Psyllid ID: psy17644

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330
Protein Sequence
MSKLEYIPAPGSPSYKGNNASADTDSDEDPLDAFMKGIDKEVKQEAKGVKTKKIEEVKGIRDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccHHHHHHHHcHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccHHHHHHHHHHcccEEEcccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHHHcccccccccccEEEEEcccHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHccccEEEEcccHHHHHHHccccccccEEEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHHcccccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHccccccccccccHcHccccccccccccccccccccccccccccccccccccccccccHHHHHccHHHHHHHHHHccEEEEccccccccccHHHccccHHHHHHHHHcccccccHHHHcHHHHHHccccEEEEEEcccHHHHHHHHHHHHHHHcccccccccccEEEEEccHHHHHHHHHHHHHHHHHHcccEEEEEEcccccHHHHHHHHcccEEEEEcccHHHHHHHcccccccEEEEEEHHHHHHHHccc
Coil and Loop (DISEMBL)
mskleyipapgspsykgnnasadtdsdedpldaFMKGIDKEVKQEAKgvktkkieevkgirddidheddeesYYRYMeenpnaglqdndsdvdleydedgnpiapkkskyidplppidhstiVYEEVEknfyqphediarlTPQEAQELRaksgitvsgadppypvssfghfgFDEVLMKALRKceytsptpiqaqavpaalsgrdiigvaktgsgktgafiWPMLVHimdqkelepgdgpmglilapTRELSQQIYNEAKRFGKGYNLSVVCcygggskwdqsKALELGAeivvgtpgrIIDMVKMGATKLNRVTFLVLDEADRMFDMG
Flexible Loop (DISEMBL)
mskleyipapgspsykgnnasadtdsDEDPLDAFMKGIDKEvkqeakgvktkkieevkgirddidhedDEESYYRYMEenpnaglqdnDSDVDLEYDEDGnpiapkkskyidplppIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKmgatklnrvtflvldeadrmfdmg
Low Complexity Region (SEG)
MSKLEYIPAPGSPSYKGNNASADTDSDEDPLDAFMKGIDKEVKQEAKGVKTKKIEEVKGIRddidheddeeSYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG
Disordered region (IsUnstruct)
*****************************************************************************************************************LPPIDHSTIVYEEVEKNFYQP*****************************YPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE**DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDE********
Disordered Region (DISOPRED)
*****YI***********************LDAFMK*******************************************************************************PIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG
Disordered Region (DISEMBL)
MSKLEYIPAPGSPS*************EDPLDAFMKGIDKEVKQEAKGVKTKKIEEVKGIRDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG
Disordered Region (DISPRO)
***************************EDPLDAFMKGIDKEVKQE*************************ESYYRY*EENPN*********V*LEYDEDGNPIAPKKSKYIDPLPPIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSKLEYIPAPGSPSYKGNNASADTDSDEDPLDAFMKGIDKEVKQEAKGVKTKKIEEVKGIRDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	330	2.2.26 [Sep-21-2011]
Q7ZY47	947	ATP-dependent RNA helicas	N/A	N/A	0.990	0.345	0.604	1e-111
Q810A7	929	ATP-dependent RNA helicas	yes	N/A	0.987	0.350	0.636	1e-109
Q5F485	944	ATP-dependent RNA helicas	yes	N/A	0.987	0.345	0.639	1e-109
Q86XP3	938	ATP-dependent RNA helicas	yes	N/A	0.987	0.347	0.633	1e-109
Q5R7D1	942	ATP-dependent RNA helicas	yes	N/A	0.987	0.346	0.633	1e-108
Q10MH8	770	DEAD-box ATP-dependent RN	yes	N/A	0.896	0.384	0.503	3e-76
Q54IV3	986	Probable ATP-dependent RN	yes	N/A	0.933	0.312	0.480	3e-75
O22907	760	DEAD-box ATP-dependent RN	yes	N/A	0.933	0.405	0.478	7e-75
Q62780	1032	Probable ATP-dependent RN	no	N/A	0.924	0.295	0.424	3e-61
Q569Z5	1032	Probable ATP-dependent RN	no	N/A	0.924	0.295	0.424	4e-61

>sp|Q7ZY47|DDX42_XENLA ATP-dependent RNA helicase DDX42 OS=Xenopus laevis GN=ddx42 PE=2 SV=1

 Score =  400 bits (1029), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 199/329 (60%), Positives = 245/329 (74%), Gaps = 2/329 (0%)

