87  E-value=7.7e-23  Score=182.32  Aligned_cols=154  Identities=15%  Similarity=0.182  Sum_probs=120.7

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .|+++|.++++.++.+++.++++|||+|||++++.++...+....  .++||++|+++|+.||.++++++... +...+.
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~--~~~lil~Pt~~L~~q~~~~l~~~~~~-~~~~~~  189 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYE--GKILIIVPTTALTTQMADDFVDYRLF-SHAMIK  189 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCS--SEEEEECSSHHHHHHHHHHHHHHTSC-CGGGEE
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcCC--CeEEEEECCHHHHHHHHHHHHHhccc-ccceEE
Confidence            799999999999999888999999999999999887776544222  28999999999999999999988643 355677


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEE
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM  227 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~  227 (423)
                      .+.++.....    ......+|+|+||+.+...   ....+.++++||+||||++.+     ..+..+...+....++++
T Consensus       190 ~~~~~~~~~~----~~~~~~~I~v~T~~~l~~~---~~~~~~~~~~vIiDEaH~~~~-----~~~~~il~~~~~~~~~l~  257 (282)
T 1rif_A          190 KIGGGASKDD----KYKNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLATG-----KSISSIISGLNNCMFKFG  257 (282)
T ss_dssp             ECSTTCSSTT----CCCTTCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCCH-----HHHHHHTTTCTTCCEEEE
T ss_pred             EEeCCCcchh----hhccCCcEEEEchHHHHhh---HHHHHhhCCEEEEECCccCCc-----ccHHHHHHHhhcCCeEEE
Confidence            7777654322    1112369999999987542   223467889999999998864     366777788777899999


Q ss_pred             EeccCCccH
Q 014486          228 FSATLSKEI  236 (423)
Q Consensus       228 ~SAT~~~~~  236 (423)
                      +|||+++..
T Consensus       258 lSATp~~~~  266 (282)
T 1rif_A          258 LSGSLRDGK  266 (282)
T ss_dssp             ECSSCCTTS
T ss_pred             EeCCCCCcc
Confidence            999998654

>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=99.87  E-value=3.2e-22  Score=173.20  Aligned_cols=161  Identities=16%  Similarity=0.179  Sum_probs=118.7

Q ss_pred             CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC--CCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           65 GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP--GQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        65 ~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~--~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      ....++++|.++++.+..|+++++.||||||||+++.++++......+  ...++++++|+++++.|+.+.+........
T Consensus        58 ~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~  137 (235)
T 3llm_A           58 ELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEP  137 (235)
T ss_dssp             HTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCT
T ss_pred             hcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhcccc
Confidence            344689999999999999999999999999999988888776543322  244899999999999999988876654322


Q ss_pred             CceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchh-hccCCcH-HHHHHHHHhCC
Q 014486          143 DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM-LESLDMR-RDVQEIFKMTP  220 (423)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~-~~~~~~~-~~~~~~~~~~~  220 (423)
                      +..+..-.....      ......++|+|+||+++.+++..   .+.++++||+||||.+ .+ .++. ..+..+.... 
T Consensus       138 ~~~~g~~~~~~~------~~~~~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~-~~~~~~~l~~i~~~~-  206 (235)
T 3llm_A          138 GKSCGYSVRFES------ILPRPHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDIN-TDFLLVVLRDVVQAY-  206 (235)
T ss_dssp             TSSEEEEETTEE------ECCCSSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHH-HHHHHHHHHHHHHHC-
T ss_pred             CceEEEeechhh------ccCCCCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcc-hHHHHHHHHHHHhhC-
Confidence            333332221110      01112358999999999998876   4789999999999985 33 4555 3555565554 


Q ss_pred             CCceEEEEeccCCccH
Q 014486          221 HDKQVMMFSATLSKEI  236 (423)
Q Consensus       221 ~~~~~v~~SAT~~~~~  236 (423)
                      ++.|++++|||++.+.
T Consensus       207 ~~~~~il~SAT~~~~~  222 (235)
T 3llm_A          207 PEVRIVLMSATIDTSM  222 (235)
T ss_dssp             TTSEEEEEECSSCCHH
T ss_pred             CCCeEEEEecCCCHHH
Confidence            4789999999999775

>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=5.5e-20  Score=158.79  Aligned_cols=138  Identities=19%  Similarity=0.175  Sum_probs=108.6

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCce-E
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIK-V  146 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~-~  146 (423)
                      .|+++|.++++.++.++++++++|||+|||.+++.++...      +.+++|++|+++|+.||.+.+.++     ++. +
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~------~~~~liv~P~~~L~~q~~~~~~~~-----~~~~v  161 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF-----GEEYV  161 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS------CSCEEEEESSHHHHHHHHHHHGGG-----CGGGE
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEeCCHHHHHHHHHHHHhC-----CCCeE
Confidence            7899999999999999899999999999999988877664      227899999999999999988873     556 7


Q ss_pred             EEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEE
Q 014486          147 AVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVM  226 (423)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v  226 (423)
                      ..+.|+...          ..+|+|+|++.+......   ....+++||+||+|.+.+ ..+.    .+...++ ..+++
T Consensus       162 ~~~~g~~~~----------~~~i~v~T~~~l~~~~~~---~~~~~~llIiDEaH~l~~-~~~~----~i~~~~~-~~~~l  222 (237)
T 2fz4_A          162 GEFSGRIKE----------LKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPA-ESYV----QIAQMSI-APFRL  222 (237)
T ss_dssp             EEESSSCBC----------CCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCT-TTHH----HHHHTCC-CSEEE
T ss_pred             EEEeCCCCC----------cCCEEEEeHHHHHhhHHH---hcccCCEEEEECCccCCC-hHHH----HHHHhcc-CCEEE
Confidence            777776542          259999999998775542   124588999999999876 3333    3444444 57789


Q ss_pred             EEeccCCcc
Q 014486          227 MFSATLSKE  235 (423)
Q Consensus       227 ~~SAT~~~~  235 (423)
                      ++|||+++.
T Consensus       223 ~LSATp~r~  231 (237)
T 2fz4_A          223 GLTATFERE  231 (237)
T ss_dssp             EEEESCC--
T ss_pred             EEecCCCCC
Confidence            999999864

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.83  E-value=1.9e-19  Score=176.13  Aligned_cols=113  Identities=15%  Similarity=0.207  Sum_probs=79.4

Q ss_pred             HHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEc--CccccCCCCCC
Q 014486          279 LNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVAT--DLVGRGIDIER  356 (423)
Q Consensus       279 l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T--~~~~~Gld~~~  356 (423)
                      +.+++... ++.++||+++....+.+++.++.  .... ...+++..++..+++.|+ ++..||+++  ..+.+|+|+++
T Consensus       440 i~~l~~~~-~g~~lvlF~Sy~~l~~v~~~l~~--~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g  514 (620)
T 4a15_A          440 IEDIILKV-KKNTIVYFPSYSLMDRVENRVSF--EHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPG  514 (620)
T ss_dssp             HHHHHHHH-CSCEEEEESCHHHHHHHTSSCCS--CCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------
T ss_pred             HHHHHHhC-CCCEEEEeCCHHHHHHHHHHHHh--cchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCC
Confidence            33444433 56799999999999999888872  2222 455566678999999999 888899997  48999999986


Q ss_pred             --CCEEEEccCCCCc-----------------------------chhhhcccccCCCCCceEEEEEecCcc
Q 014486          357 --VNIVINYDMPDSA-----------------------------DTYLHRVGRAGRFGTKGLAITFVSSAS  396 (423)
Q Consensus       357 --~~~vi~~~~~~s~-----------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~~~  396 (423)
                        +++||..+.|...                             ..+.|.+||+-|..++..+++++++..
T Consensus       515 ~~l~~viI~~lPfp~~~p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~R~  585 (620)
T 4a15_A          515 NELEMIILAGLPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDKRA  585 (620)
T ss_dssp             CCCCEEEESSCCCCCCCHHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEECGGG
T ss_pred             CceEEEEEEcCCCCCCCHHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEEEEEEccch
Confidence              7899999988631                             123699999999988888888887654

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.83  E-value=3.9e-20  Score=162.37  Aligned_cols=138  Identities=16%  Similarity=0.186  Sum_probs=104.0

Q ss_pred             ChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhC-CCCeEEEcCCCCHHHHHHHHHhhhcC-Ccc-EEEEc
Q 014486          271 SELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVEC-NFPSICIHSGMSQEERLTRYKGFKEG-NKR-ILVAT  345 (423)
Q Consensus       271 ~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~-ili~T  345 (423)
                      ....|...+.+++...  .+.++||||++...++.+...|... |+++..+||+++..+|..+++.|+++ ..+ +|++|
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             CccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEE--EEEecCc-ccHHHHHHHHHHH
Q 014486          346 DLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLA--ITFVSSA-SDSDILNQVSKFM  408 (423)
Q Consensus       346 ~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~--~~~~~~~-~~~~~~~~~~~~~  408 (423)
                      +++++|+|++.+++||+||+||++..+.||+||++|.|+.+.|  +.++... .+..+++.+.++.
T Consensus       173 ~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~TiEe~i~~~~~~K~  238 (271)
T 1z5z_A          173 KAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKR  238 (271)
T ss_dssp             CTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTSHHHHHHHHHHHCH
T ss_pred             hhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999988654  4455543 3444444444443

>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=98.84  E-value=1.1e-08  Score=100.02  Aligned_cols=146  Identities=13%  Similarity=0.137  Sum_probs=89.0

Q ss_pred             ChhhhhcccccccCCceEEEccCCCcch--hHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           70 SEVQHECIPQAILGMDVICQAKSGMGKT--AVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        70 ~~~Q~~~i~~~~~~~~~ii~~~tGsGKT--~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .+.|+.+++.++.++.+++.|++|+|||  +.++++.+...... .+.++++++||..++.++.+.+....... ++...
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~-~~~~vll~APTg~AA~~L~e~~~~~~~~l-~l~~~  228 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADG-ERCRIRLAAPTGKAAARLTESLGKALRQL-PLTDE  228 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSS-CCCCEEEEBSSHHHHHHHHHHHTHHHHHS-SCCSC
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhc-CCCeEEEEeCChhHHHHHHHHHHHHHhcC-CCCHH
Confidence            6889999999999999999999999999  55666666654322 23488999999999999988877654433 11100


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEE
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM  227 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~  227 (423)
                      .. .+..  ...    .....++-.+|... . +.........++++||||++.+.     ...+..++..++...|+|+
T Consensus       229 ~~-~~~~--~~~----~Tih~ll~~~~~~~-~-~~~~~~~~l~~d~lIIDEAsml~-----~~~~~~Ll~~l~~~~~liL  294 (608)
T 1w36_D          229 QK-KRIP--EDA----STLHRLLGAQPGSQ-R-LRHHAGNPLHLDVLVVDEASMID-----LPMMSRLIDALPDHARVIF  294 (608)
T ss_dssp             CC-CSCS--CCC----BTTTSCC-------------CTTSCCSCSEEEECSGGGCB-----HHHHHHHHHTCCTTCEEEE
T ss_pred             HH-hccc--hhh----hhhHhhhccCCCch-H-HHhccCCCCCCCEEEEechhhCC-----HHHHHHHHHhCCCCCEEEE
Confidence            00 0000  000    00012222222211 0 11111222378899999999442     4566778888888899988


Q ss_pred             Eecc
Q 014486          228 FSAT  231 (423)
Q Consensus       228 ~SAT  231 (423)
                      +.-.
T Consensus       295 vGD~  298 (608)
T 1w36_D          295 LGDR  298 (608)
T ss_dssp             EECT
T ss_pred             Ecch
Confidence            7654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.47  E-value=1.4e-07  Score=93.43  Aligned_cols=67  Identities=18%  Similarity=0.185  Sum_probs=53.1

Q ss_pred             CCChhhhhcccccccCCc-eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAILGMD-VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~-~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .+++.|++|+..++..++ .+|.||+|+|||.+..-.+.+....+   .++|+++||..-+.++.+.+...
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            568899999999887654 79999999999987655454444432   28999999999999998887653

>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=98.46  E-value=1.9e-05  Score=78.47  Aligned_cols=82  Identities=17%  Similarity=0.204  Sum_probs=59.7

Q ss_pred             CCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC-CCeEEEEEecChHHHHHHHHHHHHHhccC-CCc
Q 014486           67 EHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP-GQVTALVLCHTRELAYQICHEFERFSTYL-PDI  144 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~L~~q~~~~~~~~~~~~-~~~  144 (423)
                      ..+++.|++++.+  .+..++|.|+.|||||.+.+--+...+...+ .+.++|++++|+..+.++.+++.+..... .++
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~~~~~~~~   85 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMGTSQGGM   85 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHHCSCCTTC
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHhccccCCc
Confidence            3689999999973  3567999999999999887655555443322 23389999999999999999998775321 244


Q ss_pred             eEEEEE
Q 014486          145 KVAVFY  150 (423)
Q Consensus       145 ~~~~~~  150 (423)
                      .+..++
T Consensus        86 ~v~Tfh   91 (647)
T 3lfu_A           86 WVGTFH   91 (647)
T ss_dssp             EEEEHH
T ss_pred             EEEcHH
Confidence            555444

>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=98.39  E-value=4.3e-06  Score=73.44  Aligned_cols=132  Identities=12%  Similarity=0.014  Sum_probs=95.0

Q ss_pred             hHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccc
Q 014486          272 ELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVG  349 (423)
Q Consensus       272 ~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~  349 (423)
                      ...|...+.+++..+  .+.+++||++..+..+.+.++|...++.+..+.|.....++. .    .++...+.+.|.+++
T Consensus       107 ~SGKf~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~~k-~----~~~~~~i~Lltsag~  181 (328)
T 3hgt_A          107 NSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSAAA-A----NDFSCTVHLFSSEGI  181 (328)
T ss_dssp             TCHHHHHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCC
T ss_pred             cCccHHHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhhhh-c----ccCCceEEEEECCCC
Confidence            456777777777665  357999999999999999999999999999999985543221 1    234555556677777


Q ss_pred             cCCC-----CCCCCEEEEccCCCCcchh-hhcccccCCC--CC--ceEEEEEecCcccHHHHHHHHHHH
Q 014486          350 RGID-----IERVNIVINYDMPDSADTY-LHRVGRAGRF--GT--KGLAITFVSSASDSDILNQVSKFM  408 (423)
Q Consensus       350 ~Gld-----~~~~~~vi~~~~~~s~~~~-~Q~~GR~~R~--g~--~~~~~~~~~~~~~~~~~~~~~~~~  408 (423)
                      -|+|     +..++.||.||+.|+++.- +|++-|++|.  |+  +..++-++....-..+.-.+.+.+
T Consensus       182 ~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~TiEh~~l~~~~~~  250 (328)
T 3hgt_A          182 NFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDHCRLFFGKKF  250 (328)
T ss_dssp             CTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTSHHHHHHHHHHHT
T ss_pred             CCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCCHHHHHHHccCCC
Confidence            7776     6789999999999999986 9999999996  33  456777777666666555555543

>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=98.37  E-value=3.6e-06  Score=82.81  Aligned_cols=69  Identities=14%  Similarity=0.095  Sum_probs=52.6

Q ss_pred             CCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           67 EHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      ..+++.|..++..++.+...+|.||+|+|||.+..-.+ ..+... .+.++++++||...+.++.+.+.+.
T Consensus       179 ~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~~i-~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          179 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIV-YHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             CCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHHHH-HHHHTS-SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHHHH-HHHHHc-CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            35789999999998887779999999999998754333 332221 1238999999999999988877653

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.27  E-value=5.9e-06  Score=83.15  Aligned_cols=69  Identities=12%  Similarity=0.118  Sum_probs=52.8

Q ss_pred             CCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           67 EHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      ..+++.|..|+..++.+.-.+|.||+|+|||.+....+......  .+.++|+++||...+.++.+.+.+.
T Consensus       359 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~~l~~~--~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          359 AQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKI--HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHHHHHHH--HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             ccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhC--CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            35789999999998887778999999999998754333222211  1228999999999999999888764

>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=98.26  E-value=9.5e-06  Score=81.56  Aligned_cols=68  Identities=13%  Similarity=0.073  Sum_probs=52.0

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .+++.|..++..++.+.-.+|.||+|+|||.+..- ++..+.... +.++++++||...+.++.+.+.+.
T Consensus       356 ~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~-~i~~l~~~~-~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          356 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSAT-IVYHLARQG-NGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHH-HHHHHHTTC-SSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHHH-HHHHHHHcC-CCcEEEEcCcHHHHHHHHHHHHHh
Confidence            56889999999988877799999999999987543 333332212 238999999999999988877653

>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=98.26  E-value=3e-06  Score=80.27  Aligned_cols=69  Identities=12%  Similarity=0.091  Sum_probs=49.2

Q ss_pred             CCCCCCChhhhhcccccccC-----CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHH
Q 014486           64 SGFEHPSEVQHECIPQAILG-----MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEF  134 (423)
Q Consensus        64 ~~~~~~~~~Q~~~i~~~~~~-----~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~  134 (423)
                      +.|..+++-|++++..++..     ..++|.|+.|+|||.+.. .++..+...+. ..+++++||...+..+.+.+
T Consensus        21 ~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~-~~~~~l~~~~~-~~il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           21 MTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTK-FIIEALISTGE-TGIILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHH-HHHHHHHHTTC-CCEEEEESSHHHHHHHHHHH
T ss_pred             CccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHH-HHHHHHHhcCC-ceEEEecCcHHHHHHHHhhh
Confidence            45778999999999877542     379999999999997643 33333332222 26899999998877665544

>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=98.22  E-value=4.5e-06  Score=80.82  Aligned_cols=127  Identities=18%  Similarity=0.124  Sum_probs=78.7

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .+++.|+.++..++.++.+++.|++|+|||.+.. .++..+...+  .++++++||...+..+.+...        ....
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~-~l~~~l~~~g--~~Vl~~ApT~~Aa~~L~e~~~--------~~a~  257 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTK-AVADLAESLG--LEVGLCAPTGKAARRLGEVTG--------RTAS  257 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHH-HHHHHHHHTT--CCEEEEESSHHHHHHHHHHHT--------SCEE
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHH-HHHHHHHhcC--CeEEEecCcHHHHHHhHhhhc--------ccHH
Confidence            6889999999999988899999999999997643 2333332222  378999999988877655331        1111


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEE
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM  227 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~  227 (423)
                      .++.         .+.     .   .++    .+.........+++|||||++.+.     ...+..+...++...++++
T Consensus       258 Tih~---------ll~-----~---~~~----~~~~~~~~~~~~dvlIIDEasml~-----~~~~~~Ll~~~~~~~~lil  311 (574)
T 3e1s_A          258 TVHR---------LLG-----Y---GPQ----GFRHNHLEPAPYDLLIVDEVSMMG-----DALMLSLLAAVPPGARVLL  311 (574)
T ss_dssp             EHHH---------HTT-----E---ETT----EESCSSSSCCSCSEEEECCGGGCC-----HHHHHHHHTTSCTTCEEEE
T ss_pred             HHHH---------HHc-----C---Ccc----hhhhhhcccccCCEEEEcCccCCC-----HHHHHHHHHhCcCCCEEEE
Confidence            1110         000     0   000    001111223467899999999664     3356666777777777777


Q ss_pred             Eecc
Q 014486          228 FSAT  231 (423)
Q Consensus       228 ~SAT  231 (423)
                      +.-.
T Consensus       312 vGD~  315 (574)
T 3e1s_A          312 VGDT  315 (574)
T ss_dssp             EECT
T ss_pred             Eecc
Confidence            6443

>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=97.66  E-value=0.00046  Score=62.89  Aligned_cols=74  Identities=15%  Similarity=0.192  Sum_probs=56.6

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      .|+|+|+..+..+...+-+++..+-+.|||.+....++..+...+ +..++++.|+...|..+.+.++.+....|
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~~-g~~v~~vA~t~~qA~~vf~~i~~mi~~~P  236 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNK-DKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSSS-SCEEEEEESSHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhCC-CCeEEEEeCCHHHHHHHHHHHHHHHHhCh
Confidence            789999999877644456899999999999876655554333332 33899999999999988888888776554

>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=97.54  E-value=0.00099  Score=65.04  Aligned_cols=74  Identities=15%  Similarity=0.192  Sum_probs=57.3

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCC
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP  142 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~  142 (423)
                      .|+|+|+..+..+...+..++..+-|+|||......++..+...+ +..++++.|+...|..+.+.++.+....|
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~-~~~i~~va~t~~qA~~~~~~i~~~i~~~p  236 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNK-DKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTSS-SCEEEEEESSHHHHHHHHHHHHHHHTTSC
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhCC-CCeEEEEECCHHHHHHHHHHHHHHHHhCh
Confidence            579999999887644566899999999999876555554444333 33899999999999999988888876654

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.32  E-value=0.00097  Score=61.54  Aligned_cols=108  Identities=18%  Similarity=0.126  Sum_probs=63.4

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHh
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLK  163 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (423)
                      +-.++.|+.|+|||....-    .+.. .   ..+|++|+++++..+.+.+.+..     ..                  
T Consensus       162 ~v~~I~G~aGsGKTt~I~~----~~~~-~---~~lVlTpT~~aa~~l~~kl~~~~-----~~------------------  210 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEILS----RVNF-E---EDLILVPGRQAAEMIRRRANASG-----II------------------  210 (446)
T ss_dssp             EEEEEEECTTSCHHHHHHH----HCCT-T---TCEEEESCHHHHHHHHHHHTTTS-----CC------------------
T ss_pred             cEEEEEcCCCCCHHHHHHH----Hhcc-C---CeEEEeCCHHHHHHHHHHhhhcC-----cc------------------
Confidence            3478999999999975422    2221 1   56999999999988877663220     00                  


Q ss_pred             cCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          164 NECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       164 ~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      .. ...-+.|.++++.  +.........+++||||+-.+.     ...+..+....+. .+++++.-+
T Consensus       211 ~~-~~~~V~T~dsfL~--~~~~~~~~~~d~liiDE~sm~~-----~~~l~~l~~~~~~-~~vilvGD~  269 (446)
T 3vkw_A          211 VA-TKDNVRTVDSFLM--NYGKGARCQFKRLFIDEGLMLH-----TGCVNFLVEMSLC-DIAYVYGDT  269 (446)
T ss_dssp             CC-CTTTEEEHHHHHH--TTTSSCCCCCSEEEEETGGGSC-----HHHHHHHHHHTTC-SEEEEEECT
T ss_pred             cc-ccceEEEeHHhhc--CCCCCCCCcCCEEEEeCcccCC-----HHHHHHHHHhCCC-CEEEEecCc
Confidence            00 1334677777653  2222222347899999998542     2233333444443 556666544

>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=97.11  E-value=0.00035  Score=69.54  Aligned_cols=82  Identities=12%  Similarity=0.055  Sum_probs=59.5

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC-CCCCeEEEEEecChHHHHHHHHHHHHHhccC--CCc
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP-NPGQVTALVLCHTRELAYQICHEFERFSTYL--PDI  144 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~--~~~  144 (423)
                      .+++.|++++.+.  +..++|.|+.|||||.+.+--+...+.. +-...++|+++.|+..+.++.+++.+.....  .++
T Consensus         2 ~L~~~Q~~av~~~--~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~~~~~~~~   79 (673)
T 1uaa_A            2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGRKEARGL   79 (673)
T ss_dssp             CCCHHHHHHHHCC--SSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSCTTTTTTS
T ss_pred             CCCHHHHHHHhCC--CCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcCcccccCC
Confidence            4789999999763  6779999999999998766545444332 1123389999999999999999998765432  245


Q ss_pred             eEEEEEc
Q 014486          145 KVAVFYG  151 (423)
Q Consensus       145 ~~~~~~~  151 (423)
                      .+..+++
T Consensus        80 ~v~Tfhs   86 (673)
T 1uaa_A           80 MISTFHT   86 (673)
T ss_dssp             EEEEHHH
T ss_pred             EEEeHHH
Confidence            6665544

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.08  E-value=0.0014  Score=53.37  Aligned_cols=39  Identities=13%  Similarity=-0.059  Sum_probs=26.0

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ++-.++.||+|+|||...+-.+......+   .+++++.|..
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            45578999999999987654333332222   2788888874

>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=97.01  E-value=0.00077  Score=67.52  Aligned_cols=83  Identities=17%  Similarity=0.181  Sum_probs=60.6

Q ss_pred             CCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC-CCeEEEEEecChHHHHHHHHHHHHHhcc-CCCc
Q 014486           67 EHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP-GQVTALVLCHTRELAYQICHEFERFSTY-LPDI  144 (423)
Q Consensus        67 ~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~L~~q~~~~~~~~~~~-~~~~  144 (423)
                      ..+++.|++++.+  ....++|.|+.|||||.+.+--+...+...+ ...++|+++.|+..|.++.+++.+.... ..++
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l~~~~~~~   87 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDV   87 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHGGGGTTS
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhcccccCc
Confidence            3689999999976  3567999999999999886655554443222 3348999999999999999998876432 1245


Q ss_pred             eEEEEEc
Q 014486          145 KVAVFYG  151 (423)
Q Consensus       145 ~~~~~~~  151 (423)
                      .+..+++
T Consensus        88 ~v~Tfhs   94 (724)
T 1pjr_A           88 WISTFHS   94 (724)
T ss_dssp             EEEEHHH
T ss_pred             EEeeHHH
Confidence            6665543

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=96.96  E-value=0.00082  Score=55.47  Aligned_cols=40  Identities=13%  Similarity=0.058  Sum_probs=26.7

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      |+-.++.|++|+|||...+-.+......+.   +++++.|...
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~~g~---kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQFAKQ---HAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTTC---CEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHCCC---EEEEEEeccC
Confidence            334678999999999876555444433332   7899998763

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=96.94  E-value=0.00071  Score=56.72  Aligned_cols=91  Identities=14%  Similarity=0.086  Sum_probs=50.4

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL  162 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (423)
                      |.-.++.|++|+|||...+-.+......+.   +++++.|...-.   .  ........ ++         .        
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~g~---kVli~~~~~d~r---~--~~~i~srl-G~---------~--------   65 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYADV---KYLVFKPKIDTR---S--IRNIQSRT-GT---------S--------   65 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTTC---CEEEEEECCCGG---G--CSSCCCCC-CC---------S--------
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhcCC---EEEEEEeccCch---H--HHHHHHhc-CC---------C--------
Confidence            344788999999999876554444433322   778887765210   0  00011110 10         0        


Q ss_pred             hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       163 ~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                         ...+.+.+...+...+.... .-...++||+||++.+.
T Consensus        66 ---~~~~~~~~~~~i~~~i~~~~-~~~~~dvViIDEaQ~l~  102 (223)
T 2b8t_A           66 ---LPSVEVESAPEILNYIMSNS-FNDETKVIGIDEVQFFD  102 (223)
T ss_dssp             ---SCCEEESSTHHHHHHHHSTT-SCTTCCEEEECSGGGSC
T ss_pred             ---ccccccCCHHHHHHHHHHHh-hCCCCCEEEEecCccCc
Confidence               01344556666666555432 22457899999999754

>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=96.94  E-value=0.0013  Score=53.37  Aligned_cols=18  Identities=28%  Similarity=0.453  Sum_probs=15.8

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      ++.+++.||+|+|||..+
T Consensus        38 g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           38 GKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             CCEEEECCSSSSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            677999999999999754

>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=96.80  E-value=0.0041  Score=56.00  Aligned_cols=34  Identities=21%  Similarity=0.206  Sum_probs=24.1

Q ss_pred             CChhhhhccccccc----C---CceEEEccCCCcchhHHHH
Q 014486           69 PSEVQHECIPQAIL----G---MDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        69 ~~~~Q~~~i~~~~~----~---~~~ii~~~tGsGKT~~~~~  102 (423)
                      ++|+|..++..+..    +   +..++.||.|+|||..+..
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~   43 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYA   43 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHH
Confidence            35777777655442    2   3489999999999987654

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=96.79  E-value=0.0024  Score=52.13  Aligned_cols=39  Identities=10%  Similarity=-0.008  Sum_probs=26.2

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      |+-.++.||+|+|||...+-.+......+   .+++++.|..
T Consensus         8 g~i~v~~G~mgsGKTT~ll~~a~r~~~~g---~kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELIRRIRRAKIAK---QKIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTT---CCEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHCC---CEEEEEEecc
Confidence            44578999999999987654444333222   2789998874

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=96.77  E-value=0.0016  Score=69.15  Aligned_cols=69  Identities=25%  Similarity=0.296  Sum_probs=55.9

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC---CCeEEEEEecChHHHHHHHHHHHHHh
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP---GQVTALVLCHTRELAYQICHEFERFS  138 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~---~~~~~lil~P~~~L~~q~~~~~~~~~  138 (423)
                      .+++-|.++|..-  +++++|.|..|||||.+.+--++..+....   ...+++++++|++.+..+.+++....
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~l   81 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEAL   81 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHHH
Confidence            6899999999764  789999999999999987666666555432   33489999999999999998887643

>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=96.66  E-value=0.0021  Score=53.63  Aligned_cols=40  Identities=13%  Similarity=0.065  Sum_probs=28.2

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      |+-.++.|++|+|||...+-.+......+.   +++++.|...
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~~~~g~---kvli~kp~~D   58 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRFQIAQY---KCLVIKYAKD   58 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHTTTC---CEEEEEETTC
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHCCC---eEEEEeecCC
Confidence            445788999999999876655554443332   7899888753

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=96.62  E-value=0.0014  Score=53.89  Aligned_cols=40  Identities=10%  Similarity=-0.004  Sum_probs=25.8

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      |.-.++.|++|+|||...+-.+ .++...+  .+++++.|...
T Consensus        28 G~I~vitG~M~sGKTT~Llr~~-~r~~~~g--~kvli~kp~~D   67 (219)
T 3e2i_A           28 GWIECITGSMFSGKSEELIRRL-RRGIYAK--QKVVVFKPAID   67 (219)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH-HHHHHTT--CCEEEEEEC--
T ss_pred             ceEEEEECCCCCCHHHHHHHHH-HHHHHcC--CceEEEEeccC
Confidence            3447899999999997655444 3333222  27899999753

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.60  E-value=0.019  Score=50.87  Aligned_cols=19  Identities=5%  Similarity=-0.151  Sum_probs=16.0

Q ss_pred             CCceEEEccCCCcchhHHH
Q 014486           83 GMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~  101 (423)
                      +.++++.||+|+|||.+.-
T Consensus        45 ~~~lli~GpPGTGKT~~v~   63 (318)
T 3te6_A           45 NKLFYITNADDSTKFQLVN   63 (318)
T ss_dssp             CCEEEEECCCSHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4679999999999998653

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.55  E-value=0.0051  Score=59.78  Aligned_cols=112  Identities=17%  Similarity=0.207  Sum_probs=71.5

Q ss_pred             CCChhhhhccccccc--CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCce
Q 014486           68 HPSEVQHECIPQAIL--GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIK  145 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~--~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  145 (423)
                      .++..|++++..++.  ....++.|+-|.|||.+.-+.+.....      .++|..|+..-+....+    +...     
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a~~~~------~~~vtAP~~~a~~~l~~----~~~~-----  239 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISRIAG------RAIVTAPAKASTDVLAQ----FAGE-----  239 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHHHSSS------CEEEECSSCCSCHHHHH----HHGG-----
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHHHHHh------CcEEECCCHHHHHHHHH----HhhC-----
Confidence            578899999987776  334799999999999665544443321      46999999876654433    2211     


Q ss_pred             EEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceE
Q 014486          146 VAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQV  225 (423)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~  225 (423)
                                            .+-+..|+.+..       .....+++|||||=.+     -.+.+..+....+    .
T Consensus       240 ----------------------~i~~~~Pd~~~~-------~~~~~dlliVDEAAaI-----p~pll~~ll~~~~----~  281 (671)
T 2zpa_A          240 ----------------------KFRFIAPDALLA-------SDEQADWLVVDEAAAI-----PAPLLHQLVSRFP----R  281 (671)
T ss_dssp             ----------------------GCCBCCHHHHHH-------SCCCCSEEEEETGGGS-----CHHHHHHHHTTSS----E
T ss_pred             ----------------------CeEEeCchhhhh-------CcccCCEEEEEchhcC-----CHHHHHHHHhhCC----e
Confidence                                  133345665432       2234789999999854     3445555555332    5


Q ss_pred             EEEeccC
Q 014486          226 MMFSATL  232 (423)
Q Consensus       226 v~~SAT~  232 (423)
                      +++|.|.
T Consensus       282 v~~~tTv  288 (671)
T 2zpa_A          282 TLLTTTV  288 (671)
T ss_dssp             EEEEEEB
T ss_pred             EEEEecC
Confidence            7777775

>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=96.47  E-value=0.0021  Score=54.72  Aligned_cols=19  Identities=11%  Similarity=-0.008  Sum_probs=16.0

Q ss_pred             cCCceEEEccCCCcchhHH
Q 014486           82 LGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~  100 (423)
                      .++.+++.||+|+|||..+
T Consensus        51 ~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3567999999999999754

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=96.38  E-value=0.012  Score=52.54  Aligned_cols=18  Identities=22%  Similarity=0.285  Sum_probs=15.4

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      ++.+++.||+|+|||..+
T Consensus        37 ~~~lll~G~~GtGKT~la   54 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLL   54 (324)
T ss_dssp             CSSEEEECSSSSSHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            457999999999999764

>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=96.33  E-value=0.017  Score=48.12  Aligned_cols=40  Identities=15%  Similarity=0.297  Sum_probs=26.0

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEec
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSA  230 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SA  230 (423)
                      ....+||+||+|.+..  .....+..++...+....+++.|.
T Consensus       101 ~~~~vliiDe~~~l~~--~~~~~l~~~l~~~~~~~~~i~~~~  140 (226)
T 2chg_A          101 APFKIIFLDEADALTA--DAQAALRRTMEMYSKSCRFILSCN  140 (226)
T ss_dssp             CSCEEEEEETGGGSCH--HHHHHHHHHHHHTTTTEEEEEEES
T ss_pred             cCceEEEEeChhhcCH--HHHHHHHHHHHhcCCCCeEEEEeC
Confidence            4567899999998754  334455666666555665665543

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.32  E-value=0.0049  Score=49.98  Aligned_cols=38  Identities=13%  Similarity=0.038  Sum_probs=25.8

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT  123 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  123 (423)
                      ++=.++.||+|+|||.-.+-.+-.....+   .+++++.|.
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            44578999999999965444443333322   278999887

>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=96.09  E-value=0.028  Score=52.00  Aligned_cols=56  Identities=13%  Similarity=0.357  Sum_probs=39.3

Q ss_pred             CCccEEEEcCcchhh--ccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhc
Q 014486          189 KNVRHFILDECDKML--ESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFM  244 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~--~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~  244 (423)
                      .++++||+|++-+..  .+..+...+..+.....+..-++.++|+...+....+..+.
T Consensus       178 ~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~a~~~a~~f~  235 (433)
T 3kl4_A          178 NKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLASRFH  235 (433)
T ss_dssp             TTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGGGGGGHHHHHHHH
T ss_pred             cCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCccchHHHHHHHHHh
Confidence            467899999998764  43456667777777776677778888887666555555443

>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=96.06  E-value=0.032  Score=52.15  Aligned_cols=18  Identities=22%  Similarity=0.302  Sum_probs=15.3

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      .+.+++.||+|+|||..+
T Consensus       130 ~~~lll~Gp~G~GKTtLa  147 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLL  147 (440)
T ss_dssp             SCCEEEECSSSSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            357999999999999754

>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=96.04  E-value=0.041  Score=49.07  Aligned_cols=39  Identities=10%  Similarity=0.266  Sum_probs=24.2

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ..+++++||+|.+.. ......+..++...+...++|+.|
T Consensus       105 ~~~vliiDEi~~l~~-~~~~~~L~~~le~~~~~~~iI~~~  143 (324)
T 3u61_B          105 RQKVIVIDEFDRSGL-AESQRHLRSFMEAYSSNCSIIITA  143 (324)
T ss_dssp             CEEEEEEESCCCGGG-HHHHHHHHHHHHHHGGGCEEEEEE
T ss_pred             CCeEEEEECCcccCc-HHHHHHHHHHHHhCCCCcEEEEEe
Confidence            568899999998862 133444555555544455555544

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.00  E-value=0.0072  Score=47.16  Aligned_cols=19  Identities=21%  Similarity=0.370  Sum_probs=16.3

Q ss_pred             cCCceEEEccCCCcchhHH
Q 014486           82 LGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~  100 (423)
                      .+..+++.||+|+|||...
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            5778999999999999754

>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=95.94  E-value=0.019  Score=51.32  Aligned_cols=55  Identities=11%  Similarity=0.057  Sum_probs=33.2

Q ss_pred             ccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhh-ccc-ccccCCceEEEccCCCcchhHH
Q 014486           43 IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHE-CIP-QAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        43 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~-~i~-~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      .....|+++.-.+.+.+.|...=.   .|.... .+. .....+.+++.||+|+|||..+
T Consensus        12 ~~~~~~~di~G~~~~~~~l~~~i~---~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           12 KPNVKWEDVAGLEGAKEALKEAVI---LPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHTH---HHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             CCCCCHHHhcChHHHHHHHHHHHH---HHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            344568888877888777775411   111110 000 1122456999999999999765

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=95.87  E-value=0.023  Score=43.95  Aligned_cols=38  Identities=5%  Similarity=0.135  Sum_probs=23.9

Q ss_pred             cEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          192 RHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       192 ~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      +.+++||+|.+..  .....+..++...+...++|+.|..
T Consensus        78 g~l~ldei~~l~~--~~q~~Ll~~l~~~~~~~~~I~~t~~  115 (145)
T 3n70_A           78 GTLVLSHPEHLTR--EQQYHLVQLQSQEHRPFRLIGIGDT  115 (145)
T ss_dssp             SCEEEECGGGSCH--HHHHHHHHHHHSSSCSSCEEEEESS
T ss_pred             cEEEEcChHHCCH--HHHHHHHHHHhhcCCCEEEEEECCc
Confidence            4699999998854  3444555555555555666655544

>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=95.53  E-value=0.16  Score=45.86  Aligned_cols=43  Identities=12%  Similarity=0.319  Sum_probs=29.1

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCC
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLS  233 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~  233 (423)
                      .+.+++|+||+|.+.  ......+.+.+...+....+|+.|-.+.
T Consensus       133 ~~~~vlilDE~~~L~--~~~~~~L~~~le~~~~~~~~Il~t~~~~  175 (354)
T 1sxj_E          133 HRYKCVIINEANSLT--KDAQAALRRTMEKYSKNIRLIMVCDSMS  175 (354)
T ss_dssp             -CCEEEEEECTTSSC--HHHHHHHHHHHHHSTTTEEEEEEESCSC
T ss_pred             CCCeEEEEeCccccC--HHHHHHHHHHHHhhcCCCEEEEEeCCHH
Confidence            467899999999853  3445566666766666666666665544

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=95.45  E-value=0.066  Score=46.66  Aligned_cols=53  Identities=15%  Similarity=0.176  Sum_probs=31.6

Q ss_pred             CCCCcCCCCCHHHHHHHHhCC---CCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           45 SSGFRDFLLKPELLRAIVDSG---FEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~---~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ...|+++.-.+.+.+.|...-   ...+..++..   .+...+.+++.||+|+|||..+
T Consensus        13 ~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~---~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           13 NVRYEDIGGLEKQMQEIREVVELPLKHPELFEKV---GIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHH---CCCCCSEEEEESSSSSSHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhc---CCCCCCeEEEECCCCCcHHHHH
Confidence            445777877777777766431   0011111111   1234567999999999999764

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=95.44  E-value=0.026  Score=49.93  Aligned_cols=18  Identities=28%  Similarity=0.423  Sum_probs=15.6

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      +.++++.||+|+|||..+
T Consensus        67 ~~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           67 TLHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            456999999999999765

>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=95.37  E-value=0.054  Score=47.79  Aligned_cols=39  Identities=10%  Similarity=0.313  Sum_probs=26.8

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      .+.+++|+||+|.+..  .....+.+.++.-++...+|+++
T Consensus        81 ~~~kvviIdead~lt~--~a~naLLk~LEep~~~t~fIl~t  119 (305)
T 2gno_A           81 YTRKYVIVHDCERMTQ--QAANAFLKALEEPPEYAVIVLNT  119 (305)
T ss_dssp             SSSEEEEETTGGGBCH--HHHHHTHHHHHSCCTTEEEEEEE
T ss_pred             CCceEEEeccHHHhCH--HHHHHHHHHHhCCCCCeEEEEEE
Confidence            4678999999999864  33445666666655566566655

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=95.24  E-value=0.044  Score=50.11  Aligned_cols=18  Identities=33%  Similarity=0.383  Sum_probs=15.5

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      +..+++.||+|+|||...
T Consensus        44 ~~~vll~G~~G~GKT~l~   61 (387)
T 2v1u_A           44 PSNALLYGLTGTGKTAVA   61 (387)
T ss_dssp             CCCEEECBCTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            467999999999999764

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=95.16  E-value=0.16  Score=43.82  Aligned_cols=18  Identities=28%  Similarity=0.377  Sum_probs=15.3

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      +.+++.||+|+|||..+-
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            569999999999998653

>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=95.08  E-value=0.2  Score=46.37  Aligned_cols=55  Identities=13%  Similarity=0.247  Sum_probs=31.9

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhc
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFM  244 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~  244 (423)
                      ++++||+|.+=+...+......+..+.....+..-++.+.|+...+....+..+.
T Consensus       182 ~~DvVIIDTaGrl~~d~~lm~el~~i~~~~~pd~vlLVvDA~~gq~a~~~a~~f~  236 (443)
T 3dm5_A          182 GVDIIIVDTAGRHKEDKALIEEMKQISNVIHPHEVILVIDGTIGQQAYNQALAFK  236 (443)
T ss_dssp             TCSEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHHHHHHHHH
T ss_pred             CCCEEEEECCCcccchHHHHHHHHHHHHhhcCceEEEEEeCCCchhHHHHHHHHH
Confidence            3567888888654332234444555555555565677777776655555444443

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=95.00  E-value=0.082  Score=43.35  Aligned_cols=18  Identities=22%  Similarity=0.362  Sum_probs=15.5

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      +.+++.||+|+|||..+-
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            679999999999997643

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=94.78  E-value=0.093  Score=47.92  Aligned_cols=18  Identities=28%  Similarity=0.292  Sum_probs=15.2

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      .+.+++.||+|+|||..+
T Consensus        45 ~~~vll~G~~G~GKT~la   62 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVS   62 (384)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            346999999999999764

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=94.77  E-value=0.035  Score=50.15  Aligned_cols=40  Identities=18%  Similarity=0.272  Sum_probs=26.2