Query: 4   LEYIPAPGSPSYKGNNASADTDSDEDPLDAFMKGIDKEVKQEAKGVKTKKIEEV--KGIR 61
           L YIPA  SP+ +   +  D+DS+EDPL+AFM  ++ +  ++ + ++ +  E+   +GIR
Sbjct: 85  LPYIPAENSPTRQQLRSKTDSDSEEDPLEAFMAEVEDQAAKDMRKLEERDKEKANARGIR 144

Query: 62  DDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHST 121
           DDI+ EDD+E+Y+RYM ENP AGL   + + +LEYD DGNPIAP   + IDPLPPIDH+ 
Sbjct: 145 DDIEEEDDQEAYFRYMAENPTAGLVPEEEEDNLEYDSDGNPIAPTTKRIIDPLPPIDHTE 204

Query: 122 IVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKA 181
           I Y   EKNFY+ HE I   TPQ+  ELR K  + VSGA PP   SSF HFGFDE L+  
Sbjct: 205 IEYPPFEKNFYEEHEAITSQTPQQITELRHKLNLRVSGAAPPRLCSSFAHFGFDEQLLHQ 264

Query: 182 LRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGP 241
           +RK EYT PTPIQ Q +P ALSGRD+IG+AKTGSGKT AFIWP+LVHIMDQKEL+P DGP
Sbjct: 265 IRKSEYTQPTPIQCQGIPVALSGRDMIGIAKTGSGKTAAFIWPILVHIMDQKELQPADGP 324

Query: 242 MGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI 301
           + +I+ PTREL QQI++E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR+
Sbjct: 325 IAVIVCPTRELCQQIHSECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGRL 384

Query: 302 IDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           ID VK  AT L RVT+LV DEADRMFDMG
Sbjct: 385 IDHVKKKATNLQRVTYLVFDEADRMFDMG 413

ATP-dependent RNA helicase. Binds to RNA. May be involved in the survival of cells.
Xenopus laevis (taxid: 8355)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q810A7|DDX42_MOUSE ATP-dependent RNA helicase DDX42 OS=Mus musculus GN=Ddx42 PE=1 SV=3

 Score =  395 bits (1014), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 210/330 (63%), Positives = 251/330 (76%), Gaps = 4/330 (1%)

Query: 4   LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFMKGIDKEVKQEAKGV--KTKKIEEVKGI 60
           L YIPA  SP+ +  ++  AD+DSD+DPL+AFM  ++ +  ++ K +  K K+ + VKGI
Sbjct: 88  LPYIPAENSPTRQQFHSKPADSDSDDDPLEAFMAEVEDQAARDMKRLEEKDKERKNVKGI 147

Query: 61  RDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHS 120
           RDDI+ EDD+E+Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPIDHS
Sbjct: 148 RDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPSK-KIIDPLPPIDHS 206

Query: 121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMK 180
            I Y   EKNFY  HE+I  LTPQ+  +LR K  + VSGA PP P SSF HFGFDE LM 
Sbjct: 207 EIDYPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMH 266

Query: 181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
            +RK EYT PTPIQ Q VP ALSGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPGDG
Sbjct: 267 QIRKSEYTQPTPIQCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDG 326

Query: 241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR 300
           P+ +I+ PTREL QQI+ E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR
Sbjct: 327 PIAVIVCPTRELCQQIHAECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGR 386

Query: 301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           +ID VK  AT L RV++LV DEADRMFDMG
Sbjct: 387 LIDHVKKKATNLQRVSYLVFDEADRMFDMG 416

ATP-dependent RNA helicase. Binds to partially double-stranded RNAs (dsRNAs) in order to unwind RNA secondary structures. Unwinding is promoted in the presence of single-strand binding proteins. Mediates also RNA duplex formation thereby displacing the single-strand RNA binding protein. ATP and ADP modulate its activity: ATP binding and hydrolysis by DDX42 triggers RNA strand separation, whereas the ADP-bound form of the protein triggers annealing of complementary RNA strands. Involved in the survival of cells by interacting with TP53BP2 and thereby counteracting the apoptosis-stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5F485|DDX42_CHICK ATP-dependent RNA helicase DDX42 OS=Gallus gallus GN=DDX42 PE=2 SV=1

 Score =  393 bits (1010), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 211/330 (63%), Positives = 251/330 (76%), Gaps = 4/330 (1%)

Query: 4   LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFMKGIDKEVKQEAKGV--KTKKIEEVKGI 60
           L YIPA  SP+ +  N+ SAD+DSD+DPL+AFM  ++ +  ++ K +  K K+ +  KGI
Sbjct: 88  LPYIPAENSPTRQQFNSKSADSDSDDDPLEAFMAEVEDQAARDMKRLEDKDKEKKNAKGI 147