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEec
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSA  230 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SA  230 (423)
                      ...++|++||+|.+..  .....+..++...+....+++.+.
T Consensus       132 ~~~~vliiDE~~~l~~--~~~~~Ll~~le~~~~~~~~il~~~  171 (353)
T 1sxj_D          132 PPYKIIILDEADSMTA--DAQSALRRTMETYSGVTRFCLICN  171 (353)
T ss_dssp             CSCEEEEETTGGGSCH--HHHHHHHHHHHHTTTTEEEEEEES
T ss_pred             CCceEEEEECCCccCH--HHHHHHHHHHHhcCCCceEEEEeC
Confidence            3557999999998854  334556666666665665666543

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=94.59  E-value=0.16  Score=42.98  Aligned_cols=50  Identities=14%  Similarity=0.073  Sum_probs=29.8

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFE  135 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  135 (423)
                      .|.-+++.||+|+|||...+..+......+.   +++++.-. ....++.+.+.
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~---~v~~~~~e-~~~~~~~~~~~   71 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLKMGE---PGIYVALE-EHPVQVRQNMA   71 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHHTTC---CEEEEESS-SCHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhcCC---eEEEEEcc-CCHHHHHHHHH
Confidence            4566899999999999865443333332222   56666543 23445555444

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=94.54  E-value=0.048  Score=49.92  Aligned_cols=16  Identities=25%  Similarity=0.420  Sum_probs=14.4

Q ss_pred             ceEEEccCCCcchhHH
Q 014486           85 DVICQAKSGMGKTAVF  100 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~  100 (423)
                      .+++.||+|+|||...
T Consensus        46 ~~li~G~~G~GKTtl~   61 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTL   61 (389)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            6999999999999764

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=94.51  E-value=0.074  Score=47.29  Aligned_cols=40  Identities=15%  Similarity=0.357  Sum_probs=26.1

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEec
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSA  230 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SA  230 (423)
                      ...++||+||+|.+..  .....+..++...+....+|+.+.
T Consensus       109 ~~~~vliiDe~~~l~~--~~~~~L~~~le~~~~~~~~i~~~~  148 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQ--DAQQALRRTMEMFSSNVRFILSCN  148 (327)
T ss_dssp             CSCEEEEEETGGGSCH--HHHHHHHHHHHHTTTTEEEEEEES
T ss_pred             CCCeEEEEeCCCcCCH--HHHHHHHHHHHhcCCCCeEEEEeC
Confidence            4567899999998854  334455666666555666665543

>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=94.23  E-value=0.11  Score=51.96  Aligned_cols=78  Identities=15%  Similarity=0.211  Sum_probs=64.6

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHh----CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc-cccCCCCCCCCEEE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVE----CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL-VGRGIDIERVNIVI  361 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~-~~~Gld~~~~~~vi  361 (423)
                      .+.+++|.+++...+.++++.+++    .++++..++|+++..++...+....+|+.+|+|+|.. +...+++.++.+||
T Consensus       416 ~g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVV  495 (780)
T 1gm5_A          416 AGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVI  495 (780)
T ss_dssp             HTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEE
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEE
Confidence            357899999999988888777654    3789999999999999999999999999999999954 44567788888877


Q ss_pred             Ecc
Q 014486          362 NYD  364 (423)
Q Consensus       362 ~~~  364 (423)
                      .-.
T Consensus       496 IDE  498 (780)
T 1gm5_A          496 IDE  498 (780)
T ss_dssp             EES
T ss_pred             ecc
Confidence            533

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=94.20  E-value=0.39  Score=42.85  Aligned_cols=49  Identities=12%  Similarity=0.181  Sum_probs=28.5

Q ss_pred             cCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      .+..|+++.-.+...+.+...        -..+...-....++++.||+|+|||..+
T Consensus        24 ~p~~~~~iiG~~~~~~~l~~~--------l~~~~~~~~~~~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           24 RPSNFDGYIGQESIKKNLNVF--------IAAAKKRNECLDHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             CCCSGGGCCSCHHHHHHHHHH--------HHHHHHTTSCCCCEEEECSTTSSHHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHH--------HHHHHhcCCCCCeEEEECcCCCCHHHHH
Confidence            344677777666666655432        0000000012346999999999999764

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=94.12  E-value=0.061  Score=49.08  Aligned_cols=18  Identities=33%  Similarity=0.442  Sum_probs=15.4

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      +..+++.||+|+|||...
T Consensus        45 ~~~vli~G~~G~GKTtl~   62 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVV   62 (386)
T ss_dssp             CCCEEEEECTTSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            456999999999999754

>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=94.06  E-value=0.77  Score=40.57  Aligned_cols=48  Identities=10%  Similarity=0.153  Sum_probs=27.4

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      +..|+++.-.+...+.+...       .+. +...-.....+++.||+|+|||..+
T Consensus         8 p~~~~~~ig~~~~~~~l~~~-------l~~-~~~~~~~~~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A            8 PKTLDEYIGQERLKQKLRVY-------LEA-AKARKEPLEHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             CCSTTTCCSCHHHHHHHHHH-------HHH-HHHHCSCCCCCEEECCTTCCCHHHH
T ss_pred             cccHHHhhCHHHHHHHHHHH-------HHH-HHccCCCCCcEEEECCCCCCHHHHH
Confidence            34567776666655555421       000 0000012357999999999999754

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=93.92  E-value=0.13  Score=46.14  Aligned_cols=39  Identities=18%  Similarity=0.384  Sum_probs=27.1

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      ...+++|+||+|.+..  .....+.+++...+....+++.+
T Consensus       109 ~~~~viiiDe~~~l~~--~~~~~L~~~le~~~~~~~~il~~  147 (340)
T 1sxj_C          109 KGFKLIILDEADAMTN--AAQNALRRVIERYTKNTRFCVLA  147 (340)
T ss_dssp             CSCEEEEETTGGGSCH--HHHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCceEEEEeCCCCCCH--HHHHHHHHHHhcCCCCeEEEEEe
Confidence            3578999999998854  34455666677766666666554

>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=93.80  E-value=0.41  Score=43.33  Aligned_cols=40  Identities=8%  Similarity=0.257  Sum_probs=24.7

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEec
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSA  230 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SA  230 (423)
                      ....+||+||+|.+..  .....+.+.+...+....+|+.|.
T Consensus       118 ~~~~vliiDe~~~l~~--~~~~~Ll~~le~~~~~~~~Il~~~  157 (373)
T 1jr3_A          118 GRFKVYLIDEVHMLSR--HSFNALLKTLEEPPEHVKFLLATT  157 (373)
T ss_dssp             SSSEEEEEECGGGSCH--HHHHHHHHHHHSCCSSEEEEEEES
T ss_pred             CCeEEEEEECcchhcH--HHHHHHHHHHhcCCCceEEEEEeC
Confidence            4567999999998754  334445555555555554555543

>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=93.53  E-value=0.088  Score=46.61  Aligned_cols=44  Identities=16%  Similarity=0.200  Sum_probs=28.2

Q ss_pred             cCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      .+..|+++.-.+...+.+... +.      .      -...++++.||+|+|||..+
T Consensus        12 ~p~~~~~~~g~~~~~~~l~~~-l~------~------~~~~~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           12 RPRTLDEVVGQDEVIQRLKGY-VE------R------KNIPHLLFSGPPGTGKTATA   55 (319)
T ss_dssp             SCSSGGGSCSCHHHHHHHHTT-TT------T------TCCCCEEEESSSSSSHHHHH
T ss_pred             CCCCHHHHhCCHHHHHHHHHH-Hh------C------CCCCeEEEECcCCcCHHHHH
Confidence            345577776667777766643 10      0      01124999999999999754

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=93.48  E-value=0.099  Score=48.83  Aligned_cols=17  Identities=29%  Similarity=0.380  Sum_probs=14.8

Q ss_pred             CceEEEccCCCcchhHH
Q 014486           84 MDVICQAKSGMGKTAVF  100 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~  100 (423)
                      .++++.||+|+|||..+
T Consensus        51 ~~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLA   67 (447)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCcHHHHH
Confidence            46999999999999764

>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=93.45  E-value=0.33  Score=40.63  Aligned_cols=39  Identities=8%  Similarity=0.273  Sum_probs=23.2

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEec
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSA  230 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SA  230 (423)
                      .-.+||+||+|.+..  .....+...+...+....+|+.|.
T Consensus       126 ~~~vlviDe~~~l~~--~~~~~l~~~l~~~~~~~~~i~~t~  164 (250)
T 1njg_A          126 RFKVYLIDEVHMLSR--HSFNALLKTLEEPPEHVKFLLATT  164 (250)
T ss_dssp             SSEEEEEETGGGSCH--HHHHHHHHHHHSCCTTEEEEEEES
T ss_pred             CceEEEEECcccccH--HHHHHHHHHHhcCCCceEEEEEeC
Confidence            456899999998743  333444455554444555555543

>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=93.41  E-value=0.085  Score=46.81  Aligned_cols=39  Identities=15%  Similarity=0.302  Sum_probs=24.8

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEec
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSA  230 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SA  230 (423)
                      ...+||+||+|.+..  .....+...+...+....+|+.|.
T Consensus       107 ~~~viiiDe~~~l~~--~~~~~L~~~le~~~~~~~~il~~~  145 (323)
T 1sxj_B          107 KHKIVILDEADSMTA--GAQQALRRTMELYSNSTRFAFACN  145 (323)
T ss_dssp             CCEEEEEESGGGSCH--HHHHTTHHHHHHTTTTEEEEEEES
T ss_pred             CceEEEEECcccCCH--HHHHHHHHHHhccCCCceEEEEeC
Confidence            367999999998754  223344555555555666666553

>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=93.16  E-value=0.35  Score=38.51  Aligned_cols=72  Identities=15%  Similarity=0.272  Sum_probs=54.5

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++..+..+++.+...     ++.+..++|+.+.....   ..+.++..+|+|+|.-      -...+++.+++
T Consensus        36 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~------~~~Gid~~~~~  104 (175)
T 2rb4_A           36 QAIIFCQTRRNAKWLTVEMIQD-----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNV------CARGIDVKQVT  104 (175)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCS------CCTTTCCTTEE
T ss_pred             CEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecc------hhcCCCcccCC
Confidence            8999999999999888877653     67899999987765544   4456677899999942      13466778888


Q ss_pred             EEEEcC
Q 014486          193 HFILDE  198 (423)
Q Consensus       193 ~vVvDE  198 (423)
                      +||.-+
T Consensus       105 ~Vi~~d  110 (175)
T 2rb4_A          105 IVVNFD  110 (175)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            888543

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=93.02  E-value=0.84  Score=36.91  Aligned_cols=73  Identities=14%  Similarity=0.214  Sum_probs=54.9

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++.-+..+++.++..     ++.+..++|+.+.....   ..+.++..+|+|+|. .+     ...+++.+++
T Consensus        56 ~~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~-~~-----~~Gldi~~v~  124 (191)
T 2p6n_A           56 PVLIFAEKKADVDAIHEYLLLK-----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATD-VA-----SKGLDFPAIQ  124 (191)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECH-HH-----HTTCCCCCCS
T ss_pred             CEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcC-ch-----hcCCCcccCC
Confidence            7999999999999998888765     67889999987665443   445567789999993 22     2366778888


Q ss_pred             EEEEcCc
Q 014486          193 HFILDEC  199 (423)
Q Consensus       193 ~vVvDE~  199 (423)
                      +||.-+.
T Consensus       125 ~VI~~d~  131 (191)
T 2p6n_A          125 HVINYDM  131 (191)
T ss_dssp             EEEESSC
T ss_pred             EEEEeCC
Confidence            8886443

>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=92.87  E-value=0.5  Score=44.45  Aligned_cols=75  Identities=17%  Similarity=0.149  Sum_probs=52.2

Q ss_pred             HHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCC
Q 014486          277 RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIER  356 (423)
Q Consensus       277 ~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~  356 (423)
                      ..+...++. .+.++|+.+.+...++.+.+.|.+.++++...... .         .+..  ..|.|+...+..|+-+|.
T Consensus       372 ~~L~~~~~~-~~~rVvi~a~s~~r~erL~~~L~~~~i~~~~~~~~-~---------~~~~--g~v~i~~g~L~~GF~~p~  438 (483)
T 3hjh_A          372 DALRKFLET-FDGPVVFSVESEGRREALGELLARIKIAPQRIMRL-D---------EASD--RGRYLMIGAAEHGFVDTV  438 (483)
T ss_dssp             HHHHHHHHH-CCSCEEEEESCSSTTTTTHHHHGGGTCCCEECSCG-G---------GCCT--TCEEEEESCCCSCEEETT
T ss_pred             HHHHHHHHh-CCCeEEEEeCChHHHHHHHHHHHHcCCCceecCch-h---------hcCC--CcEEEEEcccccCcccCC
Confidence            344444433 24689999999999999999999988876544321 1         1222  356677778899999998


Q ss_pred             CCEEEEcc
Q 014486          357 VNIVINYD  364 (423)
Q Consensus       357 ~~~vi~~~  364 (423)
                      .+.+|..+
T Consensus       439 ~klaVITE  446 (483)
T 3hjh_A          439 RNLALICE  446 (483)
T ss_dssp             TTEEEEEH
T ss_pred             CCEEEEEc
Confidence            88877643

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=92.80  E-value=0.28  Score=45.24  Aligned_cols=77  Identities=18%  Similarity=0.164  Sum_probs=62.4

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHh---CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccc----cCCCCCCCCE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVE---CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVG----RGIDIERVNI  359 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~----~Gld~~~~~~  359 (423)
                      .+.++||.+|++..+.++++.++.   .++.+..++|+.+..++......+..++.+|+|+|.-.-    .-++..++++
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            557899999999999999999988   588999999999998888888888888899999995321    1145556777


Q ss_pred             EEEc
Q 014486          360 VINY  363 (423)
Q Consensus       360 vi~~  363 (423)
                      ||.-
T Consensus       143 iViD  146 (414)
T 3oiy_A          143 VFVD  146 (414)
T ss_dssp             EEES
T ss_pred             EEEe
Confidence            7653

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=92.73  E-value=0.18  Score=47.15  Aligned_cols=50  Identities=20%  Similarity=0.072  Sum_probs=28.6

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEF  134 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~  134 (423)
                      .|.-++|.|++|+|||...+-.+.......+.  .++++..- .-..|+..++
T Consensus       199 ~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~--~vl~~slE-~~~~~l~~R~  248 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFALTIAQNAALKEGV--GVGIYSLE-MPAAQLTLRM  248 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHTTCC--CEEEEESS-SCHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCC--eEEEEECC-CCHHHHHHHH
Confidence            34558999999999997655444443332221  56776542 2233444443

>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=92.66  E-value=0.25  Score=47.11  Aligned_cols=43  Identities=12%  Similarity=0.139  Sum_probs=25.9

Q ss_pred             CCccEEEEcCcchhhcc-CCcHHHHHHHHHhCCCCceEEEEeccCC
Q 014486          189 KNVRHFILDECDKMLES-LDMRRDVQEIFKMTPHDKQVMMFSATLS  233 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~-~~~~~~~~~~~~~~~~~~~~v~~SAT~~  233 (423)
                      ....+|++||+|.+... ......+..+...  ...++|+++++..
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            34568999999998652 1222444444444  2445777777643

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=92.56  E-value=0.21  Score=46.89  Aligned_cols=39  Identities=15%  Similarity=0.128  Sum_probs=24.4

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      .|.-++|.|++|+|||...+..+.......+.  .++++..
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~--~Vl~~s~  240 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATKTNE--NVAIFSL  240 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHHSSC--CEEEEES
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhCCC--cEEEEEC
Confidence            35568999999999997655444433322221  5677663

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.49  E-value=0.057  Score=49.94  Aligned_cols=54  Identities=13%  Similarity=0.177  Sum_probs=37.8

Q ss_pred             cCCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      +..+|++.+--+.+.+.|.+.   .+.+|-.++...++   ..+.+++.||+|+|||+.+
T Consensus       176 p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~---~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          176 PTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIR---APKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCC---CCCEEEEESCTTSSHHHHH
T ss_pred             CCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCC---CCCeeEEECcCCCCHHHHH
Confidence            345799998888887777754   23345555554443   2467999999999999754

>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=92.40  E-value=1.8  Score=35.01  Aligned_cols=141  Identities=13%  Similarity=0.087  Sum_probs=68.2

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH-HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE-LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDL  161 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~-L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (423)
                      ...+++..++|.|||.+++-.++..+..+.   +++++.=.+. ....=.+.+..+     ++.+.....+.........
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~G~---rV~~vQF~Kg~~~~gE~~~l~~L-----~v~~~~~g~gf~~~~~~~~   99 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGHGK---NVGVVQFIKGTWPNGERNLLEPH-----GVEFQVMATGFTWETQNRE   99 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHTTC---CEEEEESSCCSSCCHHHHHHGGG-----TCEEEECCTTCCCCGGGHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEEeeCCCCCccHHHHHHhC-----CcEEEEcccccccCCCCcH
Confidence            346899999999999998877777766544   6777732211 000000111111     1222211111110000000


Q ss_pred             HhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc-cCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHH
Q 014486          162 LKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE-SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV  239 (423)
Q Consensus       162 ~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~-~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~  239 (423)
                      -...  .    .-..|....+  .+.-..+++||+||+-.... ..--...+..++...+...-+|+.+-.+|+++...
T Consensus       100 ~~~~--~----a~~~l~~a~~--~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~~l~e~  170 (196)
T 1g5t_A          100 ADTA--A----CMAVWQHGKR--MLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDL  170 (196)
T ss_dssp             HHHH--H----HHHHHHHHHH--HTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHH
T ss_pred             HHHH--H----HHHHHHHHHH--HHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCcHHHHHh
Confidence            0000  0    0111111111  12225688999999976433 12234556666666666666777666677666554

>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=92.31  E-value=0.31  Score=43.31  Aligned_cols=55  Identities=18%  Similarity=0.113  Sum_probs=31.8

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCC------------CCC-CeEEEEEecChHH-HHHHHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEP------------NPG-QVTALVLCHTREL-AYQICHEFERF  137 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~------------~~~-~~~~lil~P~~~L-~~q~~~~~~~~  137 (423)
                      |.-+++.|++|+|||...+-.+......            ++. ..+++|+.-...+ ..++.+.++++
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            3458999999999997665544432211            111 1478888754432 44444444443

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=92.05  E-value=1.4  Score=34.47  Aligned_cols=88  Identities=13%  Similarity=0.234  Sum_probs=60.8

Q ss_pred             chhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEe
Q 014486           96 KTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVG  172 (423)
Q Consensus        96 KT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~  172 (423)
                      |.. .+..++....    ..++||.++++.-+..+++.+...     ++.+..++|+.+.....   ..+.++..+|+|+
T Consensus        17 K~~-~l~~ll~~~~----~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~   86 (165)
T 1fuk_A           17 KYE-CLTDLYDSIS----VTQAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILIS   86 (165)
T ss_dssp             HHH-HHHHHHHHTT----CSCEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEE
T ss_pred             HHH-HHHHHHHhCC----CCCEEEEECCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEE
Confidence            543 3444555432    228999999999999988887764     67888999987655443   4455677899999


Q ss_pred             chHHHHHHHhcCCCCCCCccEEEEcCc
Q 014486          173 TPGRILALARDKDLSLKNVRHFILDEC  199 (423)
Q Consensus       173 T~~~l~~~~~~~~~~~~~~~~vVvDE~  199 (423)
                      |.-      -...+++.++++||.-+.
T Consensus        87 T~~------~~~G~d~~~~~~Vi~~~~  107 (165)
T 1fuk_A           87 TDL------LARGIDVQQVSLVINYDL  107 (165)
T ss_dssp             EGG------GTTTCCCCSCSEEEESSC
T ss_pred             cCh------hhcCCCcccCCEEEEeCC
Confidence            942      134567778888876443

>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=91.83  E-value=0.41  Score=45.18  Aligned_cols=18  Identities=22%  Similarity=0.329  Sum_probs=15.6

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      ...+++.||+|+|||+.+
T Consensus       238 ~~~vLL~GppGtGKT~lA  255 (489)
T 3hu3_A          238 PRGILLYGPPGTGKTLIA  255 (489)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CCcEEEECcCCCCHHHHH
Confidence            466999999999999865

>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=91.76  E-value=0.61  Score=37.50  Aligned_cols=90  Identities=20%  Similarity=0.214  Sum_probs=53.4

Q ss_pred             CcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHH---HHHHhcCCCcEE
Q 014486           94 MGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH---KDLLKNECPQIV  170 (423)
Q Consensus        94 sGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~il  170 (423)
                      +.|-. .+.-++....   ...++||.++++.-+..+++.++..     ++.+..++|+.+....   ...+.++..+|+
T Consensus        30 ~~K~~-~L~~ll~~~~---~~~k~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vL  100 (185)
T 2jgn_A           30 SDKRS-FLLDLLNATG---KDSLTLVFVETKKGADSLEDFLYHE-----GYACTSIHGDRSQRDREEALHQFRSGKSPIL  100 (185)
T ss_dssp             GGHHH-HHHHHHHHC----CCSCEEEEESCHHHHHHHHHHHHHT-----TCCEEEEC--------CHHHHHHHHTSSSEE
T ss_pred             HHHHH-HHHHHHHhcC---CCCeEEEEECCHHHHHHHHHHHHHc-----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEE
Confidence            45653 3444555432   2238999999999999988887763     6788889987654433   344556778999


Q ss_pred             EechHHHHHHHhcCCCCCCCccEEEEcC
Q 014486          171 VGTPGRILALARDKDLSLKNVRHFILDE  198 (423)
Q Consensus       171 v~T~~~l~~~~~~~~~~~~~~~~vVvDE  198 (423)
                      |+|. .+     ...+++.++++||.=+
T Consensus       101 vaT~-~~-----~~Gldi~~~~~VI~~d  122 (185)
T 2jgn_A          101 VATA-VA-----ARGLDISNVKHVINFD  122 (185)
T ss_dssp             EEEC------------CCCSBSEEEESS
T ss_pred             EEcC-hh-----hcCCCcccCCEEEEeC
Confidence            9993 22     2355677888887643

>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=91.59  E-value=2.4  Score=33.44  Aligned_cols=91  Identities=10%  Similarity=0.073  Sum_probs=62.6

Q ss_pred             CcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEE
Q 014486           94 MGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIV  170 (423)
Q Consensus        94 sGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~il  170 (423)
                      ..|.. .+..++....    ..++||.|+++.-+..+++.+...     ++.+..++|+.......   ..+.++..+|+
T Consensus        16 ~~K~~-~L~~ll~~~~----~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vL   85 (172)
T 1t5i_A           16 NEKNR-KLFDLLDVLE----FNQVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRIL   85 (172)
T ss_dssp             GGHHH-HHHHHHHHSC----CSSEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEE
T ss_pred             HHHHH-HHHHHHHhCC----CCcEEEEECCHHHHHHHHHHHHhc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEE
Confidence            34543 3444554432    227999999999999988888764     67889999987665443   44556778999


Q ss_pred             EechHHHHHHHhcCCCCCCCccEEEEcCcc
Q 014486          171 VGTPGRILALARDKDLSLKNVRHFILDECD  200 (423)
Q Consensus       171 v~T~~~l~~~~~~~~~~~~~~~~vVvDE~h  200 (423)
                      |+|.-      -...+++.++++||.-+..
T Consensus        86 vaT~~------~~~Gldi~~~~~Vi~~d~p  109 (172)
T 1t5i_A           86 VATNL------FGRGMDIERVNIAFNYDMP  109 (172)
T ss_dssp             EESSC------CSTTCCGGGCSEEEESSCC
T ss_pred             EECCc------hhcCcchhhCCEEEEECCC
Confidence            99942      2345677888888865543

>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=91.45  E-value=4  Score=36.21  Aligned_cols=37  Identities=11%  Similarity=0.250  Sum_probs=23.2

Q ss_pred             cEEEEcCcchhhc--cCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          192 RHFILDECDKMLE--SLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       192 ~~vVvDE~h~~~~--~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      -+||+||+|.+..  ...+...+..+....+ ...+|+.+
T Consensus       139 ~vlvlDe~~~~~~~~~~~~~~~l~~~~~~~~-~~~~i~~g  177 (357)
T 2fna_A          139 VIIVLDEAQELVKLRGVNLLPALAYAYDNLK-RIKFIMSG  177 (357)
T ss_dssp             EEEEEETGGGGGGCTTCCCHHHHHHHHHHCT-TEEEEEEE
T ss_pred             eEEEEECHHHhhccCchhHHHHHHHHHHcCC-CeEEEEEc
Confidence            4799999999864  2456666666665542 34444443

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.29  E-value=0.077  Score=48.35  Aligned_cols=54  Identities=20%  Similarity=0.182  Sum_probs=36.2

Q ss_pred             cCCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      +..+|++.+=-+.+.+.|.+.   .+.+|-.++...++   ..+.+++.||+|+|||+.+
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~---~prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIA---QPKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCC---CCCCEEEESCSSSSHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCC---CCCceEEeCCCCCCHHHHH
Confidence            446788888677777777654   23344444444432   2467999999999999754

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=90.93  E-value=4.6  Score=31.35  Aligned_cols=73  Identities=16%  Similarity=0.274  Sum_probs=55.3

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.++++..+..+++.+...     ++.+..++|+.+.....   ..+.++..+|+|+|.- +     ...+++.+++
T Consensus        37 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~-~-----~~Gld~~~~~  105 (163)
T 2hjv_A           37 SCIIFCRTKEHVNQLTDELDDL-----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDV-A-----ARGIDIENIS  105 (163)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGG-G-----TTTCCCSCCS
T ss_pred             cEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECCh-h-----hcCCchhcCC
Confidence            7899999999999988888764     67899999987655443   4455677899999932 2     3467788888


Q ss_pred             EEEEcCc
Q 014486          193 HFILDEC  199 (423)
Q Consensus       193 ~vVvDE~  199 (423)
                      +||.-+.
T Consensus       106 ~Vi~~~~  112 (163)
T 2hjv_A          106 LVINYDL  112 (163)
T ss_dssp             EEEESSC
T ss_pred             EEEEeCC
Confidence            8887554

>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=90.84  E-value=0.55  Score=41.08  Aligned_cols=21  Identities=19%  Similarity=0.276  Sum_probs=16.5

Q ss_pred             cCCceEEEccCCCcchhHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~  102 (423)
                      .++.+++.|++|+|||.....
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~  124 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAK  124 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHH
Confidence            355688999999999986544

>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=90.72  E-value=1.2  Score=36.76  Aligned_cols=70  Identities=14%  Similarity=0.217  Sum_probs=54.2

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++.-+..+++.+...     ++.+..++|+.+.....   ..+.++..+|+|+|.-      -...+++.+++
T Consensus        33 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~------~~~Gidi~~v~  101 (212)
T 3eaq_A           33 RAMVFTRTKAETEEIAQGLLRL-----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDV------AARGLDIPQVD  101 (212)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHH-----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTT------TTCSSSCCCBS
T ss_pred             eEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecCh------hhcCCCCccCc
Confidence            8999999999999988888765     67889999998765554   3456677899999932      23467788888


Q ss_pred             EEEE
Q 014486          193 HFIL  196 (423)
Q Consensus       193 ~vVv  196 (423)
                      +||.
T Consensus       102 ~Vi~  105 (212)
T 3eaq_A          102 LVVH  105 (212)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8884

>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=90.04  E-value=1.8  Score=41.58  Aligned_cols=77  Identities=16%  Similarity=0.232  Sum_probs=58.6

Q ss_pred             eEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCc
Q 014486          115 VTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNV  191 (423)
Q Consensus       115 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~  191 (423)
                      .++||.|+++.-+..+++.+.+....  ++.+..++|+.......   ..+.++..+|+|+|.-      -...+++.++
T Consensus       340 ~~~iVF~~s~~~~~~l~~~L~~~~~~--~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~------~~~GiDip~v  411 (563)
T 3i5x_A          340 YKAIIFAPTVKFTSFLCSILKNEFKK--DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV------GARGMDFPNV  411 (563)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHHHTT--TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGG------GTSSCCCTTC
T ss_pred             CcEEEEcCcHHHHHHHHHHHHHhccC--CceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcch------hhcCCCcccC
Confidence            38999999999999999988876432  67899999988765543   4455677899999952      2346788889


Q ss_pred             cEEEEcCc
Q 014486          192 RHFILDEC  199 (423)
Q Consensus       192 ~~vVvDE~  199 (423)
                      ++||.-..
T Consensus       412 ~~VI~~~~  419 (563)
T 3i5x_A          412 HEVLQIGV  419 (563)
T ss_dssp             CEEEEESC
T ss_pred             CEEEEECC
Confidence            98886554

>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=90.02  E-value=6.4  Score=38.68  Aligned_cols=92  Identities=17%  Similarity=0.156  Sum_probs=65.7

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHH---HhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDL---LKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++.-+..+++.+.+.     ++++..++|+.........   +.++..+|+|+|.-      -...+++.+++
T Consensus       447 ~vlVf~~t~~~ae~L~~~L~~~-----gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~------l~~GlDip~v~  515 (661)
T 2d7d_A          447 RVLVTTLTKKMSEDLTDYLKEI-----GIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINL------LREGLDIPEVS  515 (661)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCC------CSTTCCCTTEE
T ss_pred             eEEEEECCHHHHHHHHHHHHhc-----CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecch------hhCCcccCCCC
Confidence            8999999999999888888765     6788888988765555443   55677899999852      24567888999


Q ss_pred             EEEEcCcchhhccCCcHHHHHHHHHh
Q 014486          193 HFILDECDKMLESLDMRRDVQEIFKM  218 (423)
Q Consensus       193 ~vVvDE~h~~~~~~~~~~~~~~~~~~  218 (423)
                      +||+-+++...-..+...-++++-+.
T Consensus       516 lVi~~d~d~~G~p~s~~~~iQr~GRa  541 (661)
T 2d7d_A          516 LVAILDADKEGFLRSERSLIQTIGRA  541 (661)
T ss_dssp             EEEETTTTCCTTTTSHHHHHHHHHTT
T ss_pred             EEEEeCcccccCCCCHHHHHHHhCcc
Confidence            99999987543212334444444443

>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=89.99  E-value=0.42  Score=43.93  Aligned_cols=17  Identities=29%  Similarity=0.602  Sum_probs=14.1

Q ss_pred             CceEE--EccCCCcchhHH
Q 014486           84 MDVIC--QAKSGMGKTAVF  100 (423)
Q Consensus        84 ~~~ii--~~~tGsGKT~~~  100 (423)
                      ..++|  .||+|+|||...
T Consensus        51 ~~~li~i~G~~G~GKT~L~   69 (412)
T 1w5s_A           51 VNMIYGSIGRVGIGKTTLA   69 (412)
T ss_dssp             EEEEEECTTCCSSSHHHHH
T ss_pred             CEEEEeCcCcCCCCHHHHH
Confidence            45788  899999999764

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=89.91  E-value=0.2  Score=44.74  Aligned_cols=50  Identities=24%  Similarity=0.180  Sum_probs=29.7

Q ss_pred             ccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHH
Q 014486           81 ILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEF  134 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~  134 (423)
                      ..|.-+++.|++|+|||..++-.+......   +..++|++.- .-..|+..++
T Consensus        44 ~~G~LiiIaG~pG~GKTt~al~ia~~~a~~---g~~Vl~fSlE-ms~~ql~~Rl   93 (338)
T 4a1f_A           44 NKGSLVIIGARPSMGKTSLMMNMVLSALND---DRGVAVFSLE-MSAEQLALRA   93 (338)
T ss_dssp             CTTCEEEEEECTTSCHHHHHHHHHHHHHHT---TCEEEEEESS-SCHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCC-CCHHHHHHHH
Confidence            345559999999999997655444443332   2267777642 2334444444

>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=89.79  E-value=1.1  Score=47.38  Aligned_cols=76  Identities=18%  Similarity=0.215  Sum_probs=62.9

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHh----CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEc-CccccCCCCCCCCEEE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVE----CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVAT-DLVGRGIDIERVNIVI  361 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T-~~~~~Gld~~~~~~vi  361 (423)
                      .+.+++|.+++...+.++++.+++    .+..+..+++..+..++...++....|..+|+|+| ..+...+.+.++.+||
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            456899999999999888887764    35788899999999999999999999999999999 4455567777787776


Q ss_pred             E
Q 014486          362 N  362 (423)
Q Consensus       362 ~  362 (423)
                      .
T Consensus       731 i  731 (1151)
T 2eyq_A          731 V  731 (1151)
T ss_dssp             E
T ss_pred             E
Confidence            4

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=89.74  E-value=0.72  Score=46.20  Aligned_cols=53  Identities=19%  Similarity=0.224  Sum_probs=29.4

Q ss_pred             CCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           45 SSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ...|++.+=-+...+.|.+.   .+.+|..++...+   ...+.+++.||+|+|||+.+
T Consensus       200 ~v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~---~~p~GILL~GPPGTGKT~LA  255 (806)
T 3cf2_A          200 EVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGV---KPPRGILLYGPPGTGKTLIA  255 (806)
T ss_dssp             SCCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCC---CCCCEEEEECCTTSCHHHHH
T ss_pred             CCChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCC---CCCCeEEEECCCCCCHHHHH
Confidence            44577665333333334332   2233444443322   12367999999999999754

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=89.67  E-value=0.13  Score=39.50  Aligned_cols=18  Identities=17%  Similarity=0.086  Sum_probs=15.5

Q ss_pred             cCCceEEEccCCCcchhH
Q 014486           82 LGMDVICQAKSGMGKTAV   99 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~   99 (423)
                      .+.++++.||+|+|||..
T Consensus        26 ~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           26 RTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             CSSCEEEEEETTCCHHHH
T ss_pred             CCCcEEEECCCCccHHHH
Confidence            456799999999999964

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=89.35  E-value=0.42  Score=52.63  Aligned_cols=40  Identities=15%  Similarity=0.073  Sum_probs=28.6

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      ++++++.+|+|+|||..+...+.+....+.   +++++..-..
T Consensus      1427 g~~vll~GppGtGKT~LA~ala~ea~~~G~---~v~Fi~~e~~ 1466 (2050)
T 3cmu_A         1427 GRIVEIYGPESSGKTTLTLQVIAAAQREGK---TCAFIDAEHA 1466 (2050)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHHHTTTC---CEEEECTTSC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCC---cEEEEEcccc
Confidence            577999999999999877665555444322   6777775543

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.30  E-value=0.13  Score=47.48  Aligned_cols=54  Identities=20%  Similarity=0.180  Sum_probs=35.1

Q ss_pred             cCCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      +..+|++.+--+.+.+.|...   .+.+|-.++...+   ...+.+++.||+|+|||+.+
T Consensus       176 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~---~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          176 GEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGI---KPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             CSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCC---CCCCEEEEESCTTSSHHHHH
T ss_pred             CCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeEEEECCCCCcHHHHH
Confidence            445788887666766666543   2233444444333   23467999999999999764

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=89.27  E-value=2.8  Score=38.28  Aligned_cols=71  Identities=18%  Similarity=0.192  Sum_probs=54.3

Q ss_pred             eEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCc
Q 014486          115 VTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNV  191 (423)
Q Consensus       115 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~  191 (423)
                      .++||.++++..+..+++.+.+.     ++.+..++|+.......   ..+.++..+|+|+|.-      -...+++.++
T Consensus       277 ~~~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~------~~~Gidip~v  345 (417)
T 2i4i_A          277 SLTLVFVETKKGADSLEDFLYHE-----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAV------AARGLDISNV  345 (417)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHH------HHTTSCCCCE
T ss_pred             CeEEEEECCHHHHHHHHHHHHHC-----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECCh------hhcCCCcccC
Confidence            38999999999999988888764     67899999988765443   3455677899999951      1346778888


Q ss_pred             cEEEE
Q 014486          192 RHFIL  196 (423)
Q Consensus       192 ~~vVv  196 (423)
                      ++||.
T Consensus       346 ~~Vi~  350 (417)
T 2i4i_A          346 KHVIN  350 (417)
T ss_dssp             EEEEE
T ss_pred             CEEEE
Confidence            88875

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=88.40  E-value=6.7  Score=37.82  Aligned_cols=78  Identities=15%  Similarity=0.232  Sum_probs=59.2

Q ss_pred             eEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCc
Q 014486          115 VTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNV  191 (423)
Q Consensus       115 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~  191 (423)
                      .++||.|+++.-+..+++.+.+...  .++.+..++|+.......   ..+.++..+|+|+|.-      -...+++.++
T Consensus       289 ~~~iVF~~t~~~~~~l~~~L~~~~~--~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~------~~~GiDip~v  360 (579)
T 3sqw_A          289 YKAIIFAPTVKFTSFLCSILKNEFK--KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV------GARGMDFPNV  360 (579)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHHHT--TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGG------GTSSCCCTTC
T ss_pred             CcEEEECCcHHHHHHHHHHHHHhhc--CCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcch------hhcCCCcccC
Confidence            3899999999999999998887653  267899999987765543   4455677899999952      2346788889


Q ss_pred             cEEEEcCcc
Q 014486          192 RHFILDECD  200 (423)
Q Consensus       192 ~~vVvDE~h  200 (423)
                      ++||.-..-
T Consensus       361 ~~VI~~~~p  369 (579)
T 3sqw_A          361 HEVLQIGVP  369 (579)
T ss_dssp             CEEEEESCC
T ss_pred             CEEEEcCCC
Confidence            998866543

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=88.29  E-value=0.9  Score=47.59  Aligned_cols=78  Identities=19%  Similarity=0.192  Sum_probs=62.7

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHh---CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccc-c---CCCCCCCCE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVE---CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVG-R---GIDIERVNI  359 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~-~---Gld~~~~~~  359 (423)
                      .+.++||.++++..+.++++.++.   .++.+..++|+.+..++...+..+..|..+|+|+|.-.- .   -+++.++++
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            457899999999999999999988   567899999999988888888888999999999995211 1   144567887


Q ss_pred             EEEcc
Q 014486          360 VINYD  364 (423)
Q Consensus       360 vi~~~  364 (423)
                      +|.-.
T Consensus       200 lViDE  204 (1104)
T 4ddu_A          200 VFVDD  204 (1104)
T ss_dssp             EEESC
T ss_pred             EEEeC
Confidence            77533

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=88.12  E-value=0.22  Score=44.21  Aligned_cols=53  Identities=11%  Similarity=0.092  Sum_probs=31.6

Q ss_pred             cCCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ....|++.+-.+.+.+.|...   ....+..++.    .....+.+++.||+|+|||..+
T Consensus         7 ~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~----~~~~~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A            7 PNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG----KRTPWRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCT----TCCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhC----CCCCCceEEEECCCCccHHHHH
Confidence            345688887777776666643   1111111110    1122367999999999999764

>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=88.10  E-value=0.7  Score=38.19  Aligned_cols=71  Identities=15%  Similarity=0.238  Sum_probs=53.0

Q ss_pred             CcEEEEEcChhhHHHHHHHHHhC-----CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc-c-----ccCCCCCCC
Q 014486          289 NQVVIFVKSVSRAAELNKLLVEC-----NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL-V-----GRGIDIERV  357 (423)
Q Consensus       289 ~~~ivf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~-~-----~~Gld~~~~  357 (423)
                      .++||.++++..+..+.+.++..     +..+..++|+.+.......   +..+..+|+|+|.- +     ...+++.++
T Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~---~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~  159 (220)
T 1t6n_A           83 VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALARNKSLNLKHI  159 (220)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHH---HHHSCCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             EEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHH---HhcCCCCEEEeCHHHHHHHHHhCCCCcccC
Confidence            47999999999999988887664     6888899999887665544   34466789999942 1     234667778


Q ss_pred             CEEEE
Q 014486          358 NIVIN  362 (423)
Q Consensus       358 ~~vi~  362 (423)
                      +++|.
T Consensus       160 ~~lVi  164 (220)
T 1t6n_A          160 KHFIL  164 (220)
T ss_dssp             CEEEE
T ss_pred             CEEEE
Confidence            87775

>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=88.09  E-value=1.1  Score=42.85  Aligned_cols=59  Identities=19%  Similarity=0.287  Sum_probs=54.6

Q ss_pred             CCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcC
Q 014486          288 FNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD  346 (423)
Q Consensus       288 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~  346 (423)
                      .+.+||.++.+..+....+.|...|+++..+++..+..++..+......+..+|+++|+
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            47899999999999999999999999999999999999998888888899999999984

>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=87.88  E-value=0.17  Score=44.49  Aligned_cols=55  Identities=18%  Similarity=0.213  Sum_probs=32.5

Q ss_pred             ccCCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           43 IHSSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        43 ~~~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      .....|+++.-.+.+.+.|...   ....|..++..   .+..++.+++.||+|+|||+.+
T Consensus         9 ~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~---~~~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A            9 VPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKF---GMTPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHH---CCCCCSEEEEECSSSSSHHHHH
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHc---CCCCCceEEEECCCCcCHHHHH
Confidence            3455688887667766666643   01111111111   1234567999999999999764

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.82  E-value=0.2  Score=46.21  Aligned_cols=53  Identities=15%  Similarity=0.065  Sum_probs=34.3

Q ss_pred             CCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           45 SSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ..+|++.+--+.+.+.|...   .+.+|-.++...+   ...+.+++.||+|+|||+.+
T Consensus       168 ~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~---~~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          168 DVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGI---DPPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCC---CCCCEEEEESCTTTTHHHHH
T ss_pred             CCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCceEEEECCCCCCHHHHH
Confidence            45788887666766666543   2223334444333   23467999999999999764

>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=87.73  E-value=3.4  Score=34.83  Aligned_cols=115  Identities=9%  Similarity=0.082  Sum_probs=69.4

Q ss_pred             CCcEEEEEcChhhHHHHHHHHHhC----CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc-----c--ccCCCCCC
Q 014486          288 FNQVVIFVKSVSRAAELNKLLVEC----NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL-----V--GRGIDIER  356 (423)
Q Consensus       288 ~~~~ivf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~-----~--~~Gld~~~  356 (423)
                      ..++||.++++..+..+++.++..    ++.+..++|+.+.......+.    +..+|+|+|.-     +  ..++++.+
T Consensus       111 ~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~I~v~Tp~~l~~~l~~~~~~~l~~  186 (249)
T 3ber_A          111 RLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALA----KKPHIIIATPGRLIDHLENTKGFNLRA  186 (249)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHH----TCCSEEEECHHHHHHHHHHSTTCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhc----CCCCEEEECHHHHHHHHHcCCCcCccc
Confidence            457999999999998888777654    788899999988666544332    46789999942     1  13567778


Q ss_pred             CCEEEEccCC----CCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHh
Q 014486          357 VNIVINYDMP----DSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       357 ~~~vi~~~~~----~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                      ++++|.-..-    ++....+..+-+..+.   ..-+++++........+.+++++.
T Consensus       187 ~~~lViDEah~l~~~~~~~~l~~i~~~~~~---~~~~l~~SAT~~~~v~~~~~~~l~  240 (249)
T 3ber_A          187 LKYLVMDEADRILNMDFETEVDKILKVIPR---DRKTFLFSATMTKKVQKLQRAALK  240 (249)
T ss_dssp             CCEEEECSHHHHHHTTCHHHHHHHHHSSCS---SSEEEEEESSCCHHHHHHHHHHCS
T ss_pred             cCEEEEcChhhhhccChHHHHHHHHHhCCC---CCeEEEEeccCCHHHHHHHHHHCC
Confidence            8877753211    1121122222222221   223445555555666666665554