Query: 61  RDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHS 120
           RDDI+ EDD+E+Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPIDHS
Sbjct: 148 RDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPSK-KIIDPLPPIDHS 206

Query: 121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMK 180
            I Y   EKNFY  HE+I  LTPQ+  ELR K  + VSGA PP P SSF  FGFDE LM 
Sbjct: 207 EIEYPPFEKNFYDEHEEITSLTPQQVVELRHKLNLRVSGAAPPRPGSSFARFGFDEQLMH 266

Query: 181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
            +RK EYT PTPIQ Q VP A+SGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPGDG
Sbjct: 267 QIRKSEYTQPTPIQCQGVPVAMSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDG 326

Query: 241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR 300
           P+ +I+ PTREL QQI++E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR
Sbjct: 327 PIAVIVCPTRELCQQIHSECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGR 386

Query: 301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           +ID VK  AT L RVT+LV DEADRMFDMG
Sbjct: 387 LIDHVKKKATNLQRVTYLVFDEADRMFDMG 416

ATP-dependent RNA helicase. Binds to RNA. May be involved in the survival of cells.

Gallus gallus (taxid: 9031)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q86XP3|DDX42_HUMAN ATP-dependent RNA helicase DDX42 OS=Homo sapiens GN=DDX42 PE=1 SV=1

 Score =  393 bits (1010), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 209/330 (63%), Positives = 250/330 (75%), Gaps = 4/330 (1%)

Query: 4   LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFMKGIDKEVKQEAKGV--KTKKIEEVKGI 60
           L YIPA  SP+ +  ++   D+DSD+DPL+AFM  ++ +  ++ K +  K K+ + VKGI
Sbjct: 88  LPYIPAENSPTRQQFHSKPVDSDSDDDPLEAFMAEVEDQAARDMKRLEEKDKERKNVKGI 147

Query: 61  RDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHS 120
           RDDI+ EDD+E+Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPIDHS
Sbjct: 148 RDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPTK-KIIDPLPPIDHS 206

Query: 121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMK 180
            I Y   EKNFY  HE+I  LTPQ+  +LR K  + VSGA PP P SSF HFGFDE LM 
Sbjct: 207 EIDYPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMH 266

Query: 181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
            +RK EYT PTPIQ Q VP ALSGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPGDG
Sbjct: 267 QIRKSEYTQPTPIQCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDG 326

Query: 241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR 300
           P+ +I+ PTREL QQI+ E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR
Sbjct: 327 PIAVIVCPTRELCQQIHAECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGR 386

Query: 301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           +ID VK  AT L RV++LV DEADRMFDMG
Sbjct: 387 LIDHVKKKATNLQRVSYLVFDEADRMFDMG 416

ATP-dependent RNA helicase. Binds to partially double-stranded RNAs (dsRNAs) in order to unwind RNA secondary structures. Unwinding is promoted in the presence of single-strand binding proteins. Mediates also RNA duplex formation thereby displacing the single-strand RNA binding protein. ATP and ADP modulate its activity: ATP binding and hydrolysis by DDX42 triggers RNA strand separation, whereas the ADP-bound form of the protein triggers annealing of complementary RNA strands. Involved in the survival of cells by interacting with TP53BP2 and thereby counteracting the apoptosis-stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5R7D1|DDX42_PONAB ATP-dependent RNA helicase DDX42 OS=Pongo abelii GN=DDX42 PE=2 SV=1

 Score =  392 bits (1008), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 209/330 (63%), Positives = 250/330 (75%), Gaps = 4/330 (1%)

Query: 4   LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFMKGIDKEVKQEAKGV--KTKKIEEVKGI 60
           L YIPA  SP+ +  ++   D+DSD+DPL+AFM  ++ +  ++ K +  K K+ + VKGI
Sbjct: 88  LPYIPAENSPTRQQFHSKPIDSDSDDDPLEAFMAEVEDQAARDMKRLEEKDKERKNVKGI 147

Query: 61  RDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHS 120
           RDDI+ EDD+E+Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPIDHS
Sbjct: 148 RDDIEEEDDQETYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPTK-KIIDPLPPIDHS 206

Query: 121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMK 180
            I Y   EKNFY  HE+I  LTPQ+  +LR K  + VSGA PP P SSF HFGFDE LM 
Sbjct: 207 EIDYPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMH 266

Query: 181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
            +RK EYT PTPIQ Q VP ALSGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPGDG
Sbjct: 267 QIRKSEYTQPTPIQCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDG 326

Query: 241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR 300
           P+ +I+ PTREL QQI+ E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR
Sbjct: 327 PIAVIVCPTRELCQQIHAEGKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGR 386

Query: 301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           +ID VK  AT L RV++LV DEADRMFDMG
Sbjct: 387 LIDHVKKKATNLQRVSYLVFDEADRMFDMG 416

ATP-dependent RNA helicase. Binds to partially double-stranded RNAs (dsRNAs) in order to unwind RNA secondary structures. Unwinding is promoted in the presence of single-strand binding proteins. Mediates also RNA duplex formation thereby displacing the single-strand RNA binding protein. ATP and ADP modulate its activity: ATP binding and hydrolysis by DDX42 triggers RNA strand separation, whereas the ADP-bound form of the protein triggers annealing of complementary RNA strands. Involved in the survival of cells by interacting with TP53BP2 and thereby counteracting the apoptosis-stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q10MH8|RH24_ORYSJ DEAD-box ATP-dependent RNA helicase 24 OS=Oryza sativa subsp. japonica GN=Os03g0308500 PE=2 SV=1

 Score =  285 bits (729), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 161/320 (50%), Positives = 202/320 (63%), Gaps = 24/320 (7%)

Query: 29  DPLDAFMKGIDKEVKQEAKGVKTKKIEEVKGIRDDIDHEDDE-ESYYRYMEENPNAGLQD 87
           DPLDAFM  I +E++      K + +      R D D EDD  ES+ R  +++  A   D
Sbjct: 69  DPLDAFMAEIQEEIRAPPPAPKPEALR-----RADSDDEDDPVESFLRAKKDSGLALAAD 123

Query: 88  N-----DSD---------VD---LEYDEDGNPIAPKKSKYIDPLPPIDHSTIVYEEVEKN 130
                 DSD         VD   +EYD D NPI   K K I+P+PP+DHSTI YE   K+
Sbjct: 124 AMHAGYDSDEEVYAAAKAVDAGMMEYDSDDNPIVVDKKK-IEPIPPLDHSTIEYEPFNKD 182

Query: 131 FYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSP 190
           FY+    ++ ++ QE  +      I VSG D P P+ SF   GF   LM A+ K  Y  P
Sbjct: 183 FYEEKPSVSGMSEQEVADYMKSLAIRVSGFDVPRPIKSFADCGFPVQLMNAIAKQGYEKP 242

Query: 191 TPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR 250
           T IQ QA+P  LSGRDIIG+AKTGSGKT AF+ PM+VHIMDQ ELE  +GP+G++ APTR
Sbjct: 243 TTIQCQALPIVLSGRDIIGIAKTGSGKTAAFVLPMIVHIMDQPELEKEEGPIGVVCAPTR 302

Query: 251 ELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT 310
           EL+ QIY EAK+F K YNL V   YGG SK+DQ K L+ G EIV+ TPGR+ID++KM A 
Sbjct: 303 ELAHQIYLEAKKFAKPYNLRVAAVYGGVSKFDQFKELKAGCEIVIATPGRLIDLLKMKAL 362

Query: 311 KLNRVTFLVLDEADRMFDMG 330
           K+ R T+LVLDEADRMFD+G
Sbjct: 363 KMFRATYLVLDEADRMFDLG 382

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q54IV3|DDX42_DICDI Probable ATP-dependent RNA helicase ddx42 OS=Dictyostelium discoideum GN=ddx42 PE=3 SV=1

 Score =  282 bits (721), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 159/331 (48%), Positives = 209/331 (63%), Gaps = 23/331 (6%)

Query: 19  NASADTDSDEDPLDAFMKGIDKEVKQEAKGVKTKKIEE-------VKGIRDDIDHEDDEE 71
           N + D D + DPLDAFM+ ++ +   +     +K IE+       +K  RDDID+EDDEE
Sbjct: 142 NQNEDEDDEIDPLDAFMENVNAQAAID----NSKSIEKGQQQQQSLKSKRDDIDNEDDEE 197

Query: 72  SYYRYMEEN--PNAGLQDNDSDVDLE----------YDEDGNPIAPKKSKYIDPLPPIDH 119
            +Y+  ++     +  Q  D DVD             +E       K  + I+PLPPIDH
Sbjct: 198 IFYKLRQKQLANKSSKQQQDDDVDYSSLDDDDGYFDDEESLKNGQSKGKRIIEPLPPIDH 257

Query: 120 STIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLM 179
           S   Y E  K FY+ H DIA LT ++  E+R    I ++G D   PV+SFGH+GFD++L+
Sbjct: 258 SKEEYIEFNKIFYEEHPDIANLTEEQVFEIRKNLDIRMTGTDLINPVTSFGHYGFDDILL 317