>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=87.65  E-value=8.2  Score=34.71  Aligned_cols=76  Identities=9%  Similarity=0.194  Sum_probs=58.0

Q ss_pred             eEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCc
Q 014486          115 VTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNV  191 (423)
Q Consensus       115 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~  191 (423)
                      .++||.++++.-+..+++.+++.     +..+..++|+.+.....   +.+.++..+|+|+|.-      -...+++.++
T Consensus       244 ~~~lvf~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~------~~~Gidip~~  312 (395)
T 3pey_A          244 GSSIIFVATKKTANVLYGKLKSE-----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNV------LARGIDIPTV  312 (395)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGG------GSSSCCCTTE
T ss_pred             CCEEEEeCCHHHHHHHHHHHHhc-----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECCh------hhcCCCcccC
Confidence            38999999999999988888764     66888999987655443   4455677899999952      2456788899


Q ss_pred             cEEEEcCcch
Q 014486          192 RHFILDECDK  201 (423)
Q Consensus       192 ~~vVvDE~h~  201 (423)
                      ++||.-+...
T Consensus       313 ~~Vi~~~~p~  322 (395)
T 3pey_A          313 SMVVNYDLPT  322 (395)
T ss_dssp             EEEEESSCCB
T ss_pred             CEEEEcCCCC
Confidence            9998766553

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=87.31  E-value=0.36  Score=42.19  Aligned_cols=53  Identities=13%  Similarity=0.065  Sum_probs=30.9

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhh-hccccc-ccCCceEEEccCCCcchhHH
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQH-ECIPQA-ILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~-~~i~~~-~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ...|+++.-.+.+.+.|...-.   .+... +.+..+ ...+.+++.||+|+|||..+
T Consensus        17 ~~~~~~i~G~~~~~~~l~~~i~---~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           17 KVEWTDIAGQDVAKQALQEMVI---LPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CCCGGGSCCCHHHHHHHHHHTH---HHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCHHHhCChHHHHHHHHHHHH---hhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHH
Confidence            4467777767777777664310   01100 011111 12567999999999999764

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.11  E-value=0.3  Score=44.83  Aligned_cols=54  Identities=22%  Similarity=0.237  Sum_probs=35.6

Q ss_pred             cCCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ...+|++.+=-+.+.+.|.+.   .+.+|-.++...++   ..+.+++.||+|+|||+.+
T Consensus       177 p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~---~prGvLLyGPPGTGKTlLA  233 (437)
T 4b4t_I          177 PTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIK---PPKGVILYGAPGTGKTLLA  233 (437)
T ss_dssp             CCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCC---CCSEEEEESSTTTTHHHHH
T ss_pred             CCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCC---CCCCCceECCCCchHHHHH
Confidence            345788887666666666653   23344445444432   2467999999999999754

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=86.99  E-value=1.4  Score=40.27  Aligned_cols=40  Identities=13%  Similarity=0.031  Sum_probs=24.5

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCC---CCCCeEEEEEecC
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEP---NPGQVTALVLCHT  123 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~---~~~~~~~lil~P~  123 (423)
                      .-+.|.||+|+|||......++....+   ++...+++++.-.
T Consensus       179 ei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E  221 (400)
T 3lda_A          179 SITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE  221 (400)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESS
T ss_pred             cEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCC
Confidence            458899999999997665333333322   1122367777643

>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=86.86  E-value=1.8  Score=41.91  Aligned_cols=60  Identities=10%  Similarity=0.083  Sum_probs=53.8

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhh--hcCCccEEEEcC
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGF--KEGNKRILVATD  346 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f--~~~~~~ili~T~  346 (423)
                      ..+.+||.++++..+....+.|...|+.+..++|+++..++..++...  ..+..+|+++|+
T Consensus        83 ~~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tp  144 (591)
T 2v1x_A           83 SDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTP  144 (591)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECH
T ss_pred             cCCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEECh
Confidence            357899999999999999999999999999999999999988888877  467889999996

>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=86.59  E-value=0.57  Score=41.12  Aligned_cols=42  Identities=12%  Similarity=-0.024  Sum_probs=28.3

Q ss_pred             ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHH
Q 014486           85 DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELA  127 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~  127 (423)
                      -+++.+|+|+|||...+-.+........ +.+++++..-..+.
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~-g~~vlyId~E~s~~   71 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYP-DAVCLFYDSEFGIT   71 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCT-TCEEEEEESSCCCC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCC-CceEEEEeccchhh
Confidence            5789999999999876655544443211 22888888665553

>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=86.57  E-value=0.39  Score=41.02  Aligned_cols=51  Identities=18%  Similarity=0.156  Sum_probs=27.6

Q ss_pred             CCcCCCCCHHHHHHHHhC--CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           47 GFRDFLLKPELLRAIVDS--GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        47 ~~~~~~l~~~~~~~l~~~--~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      .|+++.-.+.+.+.+.+.  .+..+..+....   +...+.+++.||+|+|||..+
T Consensus         4 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g---~~~~~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A            4 SFKDVAGMHEAKLEVREFVDYLKSPERFLQLG---AKVPKGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCCC---------CCCCCEEEEESCTTSSHHHHH
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcC---CCCCceEEEECCCCCCHHHHH
Confidence            466666556666655532  011122222211   123466999999999999764

>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=86.53  E-value=12  Score=36.87  Aligned_cols=92  Identities=17%  Similarity=0.099  Sum_probs=64.7

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHH---HhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDL---LKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++..+..+.+.+.+.     ++++..++++.........   +.++..+|+|+|.-      -...+++.+++
T Consensus       441 ~vlVf~~t~~~ae~L~~~L~~~-----gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~------l~~GlDip~v~  509 (664)
T 1c4o_A          441 RTLVTVLTVRMAEELTSFLVEH-----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINL------LREGLDIPEVS  509 (664)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCC------CCTTCCCTTEE
T ss_pred             EEEEEECCHHHHHHHHHHHHhc-----CCCceeecCCCCHHHHHHHHHHhhcCCceEEEccCh------hhcCccCCCCC
Confidence            8999999999999888887764     6788888888765555443   56677899999832      14567888999


Q ss_pred             EEEEcCcchhhccCCcHHHHHHHHHh
Q 014486          193 HFILDECDKMLESLDMRRDVQEIFKM  218 (423)
Q Consensus       193 ~vVvDE~h~~~~~~~~~~~~~~~~~~  218 (423)
                      +||+=+++...-..+....++.+-+.
T Consensus       510 lVI~~d~d~~G~p~s~~~~iQr~GRa  535 (664)
T 1c4o_A          510 LVAILDADKEGFLRSERSLIQTIGRA  535 (664)
T ss_dssp             EEEETTTTSCSGGGSHHHHHHHHGGG
T ss_pred             EEEEeCCcccCCCCCHHHHHHHHCcc
Confidence            99988876542212334444444443

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=86.17  E-value=0.24  Score=44.71  Aligned_cols=53  Identities=11%  Similarity=0.096  Sum_probs=30.7

Q ss_pred             CCCCcCCCCCHHHHHHHHhCC---CCCCChhhhhcccccccCCceEEEccCCCcchhHHH
Q 014486           45 SSGFRDFLLKPELLRAIVDSG---FEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~---~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~  101 (423)
                      ...|+++.-.+.+.+.|...=   ...+..++.    .....+.+++.||+|+|||..+-
T Consensus        47 ~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~----~~~~~~~iLL~GppGtGKT~la~  102 (355)
T 2qp9_X           47 NVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG----NRKPTSGILLYGPPGTGKSYLAK  102 (355)
T ss_dssp             CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCS----SCCCCCCEEEECSTTSCHHHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhc----CCCCCceEEEECCCCCcHHHHHH
Confidence            456777766666666665431   011111111    11224679999999999998653

>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=86.06  E-value=0.63  Score=42.86  Aligned_cols=37  Identities=19%  Similarity=0.326  Sum_probs=22.0

Q ss_pred             hhhccccccc--CCceEEEccCCCcchhHHHHHHhhccCC
Q 014486           73 QHECIPQAIL--GMDVICQAKSGMGKTAVFVLSTLQQTEP  110 (423)
Q Consensus        73 Q~~~i~~~~~--~~~~ii~~~tGsGKT~~~~~~~~~~~~~  110 (423)
                      +..++..++.  +.-+++.||||||||... -.++..+..
T Consensus       155 ~~~~L~~l~~~~ggii~I~GpnGSGKTTlL-~allg~l~~  193 (418)
T 1p9r_A          155 NHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELNS  193 (418)
T ss_dssp             HHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHCC
T ss_pred             HHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHhhcCC
Confidence            3344444333  344899999999999753 334444433

>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=86.06  E-value=1.2  Score=39.46  Aligned_cols=54  Identities=13%  Similarity=-0.028  Sum_probs=31.2

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCC---CCCeEEEEEecChHH-HHHHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPN---PGQVTALVLCHTREL-AYQICHEFER  136 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~~~L-~~q~~~~~~~  136 (423)
                      |.-+++.||+|+|||...+..+.......   +.+.+++++.-...+ ..++.+.+++
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            45589999999999986655444433321   112377887654322 3444444443

>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=86.04  E-value=9.8  Score=32.99  Aligned_cols=21  Identities=19%  Similarity=-0.051  Sum_probs=15.6

Q ss_pred             cCCceEEEccCCCcchhHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~  102 (423)
                      .++-+.+.++.|+|||.....
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~  117 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAK  117 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            455577779999999976433

>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=85.83  E-value=0.67  Score=43.09  Aligned_cols=44  Identities=7%  Similarity=0.072  Sum_probs=29.3

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAY  128 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~  128 (423)
                      ...++++.|+||+|||... ..++..+...+  ..++|+=|..++..
T Consensus        52 ~~~h~~i~G~tGsGKs~~~-~~li~~~~~~g--~~viv~Dpkge~~~   95 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL-RELAYTGLLRG--DRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHHHHTT--CEEEEEEETTHHHH
T ss_pred             CcceEEEECCCCCCHHHHH-HHHHHHHHHCC--CcEEEEeCCCchhH
Confidence            4578999999999999874 23333332222  26777778777643

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.82  E-value=0.27  Score=45.54  Aligned_cols=54  Identities=13%  Similarity=0.091  Sum_probs=35.5

Q ss_pred             cCCCCcCCCCCHHHHHHHHhC---CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDS---GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      +..+|++.+--+.+.+.|.+.   .+.+|-.++...+   ...+.+++.||+|+|||+.+
T Consensus       204 P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi---~pprGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          204 PDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGI---DPPKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             CSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTC---CCCSEEEECSCTTSSHHHHH
T ss_pred             CCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCC---CCCCceEeeCCCCCcHHHHH
Confidence            345788888777777777654   1223333333332   23567999999999999754

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=85.68  E-value=0.37  Score=39.45  Aligned_cols=22  Identities=18%  Similarity=0.226  Sum_probs=17.6

Q ss_pred             ccccCCceEEEccCCCcchhHH
Q 014486           79 QAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        79 ~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ++..+.-+++.||+|+|||...
T Consensus         8 ~~~~~~~i~l~G~sGsGKsTl~   29 (204)
T 2qor_A            8 HMARIPPLVVCGPSGVGKGTLI   29 (204)
T ss_dssp             -CCCCCCEEEECCTTSCHHHHH
T ss_pred             ccccCCEEEEECCCCCCHHHHH
Confidence            4556777999999999999754

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=85.63  E-value=0.44  Score=44.43  Aligned_cols=53  Identities=11%  Similarity=0.077  Sum_probs=31.6

Q ss_pred             CCCCcCCCCCHHHHHHHHhCC---CCCCChhhhhcccccccCCceEEEccCCCcchhHHH
Q 014486           45 SSGFRDFLLKPELLRAIVDSG---FEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~---~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~  101 (423)
                      ...|+++.-...+.+.|...-   ...+..++.    .....+.+++.||+|+|||..+-
T Consensus       130 ~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~----~~~~~~~vLL~GppGtGKT~lA~  185 (444)
T 2zan_A          130 NVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG----KRTPWRGILLFGPPGTGKSYLAK  185 (444)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSG----GGCCCSEEEEECSTTSSHHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhc----cCCCCceEEEECCCCCCHHHHHH
Confidence            456888876677767666431   111111111    11234679999999999997653

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=85.36  E-value=0.72  Score=43.77  Aligned_cols=48  Identities=10%  Similarity=0.054  Sum_probs=27.7

Q ss_pred             HHHHHhCCCCCCChhhhhcccc-cccCCceEEEccCCCcchhHHHHHHhhcc
Q 014486           58 LRAIVDSGFEHPSEVQHECIPQ-AILGMDVICQAKSGMGKTAVFVLSTLQQT  108 (423)
Q Consensus        58 ~~~l~~~~~~~~~~~Q~~~i~~-~~~~~~~ii~~~tGsGKT~~~~~~~~~~~  108 (423)
                      ...|.+.|.  +.+.+...+.. +..+..+++.||||||||... -.++..+
T Consensus       236 ~~~l~~~G~--~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTlL-~aL~~~i  284 (511)
T 2oap_1          236 PIDLIEKGT--VPSGVLAYLWLAIEHKFSAIVVGETASGKTTTL-NAIMMFI  284 (511)
T ss_dssp             HHHHHHTTS--SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHHH-HHHGGGS
T ss_pred             hhhHHhcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH-HHHHhhC
Confidence            344555553  23333333332 345778999999999999753 3344444

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=85.22  E-value=0.56  Score=41.32  Aligned_cols=19  Identities=16%  Similarity=0.305  Sum_probs=16.2

Q ss_pred             CCceEEEccCCCcchhHHH
Q 014486           83 GMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~  101 (423)
                      ++++++.||+|+|||..+.
T Consensus       152 ~~~lll~G~~GtGKT~La~  170 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLA  170 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4679999999999997654

>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=85.11  E-value=0.48  Score=38.45  Aligned_cols=20  Identities=30%  Similarity=0.614  Sum_probs=16.1

Q ss_pred             cCCceEEEccCCCcchhHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~  101 (423)
                      .++-+++.||||+|||..++
T Consensus        33 ~g~~ilI~GpsGsGKStLA~   52 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETAL   52 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHH
Confidence            35669999999999996543

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=84.95  E-value=4.5  Score=28.34  Aligned_cols=50  Identities=14%  Similarity=0.209  Sum_probs=42.3

Q ss_pred             EEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCcc
Q 014486          291 VVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKR  340 (423)
Q Consensus       291 ~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  340 (423)
                      .+||.+..+-...+...+++.|..++.++++.....|.+-+..|.....+
T Consensus         5 fvvfssdpeilkeivreikrqgvrvvllysdqdekrrrerleefekqgvd   54 (162)
T 2l82_A            5 FVVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQGVD   54 (162)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHHHTTTCE
T ss_pred             EEEecCCHHHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHHHHcCCc
Confidence            47888888888999999999999999999999988888888888754433

>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=84.93  E-value=0.44  Score=37.99  Aligned_cols=21  Identities=24%  Similarity=0.371  Sum_probs=17.1

Q ss_pred             ccCCceEEEccCCCcchhHHH
Q 014486           81 ILGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~~  101 (423)
                      ..+..+++.|++|+|||.+.-
T Consensus         9 ~~~~~i~i~G~~GsGKst~~~   29 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLGK   29 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHHH
Confidence            345679999999999998653

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=84.86  E-value=0.62  Score=38.33  Aligned_cols=32  Identities=19%  Similarity=0.074  Sum_probs=25.0

Q ss_pred             CChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           69 PSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        69 ~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      -+.-|..++..+..|.-+.+.||.|+|||+..
T Consensus         8 k~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl   39 (208)
T 3b85_A            8 KTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLA   39 (208)
T ss_dssp             CSHHHHHHHHHHHHCSEEEEECCTTSSTTHHH
T ss_pred             CCHhHHHHHHhccCCCEEEEECCCCCCHHHHH
Confidence            34456677777777888999999999999753

>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=84.78  E-value=11  Score=33.18  Aligned_cols=54  Identities=11%  Similarity=0.226  Sum_probs=36.2

Q ss_pred             ccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhc
Q 014486          191 VRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFM  244 (423)
Q Consensus       191 ~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~  244 (423)
                      .+++++|.+-...........+..+.+.+.++..++.+.++...+....++.+.
T Consensus       212 ~d~vliDtaG~~~~~~~l~~eL~~i~ral~~de~llvLDa~t~~~~~~~~~~~~  265 (328)
T 3e70_C          212 IDVVLIDTAGRSETNRNLMDEMKKIARVTKPNLVIFVGDALAGNAIVEQARQFN  265 (328)
T ss_dssp             CSEEEEEECCSCCTTTCHHHHHHHHHHHHCCSEEEEEEEGGGTTHHHHHHHHHH
T ss_pred             chhhHHhhccchhHHHHHHHHHHHHHHHhcCCCCEEEEecHHHHHHHHHHHHHH
Confidence            457889988765433455566666666666777788888887766666555543

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=84.47  E-value=0.37  Score=40.71  Aligned_cols=50  Identities=20%  Similarity=0.234  Sum_probs=28.7

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFE  135 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  135 (423)
                      |.-+++.|++|+|||..++-.+.+.....+.  .+++++-. .-..++.+++.
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~--~v~~~s~E-~~~~~~~~~~~   79 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEYGE--PGVFVTLE-ERARDLRREMA   79 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHHCC--CEEEEESS-SCHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcCC--Cceeeccc-CCHHHHHHHHH
Confidence            4558999999999997655444433322221  55666533 23444444443

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=84.45  E-value=2.6  Score=36.84  Aligned_cols=73  Identities=14%  Similarity=0.192  Sum_probs=54.3

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++.-+..+++.+...     ++.+..++|+.....+.   ..+.++..+|+|+|.-      -...+++.+++
T Consensus        30 ~~LVF~~t~~~~~~l~~~L~~~-----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~v------a~~Gidi~~v~   98 (300)
T 3i32_A           30 RAMVFTRTKAETEEIAQGLLRL-----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDV------AARGLDIPQVD   98 (300)
T ss_dssp             SEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECST------TTCSTTCCCCS
T ss_pred             CEEEEECCHHHHHHHHHHHHhC-----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEech------hhcCcccccee
Confidence            8899999999888887776553     67899999987665544   3455677899999942      23467788888


Q ss_pred             EEEEcCc
Q 014486          193 HFILDEC  199 (423)
Q Consensus       193 ~vVvDE~  199 (423)
                      +||.=+.
T Consensus        99 ~VI~~d~  105 (300)
T 3i32_A           99 LVVHYRM  105 (300)
T ss_dssp             EEEESSC
T ss_pred             EEEEcCC
Confidence            8885444

>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=84.40  E-value=4.2  Score=34.03  Aligned_cols=115  Identities=12%  Similarity=0.212  Sum_probs=70.5

Q ss_pred             CCcEEEEEcChhhHHHHHHHHHh----CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcC-----ccc-cCCCCCCC
Q 014486          288 FNQVVIFVKSVSRAAELNKLLVE----CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD-----LVG-RGIDIERV  357 (423)
Q Consensus       288 ~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~-----~~~-~Gld~~~~  357 (423)
                      +.++||.++++..+.++.+.++.    .++.+..++|+.+.......+..    ..+|+|+|.     .+. ..+++.++
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            45799999999998888777655    48889999999987776655443    478999995     222 24567788


Q ss_pred             CEEEEccCC----CCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHh
Q 014486          358 NIVINYDMP----DSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       358 ~~vi~~~~~----~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                      +++|.-..-    ++....+..+-+..+   +..-+++++........+.+.+++.
T Consensus       178 ~~lViDEah~l~~~~~~~~~~~i~~~~~---~~~q~~~~SAT~~~~~~~~~~~~l~  230 (242)
T 3fe2_A          178 TYLVLDEADRMLDMGFEPQIRKIVDQIR---PDRQTLMWSATWPKEVRQLAEDFLK  230 (242)
T ss_dssp             CEEEETTHHHHHHTTCHHHHHHHHTTSC---SSCEEEEEESCCCHHHHHHHHHHCS
T ss_pred             cEEEEeCHHHHhhhCcHHHHHHHHHhCC---ccceEEEEEeecCHHHHHHHHHHCC
Confidence            887753221    112222222211111   2234555555556666666666654

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=84.31  E-value=0.86  Score=41.13  Aligned_cols=19  Identities=26%  Similarity=0.454  Sum_probs=16.4

Q ss_pred             ccCCceEEEccCCCcchhH
Q 014486           81 ILGMDVICQAKSGMGKTAV   99 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~   99 (423)
                      ..|..+++.||||||||..
T Consensus       173 ~~G~~i~ivG~sGsGKSTl  191 (361)
T 2gza_A          173 QLERVIVVAGETGSGKTTL  191 (361)
T ss_dssp             HTTCCEEEEESSSSCHHHH
T ss_pred             hcCCEEEEECCCCCCHHHH
Confidence            3578899999999999974

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=83.97  E-value=0.63  Score=37.17  Aligned_cols=19  Identities=11%  Similarity=0.324  Sum_probs=15.7

Q ss_pred             cCCceEEEccCCCcchhHH
Q 014486           82 LGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~  100 (423)
                      .|+-+++.||+|+|||...
T Consensus         4 ~g~~i~i~GpsGsGKSTL~   22 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIK   22 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4566899999999999754

>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=84.32  E-value=0.21  Score=39.61  Aligned_cols=73  Identities=14%  Similarity=0.193  Sum_probs=49.5

Q ss_pred             eEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCc
Q 014486          115 VTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNV  191 (423)
Q Consensus       115 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~  191 (423)
                      .++||.|+++..+..+++.++..     ++.+..++|+.+.....   ..+.++..+|+|+|. .+     ...+++.++
T Consensus        31 ~~~iVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~-~~-----~~Gid~~~~   99 (170)
T 2yjt_D           31 TRSIVFVRKRERVHELANWLREA-----GINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATD-VA-----ARGIDIPDV   99 (170)
Confidence            38899999999988888777654     56778888876544333   344556678999993 22     224556666


Q ss_pred             cEEEEcC
Q 014486          192 RHFILDE  198 (423)
Q Consensus       192 ~~vVvDE  198 (423)
                      ++||.-+
T Consensus       100 ~~Vi~~~  106 (170)
T 2yjt_D          100 SHVFNFD  106 (170)
Confidence            7766533

>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=83.83  E-value=0.5  Score=37.52  Aligned_cols=18  Identities=22%  Similarity=0.313  Sum_probs=15.0

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      +.-+++.|++|||||.+.
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            345899999999999864

>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=83.76  E-value=1.4  Score=46.72  Aligned_cols=55  Identities=16%  Similarity=0.060  Sum_probs=41.9

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCC---------CCCeEEEEEecChHHHHHHHHHHHHHh
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPN---------PGQVTALVLCHTRELAYQICHEFERFS  138 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~---------~~~~~~lil~P~~~L~~q~~~~~~~~~  138 (423)
                      ...+|.|..|||||.+...-++..+...         -....+|+|+=|++-|.++.+++.+..
T Consensus        17 g~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~L   80 (1180)
T 1w36_B           17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNI   80 (1180)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHHH
Confidence            3459999999999988766666665432         123479999999999999998887653

>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=83.59  E-value=9.8  Score=34.20  Aligned_cols=74  Identities=8%  Similarity=0.086  Sum_probs=56.1

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.++++.-+..+++.+.+.     ++.+..++|+.......   +.+.++..+|+|+|.-      -...+++.+++
T Consensus       252 ~~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~------~~~Gidi~~~~  320 (391)
T 1xti_A          252 QVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL------FGRGMDIERVN  320 (391)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCC------CSSCBCCTTEE
T ss_pred             cEEEEeCcHHHHHHHHHHHHhC-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECCh------hhcCCCcccCC
Confidence            8999999999999988888764     67888999987655443   4456677899999942      23467788899


Q ss_pred             EEEEcCcc
Q 014486          193 HFILDECD  200 (423)
Q Consensus       193 ~vVvDE~h  200 (423)
                      +||.-+.-
T Consensus       321 ~Vi~~~~p  328 (391)
T 1xti_A          321 IAFNYDMP  328 (391)
T ss_dssp             EEEESSCC
T ss_pred             EEEEeCCC
Confidence            98875543

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=83.59  E-value=0.55  Score=41.67  Aligned_cols=19  Identities=16%  Similarity=0.237  Sum_probs=15.6

Q ss_pred             CceEEEccCCCcchhHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~  102 (423)
                      +-++|.||||+|||.....
T Consensus        41 ~lIvI~GPTgsGKTtLa~~   59 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSID   59 (339)
T ss_dssp             EEEEEECSTTSSHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            3589999999999986543

>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=83.58  E-value=3.1  Score=33.62  Aligned_cols=118  Identities=9%  Similarity=0.158  Sum_probs=67.1

Q ss_pred             CCcEEEEEcChhhHHHHHHHHHhC-----CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc-----ccc-CCCCCC
Q 014486          288 FNQVVIFVKSVSRAAELNKLLVEC-----NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL-----VGR-GIDIER  356 (423)
Q Consensus       288 ~~~~ivf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~-----~~~-Gld~~~  356 (423)
                      ..++||.++++..+..+.+.+...     +..+..++|+.+.......   . .+..+|+|+|.-     +.. .+++.+
T Consensus        71 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~-~~~~~i~v~T~~~l~~~~~~~~~~~~~  146 (206)
T 1vec_A           71 NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR---L-DDTVHVVIATPGRILDLIKKGVAKVDH  146 (206)
T ss_dssp             SCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHH---T-TSCCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             CeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHh---c-CCCCCEEEeCHHHHHHHHHcCCcCccc
Confidence            357999999999999888877653     5678888998876554332   2 346789999952     222 346667


Q ss_pred             CCEEEEccCCC-CcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHh
Q 014486          357 VNIVINYDMPD-SADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       357 ~~~vi~~~~~~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                      ++++|.-..-. .-..+...+.+..+.-....-+++++........+.+++++.
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            88777522110 000121111111111111233455555555666666666654

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=83.47  E-value=0.49  Score=37.81  Aligned_cols=18  Identities=28%  Similarity=0.464  Sum_probs=15.3

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      ...+++.||+|+|||..+
T Consensus        43 ~~~~ll~G~~G~GKT~l~   60 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIV   60 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            356999999999999764

>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=83.35  E-value=0.96  Score=40.23  Aligned_cols=18  Identities=39%  Similarity=0.614  Sum_probs=15.8

Q ss_pred             cCCceEEEccCCCcchhH
Q 014486           82 LGMDVICQAKSGMGKTAV   99 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~   99 (423)
                      .|..+.+.||||||||..
T Consensus       170 ~g~~v~i~G~~GsGKTTl  187 (330)
T 2pt7_A          170 IGKNVIVCGGTGSGKTTY  187 (330)
T ss_dssp             HTCCEEEEESTTSCHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            478899999999999973

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=83.27  E-value=0.51  Score=37.77  Aligned_cols=19  Identities=26%  Similarity=0.172  Sum_probs=15.8

Q ss_pred             CCceEEEccCCCcchhHHH
Q 014486           83 GMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~  101 (423)
                      .+.+++.|++|||||.+.-
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            3568999999999998654

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=83.14  E-value=1.1  Score=41.35  Aligned_cols=19  Identities=21%  Similarity=0.181  Sum_probs=15.3

Q ss_pred             CceEEEccCCCcchhHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~  102 (423)
                      ..+++.|++|+|||..+.-
T Consensus       100 ~vI~ivG~~GvGKTTla~~  118 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAK  118 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4688999999999976544

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=83.13  E-value=1.7  Score=43.57  Aligned_cols=57  Identities=19%  Similarity=0.247  Sum_probs=36.9

Q ss_pred             ccccCCCCcCCCCCHHHHHHHHhC-CC--CCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           41 VGIHSSGFRDFLLKPELLRAIVDS-GF--EHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        41 ~~~~~~~~~~~~l~~~~~~~l~~~-~~--~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      .......|++.+.-+.+.+.|.+. .+  ..|..++...   +...+.+++.||+|+|||+.+
T Consensus       469 ~~~p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g---~~~~~gvLl~GPPGtGKT~lA  528 (806)
T 3cf2_A          469 VEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFG---MTPSKGVLFYGPPGCGKTLLA  528 (806)
T ss_dssp             CBCCCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSC---CCCCSCCEEESSTTSSHHHHH
T ss_pred             ccCCCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcC---CCCCceEEEecCCCCCchHHH
Confidence            344556799998888888888775 22  2222222211   123467999999999999754

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=83.03  E-value=0.7  Score=37.60  Aligned_cols=20  Identities=20%  Similarity=0.167  Sum_probs=16.5

Q ss_pred             cCCceEEEccCCCcchhHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~  101 (423)
                      .++.+++.|++|||||...-
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            35679999999999998653

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=82.92  E-value=0.66  Score=39.71  Aligned_cols=21  Identities=14%  Similarity=0.146  Sum_probs=16.9

Q ss_pred             cccCCceEEEccCCCcchhHH
Q 014486           80 AILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        80 ~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      +..|.-+++.||||||||...
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            445667999999999999753

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=82.88  E-value=0.23  Score=42.94  Aligned_cols=54  Identities=13%  Similarity=0.142  Sum_probs=26.5

Q ss_pred             cCCCCcCCCCCHHHHHHHHhCCCCCCChhhh-hcccc--cccCCceEEEccCCCcchhHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDSGFEHPSEVQH-ECIPQ--AILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~-~~i~~--~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ...+|++.+-.+.+.+.|...=   ..|+.. .++..  +.-.+.+++.||+|+|||+.+
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~i---~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMAI---LAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             -------CCHHHHHHHHHHHHH---THHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHH---HHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHH
Confidence            3456888876667766665420   112211 11211  112344999999999999753

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=82.85  E-value=1.3  Score=39.17  Aligned_cols=51  Identities=14%  Similarity=0.007  Sum_probs=30.8

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFER  136 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  136 (423)
                      .|.-++|.|++|+|||..++..+......+   ..+++++-- .-..|+..++..
T Consensus        67 ~G~l~li~G~pG~GKTtl~l~ia~~~a~~g---~~vl~~slE-~s~~~l~~R~~~  117 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFALKQAKNMSDND---DVVNLHSLE-MGKKENIKRLIV  117 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHTTT---CEEEEEESS-SCHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHcC---CeEEEEECC-CCHHHHHHHHHH
Confidence            355699999999999976554444443332   267777643 334444444443

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=82.80  E-value=0.48  Score=42.56  Aligned_cols=25  Identities=32%  Similarity=0.700  Sum_probs=19.8

Q ss_pred             cccccccCCc--eEEEccCCCcchhHH
Q 014486           76 CIPQAILGMD--VICQAKSGMGKTAVF  100 (423)
Q Consensus        76 ~i~~~~~~~~--~ii~~~tGsGKT~~~  100 (423)
                      .+..++.|.+  ++..|.||||||.+.
T Consensus        96 lv~~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           96 VVSQALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhCCCCEEEEEeCCCCCCccEEe
Confidence            4566677877  788899999999864

>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=82.74  E-value=2.8  Score=33.90  Aligned_cols=71  Identities=13%  Similarity=0.177  Sum_probs=50.8

Q ss_pred             CCcEEEEEcChhhHHHHHHHHHhC--CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc-----cc-cCCCCCCCCE
Q 014486          288 FNQVVIFVKSVSRAAELNKLLVEC--NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL-----VG-RGIDIERVNI  359 (423)
Q Consensus       288 ~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~-----~~-~Gld~~~~~~  359 (423)
                      ..++||.++++..+..+.+.++..  +..+..++|+.+.......+.    ...+|+|+|.-     +. ..+++.++++
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            467999999999999999988875  467788888877555443332    25689999951     11 2456777887


Q ss_pred             EEE
Q 014486          360 VIN  362 (423)
Q Consensus       360 vi~  362 (423)
                      +|.
T Consensus       148 iVi  150 (207)
T 2gxq_A          148 AVL  150 (207)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            775

>1f9v_A Kinesin-like protein KAR3; kinesin-related protein, motor protein, microtubinding proteinbule, contractIle protein; HET: ADP; 1.30A {Saccharomyces cerevisiae} SCOP: c.37.1.9 PDB: 1f9t_A* 1f9w_A* 1f9u_A* 3kar_A*

Probab=82.68  E-value=0.65  Score=41.52  Aligned_cols=25  Identities=20%  Similarity=0.445  Sum_probs=20.7

Q ss_pred             cccccccCCc--eEEEccCCCcchhHH
Q 014486           76 CIPQAILGMD--VICQAKSGMGKTAVF  100 (423)
Q Consensus        76 ~i~~~~~~~~--~ii~~~tGsGKT~~~  100 (423)
                      .+..++.|.+  ++..|.||||||.+.
T Consensus        76 lv~~~l~G~n~tifAYGqTGSGKTyTM  102 (347)
T 1f9v_A           76 LVQSSLDGYNVCIFAYGQTGSGKTFTM  102 (347)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHHhcCCceeEEEEECCCCCCCcEec
Confidence            5677788877  678899999999875

>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=82.58  E-value=0.52  Score=37.18  Aligned_cols=17  Identities=18%  Similarity=0.276  Sum_probs=14.1

Q ss_pred             ceEEEccCCCcchhHHH
Q 014486           85 DVICQAKSGMGKTAVFV  101 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~  101 (423)
                      -+++.|++|||||...-
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            37899999999998653

>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=82.57  E-value=21  Score=32.75  Aligned_cols=21  Identities=19%  Similarity=-0.051  Sum_probs=15.7

Q ss_pred             cCCceEEEccCCCcchhHHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~  102 (423)
                      .+.-+.+.++.|+|||.....
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~  117 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAK  117 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            344577889999999986544

>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=82.57  E-value=0.52  Score=37.96  Aligned_cols=20  Identities=20%  Similarity=0.363  Sum_probs=16.2

Q ss_pred             ccCCceEEEccCCCcchhHH
Q 014486           81 ILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ..|.-+++.||+|||||...
T Consensus         7 ~~g~~i~l~G~~GsGKSTl~   26 (191)
T 1zp6_A            7 LGGNILLLSGHPGSGKSTIA   26 (191)
T ss_dssp             CTTEEEEEEECTTSCHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            34566899999999999753

>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=82.52  E-value=4.8  Score=36.62  Aligned_cols=72  Identities=19%  Similarity=0.332  Sum_probs=55.3

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++.-+..+++.+.+.     +..+..++|+.......   +.+.++..+|+|+|.-      -...+++.+++
T Consensus       268 ~~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~------~~~Gidip~~~  336 (412)
T 3fht_A          268 QAMIFCHTRKTASWLAAELSKE-----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNV------CARGIDVEQVS  336 (412)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGG------GTSSCCCTTEE
T ss_pred             CEEEEeCCHHHHHHHHHHHHhC-----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCc------cccCCCccCCC
Confidence            8999999999999998888765     66888999987765544   4455677899999952      24567888899


Q ss_pred             EEEEcC
Q 014486          193 HFILDE  198 (423)
Q Consensus       193 ~vVvDE  198 (423)
                      +||.-.
T Consensus       337 ~Vi~~~  342 (412)
T 3fht_A          337 VVINFD  342 (412)
T ss_dssp             EEEESS
T ss_pred             EEEEEC
Confidence            888533

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=82.41  E-value=0.66  Score=41.54  Aligned_cols=25  Identities=20%  Similarity=0.446  Sum_probs=20.9

Q ss_pred             cccccccCCc--eEEEccCCCcchhHH
Q 014486           76 CIPQAILGMD--VICQAKSGMGKTAVF  100 (423)
Q Consensus        76 ~i~~~~~~~~--~ii~~~tGsGKT~~~  100 (423)
                      .+..++.|.+  ++..|.||||||.+.
T Consensus        77 lv~~~l~G~n~tifAYGqTGSGKTyTm  103 (349)
T 3t0q_A           77 LVQSSLDGYNVCIFAYGQTGSGKTYTM  103 (349)
T ss_dssp             HHHGGGTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHCCcceeEEEeCCCCCCCceEe
Confidence            5677888887  677899999999875

>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=82.40  E-value=5  Score=37.08  Aligned_cols=72  Identities=17%  Similarity=0.220  Sum_probs=55.1

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++.-+..+++.+.+.     ++.+..++|+....+..   ..+.++..+|+|+|.-      -...+++.+++
T Consensus       302 ~~lVF~~t~~~a~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v------~~rGlDi~~v~  370 (434)
T 2db3_A          302 GTIVFVETKRGADFLASFLSEK-----EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSV------ASRGLDIKNIK  370 (434)
T ss_dssp             TEEEECSSHHHHHHHHHHHHHT-----TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGG------GTSSCCCTTCC
T ss_pred             CEEEEEeCcHHHHHHHHHHHhC-----CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchh------hhCCCCcccCC
Confidence            4899999999999988887764     67899999987765544   4456677899999962      24567888899


Q ss_pred             EEEEcC
Q 014486          193 HFILDE  198 (423)
Q Consensus       193 ~vVvDE  198 (423)
                      +||.-+
T Consensus       371 ~VI~~d  376 (434)
T 2db3_A          371 HVINYD  376 (434)
T ss_dssp             EEEESS
T ss_pred             EEEEEC
Confidence            888633

>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=82.36  E-value=0.65  Score=40.70  Aligned_cols=18  Identities=28%  Similarity=0.276  Sum_probs=14.7

Q ss_pred             ceEEEccCCCcchhHHHH
Q 014486           85 DVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~  102 (423)
                      -++|.||||+|||..+..
T Consensus         5 ~i~i~GptgsGKt~la~~   22 (322)
T 3exa_A            5 LVAIVGPTAVGKTKTSVM   22 (322)
T ss_dssp             EEEEECCTTSCHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHH
Confidence            478999999999976543

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=82.16  E-value=0.74  Score=41.49  Aligned_cols=54  Identities=11%  Similarity=-0.009  Sum_probs=29.8

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhh-hcccc-cccCCceEEEccCCCcchhHHH
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQH-ECIPQ-AILGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~-~~i~~-~~~~~~~ii~~~tGsGKT~~~~  101 (423)
                      ...|+++.-.+.+.+.|.+.=.   .+... ..+.. ....+.+++.||+|+|||..+-
T Consensus        80 ~~~~~~i~G~~~~~~~l~~~i~---~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~  135 (357)
T 3d8b_A           80 PVNWEDIAGVEFAKATIKEIVV---WPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGK  135 (357)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTH---HHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHH
T ss_pred             CCCHHHhCChHHHHHHHHHHHH---HHhhChHhHhhccCCCceEEEECCCCCCHHHHHH
Confidence            3457777666666666654310   01100 00011 1234679999999999997653

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=82.11  E-value=1.5  Score=39.54  Aligned_cols=19  Identities=37%  Similarity=0.615  Sum_probs=16.1

Q ss_pred             CCceEEEccCCCcchhHHH
Q 014486           83 GMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~  101 (423)
                      ++.+++.||+|+|||..+-
T Consensus        70 ~~~vLl~GppGtGKT~la~   88 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIAM   88 (368)
T ss_dssp             TCEEEEEESTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            4679999999999998653

>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=81.99  E-value=1.2  Score=40.67  Aligned_cols=42  Identities=19%  Similarity=0.172  Sum_probs=27.4

Q ss_pred             ccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           81 ILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      ..+.+++|.|+||+|||...-..+.... ..+  .+++++=|..+
T Consensus        33 ~~~~~~~i~G~~G~GKs~~~~~~~~~~~-~~~--~~~~~~D~~~~   74 (392)
T 4ag6_A           33 RTNSNWTILAKPGAGKSFTAKMLLLREY-MQG--SRVIIIDPERE   74 (392)
T ss_dssp             BCCCCEEEECCTTSSHHHHHHHHHHHHH-TTT--CCEEEEESSCC
T ss_pred             cccCceEEEcCCCCCHHHHHHHHHHHHH-HCC--CEEEEEeCCcC
Confidence            3567899999999999976543333333 222  26677777655

>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=81.87  E-value=0.71  Score=40.39  Aligned_cols=18  Identities=22%  Similarity=0.303  Sum_probs=14.7

Q ss_pred             ceEEEccCCCcchhHHHH
Q 014486           85 DVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~  102 (423)
                      -++|.||||+|||..+..
T Consensus        12 ~i~i~GptgsGKt~la~~   29 (316)
T 3foz_A           12 AIFLMGPTASGKTALAIE   29 (316)
T ss_dssp             EEEEECCTTSCHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHH
Confidence            378999999999976543

>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=81.85  E-value=4.8  Score=36.65  Aligned_cols=72  Identities=14%  Similarity=0.281  Sum_probs=54.9

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++.-+..+++.+.+.     ++.+..++|+.......   +.+.++..+|+|+|.-      -...+++.+++
T Consensus       278 ~~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~------~~~Gidi~~v~  346 (410)
T 2j0s_A          278 QAVIFCNTKRKVDWLTEKMREA-----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDV------WARGLDVPQVS  346 (410)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGG------GSSSCCCTTEE
T ss_pred             cEEEEEcCHHHHHHHHHHHHhC-----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECCh------hhCcCCcccCC
Confidence            8999999999999888888764     67888999987755443   4455677899999952      24567888888


Q ss_pred             EEEEcC
Q 014486          193 HFILDE  198 (423)
Q Consensus       193 ~vVvDE  198 (423)
                      +||.-+
T Consensus       347 ~Vi~~~  352 (410)
T 2j0s_A          347 LIINYD  352 (410)
T ss_dssp             EEEESS
T ss_pred             EEEEEC
Confidence            888643

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=81.66  E-value=19  Score=33.88  Aligned_cols=75  Identities=23%  Similarity=0.229  Sum_probs=52.4

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ..++++.+..-+..+++.+.+.     +.++..++|+.......   ..+.++..+|+|+|++.+..     .+++.+++
T Consensus       349 ~~~ivf~~~~~~~~l~~~L~~~-----~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~-----GiDip~v~  418 (510)
T 2oca_A          349 NAFVMFKHVSHGKAIFDLIKNE-----YDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFST-----GISVKNLH  418 (510)
T ss_dssp             EEEEEESSHHHHHHHHHHHHTT-----CSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHH-----SCCCCSEE
T ss_pred             CeEEEEecHHHHHHHHHHHHHc-----CCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhc-----ccccccCc
Confidence            4555565566665555555442     34888999988655443   44556778999999887764     66888899


Q ss_pred             EEEEcCcc
Q 014486          193 HFILDECD  200 (423)
Q Consensus       193 ~vVvDE~h  200 (423)
                      +||+....
T Consensus       419 ~vi~~~~~  426 (510)
T 2oca_A          419 HVVLAHGV  426 (510)
T ss_dssp             EEEESSCC
T ss_pred             EEEEeCCC
Confidence            99998877

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=81.55  E-value=0.63  Score=37.89  Aligned_cols=19  Identities=26%  Similarity=0.361  Sum_probs=14.7

Q ss_pred             cCCceEEEccCCCcchhHH
Q 014486           82 LGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~  100 (423)
                      .++-+.+.||+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            3566899999999999754