Query: 180 KALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGD 239
           +A+ K    +PTPIQ QA+P ALSGRD+I +AKTGSGKT  FIWP + HIMDQ  LE GD
Sbjct: 318 QAIAKQSIETPTPIQKQAIPIALSGRDLIAIAKTGSGKTATFIWPSISHIMDQPYLEKGD 377

Query: 240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPG 299
           GP+ L LAPTREL+ QIY E  ++ K + L     YGG SK  Q K L+ G EI+V TPG
Sbjct: 378 GPIALFLAPTRELAHQIYLETLKYSKYFKLKTTVLYGGVSKQQQCKELKAGCEIIVATPG 437

Query: 300 RIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           R+IDM+K+ ATKLNRV++LVLDEAD+MFD G
Sbjct: 438 RLIDMIKLKATKLNRVSYLVLDEADKMFDFG 468

probable ATP-dependent RNA helicase which may bind to partially double-stranded RNAs (dsRNAs) in order to unwind RNA secondary structures.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|O22907|RH24_ARATH DEAD-box ATP-dependent RNA helicase 24 OS=Arabidopsis thaliana GN=RH24 PE=1 SV=2

 Score =  280 bits (717), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 159/332 (47%), Positives = 209/332 (62%), Gaps = 24/332 (7%)

Query: 17  GNNASADTDSDE-DPLDAFMKGIDKEVKQEAKGVKTKKIEEVKGIRDDIDHEDDEESYYR 75
           G+ A++  + DE DPLDAFM+GI +E+K        +K+E  K      D +D  ESY +
Sbjct: 66  GSAAASGGEVDEIDPLDAFMEGIHQEMKSAPPPKPKEKLERYKD-----DDDDPVESYLK 120

Query: 76  --------YMEENPNAGLQDND------SDVD---LEYDEDGNPIAPKKSKYIDPLPPID 118
                      +  NAG   ++        VD   L+YD D NPI   K K I+P+  +D
Sbjct: 121 AKKDLGLTLAADALNAGYNSDEEVYAAAKAVDAGMLDYDSDDNPIVVDKRK-IEPITALD 179

Query: 119 HSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVL 178
           HS+I YE + K+FY+  E I+ +T QE  + R + GI VSG D   PV +F   GF   +
Sbjct: 180 HSSIDYEPINKDFYEELESISGMTEQETTDYRQRLGIRVSGFDVHRPVKTFEDCGFSSQI 239

Query: 179 MKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPG 238
           M A++K  Y  PT IQ QA+P  LSGRD+IG+AKTGSGKT AF+ PM+VHIMDQ EL+  
Sbjct: 240 MSAIKKQAYEKPTAIQCQALPIVLSGRDVIGIAKTGSGKTAAFVLPMIVHIMDQPELQRD 299

Query: 239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTP 298
           +GP+G+I APTREL+ QI+ EAK+F K Y L V   YGG SK +Q K L+ G EIVV TP
Sbjct: 300 EGPIGVICAPTRELAHQIFLEAKKFSKAYGLRVSAVYGGMSKHEQFKELKAGCEIVVATP 359

Query: 299 GRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           GR+IDM+KM A  + R ++LVLDEADRMFD+G
Sbjct: 360 GRLIDMLKMKALTMMRASYLVLDEADRMFDLG 391

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q62780|DDX46_RAT Probable ATP-dependent RNA helicase DDX46 OS=Rattus norvegicus GN=Ddx46 PE=1 SV=1

 Score =  235 bits (599), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 135/318 (42%), Positives = 186/318 (58%), Gaps = 13/318 (4%)

Query: 25  DSDEDPLDAFMKGIDKEVKQ-EAKGVKTKKIEEVKGIRDDIDHEDDEESYYRYMEENPNA 83
           D + DPLDA+M+ + +EVK+   + VK     E K             +    ++ +   
Sbjct: 222 DEELDPLDAYMEEVKEEVKKFNMRSVKGGAGNEKKSGPTVTKVVTVVTTKKAVVDADKKK 281

Query: 84  G-LQDNDSDVDLEYDED------GNPIAPKKSKYIDPLPPIDHSTIVYEEVEKNFYQPHE 136
           G L +ND D  +EY  +         +   ++K    L P+DH  I YE   KNFY    
Sbjct: 282 GELMENDQDA-MEYSSEEEEVDLQTALTGYQTKQRKLLEPVDHGKIEYEPFRKNFYVEVP 340