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=81.53  E-value=2.2  Score=49.39  Aligned_cols=69  Identities=14%  Similarity=0.046  Sum_probs=40.0

Q ss_pred             HHHHHHHHhCCCCCCChhhhhcc----cccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           55 PELLRAIVDSGFEHPSEVQHECI----PQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        55 ~~~~~~l~~~~~~~~~~~Q~~~i----~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ..+.+.+.+.|+ ++.+.+..=+    ..+...+.+++.||||+|||.++-...-..-...+......++-|-.
T Consensus       875 ~ai~~~~~~~~L-~~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~~L~~al~~l~~~~~~~~~iNPKa  947 (3245)
T 3vkg_A          875 KKIQEIAKQRHL-VTKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWEVYLEAIEQVDNIKSEAHVMDPKA  947 (3245)
T ss_dssp             HHHHHHHHHTTC-CCCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHHHHHHHHTTTTTCEEEEEEECTTT
T ss_pred             HHHHHHHHHcCC-ccCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHHHHHHHHHHhhCCCceEEEECCCC
Confidence            455666777777 5666664332    22334677999999999999886432222111112233455566653

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=81.50  E-value=0.62  Score=37.04  Aligned_cols=19  Identities=32%  Similarity=0.415  Sum_probs=15.7

Q ss_pred             CCceEEEccCCCcchhHHH
Q 014486           83 GMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~  101 (423)
                      ..++++.||+|+|||..+-
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            4568999999999997643

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=81.40  E-value=0.81  Score=38.02  Aligned_cols=23  Identities=22%  Similarity=0.238  Sum_probs=17.4

Q ss_pred             cccCCceEEEccCCCcchhHHHH
Q 014486           80 AILGMDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        80 ~~~~~~~ii~~~tGsGKT~~~~~  102 (423)
                      +..|.-+++.||+|+|||.....
T Consensus        20 i~~G~~~~i~G~~GsGKTtl~~~   42 (235)
T 2w0m_A           20 IPQGFFIALTGEPGTGKTIFSLH   42 (235)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHH
T ss_pred             CcCCCEEEEEcCCCCCHHHHHHH
Confidence            33466789999999999975433

>1bg2_A Kinesin; motor protein, ATPase, microtubule associated; HET: ADP; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 2p4n_K* 1mkj_A* 2kin_A* 3kin_A*

Probab=81.33  E-value=0.59  Score=41.36  Aligned_cols=25  Identities=16%  Similarity=0.395  Sum_probs=19.2

Q ss_pred             cccccccCCc--eEEEccCCCcchhHH
Q 014486           76 CIPQAILGMD--VICQAKSGMGKTAVF  100 (423)
Q Consensus        76 ~i~~~~~~~~--~ii~~~tGsGKT~~~  100 (423)
                      .+..++.|.+  ++..|+||||||.+.
T Consensus        69 lv~~~l~G~n~tifAYGqTGSGKTyTm   95 (325)
T 1bg2_A           69 IVKDVLEGYNGTIFAYGQTSSGKTHTM   95 (325)
T ss_dssp             HHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             hHHHHhCCCeEEEEEECCCCCCCceEe
Confidence            3455667777  788899999999864

>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=81.32  E-value=1.8  Score=36.19  Aligned_cols=25  Identities=16%  Similarity=0.001  Sum_probs=19.0

Q ss_pred             ccCCceEEEccCCCcchhHHHHHHh
Q 014486           81 ILGMDVICQAKSGMGKTAVFVLSTL  105 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~~~~~~  105 (423)
                      ..|.-+.+.||+|+|||......+.
T Consensus        22 ~~G~~~~i~G~~GsGKTtl~~~l~~   46 (243)
T 1n0w_A           22 ETGSITEMFGEFRTGKTQICHTLAV   46 (243)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHH
T ss_pred             cCCeEEEEECCCCCcHHHHHHHHHH
Confidence            3456789999999999986655444

>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=81.28  E-value=5.7  Score=36.00  Aligned_cols=72  Identities=7%  Similarity=0.117  Sum_probs=54.7

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.++++.-+..+++.+.+.     ++.+..++|+.......   +.+.++..+|+|+|.-      -...+++.+++
T Consensus       260 ~~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~------~~~Gidip~~~  328 (400)
T 1s2m_A          260 QAIIFCNSTNRVELLAKKITDL-----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL------LTRGIDIQAVN  328 (400)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC------SSSSCCCTTEE
T ss_pred             cEEEEEecHHHHHHHHHHHHhc-----CCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCc------cccCCCccCCC
Confidence            8999999999999998888775     66888899987765443   4455677899999941      23467788888


Q ss_pred             EEEEcC
Q 014486          193 HFILDE  198 (423)
Q Consensus       193 ~vVvDE  198 (423)
                      +||.-+
T Consensus       329 ~Vi~~~  334 (400)
T 1s2m_A          329 VVINFD  334 (400)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            888643

>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=81.22  E-value=1.6  Score=41.22  Aligned_cols=20  Identities=10%  Similarity=0.134  Sum_probs=16.6

Q ss_pred             ccCCceEEEccCCCcchhHH
Q 014486           81 ILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ..+.+++|.|+||||||...
T Consensus       165 ~~~pHlLIaG~TGSGKSt~L  184 (512)
T 2ius_A          165 AKMPHLLVAGTTGSGASVGV  184 (512)
T ss_dssp             GGSCSEEEECCTTSSHHHHH
T ss_pred             ccCceEEEECCCCCCHHHHH
Confidence            34578999999999999764

>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=81.17  E-value=0.72  Score=36.96  Aligned_cols=19  Identities=26%  Similarity=0.592  Sum_probs=16.0

Q ss_pred             cCCceEEEccCCCcchhHH
Q 014486           82 LGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~  100 (423)
                      .+..+++.|++|||||.+.
T Consensus         9 ~~~~I~l~G~~GsGKSTv~   27 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMA   27 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            3567999999999999865

>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=81.14  E-value=0.89  Score=37.28  Aligned_cols=18  Identities=33%  Similarity=0.558  Sum_probs=15.2

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      |.-+++.||+|+|||...
T Consensus         8 g~~i~l~GpsGsGKsTl~   25 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVR   25 (208)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CcEEEEECcCCCCHHHHH
Confidence            556889999999999764

>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=81.06  E-value=1.1  Score=36.94  Aligned_cols=36  Identities=17%  Similarity=0.098  Sum_probs=23.4

Q ss_pred             ccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           81 ILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      ..|.-+++.||+|+|||..+...+.   .  .+ .+++++.-
T Consensus        18 ~~G~~~~i~G~~GsGKTtl~~~l~~---~--~~-~~v~~i~~   53 (220)
T 2cvh_A           18 APGVLTQVYGPYASGKTTLALQTGL---L--SG-KKVAYVDT   53 (220)
T ss_dssp             CTTSEEEEECSTTSSHHHHHHHHHH---H--HC-SEEEEEES
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHH---H--cC-CcEEEEEC
Confidence            3456689999999999976544333   1  11 26666653

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=81.02  E-value=0.78  Score=39.03  Aligned_cols=16  Identities=19%  Similarity=0.219  Sum_probs=13.7

Q ss_pred             eEEEccCCCcchhHHH
Q 014486           86 VICQAKSGMGKTAVFV  101 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~  101 (423)
                      +++.||+|||||..+-
T Consensus         4 i~I~G~~GSGKSTla~   19 (253)
T 2ze6_A            4 HLIYGPTCSGKTDMAI   19 (253)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCcCHHHHHH
Confidence            6899999999997653

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=81.01  E-value=0.73  Score=37.58  Aligned_cols=20  Identities=30%  Similarity=0.423  Sum_probs=16.3

Q ss_pred             ccCCceEEEccCCCcchhHH
Q 014486           81 ILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ..|.-+.+.||+|||||...
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~   23 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVR   23 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            34666899999999999754

>3bfn_A Kinesin-like protein KIF22; limited proteolysis, structural genomics consortium domain, ADP, SGC, ATP-binding, DNA-binding, microtubule, MO protein; HET: ADP; 2.30A {Homo sapiens}

Probab=80.95  E-value=0.73  Score=41.73  Aligned_cols=23  Identities=26%  Similarity=0.469  Sum_probs=18.0

Q ss_pred             cccccCCc--eEEEccCCCcchhHH
Q 014486           78 PQAILGMD--VICQAKSGMGKTAVF  100 (423)
Q Consensus        78 ~~~~~~~~--~ii~~~tGsGKT~~~  100 (423)
                      ..++.|.+  ++..|.||||||.+.
T Consensus        92 ~~~l~G~N~tifAYGqTGSGKTyTM  116 (388)
T 3bfn_A           92 RHLLEGQNASVLAYGPTGAGKTHTM  116 (388)
T ss_dssp             HHHTTTCCEEEEEESCTTSSHHHHH
T ss_pred             HHhhcCceeeEeeecCCCCCCCeEe
Confidence            44566777  678899999999864

>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=80.95  E-value=0.68  Score=49.06  Aligned_cols=49  Identities=18%  Similarity=0.261  Sum_probs=32.9

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHH
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFE  135 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~  135 (423)
                      -+|.|..|||||.+.+--+...+.....+.++|++||.. ..-++.+++.
T Consensus         4 ~lV~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q-~TFt~~~rl~   52 (1166)
T 3u4q_B            4 EFLVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQ-MTFLMEYELA   52 (1166)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGG-GHHHHHHHHT
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCc-ccHHHHHHHH
Confidence            378899999999987766655544444445889999975 4444444443

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=80.94  E-value=0.86  Score=41.62  Aligned_cols=19  Identities=21%  Similarity=0.239  Sum_probs=16.1

Q ss_pred             CCceEEEccCCCcchhHHH
Q 014486           83 GMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~  101 (423)
                      .+++++.||+|+|||..+-
T Consensus       148 ~~~vLL~GppGtGKT~la~  166 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLAK  166 (389)
T ss_dssp             CSEEEEESSTTSCHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4679999999999997653

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=80.92  E-value=0.3  Score=38.79  Aligned_cols=57  Identities=7%  Similarity=0.025  Sum_probs=40.3

Q ss_pred             hhhhhcccccccCC--ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHH
Q 014486           71 EVQHECIPQAILGM--DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQ  129 (423)
Q Consensus        71 ~~Q~~~i~~~~~~~--~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  129 (423)
                      +-|..++..++...  -.++.++-|++|+...+..++......+.  .+.+++|+..-...
T Consensus        37 ~~~~~a~~~l~~s~~~~~iv~g~ggs~~~~~~~a~L~~~a~~~Gr--~V~vLAp~~~s~~~   95 (189)
T 2l8b_A           37 AGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGR--EVQIIAADRRSQMN   95 (189)
T ss_dssp             HHHHHHHHHHHHHSCCEECCBCSSCSHHHHHHHHHHHHHHHHTTC--CEEEECSTTHHHHH
T ss_pred             ccchhHHHHHhccCCceEEEecccchHHHHHHHHHHHHHHHhcCe--EEEEEcCchHHHHH
Confidence            45788888877644  37889999999998855554444444333  78999999765444

>1v8k_A Kinesin-like protein KIF2C; microtubule destabilizer, structural P; HET: ANP; 2.25A {Mus musculus} SCOP: c.37.1.9 PDB: 1v8j_A* 2gry_A*

Probab=80.86  E-value=0.64  Score=42.43  Aligned_cols=24  Identities=21%  Similarity=0.356  Sum_probs=18.6

Q ss_pred             ccccccCCc--eEEEccCCCcchhHH
Q 014486           77 IPQAILGMD--VICQAKSGMGKTAVF  100 (423)
Q Consensus        77 i~~~~~~~~--~ii~~~tGsGKT~~~  100 (423)
                      +..++.|.+  ++..|.||||||.+.
T Consensus       147 V~~~l~G~N~tifAYGQTGSGKTyTM  172 (410)
T 1v8k_A          147 VQTIFEGGKATCFAYGQTGSGKTHTM  172 (410)
T ss_dssp             HHHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHHhcCCceeEEeecCCCCCCCeEe
Confidence            445566776  778899999999874

>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=80.76  E-value=4.7  Score=33.24  Aligned_cols=72  Identities=13%  Similarity=0.257  Sum_probs=47.9

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhC---CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc------cccCCCCCCC
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVEC---NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL------VGRGIDIERV  357 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~------~~~Gld~~~~  357 (423)
                      .+.++||.++++..+..+.+.++..   +..+..++|+.+...+...+.    ...+|+|+|.-      ....+++.++
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~iiv~Tp~~l~~~~~~~~~~~~~~  168 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDIS----KGVDIIIATPGRLNDLQMNNSVNLRSI  168 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHHHH----SCCSEEEECHHHHHHHHHTTCCCCTTC
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHHhc----CCCCEEEECHHHHHHHHHcCCcCcccc
Confidence            3467999999999999998888774   678888888877555443332    34789999941      1235667788


Q ss_pred             CEEEE
Q 014486          358 NIVIN  362 (423)
Q Consensus       358 ~~vi~  362 (423)
                      +++|.
T Consensus       169 ~~lVi  173 (228)
T 3iuy_A          169 TYLVI  173 (228)
T ss_dssp             CEEEE
T ss_pred             eEEEE
Confidence            87775

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=80.61  E-value=5.3  Score=37.65  Aligned_cols=18  Identities=22%  Similarity=0.246  Sum_probs=14.6

Q ss_pred             ceEEEccCCCcchhHHHH
Q 014486           85 DVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~  102 (423)
                      .+++.+++|+|||..+.-
T Consensus       103 vI~ivG~~GvGKTTl~~k  120 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSK  120 (504)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            478889999999986543

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=80.59  E-value=0.78  Score=36.15  Aligned_cols=18  Identities=17%  Similarity=0.274  Sum_probs=15.0

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      +..+++.|++|||||...
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            456899999999999754

>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=80.56  E-value=6.3  Score=35.06  Aligned_cols=73  Identities=15%  Similarity=0.282  Sum_probs=53.8

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.++++.-+..+++.+++.     +..+..++|+.+.....   +.+.++..+|+|+|.- +.     ..+++.+++
T Consensus       240 ~~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~-~~-----~Gid~~~~~  308 (367)
T 1hv8_A          240 YGLVFCKTKRDTKELASMLRDI-----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDV-MS-----RGIDVNDLN  308 (367)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHT-----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTT-HH-----HHCCCSCCS
T ss_pred             cEEEEECCHHHHHHHHHHHHhc-----CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECCh-hh-----cCCCcccCC
Confidence            7899999999999988888764     67888999987655443   3455677899999942 22     245677788


Q ss_pred             EEEEcCc
Q 014486          193 HFILDEC  199 (423)
Q Consensus       193 ~vVvDE~  199 (423)
                      +||.-..
T Consensus       309 ~Vi~~~~  315 (367)
T 1hv8_A          309 CVINYHL  315 (367)
T ss_dssp             EEEESSC
T ss_pred             EEEEecC
Confidence            8876443

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=80.30  E-value=0.71  Score=41.37  Aligned_cols=24  Identities=21%  Similarity=0.476  Sum_probs=18.7

Q ss_pred             ccccccCCc--eEEEccCCCcchhHH
Q 014486           77 IPQAILGMD--VICQAKSGMGKTAVF  100 (423)
Q Consensus        77 i~~~~~~~~--~ii~~~tGsGKT~~~  100 (423)
                      +..++.|.+  ++..|.||||||.+.
T Consensus        73 v~~~l~G~n~tifAYGqTGSGKTyTm   98 (355)
T 1goj_A           73 VDDILNGYNGTVFAYGQTGAGKSYTM   98 (355)
T ss_dssp             HHHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhCCCcceEEEECCCCCCcceEe
Confidence            445667777  778899999999864

>3dc4_A Kinesin-like protein NOD; catalytic domain, ATPase, microtubule, ADP, nucleotide-binding protein, ATP-binding, coiled coil, motor protein; HET: ADP; 1.90A {Drosophila melanogaster} PDB: 3dcb_A* 3dco_N* 3pxn_A*

Probab=80.28  E-value=0.59  Score=41.70  Aligned_cols=24  Identities=17%  Similarity=0.455  Sum_probs=18.3

Q ss_pred             ccccccCCc--eEEEccCCCcchhHH
Q 014486           77 IPQAILGMD--VICQAKSGMGKTAVF  100 (423)
Q Consensus        77 i~~~~~~~~--~ii~~~tGsGKT~~~  100 (423)
                      +..++.|.+  ++..|.||||||.+.
T Consensus        87 v~~~l~G~N~tifAYGQTGSGKTyTM  112 (344)
T 3dc4_A           87 VDKLLEGFQCTALAYGQTGTGKSYSM  112 (344)
T ss_dssp             HHHHHHTCCEEEEEESSTTSSHHHHH
T ss_pred             hhHhhCCCceEEEEecCCCCCCCeEE
Confidence            344556776  678899999999864

>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=80.20  E-value=12  Score=31.32  Aligned_cols=118  Identities=11%  Similarity=0.119  Sum_probs=67.8

Q ss_pred             CCcEEEEEcChhhHHHHHHHHHhC----CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc-c-----ccCCCCCCC
Q 014486          288 FNQVVIFVKSVSRAAELNKLLVEC----NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL-V-----GRGIDIERV  357 (423)
Q Consensus       288 ~~~~ivf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~-~-----~~Gld~~~~  357 (423)
                      ..++||.++++..+..+.+.++..    +..+..++|+.+.......+    ....+|+|+|.- +     ...+++.++
T Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~  175 (253)
T 1wrb_A          100 YPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREV----QMGCHLLVATPGRLVDFIEKNKISLEFC  175 (253)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHH----SSCCSEEEECHHHHHHHHHTTSBCCTTC
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh----CCCCCEEEECHHHHHHHHHcCCCChhhC
Confidence            358999999999999888877653    56778888887755543332    246789999952 1     123567778


Q ss_pred             CEEEEccCC----CCc-chhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHh
Q 014486          358 NIVINYDMP----DSA-DTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       358 ~~vi~~~~~----~s~-~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                      +++|.-..-    ++. ..+.....+.........-+++++........+.+.+.+.
T Consensus       176 ~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~  232 (253)
T 1wrb_A          176 KYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLY  232 (253)
T ss_dssp             CEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCS
T ss_pred             CEEEEeCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcC
Confidence            877742211    111 1222223332222212334445555555555555555553

>3lre_A Kinesin-like protein KIF18A; motor protein, nucleotide binding, microtubule binding, ATP- cell projection, cytoskeleton, glycoprotein, microtubule; HET: ADP; 2.20A {Homo sapiens} SCOP: c.37.1.0

Probab=80.20  E-value=0.72  Score=41.37  Aligned_cols=25  Identities=24%  Similarity=0.437  Sum_probs=19.0

Q ss_pred             cccccccCCc--eEEEccCCCcchhHH
Q 014486           76 CIPQAILGMD--VICQAKSGMGKTAVF  100 (423)
Q Consensus        76 ~i~~~~~~~~--~ii~~~tGsGKT~~~  100 (423)
                      .+..++.|.+  ++..|+||||||.+.
T Consensus        97 lv~~~l~G~n~tifAYGqTGSGKTyTm  123 (355)
T 3lre_A           97 ILRSFLNGYNCTVLAYGATGAGKTHTM  123 (355)
T ss_dssp             HHHHHTTTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHHHhCCCceEEEEeCCCCCCceeee
Confidence            3445567777  788899999999864

>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=80.17  E-value=0.76  Score=36.85  Aligned_cols=18  Identities=22%  Similarity=0.298  Sum_probs=15.1

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      +.-+++.|++|||||.+.
T Consensus         3 ~~~I~i~G~~GsGKsT~~   20 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSS   20 (192)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            445899999999999864

>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=80.11  E-value=0.71  Score=36.27  Aligned_cols=17  Identities=18%  Similarity=0.043  Sum_probs=14.1

Q ss_pred             ceEEEccCCCcchhHHH
Q 014486           85 DVICQAKSGMGKTAVFV  101 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~  101 (423)
                      .+++.|++|||||.+.-
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            37899999999998653

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=80.02  E-value=0.69  Score=42.30  Aligned_cols=25  Identities=20%  Similarity=0.445  Sum_probs=20.5

Q ss_pred             cccccccCCc--eEEEccCCCcchhHH
Q 014486           76 CIPQAILGMD--VICQAKSGMGKTAVF  100 (423)
Q Consensus        76 ~i~~~~~~~~--~ii~~~tGsGKT~~~  100 (423)
                      .+..++.|.+  ++..|.||||||.+.
T Consensus       132 lv~~~l~G~N~tifAYGqTGSGKTyTM  158 (403)
T 4etp_A          132 LVQSSLDGYNVAIFAYGQTGSGKTFTM  158 (403)
T ss_dssp             HHHHHHTTCCEEEEEESCTTSSHHHHH
T ss_pred             HHHHHhCCcceEEEEECCCCCCCceEe
Confidence            5667778877  678899999999875

---

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	423
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	5e-60
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	1e-48
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	3e-45
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	1e-44
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	7e-41
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	2e-39
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	9e-37
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	1e-36
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	9e-33
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	3e-32
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	1e-30
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	1e-27
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	4e-22
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	7e-21
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	2e-20
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	2e-20
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	3e-20
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	1e-19
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	2e-18
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	2e-18
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	2e-18
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	2e-17
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	4e-16
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	3e-15
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	2e-14
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	3e-14
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	9e-12
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	1e-09
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	4e-09
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	6e-07
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	4e-06
d1tf5a4	175	c.37.1.19 (A:396-570) Translocation ATPase SecA, n	6e-06
d1yksa1	140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	0.004

>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 =  192 bits (488), Expect = 5e-60
 Identities = 168/207 (81%), Positives = 192/207 (92%)

Query: 46  SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTL 105
           SGFRDFLLKPELLRAIVD GFEHPSEVQHECIPQAILGMDV+CQAKSGMGKTAVFVL+TL
Sbjct: 1   SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 60

Query: 106 QQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNE 165
           QQ EP  GQV+ LV+CHTRELA+QI  E+ERFS Y+P++KVAVF+GG++IK  +++LK  
Sbjct: 61  QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 120

Query: 166 CPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQV 225
           CP IVVGTPGRILALAR+K L+LK+++HFILDECDKMLE LDMRRDVQEIF+MTPH+KQV
Sbjct: 121 CPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQV 180

Query: 226 MMFSATLSKEIRPVCKKFMQDPMEIYV 252
           MMFSATLSKEIRPVC+KFMQDPMEI+V
Sbjct: 181 MMFSATLSKEIRPVCRKFMQDPMEIFV 207

>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 =  162 bits (412), Expect = 1e-48
 Identities = 79/206 (38%), Positives = 116/206 (56%), Gaps = 6/206 (2%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILG-MDVICQAKSGMGKTAVFVLSTLQ 106
           F +  L   +L AI + GFE P+++Q + IP  +    +++ QA++G GKTA F +  ++
Sbjct: 6   FNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIE 65

Query: 107 QTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNEC 166
               N G    ++L  TRELA Q+  E E       ++K+A  YGG  I      LKN  
Sbjct: 66  LVNENNGIEA-IILTPTRELAIQVADEIESLKGN-KNLKIAKIYGGKAIYPQIKALKN-- 121

Query: 167 PQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVM 226
             IVVGTPGRIL       L+LKNV++FILDE D+ML      +DV++I      DK+++
Sbjct: 122 ANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNM-GFIKDVEKILNACNKDKRIL 180

Query: 227 MFSATLSKEIRPVCKKFMQDPMEIYV 252
           +FSAT+ +EI  + KK+M D   I  
Sbjct: 181 LFSATMPREILNLAKKYMGDYSFIKA 206

>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 =  154 bits (389), Expect = 3e-45
 Identities = 84/205 (40%), Positives = 111/205 (54%), Gaps = 2/205 (0%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  L   LLR I   GFE PS +Q   I   I G DVI QA+SG GKTA F +S LQQ
Sbjct: 14  FDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQ 73

Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            E +     ALVL  TRELA QI         Y          GG N++     L+ E P
Sbjct: 74  IELDLKATQALVLAPTRELAQQIQKVVMALGDY-MGASCHACIGGTNVRAEVQKLQMEAP 132

Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
            I+VGTPGR+  +   + LS K ++ F+LDE D+M  S   +  + +IF+    + QV++
Sbjct: 133 HIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEM-LSRGFKDQIYDIFQKLNSNTQVVL 191

Query: 228 FSATLSKEIRPVCKKFMQDPMEIYV 252
            SAT+  ++  V KKFM+DP+ I V
Sbjct: 192 LSATMPSDVLEVTKKFMRDPIRILV 216

>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 =  152 bits (384), Expect = 1e-44
 Identities = 73/205 (35%), Positives = 107/205 (52%), Gaps = 4/205 (1%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F D  L   LLR +   GFE PS +Q   I   I G DV+ QA+SG GKT  F ++ LQ+
Sbjct: 12  FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 71

Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            + +     AL+L  TRE       +      +  DIKV    GG +     + L++   
Sbjct: 72  IDTSVKAPQALMLAPTRE-LALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRD--A 128

Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
           QIVVGTPGR+    + +      ++ FILDE D+ML S   +  + +IF + P   QV++
Sbjct: 129 QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSS-GFKEQIYQIFTLLPPTTQVVL 187

Query: 228 FSATLSKEIRPVCKKFMQDPMEIYV 252
            SAT+  ++  V  KFM++P+ I V
Sbjct: 188 LSATMPNDVLEVTTKFMRNPVRILV 212

>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 =  142 bits (358), Expect = 7e-41
 Identities = 64/205 (31%), Positives = 113/205 (55%), Gaps = 2/205 (0%)

Query: 46  SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTL 105
           + F D+ LK ELL  I + G+E PS +Q E IP A+ G D++ +AK+G GK+  +++  L
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62

Query: 106 QQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNE 165
           ++ +     + A+V+  TRELA Q+     + S ++   KV    GG N++     L + 
Sbjct: 63  ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT 122

Query: 166 CPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQV 225
              + + TPGRIL L +     + +V+  +LDE DK+  S D  + +++I    P ++Q+
Sbjct: 123 VHVV-IATPGRILDLIKKGVAKVDHVQMIVLDEADKL-LSQDFVQIMEDIILTLPKNRQI 180

Query: 226 MMFSATLSKEIRPVCKKFMQDPMEI 250
           +++SAT    ++      ++ P EI
Sbjct: 181 LLYSATFPLSVQKFMNSHLEKPYEI 205

>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 =  139 bits (350), Expect = 2e-39
 Identities = 74/205 (36%), Positives = 107/205 (52%), Gaps = 3/205 (1%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQ 107
           F    L+ +LLR I   GFE PS +Q   I Q I G DVI Q++SG GKTA F +S LQ 
Sbjct: 19  FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQC 78

Query: 108 TEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECP 167
            +    +  AL+L  TRELA QI         Y  +++     GG N+      L     
Sbjct: 79  LDIQVRETQALILAPTRELAVQIQKGLLALGDY-MNVQCHACIGGTNVGEDIRKLDYGQ- 136

Query: 168 QIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM 227
            +V GTPGR+  + R + L  + ++  +LDE D+M  +   +  + ++++  P   QV++
Sbjct: 137 HVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM-LNKGFKEQIYDVYRYLPPATQVVL 195

Query: 228 FSATLSKEIRPVCKKFMQDPMEIYV 252
            SATL  EI  +  KFM DP+ I V
Sbjct: 196 ISATLPHEILEMTNKFMTDPIRILV 220

>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 =  132 bits (332), Expect = 9e-37
 Identities = 60/217 (27%), Positives = 108/217 (49%), Gaps = 14/217 (6%)

Query: 48  FRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQ- 106
           F +  L P +   I+ + ++ P+ +Q   IP  +   D++  A++G GKTA F++  +  
Sbjct: 23  FDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINH 82

Query: 107 --------QTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIH 158
                   Q          L+L  TRELA QI  E ++FS   P ++  V YGG +    
Sbjct: 83  LVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTP-LRSCVVYGGADT-HS 140

Query: 159 KDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESL---DMRRDVQEI 215
           +         ++V TPGR++       +SL+  ++ +LDE D+ML+      +R+ ++E 
Sbjct: 141 QIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEES 200

Query: 216 FKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
              +  ++Q +MFSAT  KEI+ +   F+ + + + V
Sbjct: 201 NMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV 237

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  131 bits (329), Expect = 1e-36
 Identities = 75/209 (35%), Positives = 109/209 (52%), Gaps = 3/209 (1%)

Query: 46  SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTL 105
           + F DF LK ELL  I ++GFE PS +Q E IP AI G D++ +AK+G GKTA FV+ TL
Sbjct: 1   NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL 60

Query: 106 QQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNE 165
           ++ +P   ++ AL++            +  R       I   V  GG N++     L   
Sbjct: 61  EKVKPKLNKIQALIMV-PTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNE- 118

Query: 166 CPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQV 225
              I+VGTPGR+L LA  K   L +   FI+DE DKML   D +  +++I    P   Q 
Sbjct: 119 TVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSR-DFKTIIEQILSFLPPTHQS 177

Query: 226 MMFSATLSKEIRPVCKKFMQDPMEIYVDD 254
           ++FSAT    ++    K +  P EI + +
Sbjct: 178 LLFSATFPLTVKEFMVKHLHKPYEINLME 206

>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 =  123 bits (309), Expect = 9e-33
 Identities = 44/336 (13%), Positives = 90/336 (26%), Gaps = 59/336 (17%)

Query: 83  GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP 142
               I     G GKT  ++ + +++      +   L+L  TR +A ++            
Sbjct: 9   KRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRT--LILAPTRVVAAEMEEALR------- 59

Query: 143 DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM 202
              + + Y    I+            + +              + + N    I+DE    
Sbjct: 60  --GLPIRYQTPAIRAEH----TGREIVDLMCHATFTMRLL-SPIRVPNYNLIIMDEAHFT 112

Query: 203 LESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLTLHG 262
             +    R      ++   +   +  +AT      P  +                     
Sbjct: 113 DPASIAARG-YISTRVEMGEAAGIFMTATPPGSRDPFPQSNAPIM--------------- 156

Query: 263 LVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGM 322
                 ++ E   N     + D     + V FV S+    ++   L +     I +    
Sbjct: 157 --DEEREIPERSWNSGHEWVTD--FKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKT 212

Query: 323 SQEERLTRYKGFKEGNKRILVATDLVGRGIDIE---------RVNIVINYD--------- 364
              E +      +  +   +V TD+   G + +          +  VI  D         
Sbjct: 213 FDSEYI----KTRTNDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILTDGEERVILAG 268

Query: 365 -MPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSD 399
            MP +  +   R GR GR                 +
Sbjct: 269 PMPVTHSSAAQRRGRVGRNPKNENDQYIYMGEPLEN 304

>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 =  119 bits (298), Expect = 3e-32
 Identities = 66/209 (31%), Positives = 116/209 (55%), Gaps = 3/209 (1%)

Query: 46  SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTL 105
           + F  F  +P ++ AI    F  P+E+Q   IP A+ G  ++ Q+++G GKT  ++L  +
Sbjct: 1   TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIM 60

Query: 106 QQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLK-- 163
           ++ +P   +V A++   TRELA QI HE  + + + P  ++ V    +     +  L+  
Sbjct: 61  EKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKL 120

Query: 164 NECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK 223
           N  P IV+GTPGRI    R++ L +      ++DE D M   +    DV +I    P D 
Sbjct: 121 NVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLM-LDMGFITDVDQIAARMPKDL 179

Query: 224 QVMMFSATLSKEIRPVCKKFMQDPMEIYV 252
           Q+++FSAT+ ++++P  KK+M++P  ++V
Sbjct: 180 QMLVFSATIPEKLKPFLKKYMENPTFVHV 208

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score =  116 bits (290), Expect = 1e-30
 Identities = 35/237 (14%), Positives = 70/237 (29%), Gaps = 26/237 (10%)

Query: 23  APDSVATKANGEAAKKGYVGIHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAIL 82
           A  + A  A   AA      +      DFLLK              P  +Q     + + 
Sbjct: 1   AAAAAAAAAAAAAAAAAAASL-CLFPEDFLLKE--FVEFFRKCVGEPRAIQKMWAKRILR 57

Query: 83  GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP 142
                  A +G+GKT+  +  +L             V+  T  L  Q      +++    
Sbjct: 58  KESFAATAPTGVGKTSFGLAMSLFLALKGKR---CYVIFPTSLLVIQAAETIRKYAEKAG 114

Query: 143 DIKVAV-----FYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILD 197
            +                +    +      +IV+ T   +          L +     +D
Sbjct: 115 -VGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFL----SKHYRELGHFDFIFVD 169

Query: 198 ECDKMLES----------LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFM 244
           + D +L++          L    D++    +      +M+ +AT  K  +    + +
Sbjct: 170 DVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQL 226

>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 =  109 bits (273), Expect = 1e-27
 Identities = 27/160 (16%), Positives = 48/160 (30%), Gaps = 24/160 (15%)

Query: 255 EAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFP 314
           E  L+  G +  Y K   LE  +            + +IF  S  +  EL   LV     
Sbjct: 13  EVALSTTGEIPFYGKAIPLEVIKG----------GRHLIFCHSKKKCDELAAKLVALGIN 62

Query: 315 SICIHSGMSQEERLT----------RYKGFKEGNKRILVATDLVGRG---IDIERVNIVI 361
           ++  + G+      T                 G+   ++  +          ++    + 
Sbjct: 63  AVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIE 122

Query: 362 NYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDIL 401
              +P  A +   R GR GR G  G+          S + 
Sbjct: 123 TTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPGERPSGMF 161

>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 = 90.4 bits (223), Expect = 4e-22
 Identities = 61/145 (42%), Positives = 91/145 (62%), Gaps = 2/145 (1%)

Query: 265 QHYIKLSELE-KNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMS 323
           Q Y+ + E E K   L DL D++   Q VIF  +  +  EL   L    F    I+S + 
Sbjct: 3   QFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLP 62

Query: 324 QEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFG 383
           Q+ER T  K F+ G+ RIL++TDL+ RGID+++V++VINYD+P + + Y+HR+GR GRFG
Sbjct: 63  QQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFG 122

Query: 384 TKGLAITFVSSASDSDILNQVSKFM 408
            KG+AI FV++  D   + ++ KF 
Sbjct: 123 RKGVAINFVTN-EDVGAMRELEKFY 146

>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 = 88.1 bits (217), Expect = 7e-21
 Identities = 27/183 (14%), Positives = 64/183 (34%), Gaps = 11/183 (6%)

Query: 53  LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP 112
           +    +  + + G E     Q E + +   G +++    +  GKT +  ++ +++     
Sbjct: 10  ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGG 69

Query: 113 GQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVG 172
             +    +   R LA +    F+++       K+ +  G                 I+V 
Sbjct: 70  KSLY---VVPLRALAGEKYESFKKW------EKIGLRIGISTGDYESRDEHLGDCDIIVT 120

Query: 173 TPGRILALARDKDLSLKNVRHFILDECDKMLES--LDMRRDVQEIFKMTPHDKQVMMFSA 230
           T  +  +L R++   +K V   ++DE   +           +    +      +V+  SA
Sbjct: 121 TSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSA 180

Query: 231 TLS 233
           T  
Sbjct: 181 TAP 183

>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 = 85.8 bits (211), Expect = 2e-20
 Identities = 58/153 (37%), Positives = 94/153 (61%), Gaps = 2/153 (1%)

Query: 257 KLTLHGLVQHYIKL-SELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPS 315
           +LTL G+ Q ++ +  E  K   L DL D L   Q VIF  +  +   L + + E NF  
Sbjct: 2   ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTV 61

Query: 316 ICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHR 375
             +H  M Q+ER +  K F+ G  R+L++TD+  RG+D+ +V+++INYD+P++ + Y+HR
Sbjct: 62  SSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHR 121

Query: 376 VGRAGRFGTKGLAITFVSSASDSDILNQVSKFM 408
           +GR+GR+G KG+AI FV +  D  IL  + ++ 
Sbjct: 122 IGRSGRYGRKGVAINFVKN-DDIRILRDIEQYY 153

>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 = 88.4 bits (218), Expect = 2e-20
 Identities = 37/225 (16%), Positives = 80/225 (35%), Gaps = 14/225 (6%)

Query: 184 KDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKF 243
           ++++  N     L     M   L    ++ E   ++     +               K+ 
Sbjct: 60  EEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEI 119

Query: 244 MQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRK-LNDLLDALDFNQVVIFVKSVSRAA 302
             D        +A   L    +  +   +++K ++ + + L     +++++F      A 
Sbjct: 120 FSDKRMK----KAISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAK 175

Query: 303 ELNKLLVECNFPSICIHSGMSQEERLTRY--------KGFKEGNKRILVATDLVGRGIDI 354
           ++   LV+    +       S+E                F  G   +LVAT +   G+D+
Sbjct: 176 KIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDV 235

Query: 355 ERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSD 399
             V++V+ Y+   SA   + R GR GR    G  I  ++  +  +
Sbjct: 236 PEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGTRDE 279

>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 = 84.6 bits (208), Expect = 3e-20
 Identities = 51/144 (35%), Positives = 84/144 (58%), Gaps = 2/144 (1%)

Query: 265 QHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQ 324
           Q Y++++E E+   L  LL   +F   ++F K+     EL  +L +  F +  IH  +SQ
Sbjct: 6   QSYVEVNENERFEALCRLLKNKEF-YGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQ 64

Query: 325 EERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGT 384
            +R    + FK+   RIL+ATD++ RGID+  +N VINY +P + ++Y+HR+GR GR G 
Sbjct: 65  SQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGK 124

Query: 385 KGLAITFVSSASDSDILNQVSKFM 408
           KG AI+ ++   +   L  + + M
Sbjct: 125 KGKAISIINR-REYKKLRYIERAM 147

>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 = 84.7 bits (208), Expect = 1e-19
 Identities = 27/202 (13%), Positives = 59/202 (29%), Gaps = 16/202 (7%)

Query: 56  ELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQV 115
           ++L+     G++     Q E I   + G D +    +G GK+  +      Q        
Sbjct: 15  QVLQETF--GYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCY------QIPALLLNG 66

Query: 116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPG 175
             +V+     L      + +        +            +          +++   P 
Sbjct: 67  LTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQ--IRLLYIAPE 124

Query: 176 RILALARDKDLSLKNVRHFILDECDKMLESLDMRRD---VQEIFKMTPHDKQVMMFSATL 232
           R++     + L+  N     +DE   + +     R         +        M  +AT 
Sbjct: 125 RLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATA 184

Query: 233 SKEIR-PVCKKF-MQDPMEIYV 252
               R  + +   + DP  I +
Sbjct: 185 DDTTRQDIVRLLGLNDP-LIQI 205

>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 = 82.1 bits (202), Expect = 2e-18
 Identities = 22/140 (15%), Positives = 50/140 (35%), Gaps = 17/140 (12%)

Query: 274 EKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKG 333
           E    L+ +L+ L     +I+ ++   A E+ + L            G+    +   Y+ 
Sbjct: 12  ESISTLSSILEKLG-TGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEK 64

Query: 334 FKEGNKRILVAT----DLVGRGIDI-ERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLA 388
           F EG    L+ T      + RG+D+ ER+   +    P     +   +        + + 
Sbjct: 65  FVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVK 120

Query: 389 ITFVSSASDSDILNQVSKFM 408
           +       + D + ++   +
Sbjct: 121 LLAY-LYRNVDEIERLLPAV 139

>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 = 80.1 bits (196), Expect = 2e-18
 Identities = 101/147 (68%), Positives = 117/147 (79%)

Query: 262 GLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSG 321
           GL Q+Y+KL + EKNRKL DLLD L+FNQVVIFVKSV R   L +LLVE NFP+I IH G
Sbjct: 1   GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 60

Query: 322 MSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGR 381
           M QEERL+RY+ FK+  +RILVAT+L GRG+DIERVNI  NYDMP+ +DTYLHRV RAGR
Sbjct: 61  MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 120

Query: 382 FGTKGLAITFVSSASDSDILNQVSKFM 408
           FGTKGLAITFVS  +D+ ILN V    
Sbjct: 121 FGTKGLAITFVSDENDAKILNDVQDRF 147

>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 = 77.0 bits (188), Expect = 2e-17
 Identities = 62/151 (41%), Positives = 92/151 (60%), Gaps = 1/151 (0%)

Query: 258 LTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSIC 317
           LTL G+ Q+Y  + E +K   LN L   L  NQ +IF  S +R   L K + +  +    
Sbjct: 2   LTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYY 61

Query: 318 IHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVG 377
            H+ M Q+ER   +  F++G  R LV +DL+ RGIDI+ VN+VIN+D P +A+TYLHR+G
Sbjct: 62  SHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIG 121

Query: 378 RAGRFGTKGLAITFVSSASDSDILNQVSKFM 408
           R+GRFG  GLAI  ++  +D   L ++ + +
Sbjct: 122 RSGRFGHLGLAINLINW-NDRFNLYKIEQEL 151

>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 = 74.2 bits (181), Expect = 4e-16
 Identities = 33/194 (17%), Positives = 67/194 (34%), Gaps = 24/194 (12%)

Query: 200 DKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYVDDEAKLT 259
           +K  +        + I      D   ++ ++   +      + + +              
Sbjct: 24  EKREKVYKQFLRARGITLRRAEDFNKIVMASGYDERAYEALRAWEE-------------- 69

Query: 260 LHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIH 319
                   I  +   K RKL ++L+    ++++IF +            +   F    I 
Sbjct: 70  -----ARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYR-----ISKVFLIPAIT 119

Query: 320 SGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRA 379
              S+EER    +GF+ G  R +V++ ++  GID+   N+ +      SA  Y+ R+GR 
Sbjct: 120 HRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRI 179

Query: 380 GRFGTKGLAITFVS 393
            R            
Sbjct: 180 LRPSKGKKEAVLYE 193

>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 = 70.1 bits (171), Expect = 3e-15
 Identities = 25/114 (21%), Positives = 43/114 (37%), Gaps = 12/114 (10%)

Query: 283 LDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRIL 342
           L+ +   + +IF  S  +  EL   LV     ++  + G+                  ++
Sbjct: 30  LEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGL-------DVSVIPTNGDVVV 82

Query: 343 VATDLVGRGIDIER---VNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVS 393
           VATD +  G   +    ++   +   P  A +   R GR GR G  G    FV+
Sbjct: 83  VATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR-GKPG-IYRFVA 134

>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 = 69.8 bits (169), Expect = 2e-14
 Identities = 33/212 (15%), Positives = 71/212 (33%), Gaps = 16/212 (7%)

Query: 61  IVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVL 120
           ++      P   Q           + +    +G+GKT + ++    +     G+V  L  
Sbjct: 2   VLRRDLIQPRIYQEVIY-AKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAP 60

Query: 121 CHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILAL 180
                       E  R    LP  K+    G  + +           +++V TP  I   
Sbjct: 61  TKPL---VLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWA--RAKVIVATPQTIEND 115

Query: 181 ARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLS---KEIR 237
                +SL++V   + DE  + + +      +   +K    +  V+  +A+     ++I 
Sbjct: 116 LLAGRISLEDVSLIVFDEAHRAVGN-YAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIM 174

Query: 238 PVCKKFMQDPMEIYVDDEAKLTLHGLVQHYIK 269
            V      + +E   ++         V+ Y+K
Sbjct: 175 EVINNLGIEHIEYRSENSPD------VRPYVK 200

>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 = 68.9 bits (167), Expect = 3e-14
 Identities = 29/128 (22%), Positives = 57/128 (44%)

Query: 266 HYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQE 325
            Y+ + + +   +L   +        +I+  S ++  +    L      +   H+G+   
Sbjct: 8   RYMLMEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENN 67

Query: 326 ERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTK 385
            R    + F+  + +I+VAT   G GI+   V  V+++D+P + ++Y    GRAGR G  
Sbjct: 68  VRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLP 127

Query: 386 GLAITFVS 393
             A+ F  
Sbjct: 128 AEAMLFYD 135

>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 = 61.3 bits (148), Expect = 9e-12
 Identities = 25/118 (21%), Positives = 49/118 (41%), Gaps = 10/118 (8%)

Query: 278 KLNDLLDAL-----DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYK 332
           +++DL+  +        + ++   +   A +L   L E       +HS +   ER+   +
Sbjct: 16  QIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIR 75

Query: 333 GFKEGNKRILVATDLVGRGIDIERVNIVINYDMP-----DSADTYLHRVGRAGRFGTK 385
             + G   +LV  +L+  G+DI  V++V   D        S  + +  +GRA R    
Sbjct: 76  DLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANG 133

>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 = 55.3 bits (132), Expect = 1e-09
 Identities = 32/142 (22%), Positives = 57/142 (40%), Gaps = 13/142 (9%)

Query: 278 KLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSI-CIHSGMSQEERLTRYKGFKE 336
           KL+ +      N+ +          E+++ L EC        H+G+   +R      F+ 
Sbjct: 59  KLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRR 118

Query: 337 GNKRILVATDLVGRGIDIERVNIVI-------NYDMPDSADTYLHRVGRAGRFG--TKGL 387
           GN +++VAT  +  G+++    +++        Y        Y    GRAGR G   +G 
Sbjct: 119 GNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGE 178

Query: 388 AITFVSSASDSDILNQVSKFMF 409
           AI  V      D    V +++F
Sbjct: 179 AIIIVGK---RDREIAVKRYIF 197

>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 = 53.5 bits (128), Expect = 4e-09
 Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 5/99 (5%)

Query: 290 QVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVG 349
           + ++ V +V  A EL   LVE    +  +H  +   +R    +  + G+   LV  +L+ 
Sbjct: 33  RTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLR 92

Query: 350 RGIDIERVNIVINYD-----MPDSADTYLHRVGRAGRFG 383
            G+DI  V++V   D        S  + +  +GRA R  
Sbjct: 93  EGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 131

>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 = 48.4 bits (115), Expect = 6e-07
 Identities = 20/128 (15%), Positives = 42/128 (32%), Gaps = 22/128 (17%)

Query: 290 QVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVG 349
               F+ S+  A  +   L +     + ++    + E    Y   K+     ++ATD+  
Sbjct: 38  PTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFERE----YPTIKQKKPDFILATDIAE 93

Query: 350 RGIDIERVNIV------------------INYDMPDSADTYLHRVGRAGRFGTKGLAITF 391
            G ++    ++                  I   +  SA +   R GR GR   +     +
Sbjct: 94  MGANLCVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYY 153

Query: 392 VSSASDSD 399
            S  +  +
Sbjct: 154 YSEPTSEN 161

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]} 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: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 45.2 bits (106), Expect = 4e-06
 Identities = 25/94 (26%), Positives = 41/94 (43%), Gaps = 1/94 (1%)

Query: 317 CIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHR- 375
            +H  +SQEE+      F EG   ILV+T ++  GID+ R N+++  +        LH+ 
Sbjct: 69  LMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQL 128

Query: 376 VGRAGRFGTKGLAITFVSSASDSDILNQVSKFMF 409
            GR GR G +      V    +  +       + 
Sbjct: 129 RGRVGRGGQEAYCFLVVGDVGEEAMERLRFFTLN 162

>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 = 44.1 bits (104), Expect = 6e-06
 Identities = 28/135 (20%), Positives = 54/135 (40%), Gaps = 14/135 (10%)

Query: 270 LSELEKNRKL-NDLLDALDFNQ-VVIFVKSVSRAAELNKLLVECNFPSICIHSGMS-QEE 326
            +   K + +  D+       Q V++   +V  +  ++KLL     P   +++    +E 
Sbjct: 14  RTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREA 73

Query: 327 RLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYD--------MPDSADTYLHRVGR 378
           ++    G K     + +AT++ GRG DI+    V              +S        GR
Sbjct: 74  QIIEEAGQK---GAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGR 130

Query: 379 AGRFGTKGLAITFVS 393
           +GR G  G+   ++S
Sbjct: 131 SGRQGDPGITQFYLS 145

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 140

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 35.4 bits (80), Expect = 0.004
 Identities = 17/149 (11%), Positives = 32/149 (21%), Gaps = 17/149 (11%)

Query: 83  GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLP 142
           GM  +     G GKT  F+                 +L        +             
Sbjct: 7   GMTTVLDFHPGAGKTRRFLPQ---------------ILAECARRRLRTLVLAPTRVVLSE 51

Query: 143 DIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM 202
             +                  +    I       +     +    + N    I+DE   +
Sbjct: 52  MKEAFHGLDVKFHTQAFSAHGSGREVIDAMCHATLTYRMLE-PTRVVNWEVIIMDEAHFL 110

Query: 203 LESLDMRRDVQEIFKMTPHDKQVMMFSAT 231
             +    R              ++M +AT
Sbjct: 111 DPASIAARGWAAHRARANESATILM-TAT 138

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	423
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	100.0
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	100.0
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.97
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.97
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.96
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.96
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.96
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.96
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.95
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.94
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.93
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
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.9
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.87
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.84
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.83
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.83
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.82
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.81
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.8
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.79
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.76
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.74
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.73
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.73
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.73
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.71
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.7
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.64
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.6
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.5
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.48
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.42
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	99.15
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	99.06
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.87
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.3
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.83
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.68
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.4
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.31
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.07
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.04
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.99
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	96.97
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	96.92
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.88
d1okkd2	207	GTPase domain of the signal recognition particle r	96.8
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	96.73
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	96.64
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.57
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.54
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	96.43
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	96.41
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	96.4
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.34
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.2
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	96.17
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	96.13
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	96.03
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.02
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.0
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	95.69
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.56
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	94.93
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	94.33
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	94.03
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	93.16
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	92.85
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	92.77
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	92.72
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	92.7
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	92.32
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	92.27
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	92.05
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	91.79
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	91.77
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	91.64
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	91.46
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	91.33
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	91.21
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	90.97
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	90.7
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	90.65
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	90.54
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	90.31
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	89.87
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	89.76
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	89.69
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	89.64
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	89.49
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	88.99
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	88.98
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	88.75
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	88.48
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	88.27
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	88.22
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	87.83
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	87.77
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	87.76
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	87.37
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	87.25
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	87.23
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	87.2
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	87.09
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	86.98
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	86.13
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	85.94
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	85.79
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	84.88
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	84.85
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	84.76
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	84.45
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	84.39
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	84.39
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	83.97
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	83.91
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	83.9
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	83.87
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	83.84
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	83.42
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	83.42
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	82.84
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	82.74
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	82.73
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	82.58
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	82.57
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	82.28
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	81.94
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	81.38
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	81.36
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	81.33
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	81.28
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	81.19
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	81.05
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	80.78
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	80.76
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	80.67
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	80.67
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	80.33
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	80.23

>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=3.2e-41  Score=283.05  Aligned_cols=206  Identities=81%  Similarity=1.334  Sum_probs=192.4

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      +.|+++++++.++++|.++||.+|+|+|+++||.++.|+|+++.+|||||||++|++|+++.......+++++|++|+++
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~Ptre   80 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   80 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccch
Confidence            46999999999999999999999999999999999999999999999999999999999999988888889999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~  205 (423)
                      |+.|+.+.++.+....+.+++..+.|+.....+...+.+..++|+|+||+++..+++...+.+.+++++|+||||.+.+.
T Consensus        81 L~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~  160 (207)
T d1t6na_          81 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ  160 (207)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSS
T ss_pred             hhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhhhhhc
Confidence            99999999999988877788899999999888888777666899999999999999998899999999999999999974


Q ss_pred             CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceee
Q 014486          206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIY  251 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~  251 (423)
                      .++...+..+.+.+++.+|++++|||+++.+..+.+.++.+|..+.
T Consensus       161 ~~~~~~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~  206 (207)
T d1t6na_         161 LDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  206 (207)
T ss_dssp             HHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             CCcHHHHHHHHHhCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEe
Confidence            5788999999999999999999999999999999999999887664

>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=1.5e-40  Score=278.73  Aligned_cols=204  Identities=32%  Similarity=0.563  Sum_probs=191.3

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ..+|+++++++.++++|.++||.+|+|+|+++||.++.|+|+++.+|||||||++|++|++........++.++|++|++
T Consensus         2 ~~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~   81 (206)
T d1veca_           2 GNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTR   81 (206)
T ss_dssp             CSSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCH
T ss_pred             CCChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecc
Confidence            46799999999999999999999999999999999999999999999999999999999999998888888999999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      +|+.|+.+.+..+.....+..+....|+.........+..+ ++|+|+||+++..++......+.+++++|+||||.+++
T Consensus        82 el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~-~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~  160 (206)
T d1veca_          82 ELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT-VHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLS  160 (206)
T ss_dssp             HHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSC-CSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTS
T ss_pred             hhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhc-cCeEEeCCccccccccchhccccccceEEEeccccccc
Confidence            99999999999988777778888888888888877777766 69999999999999999999999999999999999998


Q ss_pred             cCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCcee
Q 014486          205 SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEI  250 (423)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~  250 (423)
                       .+|...+..++..+++..|++++|||+++.+..+++.++.+|..+
T Consensus       161 -~~f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         161 -QDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             -TTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             -cchHHHHHHHHHhCCCCCEEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence             799999999999999999999999999999999999999998765

>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=1e-40  Score=281.42  Aligned_cols=204  Identities=37%  Similarity=0.614  Sum_probs=191.7

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      .+|+++++++.++++|+++||.+|+|+|+++||.++.|+|+++.+|||||||++|++|+++.+......++++|++|+++
T Consensus        17 ~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~Ptre   96 (222)
T d2j0sa1          17 PTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRE   96 (222)
T ss_dssp             CSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHH
T ss_pred             CCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecchHH
Confidence            46999999999999999999999999999999999999999999999999999999999999988888889999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~  205 (423)
                      |+.|+++.++.+.... ++++..+.|+.....+...+..+ ++|+|+||+++.+++......+.+++++|+||||.+++ 
T Consensus        97 La~Qi~~~~~~l~~~~-~i~~~~~~g~~~~~~~~~~l~~~-~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~-  173 (222)
T d2j0sa1          97 LAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDYG-QHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLN-  173 (222)
T ss_dssp             HHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHHHC-CSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTS-
T ss_pred             HHHHHHHHHHHHhCcc-ceeEEEEeecccchhhHHHhccC-CeEEeCCCCcHHhcccccccccccceeeeecchhHhhh-
Confidence            9999999999998765 89999999999988888888777 59999999999999999999999999999999999998 


Q ss_pred             CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeee
Q 014486          206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV  252 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  252 (423)
                      .+|...+..++..+++.+|++++|||+++++..+++.++.+|..+.+
T Consensus       174 ~~f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V  220 (222)
T d2j0sa1         174 KGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILV  220 (222)
T ss_dssp             TTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECC
T ss_pred             cCcHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEE
Confidence            79999999999999999999999999999999999999998876654

>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-39  Score=273.51  Aligned_cols=206  Identities=41%  Similarity=0.634  Sum_probs=186.6

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ..+|+++++++.+.++|.++||.+|+|+|+.+||.++.|+|+++.+|||||||++|++|+++.+......+++||++|++
T Consensus        11 i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~Pt~   90 (218)
T d2g9na1          11 VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTR   90 (218)
T ss_dssp             CCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSH
T ss_pred             cCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEEEEcccc
Confidence            45799999999999999999999999999999999999999999999999999999999999998887888999999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      +|+.|+++.+..+.... ++....+.++..............++|+|+||+++..++.+....+.+++++|+||||.+.+
T Consensus        91 eL~~Q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDEaD~ll~  169 (218)
T d2g9na1          91 ELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLS  169 (218)
T ss_dssp             HHHHHHHHHHHHHHTTT-TCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHH
T ss_pred             hhhhhHHHHHhhhcccc-ceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeeecchhhc
Confidence            99999999999998876 67777777766655554445445579999999999999999889999999999999999998


Q ss_pred             cCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeee
Q 014486          205 SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV  252 (423)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  252 (423)
                       .+|...+..++..+++..|++++|||+++.+..+.+.++.+|..+.+
T Consensus       170 -~~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v  216 (218)
T d2g9na1         170 -RGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILV  216 (218)
T ss_dssp             -TTCHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEEEC
T ss_pred             -CchHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHCCCCEEEEE
Confidence             79999999999999999999999999999999999999999987765

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.8e-38  Score=266.78  Aligned_cols=203  Identities=37%  Similarity=0.599  Sum_probs=180.1

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      ..+|+++++++.++++|.++||.+|+|+|++++|.++.|+|+++.+|||||||++|++|+++++.....++.++|++|++
T Consensus         9 ~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~   88 (212)
T d1qdea_           9 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTR   88 (212)
T ss_dssp             CCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSH
T ss_pred             ccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEcccH
Confidence            46799999999999999999999999999999999999999999999999999999999999999888889999999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      +|+.|....+..+.... .+.+....++.....+...+. + ++|+|+||+++..++....+.+.+++++|+||||.+.+
T Consensus        89 el~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~-~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~lld  165 (212)
T d1qdea_          89 ELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR-D-AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLS  165 (212)
T ss_dssp             HHHHHHHHHHHHHTTTS-CCCEEEECC----------CT-T-CSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHH
T ss_pred             HHhhhhhhhhccccccc-ccceeeEeeccchhHHHHHhc-C-CcEEEECCCccccccccCceecCcceEEeehhhhhhcc
Confidence            99999999998887665 677888888777666655544 3 69999999999999999999999999999999999998


Q ss_pred             cCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceee
Q 014486          205 SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIY  251 (423)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~  251 (423)
                       .+|...+..+++.+++.+|++++|||+++.+..+++.++.+|..+.
T Consensus       166 -~~f~~~v~~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~  211 (212)
T d1qdea_         166 -SGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRIL  211 (212)
T ss_dssp             -TTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC
T ss_pred             -cchHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence             7899999999999999999999999999999999999999987664

>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=3.1e-37  Score=259.31  Aligned_cols=204  Identities=39%  Similarity=0.633  Sum_probs=190.3

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      .+|+++++++.++++|+++||.+|+|+|+++||.++.|+|+++.+|||+|||++|++|++...........+++++|+.+
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            37999999999999999999999999999999999999999999999999999999999999888888889999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES  205 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~  205 (423)
                      ++.|....+..+.... ++++....|+.........+..+ ++|+|+||+++..+++.....+.+++++|+||||.+.+ 
T Consensus        81 ~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~-~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~-  157 (206)
T d1s2ma1          81 LALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLNET-VHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLS-  157 (206)
T ss_dssp             HHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHTTSC-CSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSS-
T ss_pred             hhhhhhhhhhhccccc-CeeEEeecCccchhhHHHHhccc-ceEEEECCcccccccccceeecccceEEEeechhhhhh-
Confidence            9999999888877665 89999999999988888777766 69999999999999999999999999999999999988 


Q ss_pred             CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeee
Q 014486          206 LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV  252 (423)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  252 (423)
                      .+|...+..+.+.+++.+|++++|||+|+.+..+++.++.+|..+.+
T Consensus       158 ~~f~~~v~~I~~~l~~~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~  204 (206)
T d1s2ma1         158 RDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINL  204 (206)
T ss_dssp             HHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESC
T ss_pred             hhhHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEe
Confidence            68999999999999999999999999999999999999998876654

>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=4.1e-37  Score=258.53  Aligned_cols=201  Identities=39%  Similarity=0.635  Sum_probs=182.0

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCC-ceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecCh
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGM-DVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTR  124 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~-~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  124 (423)
                      .+|+++++++.++++|.++||.+|+|+|+++||.++.|+ ++++.+|||+|||++|++++++...... +++++|++|++
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~~-~~~~lil~pt~   82 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENN-GIEAIILTPTR   82 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSS-SCCEEEECSCH
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccccc-CcceEEEeecc
Confidence            479999999999999999999999999999999999875 8999999999999999999998766544 45999999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhc
Q 014486          125 ELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLE  204 (423)
Q Consensus       125 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~  204 (423)
                      +|+.|+.+.++.+.... +.++....|+.+...+.+.+.+  ++|+|+||+++.++++++...+++++++|+||||.+.+
T Consensus        83 ~l~~q~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~l~~--~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~  159 (208)
T d1hv8a1          83 ELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALKN--ANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLN  159 (208)
T ss_dssp             HHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHHT--CSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHT
T ss_pred             ccchhhhhhhhhhcccC-CeEEEEeeCCCChHHHHHhcCC--CCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhc
Confidence            99999999999998765 7889999999888877766653  59999999999999999888999999999999999988


Q ss_pred             cCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceee
Q 014486          205 SLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIY  251 (423)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~  251 (423)
                       .++...+.+++..+++.+|++++|||+|+.+..+++.++.++..+.
T Consensus       160 -~~~~~~i~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~  205 (208)
T d1hv8a1         160 -MGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIK  205 (208)
T ss_dssp             -TTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEE
T ss_pred             -CCChHHHHHHHHhCCCCCeEEEEEccCCHHHHHHHHHHCCCCeEEE
Confidence             7888999999999999999999999999999999999998776553

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=100.00  E-value=9.1e-37  Score=261.10  Aligned_cols=206  Identities=28%  Similarity=0.505  Sum_probs=183.8

Q ss_pred             cCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC---------CCCC
Q 014486           44 HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP---------NPGQ  114 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~---------~~~~  114 (423)
                      ...+|+++++++.++++|.+.||.+|+|+|+.+||.++.|+|+++.+|||||||++|++|++..+..         ....
T Consensus        19 ~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~   98 (238)
T d1wrba1          19 VIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAY   98 (238)
T ss_dssp             CCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBC
T ss_pred             ccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCC
Confidence            3467999999999999999999999999999999999999999999999999999999999987632         2345


Q ss_pred             eEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEE
Q 014486          115 VTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHF  194 (423)
Q Consensus       115 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~v  194 (423)
                      ++++|++|+++|+.|+.+.+..+.... ++++..+.|+.....+......+ ++|+|+||++|..++..+...+.+++++
T Consensus        99 ~~alil~pt~el~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~ivV~TP~~l~~~~~~~~~~l~~v~~l  176 (238)
T d1wrba1          99 PKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREVQMG-CHLLVATPGRLVDFIEKNKISLEFCKYI  176 (238)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHHSSC-CSEEEECHHHHHHHHHTTSBCCTTCCEE
T ss_pred             ceEEEeccchhhhcchheeeeecccCC-CcEEEEEeccchhhHHHhhcccC-CceeecCHHHHHhHHccCceecccccee
Confidence            689999999999999999999988776 68999999998888777766666 6999999999999999988999999999


Q ss_pred             EEcCcchhhccCCcHHHHHHHHHhCCC----CceEEEEeccCCccHHHHHHHhccCCceeee
Q 014486          195 ILDECDKMLESLDMRRDVQEIFKMTPH----DKQVMMFSATLSKEIRPVCKKFMQDPMEIYV  252 (423)
Q Consensus       195 VvDE~h~~~~~~~~~~~~~~~~~~~~~----~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  252 (423)
                      |+||||.+++ .+|...+..+++.+..    .+|++++|||++..+..+++.++.+|..+.+
T Consensus       177 ViDEaD~ll~-~~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~v  237 (238)
T d1wrba1         177 VLDEADRMLD-MGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV  237 (238)
T ss_dssp             EEETHHHHHH-TTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEE
T ss_pred             eeehhhhhhh-hccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEe
Confidence            9999999998 7899999999886542    5699999999999999999999998866643

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=100.00  E-value=3.4e-35  Score=248.24  Aligned_cols=205  Identities=33%  Similarity=0.590  Sum_probs=179.9

Q ss_pred             CCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           46 SGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        46 ~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      +.|+++++++.++++|++.||.+|+|+|+++||.+++|+|+++.+|||||||++|++|+++........+..++++|+..
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~   80 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRE   80 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccc
Confidence            46999999999999999999999999999999999999999999999999999999999999888877789999999999


Q ss_pred             HHHHHHHHHHHHhccC---CCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchh
Q 014486          126 LAYQICHEFERFSTYL---PDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM  202 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~  202 (423)
                      ++.+....+.......   ....+....++.+...+......+ ++|+|+||+++..+..+....+.+++++|+||||.+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEad~l  159 (209)
T d1q0ua_          81 LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQ-PHIVIGTPGRINDFIREQALDVHTAHILVVDEADLM  159 (209)
T ss_dssp             HHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSC-CSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHH
T ss_pred             hhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccC-ceEEEecCchhhhhhhhhccccccceEEEEeecccc
Confidence            9999988887765443   234555666665555444434444 699999999999999988889999999999999999


Q ss_pred             hccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCCceeee
Q 014486          203 LESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDPMEIYV  252 (423)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~  252 (423)
                      .+ .+|...+..+...++++.|++++|||+|+++..+++.++.+|..+.+
T Consensus       160 l~-~~f~~~v~~I~~~~~~~~Q~il~SATl~~~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         160 LD-MGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             HH-TTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEEC
T ss_pred             cc-cccHHHHHHHHHHCCCCCEEEEEEccCCHHHHHHHHHHCCCCEEEEe
Confidence            98 68999999999999999999999999999999999999988876643

>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=1.2e-35  Score=267.00  Aligned_cols=273  Identities=16%  Similarity=0.131  Sum_probs=184.5

Q ss_pred             cccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH
Q 014486           80 AILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK  159 (423)
Q Consensus        80 ~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (423)
                      +..++++++.+|||||||++|+++++......+  .++||++|+++||.|++++++.+.........             
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~--~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~-------------   70 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRG--LRTLILAPTRVVAAEMEEALRGLPIRYQTPAI-------------   70 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHHT--CCEEEEESSHHHHHHHHHHTTTSCCBCCC----------------
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhcC--CEEEEEccHHHHHHHHHHHHhcCCcceeeeEE-------------
Confidence            456889999999999999999888876654333  37999999999999999887655322211111             


Q ss_pred             HHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccC-CcHHHHHHHHHhCCCCceEEEEeccCCccHHH
Q 014486          160 DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESL-DMRRDVQEIFKMTPHDKQVMMFSATLSKEIRP  238 (423)
Q Consensus       160 ~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~-~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~  238 (423)
                      .....+...++++|++.+..+... ...+.+++++|+||+|.+..+. .+...+..+.  .....+++++|||++.....
T Consensus        71 ~~~~~~~~~i~~~t~~~l~~~~~~-~~~~~~~~~vViDE~H~~~~~~~~~~~~l~~~~--~~~~~~~v~~SAT~~~~~~~  147 (305)
T d2bmfa2          71 RAEHTGREIVDLMCHATFTMRLLS-PIRVPNYNLIIMDEAHFTDPASIAARGYISTRV--EMGEAAGIFMTATPPGSRDP  147 (305)
T ss_dssp             -----CCCSEEEEEHHHHHHHHTS-SSCCCCCSEEEEESTTCCSHHHHHHHHHHHHHH--HHTSCEEEEECSSCTTCCCS
T ss_pred             eecccCccccccCCcHHHHHHHhc-CccccceeEEEeeeeeecchhhHHHHHHHHHhh--ccccceEEEeecCCCcceee
Confidence            111123358999999988776654 4456889999999999886521 1122222221  13467899999999764321


Q ss_pred             HHHHhccCCceeeeccccccccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEE
Q 014486          239 VCKKFMQDPMEIYVDDEAKLTLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICI  318 (423)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~  318 (423)
                      .    ......+..             .....+...+.... ..+ ....++++|||++++.++.+++.|.+.++.+..+
T Consensus       148 ~----~~~~~~~~~-------------~~~~~~~~~~~~~~-~~~-~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l  208 (305)
T d2bmfa2         148 F----PQSNAPIMD-------------EEREIPERSWNSGH-EWV-TDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQL  208 (305)
T ss_dssp             S----CCCSSCEEE-------------EECCCCCSCCSSCC-HHH-HSSCSCEEEECSCHHHHHHHHHHHHHHTCCCEEC
T ss_pred             e----cccCCcceE-------------EEEeccHHHHHHHH-HHH-HhhCCCEEEEeccHHHHHHHHHHHHhCCCCEEEe
Confidence            1    111100000             00000000000001 111 2245789999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE----------ccC----------CCCcchhhhcccc
Q 014486          319 HSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN----------YDM----------PDSADTYLHRVGR  378 (423)
Q Consensus       319 ~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~----------~~~----------~~s~~~~~Q~~GR  378 (423)
                      |+++.+..    ...|+++..+++|+|+++++|+|++ +++||.          ++.          |.|..+|+||+||
T Consensus       209 ~~~~~~~~----~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR  283 (305)
T d2bmfa2         209 SRKTFDSE----YIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGR  283 (305)
T ss_dssp             CTTCHHHH----GGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTT
T ss_pred             CCcChHHH----HhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCceeeeEecCCCCceEEeccccCCHHHHhhhhcC
Confidence            99986554    4467899999999999999999994 566553          333          4578899999999


Q ss_pred             cCCCCCceEEEEEecC
Q 014486          379 AGRFGTKGLAITFVSS  394 (423)
Q Consensus       379 ~~R~g~~~~~~~~~~~  394 (423)
                      +||.|+.+...+++..
T Consensus       284 ~GR~~~~~~~~~~~~~  299 (305)
T d2bmfa2         284 VGRNPKNENDQYIYMG  299 (305)
T ss_dssp             SSCSSSCCCEEEEECS
T ss_pred             cCcCCCCceEEEEECC
Confidence            9999988877766654

>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=99.97  E-value=9.9e-30  Score=203.27  Aligned_cols=150  Identities=41%  Similarity=0.697  Sum_probs=133.5

Q ss_pred             eEEEEEeC-hHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEE
Q 014486          264 VQHYIKLS-ELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRIL  342 (423)
Q Consensus       264 ~~~~~~~~-~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~il  342 (423)
                      .+.++.+. ...|...+.++++..+..++||||+++..++.+++.|...++.+..+||++++.+|..+++.|+.|+.+||
T Consensus         2 ~q~~~~v~~~e~K~~~L~~ll~~~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iL   81 (162)
T d1fuka_           2 KQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRIL   81 (162)
T ss_dssp             EEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEE
T ss_pred             EEEEEEeCCcHHHHHHHHHHHHhCCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhccccee
Confidence            34566664 45588999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhh
Q 014486          343 VATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGS  414 (423)
Q Consensus       343 i~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  414 (423)
                      |||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.++.++++ .+...+..+++.++..+..
T Consensus        82 v~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~-~d~~~~~~i~~~~~~~~~~  152 (162)
T d1fuka_          82 ISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTN-EDVGAMRELEKFYSTQIEE  152 (162)
T ss_dssp             EEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEET-TTHHHHHHHHHHSSCCCEE
T ss_pred             eccccccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCH-HHHHHHHHHHHHHcCcCCC
Confidence            9999999999999999999999999999999999999999999999999985 5777888999999877653

>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=1.1e-29  Score=205.69  Aligned_cols=154  Identities=40%  Similarity=0.654  Sum_probs=144.8

Q ss_pred             ccccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCC
Q 014486          259 TLHGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN  338 (423)
Q Consensus       259 ~~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~  338 (423)
                      ....+.++++.+...+|...|.++++..+.+++||||++++.++.++..|...|+.+..+||+++..+|..++..|++|.
T Consensus         3 tl~~i~q~yi~v~~~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~~   82 (171)
T d1s2ma2           3 TLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGK   82 (171)
T ss_dssp             BCTTEEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             CccceEEEEEEcCHHHHHHHHHHHHHhCCCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccCc
Confidence            34667888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchh
Q 014486          339 KRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIG  413 (423)
Q Consensus       339 ~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  413 (423)
                      .++||||+++++|+|+|++++||+|++|+++..|+||+||+||.|+.|.++.|+++ .+...+..+++.++..+.
T Consensus        83 ~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~-~e~~~~~~i~~~l~~~~~  156 (171)
T d1s2ma2          83 VRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINW-NDRFNLYKIEQELGTEIA  156 (171)
T ss_dssp             SSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECG-GGHHHHHHHHHHHTCCCE
T ss_pred             cccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCH-HHHHHHHHHHHHHCCCCC
Confidence            99999999999999999999999999999999999999999999999999999986 577788889999887654

>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=99.96  E-value=9.9e-30  Score=204.38  Aligned_cols=155  Identities=37%  Similarity=0.679  Sum_probs=142.2

Q ss_pred             ccccceEEEEEeCh-HHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcC
Q 014486          259 TLHGLVQHYIKLSE-LEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEG  337 (423)
Q Consensus       259 ~~~~~~~~~~~~~~-~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~  337 (423)
                      ...++.+.++.+.. ..|...|.++++..+..++||||++.+.++.++..|...++.+..+||++++.+|..+++.|++|
T Consensus         4 tl~~i~q~~v~v~~~~~K~~~L~~ll~~~~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g   83 (168)
T d2j0sa2           4 TLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG   83 (168)
T ss_dssp             SCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHT
T ss_pred             CCCCcEEEEEEecChHHHHHHHHHHHHhCCCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcC
Confidence            44667777777765 45899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhh
Q 014486          338 NKRILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGS  414 (423)
Q Consensus       338 ~~~ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  414 (423)
                      +.++||||+++++|+|+|++++||+|++|+++..|+||+||+||.|+.|.+++|+.+ .+...+..+++.++..+..
T Consensus        84 ~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~-~d~~~~~~i~~~~~~~i~e  159 (168)
T d2j0sa2          84 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKN-DDIRILRDIEQYYSTQIDE  159 (168)
T ss_dssp             SSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEG-GGHHHHHHHHHHTTCCCEE
T ss_pred             CccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECH-HHHHHHHHHHHHHcCcCCC
Confidence            999999999999999999999999999999999999999999999999999999986 4667788899988866543

>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=8.9e-30  Score=205.05  Aligned_cols=152  Identities=66%  Similarity=0.997  Sum_probs=144.2

Q ss_pred             ceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEE
Q 014486          263 LVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRIL  342 (423)
Q Consensus       263 ~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~il  342 (423)
                      +.++++.+.+.+|...+.++++....+++||||++++.++.+.+.|.+.|+++..+||++++.+|..+++.|++|+.++|
T Consensus         2 l~q~~v~~~~~~K~~~L~~ll~~~~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iL   81 (168)
T d1t5ia_           2 LQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRIL   81 (168)
T ss_dssp             CEEEEEECCGGGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEE
T ss_pred             cEEEEEEeChHHHHHHHHHHHHhCCCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccceee
Confidence            56788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhh
Q 014486          343 VATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGS  414 (423)
Q Consensus       343 i~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  414 (423)
                      |||+++++|+|+|.+++||+|++|+++..|+||+||+||.|++|.++.|+++..+..++..+++.++..+..
T Consensus        82 v~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~~~~~~~~i~~~~~~~~~e  153 (168)
T d1t5ia_          82 VATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISE  153 (168)
T ss_dssp             EESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEE
T ss_pred             eccccccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchHHHHHHHHHHHHHcCCccc
Confidence            999999999999999999999999999999999999999999999999999877888889999988866543

>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=3.2e-29  Score=199.59  Aligned_cols=152  Identities=34%  Similarity=0.558  Sum_probs=140.5

Q ss_pred             ccceEEEEEeChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCcc
Q 014486          261 HGLVQHYIKLSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKR  340 (423)
Q Consensus       261 ~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  340 (423)
                      .++.+.++.+...+|...+.++++.. +.++||||++++.++.+++.|+..|+.+..+|++++..+|..+++.|++|+.+
T Consensus         2 ~nI~~~~i~v~~~~K~~~L~~ll~~~-~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~   80 (155)
T d1hv8a2           2 ANIEQSYVEVNENERFEALCRLLKNK-EFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIR   80 (155)
T ss_dssp             SSSEEEEEECCGGGHHHHHHHHHCST-TCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSS
T ss_pred             CCeEEEEEEeChHHHHHHHHHHHccC-CCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccce
Confidence            34677888888999999999999765 46899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHhcchhh
Q 014486          341 ILVATDLVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMFLLIGS  414 (423)
Q Consensus       341 ili~T~~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  414 (423)
                      +||||+++++|+|+|++++||+|++|+|+..|+||+||+||.|+.|.+++|+++ .+...+..+++.++..+..
T Consensus        81 ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~-~d~~~~~~i~~~~~~~i~~  153 (155)
T d1hv8a2          81 ILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINR-REYKKLRYIERAMKLKIKK  153 (155)
T ss_dssp             EEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECT-TSHHHHHHHHHHHTCCCCC
T ss_pred             eeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEch-HHHHHHHHHHHHHCCCccc
Confidence            999999999999999999999999999999999999999999999999999986 5667788999999887654

>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=5.2e-28  Score=199.48  Aligned_cols=130  Identities=22%  Similarity=0.372  Sum_probs=121.5

Q ss_pred             eChHHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccc
Q 014486          270 LSELEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVG  349 (423)
Q Consensus       270 ~~~~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~  349 (423)
                      ....++...+..+++.....++||||++.+.++.++..|...++.+..+||+++..+|..+++.|++|+.+|||||++++
T Consensus        12 ~~~~~k~~~L~~~l~~~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~   91 (200)
T d1oywa3          12 MEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFG   91 (200)
T ss_dssp             EECSSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSC
T ss_pred             EcCCcHHHHHHHHHHhcCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhh
Confidence            34455778899999988889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccHH
Q 014486          350 RGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDSD  399 (423)
Q Consensus       350 ~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~  399 (423)
                      +|+|+|++++||+|++|.++..|+||+||+||.|++|.+++|+++.+...
T Consensus        92 ~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~~  141 (200)
T d1oywa3          92 MGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAW  141 (200)
T ss_dssp             TTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHH
T ss_pred             hccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHHH
Confidence            99999999999999999999999999999999999999999998754433

>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=99.94  E-value=1.7e-27  Score=199.33  Aligned_cols=182  Identities=15%  Similarity=0.231  Sum_probs=137.9

Q ss_pred             CCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHH
Q 014486           53 LKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICH  132 (423)
Q Consensus        53 l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~  132 (423)
                      +++.+...|.+.|+.+|+|+|+++++++++++++++++|||+|||++++++++......+   ++++++|+++|+.|+.+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~~~---~vl~l~P~~~L~~q~~~   86 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGG---KSLYVVPLRALAGEKYE   86 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTTC---CEEEEESSHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhccC---cceeecccHHHHHHHHH
Confidence            456788899999999999999999999999999999999999999999888887765443   79999999999999999


Q ss_pred             HHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHH-
Q 014486          133 EFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRD-  211 (423)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~-  211 (423)
                      .++++...  ...+....++......    ....+.++++||..+..++......+.++++||+||+|.+.++ ..... 
T Consensus        87 ~~~~~~~~--~~~v~~~~~~~~~~~~----~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~-~r~~~~  159 (202)
T d2p6ra3          87 SFKKWEKI--GLRIGISTGDYESRDE----HLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSE-KRGATL  159 (202)
T ss_dssp             HHTTTTTT--TCCEEEECSSCBCCSS----CSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCT-TTHHHH
T ss_pred             HHHHHhhc--cccceeeccCcccccc----cccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhccc-ccchHH
Confidence            99887654  3455555555443221    1123689999999999988888888889999999999998763 32222 


Q ss_pred             --HHHHHHhCCCCceEEEEeccCCccHHHHHHHhccC
Q 014486          212 --VQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQD  246 (423)
Q Consensus       212 --~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~  246 (423)
                        +.......++..|++++|||+++ ...+ ..++..
T Consensus       160 ~~~l~~i~~~~~~~~~l~lSATl~n-~~~~-~~~l~~  194 (202)
T d2p6ra3         160 EILVTKMRRMNKALRVIGLSATAPN-VTEI-AEWLDA  194 (202)
T ss_dssp             HHHHHHHHHHCTTCEEEEEECCCTT-HHHH-HHHTTC
T ss_pred             HHHHHHHHhcCCCCcEEEEcCCCCc-HHHH-HHHcCC
Confidence              22333445668899999999976 3434 344443

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.93  E-value=2.2e-26  Score=197.66  Aligned_cols=174  Identities=14%  Similarity=0.177  Sum_probs=126.5

Q ss_pred             HHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHH
Q 014486           58 LRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        58 ~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      .+++.+.++.+|+++|+.+++.++.|+++++.+|||+|||++++++++.....++   ++||++|+++|+.|++++++++
T Consensus        33 ~~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~~~---rvliv~Pt~~La~Q~~~~l~~~  109 (237)
T d1gkub1          33 FVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGK---RCYVIFPTSLLVIQAAETIRKY  109 (237)
T ss_dssp             HHHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTTSC---CEEEEESCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHhcC---eEEEEeccHHHHHHHHHHHHHH
Confidence            3556666888999999999999999999999999999999999998887766543   8999999999999999999998


Q ss_pred             hccCCCc----eEEEEEcCcchHHHHHHHhc-CCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHH
Q 014486          138 STYLPDI----KVAVFYGGVNIKIHKDLLKN-ECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDV  212 (423)
Q Consensus       138 ~~~~~~~----~~~~~~~~~~~~~~~~~~~~-~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~  212 (423)
                      .... ++    ......++.........+.. ..++|+|+||+.+.+.    ...+.++++||+||+|.++....-....
T Consensus       110 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~----~~~~~~~~~vVvDE~d~~l~~~~~~~~~  184 (237)
T d1gkub1         110 AEKA-GVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKH----YRELGHFDFIFVDDVDAILKASKNVDKL  184 (237)
T ss_dssp             HTTT-CCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHC----STTSCCCSEEEESCHHHHHTSTHHHHHH
T ss_pred             HHHc-CCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHh----hhhcCCCCEEEEEChhhhhhcccchhHH
Confidence            7654 33    23444444444433333322 3369999999987653    3356789999999999987521111111


Q ss_pred             HHH----------HHhCCCCceEEEEeccCCccHHHH
Q 014486          213 QEI----------FKMTPHDKQVMMFSATLSKEIRPV  239 (423)
Q Consensus       213 ~~~----------~~~~~~~~~~v~~SAT~~~~~~~~  239 (423)
                      ..+          ....+...|++++|||+++.....
T Consensus       185 ~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~  221 (237)
T d1gkub1         185 LHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAE  221 (237)
T ss_dssp             HHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTHH
T ss_pred             HHhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHHH
Confidence            111          112244668999999998765443

>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=5.8e-27  Score=196.90  Aligned_cols=188  Identities=15%  Similarity=0.150  Sum_probs=138.7

Q ss_pred             CcCCCCCHHHHHHHHhC-CCCCCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           48 FRDFLLKPELLRAIVDS-GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        48 ~~~~~l~~~~~~~l~~~-~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      .+.++|++...+.|++. ||..+||+|.+++++++.|+|+++++|||+|||++|.+|++....      ++++++|+++|
T Consensus         4 ~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~~~------~~~~v~P~~~L   77 (206)
T d1oywa2           4 AEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNG------LTVVVSPLISL   77 (206)
T ss_dssp             CCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHSSS------EEEEECSCHHH
T ss_pred             hhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhccC------ceEEeccchhh
Confidence            46678889999999987 999999999999999999999999999999999999999987643      89999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEEcCcc---hHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhh
Q 014486          127 AYQICHEFERFSTYLPDIKVAVFYGGVN---IKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKML  203 (423)
Q Consensus       127 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~  203 (423)
                      +.|+.+.++.+..     ..........   ..........+...++++||..+............+++++|+||+|.+.
T Consensus        78 ~~q~~~~l~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~  152 (206)
T d1oywa2          78 MKDQVDQLQANGV-----AAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCIS  152 (206)
T ss_dssp             HHHHHHHHHHTTC-----CEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGC
T ss_pred             hhhHHHHHHhhcc-----cccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeeeeeeeee
Confidence            9999999987642     2233322222   2222233344557999999998765333333456788999999999887


Q ss_pred             ccC-CcHH---HHHHHHHhCCCCceEEEEeccCCccHHHHH-HHh-ccCC
Q 014486          204 ESL-DMRR---DVQEIFKMTPHDKQVMMFSATLSKEIRPVC-KKF-MQDP  247 (423)
Q Consensus       204 ~~~-~~~~---~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~-~~~-~~~~  247 (423)
                      ++. .++.   .+..+...+ ++.|++++|||+++.+.+.+ +.+ +.+|
T Consensus       153 ~~~~~~~~~~~~~~~l~~~~-~~~~ii~lSATl~~~v~~di~~~L~l~~p  201 (206)
T d1oywa2         153 QWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDP  201 (206)
T ss_dssp             TTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSC
T ss_pred             ccccchHHHHHHHHHHHHhC-CCCceEEEEeCCCHHHHHHHHHHcCCCCC
Confidence            642 2222   223334444 46899999999998876544 443 4555

>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=1.9e-25  Score=186.91  Aligned_cols=165  Identities=17%  Similarity=0.225  Sum_probs=130.6

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      +|++||.+++..+. ++++++++|||+|||+++++++...+...+.  +++|++|+++|+.|+.+++.++.... +.++.
T Consensus         9 ~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~--~il~i~P~~~L~~q~~~~~~~~~~~~-~~~v~   84 (200)
T d1wp9a1           9 QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGG--KVLMLAPTKPLVLQHAESFRRLFNLP-PEKIV   84 (200)
T ss_dssp             CCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHSCS--CEEEECSSHHHHHHHHHHHHHHBCSC-GGGEE
T ss_pred             CCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhcCC--cEEEEcCchHHHHHHHHHHHHhhccc-cccee
Confidence            79999999998876 5679999999999999988877665543332  78999999999999999999987654 67788


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEE
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM  227 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~  227 (423)
                      ..+++.........+..  ++++++||+.+...+......+.++++||+||||.+... .....+...........++++
T Consensus        85 ~~~~~~~~~~~~~~~~~--~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~-~~~~~~~~~~~~~~~~~~~l~  161 (200)
T d1wp9a1          85 ALTGEKSPEERSKAWAR--AKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGN-YAYVFIAREYKRQAKNPLVIG  161 (200)
T ss_dssp             EECSCSCHHHHHHHHHH--CSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTT-CHHHHHHHHHHHHCSSCCEEE
T ss_pred             eeecccchhHHHHhhhc--ccccccccchhHHHHhhhhhhccccceEEEEehhhhhcc-hhHHHHHHHHHhcCCCCcEEE
Confidence            77787777666555554  489999999999988888888899999999999998763 333334444444455678999