Query: 137 DIARLTPQEAQELRAK-SGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQA 195
           ++A+++ +E    R +  GITV G   P P+ S+   G    ++ +L+K  Y  PTPIQ 
Sbjct: 341 ELAKMSQEEVNVFRLEMEGITVKGKGCPKPIKSWVQCGISMKILNSLKKHGYEKPTPIQT 400

Query: 196 QAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQ 255
           QA+PA +SGRD+IG+AKTGSGKT AF+ PM  HIMDQ+ LE G+GP+ +I+ PTREL+ Q
Sbjct: 401 QAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHIMDQRSLEEGEGPIAVIMTPTRELALQ 460

Query: 256 IYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA---TKL 312
           I  E K+F K   L VVC YGG    +Q   L+ GAEI+V TPGR+IDM+   +   T L
Sbjct: 461 ITKECKKFSKTLGLRVVCVYGGTGISEQIAELKRGAEIIVCTPGRMIDMLAANSGRVTNL 520

Query: 313 NRVTFLVLDEADRMFDMG 330
            RVT++VLDEADRMFDMG
Sbjct: 521 RRVTYVVLDEADRMFDMG 538

Plays an essential role in splicing, either prior to, or during A complex formation.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q569Z5|DDX46_MOUSE Probable ATP-dependent RNA helicase DDX46 OS=Mus musculus GN=Ddx46 PE=1 SV=2

 Score =  235 bits (599), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 135/318 (42%), Positives = 186/318 (58%), Gaps = 13/318 (4%)

Query: 25  DSDEDPLDAFMKGIDKEVKQ-EAKGVKTKKIEEVKGIRDDIDHEDDEESYYRYMEENPNA 83
           D + DPLDA+M+ + +EVK+   + VK     E K             +    ++ +   
Sbjct: 222 DEELDPLDAYMEEVKEEVKKFNMRSVKGGAGNEKKSGPTVTKVVTVVTTKKAVVDADKKK 281

Query: 84  G-LQDNDSDVDLEYDED------GNPIAPKKSKYIDPLPPIDHSTIVYEEVEKNFYQPHE 136
           G L +ND D  +EY  +         +   ++K    L P+DH  I YE   KNFY    
Sbjct: 282 GELMENDQDA-MEYSSEEEEVDLQTALTGYQTKQRKLLEPVDHGKIEYEPFRKNFYVEVP 340

Query: 137 DIARLTPQEAQELRAK-SGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQA 195
           ++A+++ +E    R +  GITV G   P P+ S+   G    ++ +L+K  Y  PTPIQ 
Sbjct: 341 ELAKMSQEEVNVFRLEMEGITVKGKGCPKPIKSWVQCGISMKILNSLKKHGYEKPTPIQT 400

Query: 196 QAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQ 255
           QA+PA +SGRD+IG+AKTGSGKT AF+ PM  HIMDQ+ LE G+GP+ +I+ PTREL+ Q
Sbjct: 401 QAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHIMDQRSLEEGEGPIAVIMTPTRELALQ 460

Query: 256 IYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA---TKL 312
           I  E K+F K   L VVC YGG    +Q   L+ GAEI+V TPGR+IDM+   +   T L
Sbjct: 461 ITKECKKFSKTLGLRVVCVYGGTGISEQIAELKRGAEIIVCTPGRMIDMLAANSGRVTNL 520

Query: 313 NRVTFLVLDEADRMFDMG 330
            RVT++VLDEADRMFDMG
Sbjct: 521 RRVTYVVLDEADRMFDMG 538

Plays an essential role in splicing, either prior to, or during A complex formation.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	330
345487283	793	PREDICTED: ATP-dependent RNA helicase DD	0.996	0.414	0.727	1e-139
383857449	774	PREDICTED: ATP-dependent RNA helicase DD	0.990	0.422	0.724	1e-137
322799398	764	hypothetical protein SINV_08125 [Solenop	0.996	0.430	0.725	1e-137
350426308	774	PREDICTED: ATP-dependent RNA helicase DD	0.990	0.422	0.718	1e-136
66522071	772	PREDICTED: ATP-dependent RNA helicase DD	0.990	0.423	0.727	1e-136
340723638	774	PREDICTED: ATP-dependent RNA helicase DD	0.990	0.422	0.718	1e-136
380022612	772	PREDICTED: LOW QUALITY PROTEIN: ATP-depe	0.990	0.423	0.724	1e-136
307204462	770	ATP-dependent RNA helicase DDX42 [Harpeg	0.996	0.427	0.713	1e-136
307190551	769	ATP-dependent RNA helicase DDX42 [Campon	0.996	0.427	0.716	1e-136
157117281	799	DEAD box ATP-dependent RNA helicase [Aed	0.993	0.410	0.711	1e-132

>gi|345487283|ref|XP_001603249.2| PREDICTED: ATP-dependent RNA helicase DDX42-like [Nasonia vitripennis]

 Score =  501 bits (1290), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 243/334 (72%), Positives = 276/334 (82%), Gaps = 5/334 (1%)

Query: 2   SKLEYIPAPGSPSYK----GNNASADTDSDEDPLDAFMKGIDKEV-KQEAKGVKTKKIEE 56
           S LEYIPAPGSPSY+     N    D+DS+EDPLDAFM GI+ E+ + +A  V+ +K E+
Sbjct: 85  STLEYIPAPGSPSYEEHINKNKKKEDSDSEEDPLDAFMAGIESEIERTKAPSVEDRKEEK 144

Query: 57  VKGIRDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPP 116
            KGIR DID EDDEESYYRYMEENPNAGL  +DSD ++EYDEDGNPIAP K K IDPLPP
Sbjct: 145 TKGIRADIDGEDDEESYYRYMEENPNAGLHLDDSDQEIEYDEDGNPIAPLKKKEIDPLPP 204

Query: 117 IDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDE 176
           IDHS I YE  EKNFY  HEDIA L  Q+  ELR   GI V+G  PP PV+SFGHFGFD+
Sbjct: 205 IDHSVIPYEPFEKNFYNVHEDIANLNKQQIDELRKTLGIKVTGPAPPNPVTSFGHFGFDD 264

Query: 177 VLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE 236
            L+K++RK EYT PTPIQAQ++P ALSGRD+IG+AKTGSGKT AF+WPMLVHIMDQKEL+
Sbjct: 265 SLIKSIRKHEYTQPTPIQAQSIPVALSGRDLIGIAKTGSGKTAAFVWPMLVHIMDQKELD 324

Query: 237 PGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVG 296
            GDGP+GLILAPTRELSQQIY+EAK+FGK YN+ V CCYGGGSKW+QSKALE GAEIVV 
Sbjct: 325 SGDGPIGLILAPTRELSQQIYHEAKKFGKVYNIRVCCCYGGGSKWEQSKALESGAEIVVA 384

Query: 297 TPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           TPGRIID+VKM AT L+RVTFLVLDEADRMFDMG
Sbjct: 385 TPGRIIDLVKMKATNLSRVTFLVLDEADRMFDMG 418

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383857449|ref|XP_003704217.1| PREDICTED: ATP-dependent RNA helicase DDX42-like [Megachile rotundata]

 Score =  492 bits (1267), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 242/334 (72%), Positives = 274/334 (82%), Gaps = 7/334 (2%)

Query: 4   LEYIPAPGSPSY---KGNNASADTDSDEDPLDAFMKGIDKEVKQ---EAKGVKT-KKIEE 56
           LEYIPAPGSP+Y   K +    ++DS+EDPLDAFM GID EVK+   EA+  +  +K ++
Sbjct: 85  LEYIPAPGSPTYDWMKKSTPKENSDSEEDPLDAFMAGIDAEVKKNNYEAQLAEDDRKEDK 144

Query: 57  VKGIRDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPP 116
            KG R DID EDDEESYYRYMEENP AGLQ  +SD ++EYDEDGNPIAP K K IDPLPP
Sbjct: 145 SKGFRADIDCEDDEESYYRYMEENPTAGLQQEESDQEIEYDEDGNPIAPPKKKEIDPLPP 204

Query: 117 IDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDE 176
           IDHS I YE  EKNFY  H++IA L+ Q+  +LR   GI VSG  PP PV+SFGHFGFD+
Sbjct: 205 IDHSEIQYESFEKNFYNVHDEIASLSKQQIDDLRKTLGIKVSGPSPPNPVTSFGHFGFDD 264

Query: 177 VLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE 236
            L+KA+RK EYT PTPIQAQAVPAALSGRDIIG+AKTGSGKT AFIWPMLVHIMDQ+EL+
Sbjct: 265 ALIKAIRKNEYTQPTPIQAQAVPAALSGRDIIGIAKTGSGKTAAFIWPMLVHIMDQRELK 324

Query: 237 PGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVG 296
            GDGP+GLILAPTRELSQQIY EA++FGK YN+ V CCYGGGSKW+QSKALE GAEIVV 
Sbjct: 325 AGDGPIGLILAPTRELSQQIYQEARKFGKVYNIQVCCCYGGGSKWEQSKALEGGAEIVVA 384