Q ss_pred             EeccCCccHHHH
Q 014486          228 FSATLSKEIRPV  239 (423)
Q Consensus       228 ~SAT~~~~~~~~  239 (423)
                      +|||++......
T Consensus       162 ~SATp~~~~~~~  173 (200)
T d1wp9a1         162 LTASPGSTPEKI  173 (200)
T ss_dssp             EESCSCSSHHHH
T ss_pred             EEecCCCcHHHH
Confidence            999987655544

>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=2.2e-24  Score=170.59  Aligned_cols=117  Identities=21%  Similarity=0.345  Sum_probs=103.4

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCC
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMP  366 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~  366 (423)
                      .++++||||++++.++.++..|.+.|+++..+||++++.+|.+++++|++|+++|||+|+++++|+|+|++++||++++|
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi~~~~~  109 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDAD  109 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTT
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEEEeccc
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC-----cchhhhcccccCCCCCceEEEEEecCcccHHHHHHHH
Q 014486          367 DS-----ADTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVS  405 (423)
Q Consensus       367 ~s-----~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~  405 (423)
                      .+     ...|+|++||+||.|+ |.++++... ....+...++
T Consensus       110 ~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~-~~~~~~~~i~  151 (174)
T d1c4oa2         110 KEGFLRSERSLIQTIGRAARNAR-GEVWLYADR-VSEAMQRAIE  151 (174)
T ss_dssp             SCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSS-CCHHHHHHHH
T ss_pred             cccccchhHHHHHHhhhhhhcCC-CeeEEeecC-CCHHHHHHHH
Confidence            74     4679999999999876 666666643 4444444443

>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=1.1e-23  Score=169.68  Aligned_cols=115  Identities=21%  Similarity=0.374  Sum_probs=100.8

Q ss_pred             HHHHHHHhh-cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCC
Q 014486          278 KLNDLLDAL-DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIER  356 (423)
Q Consensus       278 ~l~~ll~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~  356 (423)
                      .+..+.+.. .+.++||||+++++++.++..|+..|+++..+||++++.+|..+++.|++|+.+|||||+++++|+|+|+
T Consensus        20 ll~~i~~~~~~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~   99 (181)
T d1t5la2          20 LIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPE   99 (181)
T ss_dssp             HHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTT
T ss_pred             HHHHHHHHHhcCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCC
Confidence            344443332 4578999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCEEEEccCCC-----CcchhhhcccccCCCCCceEEEEEec
Q 014486          357 VNIVINYDMPD-----SADTYLHRVGRAGRFGTKGLAITFVS  393 (423)
Q Consensus       357 ~~~vi~~~~~~-----s~~~~~Q~~GR~~R~g~~~~~~~~~~  393 (423)
                      +++||+|++|.     |..+|+||+||+||.|+. .++++..
T Consensus       100 v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~-~~~~~~~  140 (181)
T d1t5la2         100 VSLVAILDADKEGFLRSERSLIQTIGRAARNANG-HVIMYAD  140 (181)
T ss_dssp             EEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTC-EEEEECS
T ss_pred             CCEEEEecCCcccccccHHHHHHHHHhhccccCc-eeEeecc
Confidence            99999999996     678899999999999864 3444443

>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=99.87  E-value=1.1e-22  Score=156.00  Aligned_cols=103  Identities=25%  Similarity=0.416  Sum_probs=92.2

Q ss_pred             HhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEc
Q 014486          284 DALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINY  363 (423)
Q Consensus       284 ~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~  363 (423)
                      +....+++||||++++.++.+++.|+..|+.+..+|++++.       +.|++|+.++||||+++++|+| +++++||++
T Consensus        31 ~~~~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~-------~~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~  102 (138)
T d1jr6a_          31 EVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDV-------SVIPTNGDVVVVATDALMTGFT-GDFDSVIDC  102 (138)
T ss_dssp             HHHTTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCS-------CCCTTSSCEEEEESSSSCSSSC-CCBSEEEEC
T ss_pred             hhcCCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchh-------hhhhhhhcceeehhHHHHhccc-cccceEEEE
Confidence            44567899999999999999999999999999999999984       4588999999999999999999 999999985


Q ss_pred             c----CCCCcchhhhcccccCCCCCceEEEEEecCcc
Q 014486          364 D----MPDSADTYLHRVGRAGRFGTKGLAITFVSSAS  396 (423)
Q Consensus       364 ~----~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  396 (423)
                      +    +|.++..|+||+||+|| |++|. +.|+.+.+
T Consensus       103 ~~~~~~P~~~~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_         103 NTSDGKPQDAVSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             SEETTEECCHHHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             EecCCCCCCHHHHHhHhccccC-CCCcE-EEEEcCCC
Confidence            4    69999999999999999 99995 66777643

>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=99.84  E-value=3.8e-21  Score=169.38  Aligned_cols=118  Identities=25%  Similarity=0.380  Sum_probs=102.7

Q ss_pred             HHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcC--------CCCHHHHHHHHHhhhcCCccEEEEcCccccC
Q 014486          280 NDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHS--------GMSQEERLTRYKGFKEGNKRILVATDLVGRG  351 (423)
Q Consensus       280 ~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~--------~~~~~~r~~~~~~f~~~~~~ili~T~~~~~G  351 (423)
                      .+++....+.++||||++.+.++.+++.|...++++..++|        +++..+|..+++.|++|+++|||||+++++|
T Consensus       153 ~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~~~~~G  232 (286)
T d1wp9a2         153 REQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEG  232 (286)
T ss_dssp             HHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGG
T ss_pred             HHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEccceecc
Confidence            33444556789999999999999999999999999998876        4556688999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCcccH
Q 014486          352 IDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASDS  398 (423)
Q Consensus       352 ld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  398 (423)
                      +|+|++++||+|++|+++..|+||+||+||.+ +|.++.|+++....
T Consensus       233 ld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~~e  278 (286)
T d1wp9a2         233 LDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGTRD  278 (286)
T ss_dssp             GGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTSHH
T ss_pred             ccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCCHH
Confidence            99999999999999999999999999999975 68888888875443

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.83  E-value=1.2e-19  Score=150.92  Aligned_cols=174  Identities=19%  Similarity=0.188  Sum_probs=133.3

Q ss_pred             CCCHHHHHHHHhCCCCCCChhhhhccccccc----C--CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           52 LLKPELLRAIVDSGFEHPSEVQHECIPQAIL----G--MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        52 ~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~----~--~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      ..+....+.+.+.=-..+++-|..++..+..    +  .+.+++|.||||||.+|+.++...+..+.   ++++++|+..
T Consensus        39 ~~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~---qv~~l~Pt~~  115 (233)
T d2eyqa3          39 KHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHK---QVAVLVPTTL  115 (233)
T ss_dssp             CCCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTC---EEEEECSSHH
T ss_pred             CCCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCC---ceEEEccHHH
Confidence            3445666666654233799999999988764    2  35899999999999999998888886544   9999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchh
Q 014486          126 LAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM  202 (423)
Q Consensus       126 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~  202 (423)
                      |+.|+++.++++...+ ++++..+++........   ..+.++..+|+|+|...+.     ..+.+.++++||+||-|++
T Consensus       116 La~Q~~~~~~~~~~~~-~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~-----~~~~f~~LgLiIiDEeH~f  189 (233)
T d2eyqa3         116 LAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEHRF  189 (233)
T ss_dssp             HHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGGGS
T ss_pred             hHHHHHHHHHHHHhhC-CCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc-----cCCccccccceeeechhhh
Confidence            9999999999987776 67999999988765544   4566788899999987765     3567789999999999975


Q ss_pred             hccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHH
Q 014486          203 LESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVC  240 (423)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~  240 (423)
                      .    +...  ..+.....+..++++||||-++.....
T Consensus       190 g----~kQ~--~~l~~~~~~~~~l~~SATPiprtl~~~  221 (233)
T d2eyqa3         190 G----VRHK--ERIKAMRANVDILTLTATPIPRTLNMA  221 (233)
T ss_dssp             C----HHHH--HHHHHHHTTSEEEEEESSCCCHHHHHH
T ss_pred             h----hHHH--HHHHhhCCCCCEEEEecchhHHHHHHH
Confidence            3    3332  122223446789999999987765443

>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=99.83  E-value=4.1e-20  Score=156.77  Aligned_cols=166  Identities=23%  Similarity=0.214  Sum_probs=127.3

Q ss_pred             HHHHHhCCCCCCChhhhhccccccc----C--CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHH
Q 014486           58 LRAIVDSGFEHPSEVQHECIPQAIL----G--MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQIC  131 (423)
Q Consensus        58 ~~~l~~~~~~~~~~~Q~~~i~~~~~----~--~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  131 (423)
                      .+.+....| .+|+.|.+++..+..    +  .+.+++|.||||||.+|+.+++..+..+.   ++++++|+..|+.|++
T Consensus        74 ~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~---q~~~m~Pt~~La~Qh~  149 (264)
T d1gm5a3          74 EEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGF---QTAFMVPTSILAIQHY  149 (264)
T ss_dssp             HHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTS---CEEEECSCHHHHHHHH
T ss_pred             HHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhccc---ceeEEeehHhhhHHHH
Confidence            344445567 799999999988864    2  35799999999999999998887776544   8999999999999999


Q ss_pred             HHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCc
Q 014486          132 HEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDM  208 (423)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~  208 (423)
                      +.++++.... ++++..++|+.+..+..   ..+.+|.++|+|+|...+..     .+.+.++++||+||-|++.-.  .
T Consensus       150 ~~~~~~f~~~-~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~-----~~~f~~LglviiDEqH~fgv~--Q  221 (264)
T d1gm5a3         150 RRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVK--Q  221 (264)
T ss_dssp             HHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC------
T ss_pred             HHHHHhhhhc-cccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC-----CCCccccceeeeccccccchh--h
Confidence            9999998776 78999999988765544   44567889999999877653     456788999999999987431  1


Q ss_pred             HHHHHHHHHhCCCCceEEEEeccCCccHHHH
Q 014486          209 RRDVQEIFKMTPHDKQVMMFSATLSKEIRPV  239 (423)
Q Consensus       209 ~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~  239 (423)
                      +    ..+......+.++++||||-+.....
T Consensus       222 r----~~l~~~~~~~~~l~~SATPiprtl~~  248 (264)
T d1gm5a3         222 R----EALMNKGKMVDTLVMSATPIPRSMAL  248 (264)
T ss_dssp             -----CCCCSSSSCCCEEEEESSCCCHHHHH
T ss_pred             H----HHHHHhCcCCCEEEEECCCCHHHHHH
Confidence            1    11222334678999999988766544

>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=99.82  E-value=4e-20  Score=154.02  Aligned_cols=136  Identities=19%  Similarity=0.169  Sum_probs=101.4

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      +|++||++++..++.+++.++.+|||+|||++++..+... .     .++||+||+++|+.||.++++.+..    ..+.
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~-~-----~~~Liv~p~~~L~~q~~~~~~~~~~----~~~~  139 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL-S-----TPTLIVVPTLALAEQWKERLGIFGE----EYVG  139 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS-C-----SCEEEEESSHHHHHHHHHHHGGGCG----GGEE
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHHHHh-c-----CceeEEEcccchHHHHHHHHHhhcc----cchh
Confidence            6999999999999999999999999999999876544333 1     2789999999999999999987642    2344


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEE
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM  227 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~  227 (423)
                      ...|+..          ....++++|++.+......   ...++++||+||||++.. ..    +..+...++ ...+++
T Consensus       140 ~~~~~~~----------~~~~i~i~t~~~~~~~~~~---~~~~~~lvIiDEaH~~~a-~~----~~~i~~~~~-~~~~lg  200 (206)
T d2fz4a1         140 EFSGRIK----------ELKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPA-ES----YVQIAQMSI-APFRLG  200 (206)
T ss_dssp             EESSSCB----------CCCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCT-TT----HHHHHHTCC-CSEEEE
T ss_pred             hcccccc----------cccccccceehhhhhhhHh---hCCcCCEEEEECCeeCCc-HH----HHHHHhccC-CCcEEE
Confidence            4444322          2248999999988765443   235688999999998864 22    344455443 445789


Q ss_pred             EeccC
Q 014486          228 FSATL  232 (423)
Q Consensus       228 ~SAT~  232 (423)
                      ||||+
T Consensus       201 LTATl  205 (206)
T d2fz4a1         201 LTATF  205 (206)
T ss_dssp             EEESC
T ss_pred             EecCC
Confidence            99997

>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=99.81  E-value=1e-20  Score=164.85  Aligned_cols=153  Identities=15%  Similarity=0.193  Sum_probs=111.1

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      .||+||.+++..++.++..++.+|||+|||+++...+....... . .++||++|+++|+.||++++.++.... ...+.
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~~-~-~k~Liivp~~~Lv~Q~~~~f~~~~~~~-~~~~~  189 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY-E-GKILIIVPTTALTTQMADDFVDYRLFS-HAMIK  189 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC-S-SEEEEECSSHHHHHHHHHHHHHHTSCC-GGGEE
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhcc-c-ceEEEEEcCchhHHHHHHHHHHhhccc-cccce
Confidence            79999999999999999999999999999998765443322222 2 289999999999999999999886443 33455


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEE
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMM  227 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~  227 (423)
                      ...+|......   . .....++++|++.+....   ...+.++++||+||||++.     ...+..++..+.+....++
T Consensus       190 ~~~~g~~~~~~---~-~~~~~i~i~t~qs~~~~~---~~~~~~f~~VIvDEaH~~~-----a~~~~~il~~~~~~~~rlG  257 (282)
T d1rifa_         190 KIGGGASKDDK---Y-KNDAPVVVGTWQTVVKQP---KEWFSQFGMMMNDECHLAT-----GKSISSIISGLNNCMFKFG  257 (282)
T ss_dssp             ECSTTCSSTTC---C-CTTCSEEEECHHHHTTSC---GGGGGGEEEEEEETGGGCC-----HHHHHHHTTTCTTCCEEEE
T ss_pred             eecceeccccc---c-cccceEEEEeeehhhhhc---ccccCCCCEEEEECCCCCC-----chhHHHHHHhccCCCeEEE
Confidence            55555432211   1 122589999998876432   2345789999999999764     3455667666665566799


Q ss_pred             EeccCCcc
Q 014486          228 FSATLSKE  235 (423)
Q Consensus       228 ~SAT~~~~  235 (423)
                      +|||++..
T Consensus       258 lTaT~~~~  265 (282)
T d1rifa_         258 LSGSLRDG  265 (282)
T ss_dssp             ECSSCCTT
T ss_pred             EEeecCCC
Confidence            99998754

>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=1.1e-20  Score=156.94  Aligned_cols=108  Identities=27%  Similarity=0.443  Sum_probs=99.5

Q ss_pred             HHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCC
Q 014486          274 EKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGID  353 (423)
Q Consensus       274 ~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld  353 (423)
                      .|...+.++++..++.++||||++.+.++.+.+.|.     +..+||+++..+|..+++.|++|+.+|||+|+++++|+|
T Consensus        79 ~K~~~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l~-----~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gid  153 (200)
T d2fwra1          79 NKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGID  153 (200)
T ss_dssp             HHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSC
T ss_pred             HHHHHHHHHHHhCCCCcEEEEeCcHHHHHHHHhhcC-----cceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcccC
Confidence            467788899999888999999999999999988774     345799999999999999999999999999999999999


Q ss_pred             CCCCCEEEEccCCCCcchhhhcccccCCCCCce
Q 014486          354 IERVNIVINYDMPDSADTYLHRVGRAGRFGTKG  386 (423)
Q Consensus       354 ~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~  386 (423)
                      +|.+++||++++|+|+..+.||+||++|.|+.+
T Consensus       154 l~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~k  186 (200)
T d2fwra1         154 VPDANVGVIMSGSGSAREYIQRLGRILRPSKGK  186 (200)
T ss_dssp             SCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTT
T ss_pred             CCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCCC
Confidence            999999999999999999999999999998743

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.79  E-value=7.9e-20  Score=150.64  Aligned_cols=119  Identities=22%  Similarity=0.357  Sum_probs=99.0

Q ss_pred             HHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhC------------------------------CCCeEEEcCCCCHHH
Q 014486          277 RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVEC------------------------------NFPSICIHSGMSQEE  326 (423)
Q Consensus       277 ~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~------------------------------~~~~~~~~~~~~~~~  326 (423)
                      ..+.++++.  ++++||||++++.+..++..|...                              ...+..+|++|++.+
T Consensus        31 ~l~~~~i~~--~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~  108 (201)
T d2p6ra4          31 ELVEECVAE--NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQ  108 (201)
T ss_dssp             HHHHHHHHT--TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHH
T ss_pred             HHHHHHHHc--CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhh
Confidence            344454443  578999999999988887776541                              123678999999999


Q ss_pred             HHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEE-------ccCCCCcchhhhcccccCCCCC--ceEEEEEecCccc
Q 014486          327 RLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVIN-------YDMPDSADTYLHRVGRAGRFGT--KGLAITFVSSASD  397 (423)
Q Consensus       327 r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~-------~~~~~s~~~~~Q~~GR~~R~g~--~~~~~~~~~~~~~  397 (423)
                      |..+.+.|++|.++|||||+++++|+|+|..++||.       ++.|.++.+|.||+|||||.|.  .|.+++++.+.+.
T Consensus       109 r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~~~  188 (201)
T d2p6ra4         109 RRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDR  188 (201)
T ss_dssp             HHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGGH
T ss_pred             HHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCCCh
Confidence            999999999999999999999999999999998886       6678899999999999999985  6888887766443

>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=99.76  E-value=4e-19  Score=138.99  Aligned_cols=136  Identities=17%  Similarity=0.150  Sum_probs=88.7

Q ss_pred             ccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHH
Q 014486           81 ILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKD  160 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (423)
                      ..|+++++.+|||+|||.+++..++......+  .++++++|++.++.|+.+.+...       ............    
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~--~~vli~~p~~~l~~q~~~~~~~~-------~~~~~~~~~~~~----   71 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECARRR--LRTLVLAPTRVVLSEMKEAFHGL-------DVKFHTQAFSAH----   71 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHTT--CCEEEEESSHHHHHHHHHHTTTS-------CEEEESSCCCCC----
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhhcC--ceeeeeecchhHHHHHHHHhhhh-------hhhhcccccccc----
Confidence            34788999999999999988776666554433  38999999999999987665322       222221111100    


Q ss_pred             HHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCC
Q 014486          161 LLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLS  233 (423)
Q Consensus       161 ~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~  233 (423)
                        ......+.++|...+.... .....+.++++||+||||.+.........+...... .++.++++||||||
T Consensus        72 --~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1          72 --GSGREVIDAMCHATLTYRM-LEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATPP  140 (140)
T ss_dssp             --CCSSCCEEEEEHHHHHHHH-TSSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             --cccccchhhhhHHHHHHHH-hccccccceeEEEEccccccChhhHHHHHHHHHHhh-CCCCCEEEEEcCCC
Confidence              0112367778877776644 335567899999999999874421111222222333 35789999999997

>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=99.74  E-value=1.3e-19  Score=152.84  Aligned_cols=108  Identities=17%  Similarity=0.215  Sum_probs=94.2

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHH----------HHHHHhhhcCCccEEEEcCcccc---CCC
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEER----------LTRYKGFKEGNKRILVATDLVGR---GID  353 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r----------~~~~~~f~~~~~~ili~T~~~~~---Gld  353 (423)
                      .++++||||++++.++.+++.|++.|+++..+|+++++..|          ..++..|..|+.+++|+|+++++   |+|
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            46899999999999999999999999999999999998876          45678899999999999999888   678


Q ss_pred             CCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCc
Q 014486          354 IERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       354 ~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      ++.+.+||+++.|.|+..|+||+||+|| |++|...++....
T Consensus       115 id~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~~t  155 (299)
T d1a1va2         115 LDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPGE  155 (299)
T ss_dssp             CSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCSCC
T ss_pred             CCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEecCC
Confidence            8888899999999999999999999999 8888776655443

>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=99.73  E-value=3e-19  Score=145.75  Aligned_cols=121  Identities=22%  Similarity=0.332  Sum_probs=95.0

Q ss_pred             HHHHHHHHh-h-cCCcEEEEEcChhhHHH--------HHHHHHhC---CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEE
Q 014486          277 RKLNDLLDA-L-DFNQVVIFVKSVSRAAE--------LNKLLVEC---NFPSICIHSGMSQEERLTRYKGFKEGNKRILV  343 (423)
Q Consensus       277 ~~l~~ll~~-~-~~~~~ivf~~~~~~~~~--------l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili  343 (423)
                      ..+.+.++. + .++++.++||.++..+.        ..+.|.+.   ++++..+||.|++.+|.+++.+|++|+++|||
T Consensus        16 ~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLV   95 (206)
T d1gm5a4          16 NEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILV   95 (206)
T ss_dssp             HHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCC
T ss_pred             HHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEE
Confidence            344444433 2 45678888987765443        33444433   56677899999999999999999999999999


Q ss_pred             EcCccccCCCCCCCCEEEEccCCC-CcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          344 ATDLVGRGIDIERVNIVINYDMPD-SADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       344 ~T~~~~~Gld~~~~~~vi~~~~~~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      ||.++++|+|+|+++++|+++.|. ..+++.|..||+||.|++|.|++++++..+
T Consensus        96 aTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~~  150 (206)
T d1gm5a4          96 STTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGE  150 (206)
T ss_dssp             CSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCH
T ss_pred             EehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeeccccc
Confidence            999999999999999999999886 788999999999999999999999876443

>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=99.73  E-value=8.4e-18  Score=130.35  Aligned_cols=127  Identities=18%  Similarity=0.095  Sum_probs=86.4

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL  162 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (423)
                      .+..++.+|||+|||+++...+...      +.+++|++|++.|+.|+.+.+.++....    .....++....      
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~~~~------~~~vli~~P~~~l~~q~~~~~~~~~~~~----~~~~~~~~~~~------   71 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAHGVD----PNIRTGVRTIT------   71 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHHHTT------TCCEEEEESCHHHHHHHHHHHHHHHSCC----CEEECSSCEEC------
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHc------CCcEEEEcChHHHHHHHHHHHHHHhhcc----ccccccccccc------
Confidence            3558999999999998764433321      2289999999999999999998876432    22333332211      


Q ss_pred             hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCC--CCceEEEEeccC
Q 014486          163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTP--HDKQVMMFSATL  232 (423)
Q Consensus       163 ~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~--~~~~~v~~SAT~  232 (423)
                        ....+.++|.+.+...   ....+.++++||+||+|.+..  .....+..+.+.+.  ...+++++||||
T Consensus        72 --~~~~~~~~~~~~~~~~---~~~~~~~~~~vIiDE~H~~~~--~~~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1          72 --TGSPITYSTYGKFLAD---GGCSGGAYDIIICDECHSTDA--TSILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             --CCCSEEEEEHHHHHHT---TGGGGCCCSEEEEETTTCCSH--HHHHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             --cccceEEEeeeeeccc---cchhhhcCCEEEEecccccCH--HHHHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence              1137889998876643   334567899999999998743  23334555555443  456799999996

>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=99.73  E-value=6.2e-17  Score=130.33  Aligned_cols=109  Identities=21%  Similarity=0.211  Sum_probs=101.1

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhC--CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEcc
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVEC--NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYD  364 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~  364 (423)
                      .++++-+.||..+..+.+.+.+++.  +.++..+||.|++.++..++.+|.+|+++|||||.+++.|+|+|+++++|..+
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            5689999999999999999998874  67899999999999999999999999999999999999999999999999988


Q ss_pred             CCC-CcchhhhcccccCCCCCceEEEEEecCc
Q 014486          365 MPD-SADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       365 ~~~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      ... ..+++.|..||+||.+.++.|++++.+.
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            775 8999999999999999999999998653

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.71  E-value=2.3e-19  Score=154.09  Aligned_cols=112  Identities=17%  Similarity=0.287  Sum_probs=96.1

Q ss_pred             HHHHHHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEc----Ccc
Q 014486          273 LEKNRKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVAT----DLV  348 (423)
Q Consensus       273 ~~~~~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T----~~~  348 (423)
                      .++...+..+++... .++||||++++.++.+++.|...      +||++++.+|..++++|++|+++|||||    +.+
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            445667788887654 67999999999999999999863      7999999999999999999999999999    678


Q ss_pred             ccCCCCCC-CCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCc
Q 014486          349 GRGIDIER-VNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSA  395 (423)
Q Consensus       349 ~~Gld~~~-~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  395 (423)
                      ++|+|+|+ +++||+|++|+    |.|++||+||.|+.+.+++++...
T Consensus        84 ~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~  127 (248)
T d1gkub2          84 VRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYR  127 (248)
T ss_dssp             -CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTS
T ss_pred             hhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHh
Confidence            99999996 99999999995    889999999999998888777653

>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=99.70  E-value=1.6e-16  Score=141.55  Aligned_cols=138  Identities=17%  Similarity=0.190  Sum_probs=115.6

Q ss_pred             HHHHHHHHHHHHh---hcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCcc---EEEEcC
Q 014486          273 LEKNRKLNDLLDA---LDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKR---ILVATD  346 (423)
Q Consensus       273 ~~~~~~l~~ll~~---~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~---ili~T~  346 (423)
                      ..|...+..++..   .+++|+|||++.....+.+.+.|...|+++..++|.++..+|..+++.|+++...   +|++|.
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            4566666666653   4578999999999999999999999999999999999999999999999987543   677899


Q ss_pred             ccccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEEEE--Eec-CcccHHHHHHHHHHHhc
Q 014486          347 LVGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAIT--FVS-SASDSDILNQVSKFMFL  410 (423)
Q Consensus       347 ~~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~--~~~-~~~~~~~~~~~~~~~~~  410 (423)
                      +++.|+|+..+++||+|+++|++..+.|++||++|.||+..|.+  ++. ...+..+++...++.++
T Consensus       180 agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~TiEe~i~~~~~~K~~l  246 (346)
T d1z3ix1         180 AGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKILQRQAHKKAL  246 (346)
T ss_dssp             GSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSHHHHHHHHHHHHHHT
T ss_pred             hhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEEEEEeCCCHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999998865543  333 34556666666666553

>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=99.64  E-value=1.1e-15  Score=130.58  Aligned_cols=136  Identities=16%  Similarity=0.183  Sum_probs=97.3

Q ss_pred             HHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhC-CCCeEEEcCCCCHHHHHHHHHhhhcCC-ccEEE-EcCc
Q 014486          273 LEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVEC-NFPSICIHSGMSQEERLTRYKGFKEGN-KRILV-ATDL  347 (423)
Q Consensus       273 ~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~ili-~T~~  347 (423)
                      ..|...+.+++...  +++++||||+.....+.+...+... +..+..+||+++..+|..+++.|.++. ..+++ ++.+
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  5679999999999999998888654 888899999999999999999998764 56665 5689


Q ss_pred             cccCCCCCCCCEEEEccCCCCcchhhhcccccCCCCCceEE--EEEecCc-ccHHHHHHHHHHH
Q 014486          348 VGRGIDIERVNIVINYDMPDSADTYLHRVGRAGRFGTKGLA--ITFVSSA-SDSDILNQVSKFM  408 (423)
Q Consensus       348 ~~~Gld~~~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~--~~~~~~~-~~~~~~~~~~~~~  408 (423)
                      ++.|+|++.+++||++++||++..+.|+.||++|.||...|  +.++... .+..++..+.++.
T Consensus       148 ~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~Tiee~i~~~~~~K~  211 (244)
T d1z5za1         148 GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKR  211 (244)
T ss_dssp             TCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTSHHHHHHHHHHHCH
T ss_pred             cccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999986544  4344443 4555555555444

>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=99.60  E-value=9.4e-15  Score=128.59  Aligned_cols=158  Identities=16%  Similarity=0.150  Sum_probs=102.0

Q ss_pred             CCChhhhhcccccc---------cCCceEEEccCCCcchhHHHHHHhhccCC----CCCCeEEEEEecChHHHHHHHHHH
Q 014486           68 HPSEVQHECIPQAI---------LGMDVICQAKSGMGKTAVFVLSTLQQTEP----NPGQVTALVLCHTRELAYQICHEF  134 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~---------~~~~~ii~~~tGsGKT~~~~~~~~~~~~~----~~~~~~~lil~P~~~L~~q~~~~~  134 (423)
                      .++|||.+++..+.         .+..+|++.++|+|||++.+..+......    .+....+|||||. .|..||.+++
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~-sl~~qW~~Ei  133 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccc-hhhHHHHHHH
Confidence            68999999997653         24569999999999998654333222211    1122368999997 5889999999


Q ss_pred             HHHhccCCCceEEEEEcCcchHHHHHH--H-hc----CCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCC
Q 014486          135 ERFSTYLPDIKVAVFYGGVNIKIHKDL--L-KN----ECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLD  207 (423)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--~-~~----~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~  207 (423)
                      .++...  ...+..++++.........  . ..    ...+++++|++.+.....  .+...++++||+||+|.+.+. .
T Consensus       134 ~k~~~~--~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~--~l~~~~~~~vI~DEaH~ikn~-~  208 (298)
T d1z3ix2         134 GKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKNS-D  208 (298)
T ss_dssp             HHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCTT-C
T ss_pred             HhhcCC--ceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchh--cccccceeeeecccccccccc-c
Confidence            998764  3455556665543322221  1 11    234799999998875433  233356789999999999762 2


Q ss_pred             cHHHHHHHHHhCCCCceEEEEeccCCc
Q 014486          208 MRRDVQEIFKMTPHDKQVMMFSATLSK  234 (423)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~v~~SAT~~~  234 (423)
                       ......+.. + +....+++||||-.
T Consensus       209 -s~~~~a~~~-l-~~~~rllLTGTPi~  232 (298)
T d1z3ix2         209 -NQTYLALNS-M-NAQRRVLISGTPIQ  232 (298)
T ss_dssp             -HHHHHHHHH-H-CCSEEEEECSSCSG
T ss_pred             -chhhhhhhc-c-ccceeeeecchHHh
Confidence             222222222 2 34557999999854

>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=99.50  E-value=1e-14  Score=123.32  Aligned_cols=149  Identities=17%  Similarity=0.190  Sum_probs=97.3

Q ss_pred             CCChhhhhccccccc----CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCC
Q 014486           68 HPSEVQHECIPQAIL----GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPD  143 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~  143 (423)
                      .|+|||.+++..+..    +..++++.++|.|||++++..+......... .++||+||. .+..||.+++.++...   
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~~~~~~~~~-~~~LIv~p~-~l~~~W~~e~~~~~~~---   86 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENEL-TPSLVICPL-SVLKNWEEELSKFAPH---   86 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTTCC-SSEEEEECS-TTHHHHHHHHHHHCTT---
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhhhhhhcccc-cccceecch-hhhhHHHHHHHhhccc---
Confidence            689999999976643    4568999999999999876544443333332 378999995 6789999999888643   


Q ss_pred             ceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCc
Q 014486          144 IKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDK  223 (423)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~  223 (423)
                      ..+...........      ...++|+++|++.+.....   +.-..+.+||+||+|.+.+. ... .. .....+. ..
T Consensus        87 ~~~~~~~~~~~~~~------~~~~~vvi~~~~~~~~~~~---l~~~~~~~vI~DEah~~k~~-~s~-~~-~~~~~l~-a~  153 (230)
T d1z63a1          87 LRFAVFHEDRSKIK------LEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNP-QTK-IF-KAVKELK-SK  153 (230)
T ss_dssp             SCEEECSSSTTSCC------GGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCT-TSH-HH-HHHHTSC-EE
T ss_pred             ccceeeccccchhh------ccCcCEEEeeHHHHHhHHH---HhcccceEEEEEhhhccccc-chh-hh-hhhhhhc-cc
Confidence            34444333221111      1125999999998764322   11235678999999999763 222 22 2233333 45


Q ss_pred             eEEEEeccCCc
Q 014486          224 QVMMFSATLSK  234 (423)
Q Consensus       224 ~~v~~SAT~~~  234 (423)
                      ..+++||||-.
T Consensus       154 ~r~~LTgTPi~  164 (230)
T d1z63a1         154 YRIALTGTPIE  164 (230)
T ss_dssp             EEEEECSSCST
T ss_pred             eEEEEecchHH
Confidence            57999999853

>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=99.48  E-value=4.3e-14  Score=121.88  Aligned_cols=101  Identities=20%  Similarity=0.235  Sum_probs=80.0

Q ss_pred             CCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCCCCEEEEccCC-
Q 014486          288 FNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIERVNIVINYDMP-  366 (423)
Q Consensus       288 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~~~~vi~~~~~-  366 (423)
                      +++++|||++...++.+++.|++.|.++..+||.+...+++    .|.+++.++||||+++++|+|+ ++.+||+.+.+ 
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            58999999999999999999999999999999999988755    4678999999999999999999 59999976642 


Q ss_pred             ------------------CCcchhhhcccccCCCCCceEEEEEec
Q 014486          367 ------------------DSADTYLHRVGRAGRFGTKGLAITFVS  393 (423)
Q Consensus       367 ------------------~s~~~~~Q~~GR~~R~g~~~~~~~~~~  393 (423)
                                        .|.++..||.||+||.+....++.++.
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         111 KPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             EEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             ceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence                              255667899999999865544444554

>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=99.42  E-value=3.3e-12  Score=99.03  Aligned_cols=127  Identities=19%  Similarity=0.219  Sum_probs=100.6

Q ss_pred             EeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcC
Q 014486          269 KLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD  346 (423)
Q Consensus       269 ~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~  346 (423)
                      .....+|...+.+-+...  .+.++||++.+++.++.+++.|++.+++..+++......+-.  +-...-....|.|||+
T Consensus        13 f~T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~--II~~Ag~~g~VtIATN   90 (175)
T d1tf5a4          13 YRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQ--IIEEAGQKGAVTIATN   90 (175)
T ss_dssp             ESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHH--HHTTTTSTTCEEEEET
T ss_pred             EcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHH--HHHhccCCCceeehhh
Confidence            345566766665555332  468999999999999999999999999999999876543333  3333333446999999


Q ss_pred             ccccCCCCC--------CCCEEEEccCCCCcchhhhcccccCCCCCceEEEEEecCccc
Q 014486          347 LVGRGIDIE--------RVNIVINYDMPDSADTYLHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       347 ~~~~Gld~~--------~~~~vi~~~~~~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      ++++|.|+.        +--|||....|.|.....|..||+||.|.+|....|++..++
T Consensus        91 mAGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD~  149 (175)
T d1tf5a4          91 MAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  149 (175)
T ss_dssp             TSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             HHHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCHH
Confidence            999999985        344799999999999999999999999999999999986554

>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=99.15  E-value=2.8e-10  Score=93.87  Aligned_cols=168  Identities=17%  Similarity=0.194  Sum_probs=124.7

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEE
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVA  147 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  147 (423)
                      +|++.|--+--.+..|  -|..+.||-|||+++.+|+......++   .+-|++.+.-||..=++++..+...+ ++++.
T Consensus        80 RhyDVQLiGgi~L~~G--~iaem~TGEGKTL~a~l~a~l~al~g~---~vhvvTvNdyLA~RDae~m~~iy~~l-Glsvg  153 (273)
T d1tf5a3          80 FPFKVQLMGGVALHDG--NIAEMKTGEGKTLTSTLPVYLNALTGK---GVHVVTVNEYLASRDAEQMGKIFEFL-GLTVG  153 (273)
T ss_dssp             CCCHHHHHHHHHHHTT--SEEECCTTSCHHHHHHHHHHHHHTTSS---CEEEEESSHHHHHHHHHHHHHHHHHT-TCCEE
T ss_pred             EEehhHHHHHHHHHhh--hheeecCCCcchhHHHHHHHHHHhcCC---CceEEecCccccchhhhHHhHHHHHc-CCCcc
Confidence            6777777665555554  699999999999999998888777665   67888889999999999999998888 99999


Q ss_pred             EEEcCcchHHHHHHHhcCCCcEEEechHHH-HHHHhcCCC------CCCCccEEEEcCcchhhccCCc------------
Q 014486          148 VFYGGVNIKIHKDLLKNECPQIVVGTPGRI-LALARDKDL------SLKNVRHFILDECDKMLESLDM------------  208 (423)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l-~~~~~~~~~------~~~~~~~vVvDE~h~~~~~~~~------------  208 (423)
                      +...+.........+.   .+|+++|...| +++++.+..      ....+.+.||||+|.++-+...            
T Consensus       154 ~~~~~~~~~~r~~~Y~---~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDeartpliisg~~~~~  230 (273)
T d1tf5a3         154 LNLNSMSKDEKREAYA---ADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQSMTL  230 (273)
T ss_dssp             ECCTTSCHHHHHHHHH---SSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEEEEE
T ss_pred             ccccccCHHHHHHHhh---CCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhccCCceEeccCccch
Confidence            9988777666555554   49999999877 345554322      2466889999999988743111            


Q ss_pred             -HHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhccCC
Q 014486          209 -RRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFMQDP  247 (423)
Q Consensus       209 -~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~~~~  247 (423)
                       .-.++.+++..   .++.+||+|...+...+.+.+....
T Consensus       231 a~it~q~~f~~y---~~l~gmtgta~~~~~e~~~iy~l~v  267 (273)
T d1tf5a3         231 ATITFQNYFRMY---EKLAGMTGTAKTEEEEFRNIYNMQV  267 (273)
T ss_dssp             EEEEHHHHHTTS---SEEEEEESCCGGGHHHHHHHHCCCE
T ss_pred             hhhhHHHHHHHH---HHHhCCccccHHHHHHHHhccCCce
Confidence             01244555544   4789999999887777766665443

>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=98.87  E-value=2.8e-08  Score=78.04  Aligned_cols=127  Identities=24%  Similarity=0.268  Sum_probs=97.5

Q ss_pred             EEeChHHHHHHHHHHHHhh--cCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCC-ccEEEE
Q 014486          268 IKLSELEKNRKLNDLLDAL--DFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGN-KRILVA  344 (423)
Q Consensus       268 ~~~~~~~~~~~l~~ll~~~--~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~ili~  344 (423)
                      +......|...+.+-+...  .+.|+||-+.+++..+.+.+.|.+.+++..+++......+ ..++.  ..|. ..|-||
T Consensus        12 Vy~T~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herE-AeIIA--qAG~~GaVTIA   88 (219)
T d1nkta4          12 IYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQE-ATIIA--VAGRRGGVTVA   88 (219)
T ss_dssp             EESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHH-HHHHH--TTTSTTCEEEE
T ss_pred             EEcCHHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHH-HHHHH--hcccCCcEEee
Confidence            3345566766666555433  5689999999999999999999999999999999754322 33333  2344 469999


Q ss_pred             cCccccCCCCCC----------------------------------------------------CCEEEEccCCCCcchh
Q 014486          345 TDLVGRGIDIER----------------------------------------------------VNIVINYDMPDSADTY  372 (423)
Q Consensus       345 T~~~~~Gld~~~----------------------------------------------------~~~vi~~~~~~s~~~~  372 (423)
                      |+++++|.|+.=                                                    --+||-.....|-.--
T Consensus        89 TNMAGRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRID  168 (219)
T d1nkta4          89 TNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRID  168 (219)
T ss_dssp             ETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHH
T ss_pred             ccccCCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEecccccccccc
Confidence            999999999831                                                    2357777777787788


Q ss_pred             hhcccccCCCCCceEEEEEecCccc
Q 014486          373 LHRVGRAGRFGTKGLAITFVSSASD  397 (423)
Q Consensus       373 ~Q~~GR~~R~g~~~~~~~~~~~~~~  397 (423)
                      .|-.||+||.|.+|....|++-.++
T Consensus       169 nQLRGRsGRQGDPGsSrFflSLeDd  193 (219)
T d1nkta4         169 NQLRGRSGRQGDPGESRFYLSLGDE  193 (219)
T ss_dssp             HHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             ccccccccccCCCccceeEEeccHH
Confidence            8999999999999999999986444

>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=98.30  E-value=1.4e-06  Score=76.84  Aligned_cols=148  Identities=13%  Similarity=0.114  Sum_probs=84.2

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHH--HHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCce
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVL--STLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIK  145 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~--~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~  145 (423)
                      ...+.|+.|+...+.++-++|.||+|+|||.+..-  ..+...... .+.++++++||..-+..+.+.........+...
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~-~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~~~~  226 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADG-ERCRIRLAAPTGKAAARLTESLGKALRQLPLTD  226 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSS-CCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCS
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHHhc-cCCeEEEecCcHHHHHHHHHHHHHHHhhcCchh
Confidence            45678999999999888899999999999986432  223332222 233899999999888887776654433221100


Q ss_pred             EEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceE
Q 014486          146 VAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQV  225 (423)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~  225 (423)
                      ........    ..    .....++-.++..  ..+.........+++|||||+-.+.     ...+..+...++...++
T Consensus       227 ~~~~~~~~----~~----~t~~~ll~~~~~~--~~~~~~~~~~l~~d~lIIDEaSmv~-----~~l~~~ll~~~~~~~~l  291 (359)
T d1w36d1         227 EQKKRIPE----DA----STLHRLLGAQPGS--QRLRHHAGNPLHLDVLVVDEASMID-----LPMMSRLIDALPDHARV  291 (359)
T ss_dssp             CCCCSCSC----CC----BTTTSCC-------------CTTSCCSCSEEEECSGGGCB-----HHHHHHHHHTCCTTCEE
T ss_pred             hhhhhhhh----hh----hHHHHHHhhhhcc--hHHHHhhhcccccceeeehhhhccC-----HHHHHHHHHHhcCCCEE
Confidence            00000000    00    0000111111110  1112223344568899999998653     34566777888888888


Q ss_pred             EEEecc
Q 014486          226 MMFSAT  231 (423)
Q Consensus       226 v~~SAT  231 (423)
                      |++.=.
T Consensus       292 ILvGD~  297 (359)
T d1w36d1         292 IFLGDR  297 (359)
T ss_dssp             EEEECT
T ss_pred             EEECCh
Confidence            877543

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=97.83  E-value=6.7e-06  Score=71.29  Aligned_cols=69  Identities=13%  Similarity=0.056  Sum_probs=50.5

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCC-CCCCeEEEEEecChHHHHHHHHHHHHHh
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP-NPGQVTALVLCHTRELAYQICHEFERFS  138 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q~~~~~~~~~  138 (423)
                      +|+|-|++++.+  ....++|.|+.|||||.+.+--+...+.. .....+++++++|++++..+.+.+.+..
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            478999999975  34569999999999998765433332221 1122379999999999999888887654

>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=97.68  E-value=2.9e-05  Score=67.54  Aligned_cols=69  Identities=17%  Similarity=0.194  Sum_probs=52.0

Q ss_pred             CCChhhhhcccccccCCceEEEccCCCcchhHHHHHHhhccCCCC-CCeEEEEEecChHHHHHHHHHHHHHh
Q 014486           68 HPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEPNP-GQVTALVLCHTRELAYQICHEFERFS  138 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~-~~~~~lil~P~~~L~~q~~~~~~~~~  138 (423)
                      .+++-|++++.+.  +..++|.|+.|||||.+.+-.+...+.... .+.+++++++++..+..+...+....
T Consensus        11 ~L~~eQ~~~v~~~--~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~~   80 (318)
T d1pjra1          11 HLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLL   80 (318)
T ss_dssp             TSCHHHHHHHHCC--SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhCC--CCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhhc
Confidence            4889999999863  456999999999999887654444333221 22379999999999999988887654

>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=97.40  E-value=0.0001  Score=59.49  Aligned_cols=42  Identities=5%  Similarity=0.158  Sum_probs=30.5

Q ss_pred             CCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      ....+++|+||+|.+..  .....+.++++.-++...++++|-.
T Consensus       106 ~~~~kviIide~d~l~~--~a~n~Llk~lEep~~~~~fIl~t~~  147 (207)
T d1a5ta2         106 LGGAKVVWVTDAALLTD--AAANALLKTLEEPPAETWFFLATRE  147 (207)
T ss_dssp             TSSCEEEEESCGGGBCH--HHHHHHHHHHTSCCTTEEEEEEESC
T ss_pred             cCccceEEechhhhhhh--hhhHHHHHHHHhhcccceeeeeecC
Confidence            35678999999999865  4566677777777767766665544

>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=97.31  E-value=0.00044  Score=55.17  Aligned_cols=133  Identities=14%  Similarity=0.152  Sum_probs=70.3

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec-ChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhc
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH-TRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKN  164 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P-~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (423)
                      +++.||||+|||.+..-.+.... ..+.+ .+++-+. .|.-+.++   ++.+.... ++.+...........-...   
T Consensus        13 i~lvGp~GvGKTTTiaKLA~~~~-~~g~k-V~lit~Dt~R~gA~eQ---L~~~a~~l-~v~~~~~~~~~~~~~~~~~---   83 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAKLALYYK-GKGRR-PLLVAADTQRPAAREQ---LRLLGEKV-GVPVLEVMDGESPESIRRR---   83 (207)
T ss_dssp             EEEECCTTTTHHHHHHHHHHHHH-HTTCC-EEEEECCSSCHHHHHH---HHHHHHHH-TCCEEECCTTCCHHHHHHH---
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH-HCCCc-EEEEecccccchHHHH---HHHHHHhc-CCccccccccchhhHHHHH---
Confidence            67799999999987544333332 22222 3344343 33333333   33333332 4444443332221111000   


Q ss_pred             CCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHhc
Q 014486          165 ECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKFM  244 (423)
Q Consensus       165 ~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~~  244 (423)
                                  ...+.     ...+.++|++|=+-+...+......+..+.....+...++.++|+.+.+....+..+.
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     1234467888877765443345566777777777777788999998877766666554

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.04  E-value=0.001  Score=52.86  Aligned_cols=43  Identities=9%  Similarity=0.271  Sum_probs=33.0

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCC
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLS  233 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~  233 (423)
                      ...+++|+||||.+..  .....+.+.++.-+....++++|..+.
T Consensus        78 ~~~KviIId~ad~l~~--~aqNaLLK~LEEPp~~t~fiLit~~~~  120 (198)
T d2gnoa2          78 YTRKYVIVHDCERMTQ--QAANAFLKALEEPPEYAVIVLNTRRWH  120 (198)
T ss_dssp             SSSEEEEETTGGGBCH--HHHHHTHHHHHSCCTTEEEEEEESCGG
T ss_pred             CCCEEEEEeCccccch--hhhhHHHHHHhCCCCCceeeeccCChh
Confidence            5668999999999864  566677888888777887777766543

>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=96.99  E-value=0.0013  Score=52.42  Aligned_cols=134  Identities=15%  Similarity=0.206  Sum_probs=67.6

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcC
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNE  165 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (423)
                      +++.||||+|||.+..-.+ .++...+. ..+||-+.+--.+  -.++++.+.... ++.+.....+.....-       
T Consensus        12 i~lvGptGvGKTTTiAKLA-~~~~~~g~-kV~lit~Dt~R~g--A~eQL~~~a~~l-~v~~~~~~~~~d~~~~-------   79 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLA-RQFEQQGK-SVMLAAGDTFRAA--AVEQLQVWGQRN-NIPVIAQHTGADSASV-------   79 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HHHHTTTC-CEEEECCCTTCHH--HHHHHHHHHHHT-TCCEECCSTTCCHHHH-------
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHCCC-cEEEEeccccccc--chhhhhhhhhhc-CCcccccccCCCHHHH-------
Confidence            6679999999998765433 33333333 2455555543221  133445555444 5555443333221111       


Q ss_pred             CCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCC------CCceEEEEeccCCccHHHH
Q 014486          166 CPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTP------HDKQVMMFSATLSKEIRPV  239 (423)
Q Consensus       166 ~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~------~~~~~v~~SAT~~~~~~~~  239 (423)
                                 +.+....  ....++++|++|=+=+.-.+......+..+.+...      +...++.++|+...+....
T Consensus        80 -----------l~~~~~~--a~~~~~d~ilIDTaGr~~~d~~~~~el~~l~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~  146 (211)
T d2qy9a2          80 -----------IFDAIQA--AKARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQ  146 (211)
T ss_dssp             -----------HHHHHHH--HHHTTCSEEEECCCCCGGGHHHHHHHHHHHHHHHTTTCTTCCSEEEEEEEGGGTHHHHHH
T ss_pred             -----------HHHHHHH--HHHcCCCEEEeccCCCccccHHHHHHHHHHHHHHhhhcccCcceeeeehhcccCcchHHH
Confidence                       1111110  01134567888887655332333444555544332      3456788899987665554


Q ss_pred             HHHhc
Q 014486          240 CKKFM  244 (423)
Q Consensus       240 ~~~~~  244 (423)
                      ...++
T Consensus       147 ~~~~~  151 (211)
T d2qy9a2         147 AKLFH  151 (211)
T ss_dssp             HHHHH
T ss_pred             Hhhhh
Confidence            44433

>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=96.97  E-value=0.00046  Score=57.37  Aligned_cols=48  Identities=13%  Similarity=0.113  Sum_probs=33.0

Q ss_pred             ccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHH
Q 014486           43 IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        43 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~  102 (423)
                      ..+..|+++...+.+.+.|...- .     |..      ...++++.||+|+|||..+-.
T Consensus         5 y~P~~~~diig~~~~~~~L~~~~-~-----~~~------~~~~lll~Gp~G~GKTt~~~~   52 (252)
T d1sxje2           5 YRPKSLNALSHNEELTNFLKSLS-D-----QPR------DLPHLLLYGPNGTGKKTRCMA   52 (252)
T ss_dssp             TCCCSGGGCCSCHHHHHHHHTTT-T-----CTT------CCCCEEEECSTTSSHHHHHHT
T ss_pred             cCCCCHHHccCcHHHHHHHHHHH-H-----cCC------CCCeEEEECCCCCCHHHHHHH
Confidence            34567888988888888887541 0     111      123589999999999986543

>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=96.92  E-value=0.0039  Score=51.03  Aligned_cols=47  Identities=19%  Similarity=0.329  Sum_probs=31.4

Q ss_pred             cCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHHHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~~  102 (423)
                      .+.+|+++...+.+.+.|...       ++..     .-.+.+++.||+|+|||..+..
T Consensus         7 rP~~~~dlig~~~~~~~L~~~-------i~~~-----~~~~~~Ll~Gp~G~GKtt~a~~   53 (239)
T d1njfa_           7 RPQTFADVVGQEHVLTALANG-------LSLG-----RIHHAYLFSGTRGVGKTSIARL   53 (239)
T ss_dssp             CCSSGGGSCSCHHHHHHHHHH-------HHTT-----CCCSEEEEECSTTSSHHHHHHH
T ss_pred             CCCCHHHccChHHHHHHHHHH-------HHcC-----CCCeeEEEECCCCCcHHHHHHH
Confidence            345788888888887777643       0000     0123489999999999987654

>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=96.88  E-value=0.0015  Score=53.92  Aligned_cols=89  Identities=15%  Similarity=0.160  Sum_probs=67.7

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHh----CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc-cccCCCCCCCCEEE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVE----CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL-VGRGIDIERVNIVI  361 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~-~~~Gld~~~~~~vi  361 (423)
                      .+.++++.+++.-.+.+.++.+++    .|+.+..+||+++..+|..++....+|+++|+|+|.+ +...+.+.++..||
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            457899999998888776665544    4789999999999999999999999999999999955 55578888888877


Q ss_pred             EccCCCCcchhhhccc
Q 014486          362 NYDMPDSADTYLHRVG  377 (423)
Q Consensus       362 ~~~~~~s~~~~~Q~~G  377 (423)
                      .-..-+  ..+.||.+
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            655433  24667654

>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=96.80  E-value=0.0031  Score=49.99  Aligned_cols=133  Identities=11%  Similarity=0.077  Sum_probs=61.8

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecC-hHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHT-RELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLL  162 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~-~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (423)
                      +-+++.||||+|||.+..-.+. ++...+.+ .+||-+.+ |.=+.++.   +.+.... ++.+.....+..........
T Consensus         7 ~vi~lvGptGvGKTTTiaKLA~-~~~~~g~k-V~lit~Dt~R~gA~eQL---~~~a~~l-~i~~~~~~~~~d~~~~~~~~   80 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTTIAKLGR-YYQNLGKK-VMFCAGDTFRAAGGTQL---SEWGKRL-SIPVIQGPEGTDPAALAYDA   80 (207)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHH-HHHTTTCC-EEEECCCCSSTTHHHHH---HHHHHHH-TCCEECCCTTCCHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH-HHHHCCCc-EEEEEeccccccchhhH---hhccccc-CceEEeccCCccHHHHHHHH
Confidence            4478899999999987654333 33333332 44555544 33333332   2332222 44443332222211111000


Q ss_pred             hcCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhC------CCCceEEEEeccCCccH
Q 014486          163 KNECPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMT------PHDKQVMMFSATLSKEI  236 (423)
Q Consensus       163 ~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~------~~~~~~v~~SAT~~~~~  236 (423)
                                     ....     ...+.++|++|=+=+...+......+..+.+..      .+...++.++||...+.
T Consensus        81 ---------------~~~~-----~~~~~d~ilIDTaGr~~~d~~l~~el~~~~~~~~~~~~~~p~~~~LVl~a~~~~~~  140 (207)
T d1okkd2          81 ---------------VQAM-----KARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNG  140 (207)
T ss_dssp             ---------------HHHH-----HHHTCSEEEECCCCCCTTCHHHHHHHHHHHHHHHHHCTTCCSEEEEEEETTBCTHH
T ss_pred             ---------------HHHH-----HHCCCCEEEcCccccchhhHHHHHHHHHHHHHhhhcccCCCceEEEEeecccCchH
Confidence                           0000     112345677777765533222333343443322      33445778889887655


Q ss_pred             HHHHHH
Q 014486          237 RPVCKK  242 (423)
Q Consensus       237 ~~~~~~  242 (423)
                      ...+..
T Consensus       141 ~~~~~~  146 (207)
T d1okkd2         141 LEQAKK  146 (207)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444433

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.73  E-value=0.0032  Score=50.50  Aligned_cols=46  Identities=17%  Similarity=0.257  Sum_probs=27.9

Q ss_pred             CccEEEEcCcchhhccCCcHHHHHHHHHhC-CCCceEEEEeccCCcc
Q 014486          190 NVRHFILDECDKMLESLDMRRDVQEIFKMT-PHDKQVMMFSATLSKE  235 (423)
Q Consensus       190 ~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~-~~~~~~v~~SAT~~~~  235 (423)
                      ..+++++|++|.+.........+-.+...+ ....++|+.|...|..
T Consensus        97 ~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~  143 (213)
T d1l8qa2          97 SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQK  143 (213)
T ss_dssp             TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGG
T ss_pred             hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchh
Confidence            457899999999876334444444444433 3456666665555543

>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=96.64  E-value=0.0019  Score=52.42  Aligned_cols=44  Identities=14%  Similarity=0.233  Sum_probs=30.0

Q ss_pred             CCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCC
Q 014486          188 LKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLS  233 (423)
Q Consensus       188 ~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~  233 (423)
                      ....+++|+||+|.+..  .....+.......+....+++.+....
T Consensus        99 ~~~~kviiiDe~d~~~~--~~~~~ll~~~e~~~~~~~~i~~~~~~~  142 (224)
T d1sxjb2          99 PGKHKIVILDEADSMTA--GAQQALRRTMELYSNSTRFAFACNQSN  142 (224)
T ss_dssp             TTCCEEEEEESGGGSCH--HHHHTTHHHHHHTTTTEEEEEEESCGG
T ss_pred             CcceEEEEEecccccch--hHHHHHhhhccccccceeeeeccCchh
Confidence            34567999999998875  344455566666666776777665544

>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=96.57  E-value=0.004  Score=50.29  Aligned_cols=89  Identities=16%  Similarity=0.136  Sum_probs=71.7

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHh----CCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc-cccCCCCCCCCEEE
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVE----CNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL-VGRGIDIERVNIVI  361 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~-~~~Gld~~~~~~vi  361 (423)
                      .+.++++.+|+.-.+.+.++.+++    .+..+..+|+.++..+|..++....+|+.+|+|+|.+ +...+.++++..||
T Consensus       103 ~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~~~f~~LgLiI  182 (233)
T d2eyqa3         103 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLI  182 (233)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEE
T ss_pred             cCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccCCcccccccee
Confidence            467899999999999999888875    4778899999999999999999999999999999965 44568888888777


Q ss_pred             EccCCCCcchhhhccc
Q 014486          362 NYDMPDSADTYLHRVG  377 (423)
Q Consensus       362 ~~~~~~s~~~~~Q~~G  377 (423)
                      .-..-.  ..|.|+.+
T Consensus       183 iDEeH~--fg~kQ~~~  196 (233)
T d2eyqa3         183 VDEEHR--FGVRHKER  196 (233)
T ss_dssp             EESGGG--SCHHHHHH
T ss_pred             eechhh--hhhHHHHH
Confidence            654332  23556543

>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=96.54  E-value=0.0022  Score=51.16  Aligned_cols=131  Identities=13%  Similarity=0.130  Sum_probs=61.7

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcC
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNE  165 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (423)
                      +++.||||+|||.+..-.+ .++...+. ..+|+-+.+--.+.  .++++.+.... ++.+.....+.....-...    
T Consensus        14 i~lvGptGvGKTTTiAKLA-a~~~~~~~-kV~lit~Dt~R~gA--~eQL~~~a~~l-~i~~~~~~~~~d~~~~~~~----   84 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLA-KMFVDEGK-SVVLAAADTFRAAA--IEQLKIWGERV-GATVISHSEGADPAAVAFD----   84 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHH-HHHHHTTC-CEEEEEECTTCHHH--HHHHHHHHHHH-TCEEECCSTTCCHHHHHHH----
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHCCC-ceEEEeecccccch--hHHHHHHhhhc-CccccccCCCCcHHHHHHH----
Confidence            6789999999998754333 33333332 25566665443222  12344444332 4444332222211110000    


Q ss_pred             CCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCC------CCceEEEEeccCCccHHHH
Q 014486          166 CPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTP------HDKQVMMFSATLSKEIRPV  239 (423)
Q Consensus       166 ~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~------~~~~~v~~SAT~~~~~~~~  239 (423)
                                 .....     ...++++|++|=+=+.-.+......+..+.+...      +...++.++||........
T Consensus        85 -----------~~~~~-----~~~~~d~ilIDTaGr~~~d~~~~~el~~~~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~  148 (213)
T d1vmaa2          85 -----------AVAHA-----LARNKDVVIIDTAGRLHTKKNLMEELRKVHRVVKKKIPDAPHETLLVIDATTGQNGLVQ  148 (213)
T ss_dssp             -----------HHHHH-----HHTTCSEEEEEECCCCSCHHHHHHHHHHHHHHGGGTCTTCCSEEEEEEEGGGHHHHHHH
T ss_pred             -----------HHHHH-----HHcCCCEEEEeccccccchHHHHHHHHHHHhhhhhccccccceeEEeeccccCcchhhh
Confidence                       00000     1134567778777654332233344444544332      2345788888876554444


Q ss_pred             HH
Q 014486          240 CK  241 (423)
Q Consensus       240 ~~  241 (423)
                      +.
T Consensus       149 ~~  150 (213)
T d1vmaa2         149 AK  150 (213)
T ss_dssp             HH
T ss_pred             hh
Confidence            33

>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=0.0071  Score=48.91  Aligned_cols=43  Identities=16%  Similarity=0.339  Sum_probs=28.2

Q ss_pred             CCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          185 DLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       185 ~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      .....+.+++|+||+|.+..  .....+..++...++...+++.+
T Consensus        94 ~~~~~~~kiiiiDe~d~~~~--~~~~~Ll~~le~~~~~~~~~~~~  136 (227)
T d1sxjc2          94 QIFSKGFKLIILDEADAMTN--AAQNALRRVIERYTKNTRFCVLA  136 (227)
T ss_dssp             CSSSCSCEEEEETTGGGSCH--HHHHHHHHHHHHTTTTEEEEEEE
T ss_pred             cccCCCeEEEEEeccccchh--hHHHHHHHHhhhcccceeecccc
Confidence            34445667999999998864  34555666666666666555444

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=96.41  E-value=0.0045  Score=48.72  Aligned_cols=101  Identities=10%  Similarity=0.162  Sum_probs=72.5

Q ss_pred             HhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHH
Q 014486          104 TLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILAL  180 (423)
Q Consensus       104 ~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~  180 (423)
                      +...+..++   ++.||||..+-.....+.+++.   +|+.++..+||..+..+..   ..+.++..+|+|||.-.    
T Consensus        24 I~~El~rGg---Qvy~V~p~I~~~e~~~~~l~~~---~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvI----   93 (211)
T d2eyqa5          24 ILREILRGG---QVYYLYNDVENIQKAAERLAEL---VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTII----   93 (211)
T ss_dssp             HHHHHTTTC---EEEEECCCSSCHHHHHHHHHHH---CTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTT----
T ss_pred             HHHHHHcCC---eEEEEEcCccchhhHHHHHHHh---CCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhh----
Confidence            444444333   9999999998888887777665   4788999999988765543   45677888999999632    


Q ss_pred             HhcCCCCCCCccEEEEcCcchhhccCCcHHHHHHHHHhCCC
Q 014486          181 ARDKDLSLKNVRHFILDECDKMLESLDMRRDVQEIFKMTPH  221 (423)
Q Consensus       181 ~~~~~~~~~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~  221 (423)
                        ...++..+.+++|+..|+++.     ...+..+..+...
T Consensus        94 --EvGiDvpnA~~iiI~~a~rfG-----LaQLhQLRGRVGR  127 (211)
T d2eyqa5          94 --ETGIDIPTANTIIIERADHFG-----LAQLHQLRGRVGR  127 (211)
T ss_dssp             --GGGSCCTTEEEEEETTTTSSC-----HHHHHHHHTTCCB
T ss_pred             --hhccCCCCCcEEEEecchhcc-----ccccccccceeee
Confidence              345788999999999999652     2335555554433

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.40  E-value=0.0026  Score=51.98  Aligned_cols=44  Identities=16%  Similarity=0.278  Sum_probs=27.4

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEeccCCc
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSATLSK  234 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~  234 (423)
                      ...+++|+||+|.+..  .....+..+.........+++.+.....
T Consensus       107 ~~~~viiiDe~d~l~~--~~~~~l~~~~~~~~~~~~~i~~~~~~~~  150 (237)
T d1sxjd2         107 PPYKIIILDEADSMTA--DAQSALRRTMETYSGVTRFCLICNYVTR  150 (237)
T ss_dssp             CSCEEEEETTGGGSCH--HHHHHHHHHHHHTTTTEEEEEEESCGGG
T ss_pred             cCceEEEEecccccCH--HHHHHHhhcccccccccccccccccccc
Confidence            3456899999998865  3344555556665556655555544433

>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=96.34  E-value=0.0098  Score=48.70  Aligned_cols=53  Identities=19%  Similarity=0.251  Sum_probs=31.9

Q ss_pred             CCCCcCCCCCHHHHHHHHhC-C-CCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           45 SSGFRDFLLKPELLRAIVDS-G-FEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~-~-~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ..+|++..-.+.+.+.|.+. . +..+..+|....   ...+.+++.||+|+|||+.+
T Consensus         5 ~~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~---~~~~giLl~GppGtGKT~la   59 (247)
T d1ixza_           5 KVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGA---RIPKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             SCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTC---CCCSEEEEECCTTSSHHHHH
T ss_pred             CCcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCC---CCCceEEEecCCCCChhHHH
Confidence            35688887677766666532 0 112222333221   12356999999999999864

>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=96.20  E-value=0.0028  Score=50.44  Aligned_cols=133  Identities=11%  Similarity=0.119  Sum_probs=60.6

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcC
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNE  165 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (423)
                      +++.||||+|||.+..-.+ .++...+.+ .++|-+.+--.+.  .++++.+.... ++.+...............    
T Consensus        15 i~lvGptGvGKTTTiAKLA-~~~~~~g~k-V~lit~Dt~R~ga--~eQL~~~a~~l-~v~~~~~~~~~~~~~~~~~----   85 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLA-YFYKKKGFK-VGLVGADVYRPAA--LEQLQQLGQQI-GVPVYGEPGEKDVVGIAKR----   85 (211)
T ss_dssp             EEEECSCCC----HHHHHH-HHHHHTTCC-EEEEECCCSSHHH--HHHHHHHHHHH-TCCEECCTTCCCHHHHHHH----
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHCCCc-eEEEEeeccccch--hHHHHHhcccc-CcceeecccchhhhHHHHH----
Confidence            6678999999998754433 333333332 4555554332221  22334443332 4444332222111110000    


Q ss_pred             CCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchhhcc--CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHHHHHh
Q 014486          166 CPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKMLES--LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPVCKKF  243 (423)
Q Consensus       166 ~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~~~~--~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~~~~~  243 (423)
                                .+ ...     ...+.++|++|=+=+.-.+  ......+..+.....+....+.++|+...+.......+
T Consensus        86 ----------a~-~~~-----~~~~~d~IlIDTaGr~~~~~~~~~~~el~~~~~~~~~~~~~LVl~a~~~~~~~~~~~~~  149 (211)
T d1j8yf2          86 ----------GV-EKF-----LSEKMEIIIVDTAGRHGYGEEAALLEEMKNIYEAIKPDEVTLVIDASIGQKAYDLASKF  149 (211)
T ss_dssp             ----------HH-HHH-----HHTTCSEEEEECCCSCCTTCHHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHHHHHHHH
T ss_pred             ----------HH-HHh-----hccCCceEEEecCCcCccchhhHHHHHHHHHHhhcCCceEEEEEecccCcchHHHHhhh
Confidence                      00 000     1134567888876542110  11234566667776666678888999876655544443

>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=96.17  E-value=0.067  Score=40.58  Aligned_cols=105  Identities=15%  Similarity=0.073  Sum_probs=74.3

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++.-+..+++.+.+.     ++++..++|+.+..+..   ..+.++..+|+|+|.-      ....++..+++
T Consensus        33 r~lvfc~t~~~~~~l~~~L~~~-----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v------~~~GiDip~V~  101 (174)
T d1c4oa2          33 RTLVTVLTVRMAEELTSFLVEH-----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINL------LREGLDIPEVS  101 (174)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCC------CCTTCCCTTEE
T ss_pred             cEEEEEcchhHHHHHHHHHHhc-----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeeee------eeeeccCCCCc
Confidence            8999999999999988888774     88999999998866554   4566788999999952      24578899999


Q ss_pred             EEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          193 HFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       193 ~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      +||+=.++...........+..+-+..+...-.+++-+.
T Consensus       102 ~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~g~~~~~~~  140 (174)
T d1c4oa2         102 LVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYAD  140 (174)
T ss_dssp             EEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECS
T ss_pred             EEEEeccccccccchhHHHHHHhhhhhhcCCCeeEEeec
Confidence            999877765332123344555555555544333433333

>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=96.13  E-value=0.0035  Score=46.27  Aligned_cols=87  Identities=18%  Similarity=0.164  Sum_probs=49.8

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcC
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNE  165 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (423)
                      -++.||+.||||.-.+- .+.+....+.  +++++-|...-         +..   ..  +... .|..           
T Consensus         5 ~~i~GpMfsGKTteLi~-~~~~~~~~~~--kv~~ikp~~D~---------R~~---~~--i~s~-~g~~-----------   55 (139)
T d2b8ta1           5 EFITGPMFAGKTAELIR-RLHRLEYADV--KYLVFKPKIDT---------RSI---RN--IQSR-TGTS-----------   55 (139)
T ss_dssp             EEEECSTTSCHHHHHHH-HHHHHHHTTC--CEEEEEECCCG---------GGC---SS--CCCC-CCCS-----------
T ss_pred             EEEEccccCHHHHHHHH-HHHHHHHCCC--cEEEEEEcccc---------ccc---ce--EEcc-cCce-----------
Confidence            47889999999976443 3333332222  78899997542         110   01  1111 1111           


Q ss_pred             CCcEEEechHHHHHHHhcCCCCCCCccEEEEcCcchh
Q 014486          166 CPQIVVGTPGRILALARDKDLSLKNVRHFILDECDKM  202 (423)
Q Consensus       166 ~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~~  202 (423)
                      ...+.+.+...+...+..... ..+.++|.+||++-+
T Consensus        56 ~~~~~~~~~~~~~~~~~~~~~-~~~~dvI~IDE~QFf   91 (139)
T d2b8ta1          56 LPSVEVESAPEILNYIMSNSF-NDETKVIGIDEVQFF   91 (139)
T ss_dssp             SCCEEESSTHHHHHHHHSTTS-CTTCCEEEECSGGGS
T ss_pred             eeeEEeccchhhHHHHHhhcc-ccCcCEEEechhhhc
Confidence            124666666666665554332 357889999999965

>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=96.03  E-value=0.0035  Score=46.29  Aligned_cols=37  Identities=8%  Similarity=0.077  Sum_probs=24.5

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      -++.||+.||||.-.+ -.+.+....+.  +++++-|...
T Consensus        10 ~lI~GpMfSGKTteLi-~~~~~~~~~g~--~vl~i~~~~D   46 (141)
T d1xx6a1          10 EVIVGPMYSGKSEELI-RRIRRAKIAKQ--KIQVFKPEID   46 (141)
T ss_dssp             EEEECSTTSSHHHHHH-HHHHHHHHTTC--CEEEEEEC--
T ss_pred             EEEEeccccHHHHHHH-HHHHHhhhcCC--cEEEEEeccc
Confidence            5789999999997643 34444333332  7899999754

>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=96.02  E-value=0.0034  Score=55.49  Aligned_cols=66  Identities=26%  Similarity=0.394  Sum_probs=48.0

Q ss_pred             CCChhhhhccccccc----C-CceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhc
Q 014486           68 HPSEVQHECIPQAIL----G-MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFST  139 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~-~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  139 (423)
                      .|.--|=++|..+..    | +..++.|-||||||++.. .+++...    + .+|||+|+..+|.|+++.++.+..
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~~----r-p~LVVt~n~~~A~qL~~dL~~~l~   81 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQVN----K-PTLVIAHNKTLAGQLYSELKEFFP   81 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHHT----C-CEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHhC----C-CEEEEeCCHHHHHHHHHHHHHHcC
Confidence            456666666655554    3 458899999999997542 2333322    1 679999999999999999998863

>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=96.00  E-value=0.017  Score=46.67  Aligned_cols=45  Identities=13%  Similarity=0.231  Sum_probs=31.4

Q ss_pred             ccCCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           43 IHSSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        43 ~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ..+..|+++-..+.+.+.|...       .+..      ...++++.||+|+|||..+
T Consensus        18 y~P~~~~diig~~~~~~~l~~~-------i~~~------~~~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          18 YRPQRLDDIVGQEHIVKRLKHY-------VKTG------SMPHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             TCCCSTTTCCSCHHHHHHHHHH-------HHHT------CCCEEEEESCTTSSHHHHH
T ss_pred             hCCCCHHHccCcHHHHHHHHHH-------HHcC------CCCeEEEECCCCCcHHHHH
Confidence            3456788998888887777643       1111      1235899999999999765

>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=95.69  E-value=0.11  Score=39.89  Aligned_cols=105  Identities=18%  Similarity=0.125  Sum_probs=74.7

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      +++|.|+++.-+..++..+++.     ++++..++|+.+..+..   ..+.++..+|+|||.-      -...+++.+++
T Consensus        33 ~~iif~~~~~~~~~~~~~l~~~-----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv------~~rGiDip~v~  101 (181)
T d1t5la2          33 RTLVTTLTKKMAEDLTDYLKEA-----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINL------LREGLDIPEVS  101 (181)
T ss_dssp             EEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCC------CSSSCCCTTEE
T ss_pred             eEEEEeehhhhhHHHHHHHHhC-----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhH------HHccCCCCCCC
Confidence            8999999999988888777654     88999999999876654   4556788999999942      24578899999


Q ss_pred             EEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEecc
Q 014486          193 HFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFSAT  231 (423)
Q Consensus       193 ~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT  231 (423)
                      +||.-++............+.++-+..+.....+++...
T Consensus       102 ~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~~~~~~~~  140 (181)
T d1t5la2         102 LVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYAD  140 (181)
T ss_dssp             EEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECS
T ss_pred             EEEEecCCcccccccHHHHHHHHHhhccccCceeEeecc
Confidence            999888875321124455566666555544334444333

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=95.56  E-value=0.019  Score=48.86  Aligned_cols=65  Identities=23%  Similarity=0.326  Sum_probs=39.0

Q ss_pred             HHHHHhCCCCCC---Chhhhhcccccc-cCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHH
Q 014486           58 LRAIVDSGFEHP---SEVQHECIPQAI-LGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTREL  126 (423)
Q Consensus        58 ~~~l~~~~~~~~---~~~Q~~~i~~~~-~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  126 (423)
                      ...+.+.|+...   .+-+...+..+. .+++++++|+||||||.. +-+++.......   +++.+-.+.+|
T Consensus       137 l~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i~~~~---rivtiEd~~El  205 (323)
T d1g6oa_         137 HSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFIPKEE---RIISIEDTEEI  205 (323)
T ss_dssp             HHHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGSCTTC---CEEEEESSCCC
T ss_pred             hHHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhccccc---ceeeccchhhh
Confidence            345555555432   233334443333 478899999999999975 344555443322   67777676665

>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=94.93  E-value=0.042  Score=45.17  Aligned_cols=18  Identities=22%  Similarity=0.329  Sum_probs=15.1

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      .+.+++.||+|+|||+.+
T Consensus        38 ~~giLL~GppGtGKT~l~   55 (258)
T d1e32a2          38 PRGILLYGPPGTGKTLIA   55 (258)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CceeEEecCCCCCchHHH
Confidence            356999999999999753

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=94.33  E-value=0.015  Score=51.30  Aligned_cols=39  Identities=18%  Similarity=0.350  Sum_probs=26.4

Q ss_pred             ChhhhhcccccccCCc--eEEEccCCCcchhHHHHHHhhccC
Q 014486           70 SEVQHECIPQAILGMD--VICQAKSGMGKTAVFVLSTLQQTE  109 (423)
Q Consensus        70 ~~~Q~~~i~~~~~~~~--~ii~~~tGsGKT~~~~~~~~~~~~  109 (423)
                      .+.|.+.+..++....  +++.||||||||.+. ..++..+.
T Consensus       143 ~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl-~~~l~~~~  183 (401)
T d1p9ra_         143 TAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELN  183 (401)
T ss_dssp             CHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHC
T ss_pred             cHHHHHHHHHHHhhhhceEEEEcCCCCCccHHH-HHHhhhhc
Confidence            3566666666665433  899999999999764 44555543

>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=94.03  E-value=0.085  Score=39.68  Aligned_cols=73  Identities=14%  Similarity=0.282  Sum_probs=56.9

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHH---HHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKD---LLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|.++.-+.++++.+...     ++.+..++|+.+......   .+.++...|+|||--      -..+.++.+++
T Consensus        29 k~iIF~~s~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv------~~rGiDi~~v~   97 (162)
T d1fuka_          29 QAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDL------LARGIDVQQVS   97 (162)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGG------GTTTCCCCSCS
T ss_pred             cEEEEEEEEchHHHHHHHHhhc-----CceEEEeccCCchhhHHHHHHHHhhcccceeecccc------ccccccCCCce
Confidence            7999999999999998877664     678999999887766554   455677899999963      24567888999


Q ss_pred             EEEEcCc
Q 014486          193 HFILDEC  199 (423)
Q Consensus       193 ~vVvDE~  199 (423)
                      +||.=+.
T Consensus        98 ~VI~~d~  104 (162)
T d1fuka_          98 LVINYDL  104 (162)
T ss_dssp             EEEESSC
T ss_pred             EEEEecc
Confidence            8886554

>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=93.16  E-value=0.052  Score=47.67  Aligned_cols=66  Identities=27%  Similarity=0.363  Sum_probs=46.0

Q ss_pred             CCChhhhhccccccc----CCc-eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhc
Q 014486           68 HPSEVQHECIPQAIL----GMD-VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFST  139 (423)
Q Consensus        68 ~~~~~Q~~~i~~~~~----~~~-~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  139 (423)
                      .|+.-|-++|..+..    |.. ..+.|-+||+||++.. .+..... .    .+|||+|+...|.++++.+..+..
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A-~l~~~~~-r----p~LvVt~~~~~A~~l~~dL~~~l~   78 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEALG-R----PALVLAPNKILAAQLAAEFRELFP   78 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHHT-C----CEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHH-HHHHHhC-C----CEEEEeCCHHHHHHHHHHHHHhcC
Confidence            455556556665543    443 6889999999997532 2222222 1    579999999999999999998863

>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=92.85  E-value=0.021  Score=44.00  Aligned_cols=30  Identities=17%  Similarity=0.211  Sum_probs=20.6

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCCCCCC
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEPNPGQ  114 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~  114 (423)
                      ++++|.||+|+|||... ..++..+...+..
T Consensus         2 k~v~ItG~~GtGKTtl~-~~i~~~l~~~~~~   31 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLI-HKASEVLKSSGVP   31 (189)
T ss_dssp             CCEEEESCCSSCHHHHH-HHHHHHHHHTTCC
T ss_pred             cEEEEECCCCCcHHHHH-HHHHHHHHHCCCE
Confidence            57999999999999753 3445554444433

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.77  E-value=0.019  Score=47.11  Aligned_cols=58  Identities=10%  Similarity=0.093  Sum_probs=33.5

Q ss_pred             cCCCCcCCCCCHHHHHHHHhC--CCCCCChh--hhhcccccccCCceEEEccCCCcchhHHH
Q 014486           44 HSSGFRDFLLKPELLRAIVDS--GFEHPSEV--QHECIPQAILGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        44 ~~~~~~~~~l~~~~~~~l~~~--~~~~~~~~--Q~~~i~~~~~~~~~ii~~~tGsGKT~~~~  101 (423)
                      .+.+|+++...+...+.|...  .+....+.  |-.........+.+++.||+|+|||.++-
T Consensus         9 ~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~   70 (253)
T d1sxja2           9 APTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAH   70 (253)
T ss_dssp             CCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHH
T ss_pred             CCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHH
Confidence            456799999999888777653  11000010  10010011112469999999999997653

>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=92.72  E-value=0.3  Score=36.15  Aligned_cols=73  Identities=15%  Similarity=0.282  Sum_probs=54.4

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++.-+.++++.+++.     ++.+..++++.+..+..   ..+.++...|+|||.. +.     .++++..++
T Consensus        30 k~IIF~~s~~~~~~l~~~L~~~-----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~-~~-----~Gid~~~v~   98 (155)
T d1hv8a2          30 YGLVFCKTKRDTKELASMLRDI-----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDV-MS-----RGIDVNDLN   98 (155)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHT-----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTT-HH-----HHCCCSCCS
T ss_pred             CEEEEECchHHHHHHHhhhccc-----ccccccccccchhhhhhhhhhhhhcccceeeeehhH-Hh-----hhhhhccCc
Confidence            7899999999999988888764     67888999987665554   4455677899999953 22     246777888


Q ss_pred             EEEEcCc
Q 014486          193 HFILDEC  199 (423)
Q Consensus       193 ~vVvDE~  199 (423)
                      +||.=++
T Consensus        99 ~Vi~~d~  105 (155)
T d1hv8a2          99 CVINYHL  105 (155)
T ss_dssp             EEEESSC
T ss_pred             EEEEecC
Confidence            8885433

>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=92.70  E-value=0.52  Score=35.41  Aligned_cols=84  Identities=7%  Similarity=0.103  Sum_probs=62.4

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++.-+..++..+...     ++.+..++|+.+..+..   ..+.++..+++|||..      -...+++.+++
T Consensus        34 k~iVF~~~~~~~~~l~~~L~~~-----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~------~~~Gid~~~v~  102 (171)
T d1s2ma2          34 QAIIFCNSTNRVELLAKKITDL-----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL------LTRGIDIQAVN  102 (171)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC------SSSSCCCTTEE
T ss_pred             ceEEEEeeeehhhHhHHhhhcc-----cccccccccccchhhhhhhhhhcccCccccccchhH------hhhccccceeE
Confidence            8999999999999888887765     67888999988765554   4455677899999963      24567888899


Q ss_pred             EEEEcCcchhhccCCcHHHHHHH
Q 014486          193 HFILDECDKMLESLDMRRDVQEI  215 (423)
Q Consensus       193 ~vVvDE~h~~~~~~~~~~~~~~~  215 (423)
                      +||.=++.     .+...-+.++
T Consensus       103 ~VI~~d~p-----~~~~~y~qr~  120 (171)
T d1s2ma2         103 VVINFDFP-----KTAETYLHRI  120 (171)
T ss_dssp             EEEESSCC-----SSHHHHHHHH
T ss_pred             EEEecCCc-----chHHHHHHHh
Confidence            88866664     3444444554

>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=92.32  E-value=0.063  Score=43.33  Aligned_cols=48  Identities=13%  Similarity=0.230  Sum_probs=28.5

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      +.+|+++.-.+.+.+.|...       .+. ....-....++++.||+|+|||..+
T Consensus         5 P~~~~divGqe~~~~~l~~~-------i~~-~~~~~~~~~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2           5 PKSLDEFIGQENVKKKLSLA-------LEA-AKMRGEVLDHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             CSSGGGCCSCHHHHHHHHHH-------HHH-HHHHTCCCCCEEEESSTTSSHHHHH
T ss_pred             CCcHHHcCChHHHHHHHHHH-------HHH-HHhcCCCCCeEEEECCCCCcHHHHH
Confidence            34678887777776665532       000 0000001246999999999999865

>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=92.27  E-value=0.19  Score=39.19  Aligned_cols=72  Identities=18%  Similarity=0.317  Sum_probs=55.0

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.++|+.-+..++..+...     ++.+..++|+.+.....   ..+.++..+|+|+|-.      ....+++.+++
T Consensus        32 ~~IIF~~t~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~------~~~GiD~p~v~  100 (200)
T d1oywa3          32 SGIIYCNSRAKVEDTAARLQSK-----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVA------FGMGINKPNVR  100 (200)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTT------SCTTTCCTTCC
T ss_pred             CEEEEEeeehhhHHhhhhhccC-----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecch------hhhccCCCCCC
Confidence            7899999999999888777664     77899999998765544   4456677899999963      23467778888


Q ss_pred             EEEEcC
Q 014486          193 HFILDE  198 (423)
Q Consensus       193 ~vVvDE  198 (423)
                      +||.=+
T Consensus       101 ~VI~~~  106 (200)
T d1oywa3         101 FVVHFD  106 (200)
T ss_dssp             EEEESS
T ss_pred             EEEECC
Confidence            887433

>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=92.05  E-value=0.029  Score=50.00  Aligned_cols=19  Identities=21%  Similarity=0.417  Sum_probs=16.3

Q ss_pred             cCCceEEEccCCCcchhHH
Q 014486           82 LGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~  100 (423)
                      ..+|+++.||||+|||+.+
T Consensus        48 ~ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             ccccEEEECCCCCCHHHHH
Confidence            3578999999999999854

>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=91.79  E-value=0.025  Score=46.37  Aligned_cols=53  Identities=21%  Similarity=0.182  Sum_probs=31.0

Q ss_pred             CCCCcCCCCCHHHHHHHHhC--CCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           45 SSGFRDFLLKPELLRAIVDS--GFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~--~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      ..+|++..-.+.+.+.|.+.  -+.++..+|...+   -..+.+++.||+|+|||+.+
T Consensus         8 ~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~---~~~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_           8 KTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGG---KIPKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcCC---CCCCeEEeeCCCCCCccHHH
Confidence            34588887777776666542  1222333333222   12466999999999999864

>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=91.77  E-value=0.59  Score=35.00  Aligned_cols=97  Identities=11%  Similarity=0.172  Sum_probs=67.1

Q ss_pred             EEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHh
Q 014486           87 ICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLK  163 (423)
Q Consensus        87 ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~  163 (423)
                      .+..+....|.. ++..++....    ..++||.|+++.-+..+++.++..     ++++..++|+.......   ..+.
T Consensus        12 ~v~v~~~~~K~~-~L~~ll~~~~----~~k~iiF~~~~~~~~~~~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~fk   81 (168)
T d2j0sa2          12 FVAVEREEWKFD-TLCDLYDTLT----ITQAVIFCNTKRKVDWLTEKMREA-----NFTVSSMHGDMPQKERESIMKEFR   81 (168)
T ss_dssp             EEEESSTTHHHH-HHHHHHHHHT----SSEEEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEecChHHHHH-HHHHHHHhCC----CCceEEEeeeHHHHHHHHHHhhhc-----ccchhhhhhhhhHHHHHHHHHHHh
Confidence            344444445643 3444554432    228999999999999988877764     67888999988776554   3455


Q ss_pred             cCCCcEEEechHHHHHHHhcCCCCCCCccEEEEcCc
Q 014486          164 NECPQIVVGTPGRILALARDKDLSLKNVRHFILDEC  199 (423)
Q Consensus       164 ~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vVvDE~  199 (423)
                      ++..+|+|||--      -..+.++.++++||.=++
T Consensus        82 ~g~~~iLv~Td~------~~rGiDi~~v~~VIn~d~  111 (168)
T d2j0sa2          82 SGASRVLISTDV------WARGLDVPQVSLIINYDL  111 (168)
T ss_dssp             HTSSCEEEECGG------GSSSCCCTTEEEEEESSC
T ss_pred             cCCccEEeccch------hcccccccCcceEEEecC
Confidence            677899999963      245778889998885544

>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=91.64  E-value=0.13  Score=41.36  Aligned_cols=48  Identities=10%  Similarity=0.159  Sum_probs=28.3

Q ss_pred             CCCCcCCCCCHHHHHHHHhCCCCCCChhhhhcccccccCCceEEEccCCCcchhHH
Q 014486           45 SSGFRDFLLKPELLRAIVDSGFEHPSEVQHECIPQAILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        45 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      +.+|+++--.+.+.+.|...       .+ .+...-..-.++++.||+|+|||..+
T Consensus         5 P~~~ddivGq~~~~~~L~~~-------i~-~~~~~~~~~~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2           5 PKTLDEYIGQERLKQKLRVY-------LE-AAKARKEPLEHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             CCSGGGSCSCHHHHHHHHHH-------HH-HHTTSSSCCCCEEEECCTTSCHHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHH-------HH-HHHhcCCCCCeEEEECCCCCCHHHHH
Confidence            45688876666666665532       00 00000001246899999999999765

>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=91.33  E-value=0.085  Score=37.15  Aligned_cols=75  Identities=17%  Similarity=0.167  Sum_probs=55.2

Q ss_pred             HHHHHHHHhhcCCcEEEEEcChhhHHHHHHHHHhCCCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCccccCCCCCC
Q 014486          277 RKLNDLLDALDFNQVVIFVKSVSRAAELNKLLVECNFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDLVGRGIDIER  356 (423)
Q Consensus       277 ~~l~~ll~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~~~~Gld~~~  356 (423)
                      ..+..+++.. .+++|+.|.+...++.+.+.|++.++++..+.+- +         .|.++.  +.|+...+..|+-+++
T Consensus        24 ~~L~~~i~~~-~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~~-~---------~~~~~~--~~i~~~~l~~GF~~~~   90 (117)
T d2eyqa2          24 DALRKFLETF-DGPVVFSVESEGRREALGELLARIKIAPQRIMRL-D---------EASDRG--RYLMIGAAEHGFVDTV   90 (117)
T ss_dssp             HHHHHHHTTC-CSCCCEEESSHHHHHHHHHHHGGGTCCCEECSSG-G---------GCCTTC--CEEEECCCCSCEEETT
T ss_pred             HHHHHHHHhC-CCeEEEEECCccHHHHHHHHHHHcCCCceEecCh-h---------hhcCce--EEEEEecCccccccCC
Confidence            3455566543 4678999999999999999999999987665542 1         233333  5566678999998888


Q ss_pred             CCEEEEcc
Q 014486          357 VNIVINYD  364 (423)
Q Consensus       357 ~~~vi~~~  364 (423)
                      .+.+|..+
T Consensus        91 ~~l~vItE   98 (117)
T d2eyqa2          91 RNLALICE   98 (117)
T ss_dssp             TTEEEEEH
T ss_pred             CCEEEEEc
Confidence            88888643

>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=91.21  E-value=0.55  Score=36.02  Aligned_cols=117  Identities=13%  Similarity=0.112  Sum_probs=61.0

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccC---CCC-CCeEEEEEecChHHH------HHHHHHHHHHhccC--CCceEEEEE
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTE---PNP-GQVTALVLCHTRELA------YQICHEFERFSTYL--PDIKVAVFY  150 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~---~~~-~~~~~lil~P~~~L~------~q~~~~~~~~~~~~--~~~~~~~~~  150 (423)
                      ..++++.||+|.|||...--.+.....   +.. .. +.++-+....|.      -+|.++++......  ..-++..+.
T Consensus        43 k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~-~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfI  121 (195)
T d1jbka_          43 KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKG-RRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFI  121 (195)
T ss_dssp             SCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTT-CEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEE
T ss_pred             CCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcC-ceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEc
Confidence            357999999999999754322221111   111 12 335554444444      36766666544221  011222221


Q ss_pred             c-------------Ccch-HHHHHHHhcCCCcEE-EechHHHHHHHhcCCCCCCCccEEEEcCcc
Q 014486          151 G-------------GVNI-KIHKDLLKNECPQIV-VGTPGRILALARDKDLSLKNVRHFILDECD  200 (423)
Q Consensus       151 ~-------------~~~~-~~~~~~~~~~~~~il-v~T~~~l~~~~~~~~~~~~~~~~vVvDE~h  200 (423)
                      .             +.+. ......+..+...+| -|||+.+..+++...-....|..|-++|..
T Consensus       122 Deih~l~~~g~~~g~~d~~~~Lkp~L~rg~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~  186 (195)
T d1jbka_         122 DELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPS  186 (195)
T ss_dssp             ETGGGGTT------CCCCHHHHHHHHHTTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCC
T ss_pred             chHHHHhcCCCCCCcccHHHHHHHHHhCCCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCCC
Confidence            1             1111 222333445655655 466777777666554445678889898875

>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=90.97  E-value=0.19  Score=45.09  Aligned_cols=55  Identities=16%  Similarity=0.069  Sum_probs=38.8

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCC---------CCeEEEEEecChHHHHHHHHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNP---------GQVTALVLCHTRELAYQICHEFERF  137 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~---------~~~~~lil~P~~~L~~q~~~~~~~~  137 (423)
                      ....+|.|..|||||.+.+--++..+....         ..-.+|+|+=|+.-|.++.+++.+.
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~   79 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHH
Confidence            456899999999999876655555443211         1125889998888888888777554

>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=90.70  E-value=0.061  Score=40.22  Aligned_cols=19  Identities=16%  Similarity=0.225  Sum_probs=15.9

Q ss_pred             CCceEEEccCCCcchhHHH
Q 014486           83 GMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~  101 (423)
                      .+++++.||+|+|||.++-
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            3678999999999998654

>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=90.65  E-value=0.54  Score=35.21  Aligned_cols=74  Identities=8%  Similarity=0.086  Sum_probs=55.7

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHH---HHHhcCCCcEEEechHHHHHHHhcCCCCCCCcc
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHK---DLLKNECPQIVVGTPGRILALARDKDLSLKNVR  192 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~  192 (423)
                      ++||.|+++.-+..+.+.+.+.     ++++..++|+.+..+..   +.+.++..+|+|+|..      -...+++..++
T Consensus        29 k~iIF~~~~~~~~~l~~~L~~~-----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~------~~~Gid~~~~~   97 (168)
T d1t5ia_          29 QVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL------FGRGMDIERVN   97 (168)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC------CSTTCCGGGCS
T ss_pred             eEEEEEeeeecchhhhhhhccc-----cccccccccccchhhhhhhhhhhccccceeeecccc------ccchhhcccch
Confidence            7899999999988888777664     67899999998766554   4456677899999943      13456777888


Q ss_pred             EEEEcCcc
Q 014486          193 HFILDECD  200 (423)
Q Consensus       193 ~vVvDE~h  200 (423)
                      +||.=+.-
T Consensus        98 ~vi~~~~p  105 (168)
T d1t5ia_          98 IAFNYDMP  105 (168)
T ss_dssp             EEEESSCC
T ss_pred             hhhhhhcc
Confidence            87766553

>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=90.54  E-value=0.047  Score=46.16  Aligned_cols=18  Identities=22%  Similarity=0.464  Sum_probs=15.7

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      .+++++.||||+|||+.+
T Consensus        49 ~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            467999999999999865

>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=90.31  E-value=0.05  Score=41.35  Aligned_cols=19  Identities=21%  Similarity=0.333  Sum_probs=16.0

Q ss_pred             cCCceEEEccCCCcchhHH
Q 014486           82 LGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~  100 (423)
                      .|+-+++.||+|||||.++
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            4566889999999999864

>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=89.87  E-value=0.14  Score=41.83  Aligned_cols=26  Identities=15%  Similarity=0.160  Sum_probs=18.7

Q ss_pred             CceEEEccCCCcchhHHHHHHhhccCC
Q 014486           84 MDVICQAKSGMGKTAVFVLSTLQQTEP  110 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~~~~~~~~~  110 (423)
                      .++++.||+|+|||.+. -.+...+..
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            56999999999999764 334444443

>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=89.76  E-value=0.13  Score=41.43  Aligned_cols=37  Identities=14%  Similarity=0.179  Sum_probs=26.2

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      |.-+++.|++|+|||...+-.+.+......   ++++++-
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~~~~~~~---~~~~is~   62 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVENACANKE---RAILFAY   62 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHHTTTC---CEEEEES
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcc---ccceeec
Confidence            456999999999999877665655544333   5666663

>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=89.69  E-value=0.07  Score=40.42  Aligned_cols=19  Identities=26%  Similarity=0.595  Sum_probs=15.7

Q ss_pred             CCceEEEccCCCcchhHHH
Q 014486           83 GMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~  101 (423)
                      +.++++.||+|+|||.++-
T Consensus         5 ~~~I~i~G~~GsGKTT~~~   23 (174)
T d1y63a_           5 GINILITGTPGTGKTSMAE   23 (174)
T ss_dssp             SCEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHH
Confidence            3469999999999998653

>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=89.64  E-value=0.15  Score=45.19  Aligned_cols=44  Identities=7%  Similarity=0.103  Sum_probs=29.4

Q ss_pred             ccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChHHH
Q 014486           81 ILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRELA  127 (423)
Q Consensus        81 ~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~  127 (423)
                      ...++++|.|+||+|||... ..++..+...+.  .++|+=|..++.
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l-~~li~~~~~~g~--~~iiiD~kge~~   91 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLL-RELAYTGLLRGD--RMVIVDPNGDML   91 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHH-HHHHHHHHHTTC--EEEEEEETTHHH
T ss_pred             cccceEEEEeCCCCcHHHHH-HHHHHHHHhCCC--CEEEEeCChhHH
Confidence            44678999999999999764 334444333222  677777877653

>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=89.49  E-value=0.065  Score=39.60  Aligned_cols=16  Identities=19%  Similarity=0.210  Sum_probs=13.4

Q ss_pred             ceEEEccCCCcchhHH
Q 014486           85 DVICQAKSGMGKTAVF  100 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~  100 (423)
                      -+++.|++|||||..+
T Consensus         4 lIii~G~pGsGKTTla   19 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3788999999999754

>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=88.99  E-value=0.074  Score=40.18  Aligned_cols=16  Identities=25%  Similarity=0.378  Sum_probs=13.9

Q ss_pred             ceEEEccCCCcchhHH
Q 014486           85 DVICQAKSGMGKTAVF  100 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~  100 (423)
                      -+++.||+|||||+++
T Consensus         4 lI~i~G~~GsGKTTva   19 (176)
T d2bdta1           4 LYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999864

>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=88.98  E-value=0.22  Score=41.03  Aligned_cols=41  Identities=22%  Similarity=0.141  Sum_probs=26.3

Q ss_pred             cccCCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           80 AILGMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        80 ~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      +..|.-+++.|+||+|||...+-.+.+.....+.  ++++++.
T Consensus        32 ~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~--~v~~~s~   72 (277)
T d1cr2a_          32 ARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGK--KVGLAML   72 (277)
T ss_dssp             BCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCC--CEEEEES
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhccc--ceeEeee
Confidence            3446669999999999997554444443322222  6677764

>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=88.75  E-value=0.081  Score=40.25  Aligned_cols=21  Identities=24%  Similarity=0.319  Sum_probs=16.8

Q ss_pred             cccCCceEEEccCCCcchhHH
Q 014486           80 AILGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        80 ~~~~~~~ii~~~tGsGKT~~~  100 (423)
                      -.+|.-+++.|++|||||.++
T Consensus         3 ~~~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           3 ATQGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             TTCCEEEEEECSTTSSHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHH
Confidence            345566889999999999865

>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=88.48  E-value=0.25  Score=39.55  Aligned_cols=40  Identities=15%  Similarity=0.078  Sum_probs=25.1

Q ss_pred             cCCceEEEccCCCcchhHHHHHHhhccCC---CCCCeEEEEEe
Q 014486           82 LGMDVICQAKSGMGKTAVFVLSTLQQTEP---NPGQVTALVLC  121 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~~~~~~~~~~---~~~~~~~lil~  121 (423)
                      .|+-+++.||+|+|||...+-.+......   ...+..++++.
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~   75 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYID   75 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEE
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEe
Confidence            34669999999999998665544443221   11223566664

>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=88.27  E-value=0.13  Score=38.60  Aligned_cols=18  Identities=22%  Similarity=0.394  Sum_probs=15.1

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      ..+++.||+|||||.++-
T Consensus         5 ~~I~i~G~pGsGKTTia~   22 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGK   22 (173)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            468999999999998653

>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=88.22  E-value=0.1  Score=39.46  Aligned_cols=19  Identities=21%  Similarity=0.274  Sum_probs=15.5

Q ss_pred             cCCceEEEccCCCcchhHH
Q 014486           82 LGMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~  100 (423)
                      ..+-+++.|++|||||.++
T Consensus         2 ~~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3456889999999999765

>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=87.83  E-value=1.7  Score=37.36  Aligned_cols=118  Identities=14%  Similarity=0.121  Sum_probs=56.1

Q ss_pred             CCceEEEccCCCcchhHHHHHH---hhccCCCC-CCeEEEEEecChHHH-----HHHHHHHHHHhccC--CCceEEEEE-
Q 014486           83 GMDVICQAKSGMGKTAVFVLST---LQQTEPNP-GQVTALVLCHTRELA-----YQICHEFERFSTYL--PDIKVAVFY-  150 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~---~~~~~~~~-~~~~~lil~P~~~L~-----~q~~~~~~~~~~~~--~~~~~~~~~-  150 (423)
                      .+|.++.||+|.|||...--.+   ...-.+.. .+.+++.+-+.+-++     .+|.+++..+....  ..-++..+. 
T Consensus        43 k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfid  122 (387)
T d1qvra2          43 KNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFID  122 (387)
T ss_dssp             CCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEEC
T ss_pred             CCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchhHHHHHHHHHHHhccCCCceEEEec
Confidence            3569999999999997542111   12111111 222444444444333     25666665543221  011122211 


Q ss_pred             --------cCc----ch-HHHHHHHhcCCCcEE-EechHHHHHHHhcCCCCCCCccEEEEcCcch
Q 014486          151 --------GGV----NI-KIHKDLLKNECPQIV-VGTPGRILALARDKDLSLKNVRHFILDECDK  201 (423)
Q Consensus       151 --------~~~----~~-~~~~~~~~~~~~~il-v~T~~~l~~~~~~~~~~~~~~~~vVvDE~h~  201 (423)
                              |+.    +. ......+..+...+| -+||+-+.. +....-....|..|-|+|-+.
T Consensus       123 e~h~l~~~g~~~g~~d~a~~Lkp~L~rg~~~~I~~tT~~ey~~-~e~d~al~rrF~~v~v~ep~~  186 (387)
T d1qvra2         123 ELHTVVGAGKAEGAVDAGNMLKPALARGELRLIGATTLDEYRE-IEKDPALERRFQPVYVDEPTV  186 (387)
T ss_dssp             CC-------------------HHHHHTTCCCEEEEECHHHHHH-HTTCTTTCSCCCCEEECCCCH
T ss_pred             cHHHHhcCCCCCCcccHHHHHHHHHhCCCcceeeecCHHHHHH-hcccHHHHHhcccccCCCCcH
Confidence                    111    11 222333455656655 556666654 555444457789999999984

>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=87.77  E-value=0.11  Score=39.02  Aligned_cols=18  Identities=17%  Similarity=0.274  Sum_probs=15.1

Q ss_pred             CceEEEccCCCcchhHHH
Q 014486           84 MDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~  101 (423)
                      +++++.|++|+|||.+.-
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            468899999999998653

>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=87.76  E-value=0.089  Score=43.24  Aligned_cols=17  Identities=24%  Similarity=0.376  Sum_probs=14.6

Q ss_pred             CceEEEccCCCcchhHH
Q 014486           84 MDVICQAKSGMGKTAVF  100 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~  100 (423)
                      +.+++.||+|+|||..+
T Consensus        33 ~~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEEECCTTSCTHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            35899999999999864

>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=87.37  E-value=0.085  Score=40.37  Aligned_cols=18  Identities=17%  Similarity=0.204  Sum_probs=15.4

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      .+.+++.||+|+|||..+
T Consensus         7 ~K~I~i~G~~GsGKTTla   24 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLV   24 (192)
T ss_dssp             CEEEEEECCTTSHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            467999999999999754

>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=87.25  E-value=1  Score=34.93  Aligned_cols=114  Identities=17%  Similarity=0.161  Sum_probs=70.7

Q ss_pred             cCCcEEEEEcChhhHHHHHHHHHhC----CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcCc-----c-ccCCCCCC
Q 014486          287 DFNQVVIFVKSVSRAAELNKLLVEC----NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATDL-----V-GRGIDIER  356 (423)
Q Consensus       287 ~~~~~ivf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~~-----~-~~Gld~~~  356 (423)
                      .+.++||.+++.+.+..+.+.+...    +..+..++|+.+..+....++     ..+|+|+|+-     + ...+++.+
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            3457999999999999987777653    677888899888776655443     3689999942     2 34678889


Q ss_pred             CCEEEEccCC----CCc-chhhhcccccCCCCCceEEEEEecCcccHHHHHHHHHHHh
Q 014486          357 VNIVINYDMP----DSA-DTYLHRVGRAGRFGTKGLAITFVSSASDSDILNQVSKFMF  409 (423)
Q Consensus       357 ~~~vi~~~~~----~s~-~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (423)
                      ++++|.-+..    ... ....+...+.   .. ..-+++++.....++.+..++.|.
T Consensus       146 l~~lViDEad~l~~~~~~~~i~~I~~~~---~~-~~Q~i~~SAT~~~~v~~~~~~~l~  199 (208)
T d1hv8a1         146 VKYFILDEADEMLNMGFIKDVEKILNAC---NK-DKRILLFSATMPREILNLAKKYMG  199 (208)
T ss_dssp             CCEEEEETHHHHHTTTTHHHHHHHHHTS---CS-SCEEEEECSSCCHHHHHHHHHHCC
T ss_pred             CcEEEEEChHHhhcCCChHHHHHHHHhC---CC-CCeEEEEEccCCHHHHHHHHHHCC
Confidence            9988753311    111 1222222222   11 233556665555565665555553

>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=87.23  E-value=1.3  Score=32.42  Aligned_cols=51  Identities=16%  Similarity=0.195  Sum_probs=37.5

Q ss_pred             CCccEEEEcCcchhhcc-CCcHHHHHHHHHhCCCCceEEEEeccCCccHHHH
Q 014486          189 KNVRHFILDECDKMLES-LDMRRDVQEIFKMTPHDKQVMMFSATLSKEIRPV  239 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~-~~~~~~~~~~~~~~~~~~~~v~~SAT~~~~~~~~  239 (423)
                      ..+++||+||+-..... .-....+..+++..|...-+|+....+|+++...
T Consensus        93 ~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~p~~L~e~  144 (157)
T d1g5ta_          93 PLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDL  144 (157)
T ss_dssp             TTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHH
T ss_pred             CccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHh
Confidence            55789999999987662 2235667777887787887887777788776654

>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=87.20  E-value=0.46  Score=34.26  Aligned_cols=64  Identities=16%  Similarity=0.438  Sum_probs=47.3

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEechHHHHHHHhcCCCCCCCccEEE
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTPGRILALARDKDLSLKNVRHFI  195 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vV  195 (423)
                      ++||.|+++.-|+++++.++..     ++++..++++.....    +.++..+++|||--     + ...++ .++++||
T Consensus        37 k~IVFc~t~~~ae~la~~L~~~-----G~~~~~~H~~~~~~~----~~~~~~~vlvaTd~-----~-~~GiD-~~v~~Vi  100 (138)
T d1jr6a_          37 RHLIFCHSKKKCDELAAKLVAL-----GINAVAYYRGLDVSV----IPTNGDVVVVATDA-----L-MTGFT-GDFDSVI  100 (138)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHH-----TCEEEEECTTCCSCC----CTTSSCEEEEESSS-----S-CSSSC-CCBSEEE
T ss_pred             CEEEEeCcHHHHHHHHHHHhcc-----ccchhhhhccchhhh----hhhhhcceeehhHH-----H-Hhccc-cccceEE
Confidence            7899999999999999888775     788999999876443    34566799999941     1 22344 4667664

>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=87.09  E-value=0.1  Score=42.35  Aligned_cols=17  Identities=29%  Similarity=0.397  Sum_probs=14.7

Q ss_pred             CceEEEccCCCcchhHH
Q 014486           84 MDVICQAKSGMGKTAVF  100 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~  100 (423)
                      +++++.||+|+|||..+
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            46999999999999764

>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=86.98  E-value=0.24  Score=35.60  Aligned_cols=37  Identities=11%  Similarity=0.130  Sum_probs=25.1

Q ss_pred             eEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEecChH
Q 014486           86 VICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCHTRE  125 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  125 (423)
                      -++.||+.||||.-. +-.+......+.  +++++-|...
T Consensus         5 ~li~GpMfsGKTt~L-i~~~~~~~~~g~--~v~~ikp~~D   41 (133)
T d1xbta1           5 QVILGPMFSGKSTEL-MRRVRRFQIAQY--KCLVIKYAKD   41 (133)
T ss_dssp             EEEECCTTSCHHHHH-HHHHHHHHTTTC--CEEEEEETTC
T ss_pred             EEEEecccCHHHHHH-HHHHHHHHHcCC--cEEEEecccc
Confidence            578999999999754 444444333332  6889988754

>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=86.13  E-value=0.23  Score=38.98  Aligned_cols=26  Identities=15%  Similarity=0.022  Sum_probs=19.9

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhcc
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQT  108 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~  108 (423)
                      |.-+++.||+|+|||...+-.+.+..
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            56699999999999987665555443

>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=85.94  E-value=0.14  Score=38.45  Aligned_cols=17  Identities=35%  Similarity=0.309  Sum_probs=14.3

Q ss_pred             ceEEEccCCCcchhHHH
Q 014486           85 DVICQAKSGMGKTAVFV  101 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~  101 (423)
                      -+++.|++|||||..+-
T Consensus         8 iivl~G~~GsGKsT~a~   24 (171)
T d1knqa_           8 IYVLMGVSGSGKSAVAS   24 (171)
T ss_dssp             EEEEECSTTSCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            37889999999998653

>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=85.79  E-value=0.15  Score=44.01  Aligned_cols=17  Identities=24%  Similarity=0.399  Sum_probs=14.9

Q ss_pred             CceEEEccCCCcchhHH
Q 014486           84 MDVICQAKSGMGKTAVF  100 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~  100 (423)
                      .+++..||||+|||..+
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            56999999999999754

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {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: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=84.88  E-value=1.1  Score=36.13  Aligned_cols=18  Identities=11%  Similarity=0.161  Sum_probs=14.8

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      ++.++|.||.|+|||...
T Consensus        29 ~~~i~i~G~~G~GKTsLl   46 (283)
T d2fnaa2          29 APITLVLGLRRTGKSSII   46 (283)
T ss_dssp             SSEEEEEESTTSSHHHHH
T ss_pred             CCEEEEEcCCCCcHHHHH
Confidence            356889999999999754

>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=84.85  E-value=0.24  Score=37.31  Aligned_cols=19  Identities=21%  Similarity=0.113  Sum_probs=15.5

Q ss_pred             CceEEEccCCCcchhHHHH
Q 014486           84 MDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~~~  102 (423)
                      +.+++.|++|+|||.++-+
T Consensus         3 ~~Iil~G~~GsGKSTia~~   21 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRE   21 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHH
Confidence            5688899999999987543

>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=84.76  E-value=0.17  Score=38.54  Aligned_cols=18  Identities=28%  Similarity=0.294  Sum_probs=15.1

Q ss_pred             ceEEEccCCCcchhHHHH
Q 014486           85 DVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~  102 (423)
                      ++++.||+|||||+++-.
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            478999999999987644

>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=84.45  E-value=0.27  Score=37.78  Aligned_cols=20  Identities=20%  Similarity=0.265  Sum_probs=16.0

Q ss_pred             CCceEEEccCCCcchhHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~  102 (423)
                      |-.+++.||+|||||+++-.
T Consensus         3 ~~riil~G~pGSGKsT~a~~   22 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPK   22 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHH
Confidence            34578899999999987644

>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=84.39  E-value=0.24  Score=38.08  Aligned_cols=18  Identities=22%  Similarity=0.265  Sum_probs=14.9

Q ss_pred             ceEEEccCCCcchhHHHH
Q 014486           85 DVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~  102 (423)
                      .+++.||+|||||..+-.
T Consensus         5 ~I~i~GppGsGKsT~a~~   22 (189)
T d1zaka1           5 KVMISGAPASGKGTQCEL   22 (189)
T ss_dssp             CEEEEESTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            478999999999987643

>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=84.39  E-value=0.21  Score=39.77  Aligned_cols=38  Identities=16%  Similarity=0.160  Sum_probs=23.9

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCCCCCeEEEEEec
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPNPGQVTALVLCH  122 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  122 (423)
                      |.-+++.|++|+|||..++-.+.+.+...+.  +++++..
T Consensus        26 G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~--~~~~~s~   63 (242)
T d1tf7a1          26 GRSTLVSGTSGTGKTLFSIQFLYNGIIEFDE--PGVFVTF   63 (242)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHHHCC--CEEEEES
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcCC--Ccccccc
Confidence            4569999999999997654434333322222  5666654

>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=83.97  E-value=0.25  Score=37.48  Aligned_cols=17  Identities=18%  Similarity=0.255  Sum_probs=14.6

Q ss_pred             ceEEEccCCCcchhHHH
Q 014486           85 DVICQAKSGMGKTAVFV  101 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~  101 (423)
                      .+++.||+|||||+++-
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            37899999999998764

>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=83.91  E-value=0.75  Score=37.40  Aligned_cols=63  Identities=14%  Similarity=0.145  Sum_probs=37.2

Q ss_pred             hcccccccCCceEEEccCCCcchhHHHHHHhhccCC-------CCCCeEEEEEecChHHHHHHHHHHHHHh
Q 014486           75 ECIPQAILGMDVICQAKSGMGKTAVFVLSTLQQTEP-------NPGQVTALVLCHTRELAYQICHEFERFS  138 (423)
Q Consensus        75 ~~i~~~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~~-------~~~~~~~lil~P~~~L~~q~~~~~~~~~  138 (423)
                      ..++-++.|.-+++.|++|+|||...+..++.....       ...+.+++++.- ..-..++..++..+.
T Consensus        21 ~li~G~~pg~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~-E~~~~~~~~Rl~~~~   90 (274)
T d1nlfa_          21 YVLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPA-EDPPTAIHHRLHALG   90 (274)
T ss_dssp             EEETTEETTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEES-SSCHHHHHHHHHHHH
T ss_pred             HHhCCccCCcEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEec-cchHHHHHHHHHHHh
Confidence            356677777779999999999997665544432211       111225666653 223445555665554

>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=83.90  E-value=0.2  Score=38.10  Aligned_cols=17  Identities=18%  Similarity=0.085  Sum_probs=14.4

Q ss_pred             ceEEEccCCCcchhHHH
Q 014486           85 DVICQAKSGMGKTAVFV  101 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~  101 (423)
                      .+++.||+|||||+++-
T Consensus         2 ~I~i~G~pGSGKsT~~~   18 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQ   18 (179)
T ss_dssp             EEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            46889999999998763

>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=83.87  E-value=0.54  Score=37.65  Aligned_cols=26  Identities=15%  Similarity=-0.005  Sum_probs=19.5

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhcc
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQT  108 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~  108 (423)
                      |+-++|.||+|+|||...+-.+.+..
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            45699999999999987665554443

>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=83.84  E-value=1.8  Score=33.84  Aligned_cols=70  Identities=14%  Similarity=0.252  Sum_probs=53.1

Q ss_pred             CcEEEEEcChhhHHHHHHHHHhC----CCCeEEEcCCCCHHHHHHHHHhhhcCCccEEEEcC------ccccCCCCCCCC
Q 014486          289 NQVVIFVKSVSRAAELNKLLVEC----NFPSICIHSGMSQEERLTRYKGFKEGNKRILVATD------LVGRGIDIERVN  358 (423)
Q Consensus       289 ~~~ivf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~ili~T~------~~~~Gld~~~~~  358 (423)
                      -+.+|.+++++.+..+++.+...    ++.+..+.|+.+.......++.    ..+|||+|+      .-...+++.+++
T Consensus        86 ~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~----~~~Ilv~TPgrl~~~~~~~~~~~~~l~  161 (222)
T d2j0sa1          86 TQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY----GQHVVAGTPGRVFDMIRRRSLRTRAIK  161 (222)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHTTSSCCTTCC
T ss_pred             ceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhcc----CCeEEeCCCCcHHhcccccccccccce
Confidence            46899999999999998877653    5678888898887766555432    458999994      224567888899


Q ss_pred             EEEE
Q 014486          359 IVIN  362 (423)
Q Consensus       359 ~vi~  362 (423)
                      ++|.
T Consensus       162 ~lVl  165 (222)
T d2j0sa1         162 MLVL  165 (222)
T ss_dssp             EEEE
T ss_pred             eeee
Confidence            8885

>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=83.42  E-value=0.28  Score=37.38  Aligned_cols=18  Identities=17%  Similarity=0.206  Sum_probs=14.8

Q ss_pred             ceEEEccCCCcchhHHHH
Q 014486           85 DVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~  102 (423)
                      .+++.||+|||||+++-.
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            378999999999987643

>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=83.42  E-value=0.23  Score=37.73  Aligned_cols=17  Identities=24%  Similarity=0.307  Sum_probs=14.4

Q ss_pred             CceEEEccCCCcchhHH
Q 014486           84 MDVICQAKSGMGKTAVF  100 (423)
Q Consensus        84 ~~~ii~~~tGsGKT~~~  100 (423)
                      +-+++.|++|||||...
T Consensus         2 kiI~i~G~~GsGKsT~~   18 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSS   18 (190)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            45789999999999764

>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=82.84  E-value=0.78  Score=35.56  Aligned_cols=81  Identities=12%  Similarity=0.208  Sum_probs=52.2

Q ss_pred             EEEEEecChHHHHH-----HHHHHHHHh-ccCCCceEEEEEcCcchH---HHHHHHhcCCCcEEEechHHHHHHHhcCCC
Q 014486          116 TALVLCHTRELAYQ-----ICHEFERFS-TYLPDIKVAVFYGGVNIK---IHKDLLKNECPQIVVGTPGRILALARDKDL  186 (423)
Q Consensus       116 ~~lil~P~~~L~~q-----~~~~~~~~~-~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~  186 (423)
                      ++.||||..+-...     ..+.+..+. ...|+.++..+||..+..   .-...+.++..+|+|||.-      -...+
T Consensus        31 QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTtV------iE~GI  104 (206)
T d1gm5a4          31 QAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTV------IEVGI  104 (206)
T ss_dssp             CBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSC------CCSCS
T ss_pred             CEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEehh------hhccc
Confidence            78999998643322     122223332 234678888999987543   3456677888999999952      24567


Q ss_pred             CCCCccEEEEcCcchh
Q 014486          187 SLKNVRHFILDECDKM  202 (423)
Q Consensus       187 ~~~~~~~vVvDE~h~~  202 (423)
                      +..+.+++|+..++++
T Consensus       105 Dip~a~~iii~~a~~f  120 (206)
T d1gm5a4         105 DVPRANVMVIENPERF  120 (206)
T ss_dssp             CCTTCCEEEBCSCSSS
T ss_pred             cccCCcEEEEEccCCc
Confidence            8899999999999965

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.74  E-value=0.23  Score=42.06  Aligned_cols=25  Identities=16%  Similarity=0.395  Sum_probs=19.9

Q ss_pred             cccccccCCc--eEEEccCCCcchhHH
Q 014486           76 CIPQAILGMD--VICQAKSGMGKTAVF  100 (423)
Q Consensus        76 ~i~~~~~~~~--~ii~~~tGsGKT~~~  100 (423)
                      .++.++.|.+  ++..|+||||||.+.
T Consensus        67 lv~~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          67 IVKDVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHcCCCcceeeecccCCCCceec
Confidence            3556677877  788999999999863

>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=82.73  E-value=0.24  Score=37.45  Aligned_cols=14  Identities=29%  Similarity=0.501  Sum_probs=12.7

Q ss_pred             eEEEccCCCcchhH
Q 014486           86 VICQAKSGMGKTAV   99 (423)
Q Consensus        86 ~ii~~~tGsGKT~~   99 (423)
                      ++++|++|||||..
T Consensus        17 iil~G~pGsGKST~   30 (172)
T d1yj5a2          17 VVAVGFPGAGKSTF   30 (172)
T ss_dssp             EEEECCTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            88999999999964

>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=82.58  E-value=1.5  Score=33.72  Aligned_cols=76  Identities=18%  Similarity=0.188  Sum_probs=50.2

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCC-------------------------ceEEEEEcCcchHHHH---HHHhcCCC
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPD-------------------------IKVAVFYGGVNIKIHK---DLLKNECP  167 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~-------------------------~~~~~~~~~~~~~~~~---~~~~~~~~  167 (423)
                      .+||.||++.-+...+..+.........                         -.++.++++.......   ..+.++..
T Consensus        42 ~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f~~g~i  121 (201)
T d2p6ra4          42 GVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNI  121 (201)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             cEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHHhCCCc
Confidence            6899999998888887777664322110                         1267788887655443   44667888


Q ss_pred             cEEEechHHHHHHHhcCCCCCCCccEEEEc
Q 014486          168 QIVVGTPGRILALARDKDLSLKNVRHFILD  197 (423)
Q Consensus       168 ~ilv~T~~~l~~~~~~~~~~~~~~~~vVvD  197 (423)
                      +|+|||...-      ..+++....+||.|
T Consensus       122 ~vlvaT~~l~------~Gin~p~~~vvi~~  145 (201)
T d2p6ra4         122 KVVVATPTLA------AGVNLPARRVIVRS  145 (201)
T ss_dssp             CEEEECSTTT------SSSCCCBSEEEECC
T ss_pred             eEEEechHHH------hhcCCCCceEEEec
Confidence            9999997532      35566666666643

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.57  E-value=0.063  Score=44.23  Aligned_cols=18  Identities=28%  Similarity=0.360  Sum_probs=15.4

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      .+.+++.||+|+|||+.+
T Consensus        41 ~~giLL~Gp~GtGKT~l~   58 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLLA   58 (265)
T ss_dssp             CCEEEEBCCTTSSHHHHH
T ss_pred             CCeEEEECCCCCcchhHH
Confidence            467999999999999754

>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=82.28  E-value=0.32  Score=37.50  Aligned_cols=17  Identities=18%  Similarity=0.221  Sum_probs=14.3

Q ss_pred             eEEEccCCCcchhHHHH
Q 014486           86 VICQAKSGMGKTAVFVL  102 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~~  102 (423)
                      +++.||+|||||.++-.
T Consensus        11 I~i~GppGSGKsT~a~~   27 (196)
T d1ukza_          11 IFVLGGPGAGKGTQCEK   27 (196)
T ss_dssp             EEEECSTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            78889999999987643

>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=81.94  E-value=0.34  Score=37.30  Aligned_cols=16  Identities=25%  Similarity=0.312  Sum_probs=13.9

Q ss_pred             eEEEccCCCcchhHHH
Q 014486           86 VICQAKSGMGKTAVFV  101 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~  101 (423)
                      +++.||+|||||.++-
T Consensus         9 I~i~G~pGSGKsT~a~   24 (194)
T d1qf9a_           9 VFVLGGPGSGKGTQCA   24 (194)
T ss_dssp             EEEEESTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            7889999999998653

>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=81.38  E-value=0.36  Score=37.16  Aligned_cols=20  Identities=15%  Similarity=0.099  Sum_probs=16.2

Q ss_pred             cCCceEEEccCCCcchhHHH
Q 014486           82 LGMDVICQAKSGMGKTAVFV  101 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~~~  101 (423)
                      ..+-+++.||+|||||.++-
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~   26 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCE   26 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            34568899999999998654

>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=81.36  E-value=0.46  Score=38.12  Aligned_cols=48  Identities=8%  Similarity=-0.095  Sum_probs=28.8

Q ss_pred             CCceEEEccCCCcchhHHHHHHhhccCCC---CCCeEEEEEecChHHHHHH
Q 014486           83 GMDVICQAKSGMGKTAVFVLSTLQQTEPN---PGQVTALVLCHTRELAYQI  130 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~~~~~~~~~~~~---~~~~~~lil~P~~~L~~q~  130 (423)
                      |.-+++.|++|+|||..++-.+.+.....   .....++++.....+...+
T Consensus        37 G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (258)
T d1v5wa_          37 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDR   87 (258)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHH
Confidence            45699999999999987665554433321   2223556665544443333

>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=81.33  E-value=0.37  Score=37.00  Aligned_cols=18  Identities=22%  Similarity=0.174  Sum_probs=15.2

Q ss_pred             ceEEEccCCCcchhHHHH
Q 014486           85 DVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~  102 (423)
                      .+++.||+|||||.++-.
T Consensus         8 rIiliG~PGSGKtT~a~~   25 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSR   25 (189)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            588999999999987644

>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=81.28  E-value=0.37  Score=37.03  Aligned_cols=16  Identities=25%  Similarity=0.327  Sum_probs=14.0

Q ss_pred             eEEEccCCCcchhHHH
Q 014486           86 VICQAKSGMGKTAVFV  101 (423)
Q Consensus        86 ~ii~~~tGsGKT~~~~  101 (423)
                      +++.||+|||||+++-
T Consensus         4 I~i~GppGSGKsT~a~   19 (194)
T d1teva_           4 VFVLGGPGAGKGTQCA   19 (194)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6899999999998764

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=81.19  E-value=0.58  Score=37.42  Aligned_cols=28  Identities=21%  Similarity=0.206  Sum_probs=19.7

Q ss_pred             cccCCceEEEccCCCcchhHHHHHHhhccC
Q 014486           80 AILGMDVICQAKSGMGKTAVFVLSTLQQTE  109 (423)
Q Consensus        80 ~~~~~~~ii~~~tGsGKT~~~~~~~~~~~~  109 (423)
                      +..|..+.|.||+|||||..  +-++..+.
T Consensus        26 i~~Ge~vaIvG~sGsGKSTL--l~ll~gl~   53 (241)
T d2pmka1          26 IKQGEVIGIVGRSGSGKSTL--TKLIQRFY   53 (241)
T ss_dssp             EETTCEEEEECSTTSSHHHH--HHHHTTSS
T ss_pred             EcCCCEEEEECCCCCCHHHH--HHHHHhcC
Confidence            33477799999999999963  34444443

>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=81.05  E-value=0.97  Score=37.33  Aligned_cols=53  Identities=11%  Similarity=0.094  Sum_probs=37.9

Q ss_pred             EEEEEecChHHHHHHHHHHHHHhccCCCceEEEEEcCcchHHHHHHHhcCCCcEEEech
Q 014486          116 TALVLCHTRELAYQICHEFERFSTYLPDIKVAVFYGGVNIKIHKDLLKNECPQIVVGTP  174 (423)
Q Consensus       116 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~  174 (423)
                      +++|+||+..-+.++++.+++.     +.++..++|.....+. ..+.++..+|+|+|.
T Consensus        38 ~~~~F~~s~~~~~~~a~~L~~~-----g~~V~~l~~~~~~~e~-~~~~~~~~~~~~~t~   90 (299)
T d1yksa2          38 PTAWFLPSIRAANVMAASLRKA-----GKSVVVLNRKTFEREY-PTIKQKKPDFILATD   90 (299)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHT-----TCCEEECCSSSCC---------CCCSEEEESS
T ss_pred             CEEEEeCCHHHHHHHHHHHHhc-----CCeEEEEcCcCcHhHH-hhhhcCCcCEEEEec
Confidence            7899999999999998888774     5678888887665444 456677789999995

>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=80.78  E-value=0.4  Score=36.39  Aligned_cols=18  Identities=17%  Similarity=0.148  Sum_probs=14.7

Q ss_pred             ceEEEccCCCcchhHHHH
Q 014486           85 DVICQAKSGMGKTAVFVL  102 (423)
Q Consensus        85 ~~ii~~~tGsGKT~~~~~  102 (423)
                      .+++.||+|||||.++-.
T Consensus         4 rIvl~G~pGSGKtT~a~~   21 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPN   21 (180)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            478889999999987643

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=80.76  E-value=0.3  Score=41.95  Aligned_cols=24  Identities=21%  Similarity=0.356  Sum_probs=18.6

Q ss_pred             ccccccCCc--eEEEccCCCcchhHH
Q 014486           77 IPQAILGMD--VICQAKSGMGKTAVF  100 (423)
Q Consensus        77 i~~~~~~~~--~ii~~~tGsGKT~~~  100 (423)
                      +..++.|.+  ++..|+||||||.+.
T Consensus       106 v~~~l~G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_         106 VQTIFEGGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             HHHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhccCceEEeeccCCCCCceee
Confidence            455667777  667799999999874

>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=80.67  E-value=0.16  Score=39.11  Aligned_cols=18  Identities=44%  Similarity=0.479  Sum_probs=14.4

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      |.-+++.|++|||||.++
T Consensus        19 g~vI~L~G~pGSGKTTiA   36 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVS   36 (195)
T ss_dssp             CEEEEEESSCHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            344678899999999865

>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=80.67  E-value=0.2  Score=42.54  Aligned_cols=18  Identities=22%  Similarity=0.189  Sum_probs=15.6

Q ss_pred             cCCceEEEccCCCcchhH
Q 014486           82 LGMDVICQAKSGMGKTAV   99 (423)
Q Consensus        82 ~~~~~ii~~~tGsGKT~~   99 (423)
                      .++++++.||+|+|||..
T Consensus        27 ~~h~vLl~G~pG~GKT~l   44 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTA   44 (333)
T ss_dssp             GGCCEEEECCGGGCTTHH
T ss_pred             CCCeEEEECCCCccHHHH
Confidence            357899999999999975

>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=80.33  E-value=0.42  Score=35.96  Aligned_cols=39  Identities=13%  Similarity=0.079  Sum_probs=22.0

Q ss_pred             CCccEEEEcCcchhhccCCcHHHHHHHHHhCCCCceEEEEe
Q 014486          189 KNVRHFILDECDKMLESLDMRRDVQEIFKMTPHDKQVMMFS  229 (423)
Q Consensus       189 ~~~~~vVvDE~h~~~~~~~~~~~~~~~~~~~~~~~~~v~~S  229 (423)
                      .+.+++++||++....  ........+...+......++++
T Consensus        98 ~~~~vlllDE~~~~~~--~~~~~~~~l~~~l~~~~~~il~~  136 (178)
T d1ye8a1          98 DRRKVIIIDEIGKMEL--FSKKFRDLVRQIMHDPNVNVVAT  136 (178)
T ss_dssp             CTTCEEEECCCSTTGG--GCHHHHHHHHHHHTCTTSEEEEE
T ss_pred             cCCCceeecCCCccch--hhHHHHHHHHHHhccCCCEEEEE
Confidence            4567899999875543  23344444444444444445554

>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=80.23  E-value=0.36  Score=36.71  Aligned_cols=18  Identities=33%  Similarity=0.497  Sum_probs=15.0

Q ss_pred             CCceEEEccCCCcchhHH
Q 014486           83 GMDVICQAKSGMGKTAVF  100 (423)
Q Consensus        83 ~~~~ii~~~tGsGKT~~~  100 (423)
                      |+-+++.||+|+|||...
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            456899999999999753