Query: 297 TPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           TPGRIID+VKM AT L RVTFLVLDEADRMFDMG
Sbjct: 385 TPGRIIDLVKMKATNLTRVTFLVLDEADRMFDMG 418

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322799398|gb|EFZ20748.1| hypothetical protein SINV_08125 [Solenopsis invicta]

 Score =  492 bits (1267), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 243/335 (72%), Positives = 271/335 (80%), Gaps = 6/335 (1%)

Query: 2   SKLEYIPAPGSPSYKGNNASA---DTDSDEDPLDAFMKGIDKEVKQE---AKGVKTKKIE 55
           S LEYIPAPGSP+Y     SA   D+DS+ED LDAFM GID EVK+    A+     K +
Sbjct: 83  SSLEYIPAPGSPTYDLMKKSATKDDSDSEEDTLDAFMAGIDAEVKRNNCAAQRGDNHKED 142

Query: 56  EVKGIRDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLP 115
           + KGIR DID EDDEESYYRYMEENP AGLQ  +SD ++EYDEDGNPIAP K K IDPLP
Sbjct: 143 KSKGIRADIDGEDDEESYYRYMEENPTAGLQQEESDQEIEYDEDGNPIAPPKKKEIDPLP 202

Query: 116 PIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFD 175
           PIDHS I YE  EKNFY  HE+IA L+ Q+  +L+   GI VSG  PP PV+SFGHFGFD
Sbjct: 203 PIDHSEIEYEPFEKNFYNVHEEIASLSKQQIDDLKKTLGIKVSGPSPPNPVTSFGHFGFD 262

Query: 176 EVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL 235
           + L+K +RK EYT PTPIQAQAVPAALSGRDIIG+AKTGSGKT AFIWPMLVHIMDQ+EL
Sbjct: 263 DALIKTIRKNEYTQPTPIQAQAVPAALSGRDIIGIAKTGSGKTAAFIWPMLVHIMDQREL 322

Query: 236 EPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVV 295
           + GDGP+GLILAPTRELSQQIY EAK+FGK YN+ V CCYGGGSKW+QSKALE GAEIVV
Sbjct: 323 KAGDGPIGLILAPTRELSQQIYQEAKKFGKVYNIQVCCCYGGGSKWEQSKALESGAEIVV 382

Query: 296 GTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            TPGR+ID+VKM AT L RVTFLVLDEADRMFDMG
Sbjct: 383 ATPGRMIDLVKMKATNLTRVTFLVLDEADRMFDMG 417

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350426308|ref|XP_003494399.1| PREDICTED: ATP-dependent RNA helicase DDX42-like [Bombus impatiens]

 Score =  491 bits (1265), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 240/334 (71%), Positives = 275/334 (82%), Gaps = 7/334 (2%)

Query: 4   LEYIPAPGSPSY---KGNNASADTDSDEDPLDAFMKGIDKEVKQ---EAKGVKTKKIEE- 56
           LEYIPAPGSP+Y   K + +  D+DS+EDPLDAFM GID EVK+   EA+  + ++ EE 
Sbjct: 85  LEYIPAPGSPTYDWMKKSTSKEDSDSEEDPLDAFMAGIDAEVKRNNYEAQLAEDERKEEK 144

Query: 57  VKGIRDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPP 116
            KG R DID EDDEESYYRYMEENP AGLQ  +SD +++YDEDGNPIAP K K IDPLPP
Sbjct: 145 SKGFRADIDGEDDEESYYRYMEENPTAGLQQEESDQEIDYDEDGNPIAPPKKKDIDPLPP 204

Query: 117 IDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDE 176
           +DHS I YE  EKNFY  H++IA L+ Q+  +L+   GI VSG  PP PV+SFGHFGFD+
Sbjct: 205 VDHSEIKYESFEKNFYNVHDEIANLSKQQIDDLKKTLGIKVSGPSPPNPVTSFGHFGFDD 264

Query: 177 VLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE 236
            L+KA+RK EYT PTPIQAQAVPAALSGRDIIG+AKTGSGKT AFIWPMLVHIMDQ+EL+
Sbjct: 265 ALIKAIRKNEYTQPTPIQAQAVPAALSGRDIIGIAKTGSGKTAAFIWPMLVHIMDQRELK 324

Query: 237 PGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVG 296
            GDGP+GLILAPTRELSQQIY EA++FGK YN+ V CCYGGGSKW+QSKALE GAEIVV 
Sbjct: 325 AGDGPIGLILAPTRELSQQIYQEARKFGKVYNIQVCCCYGGGSKWEQSKALEGGAEIVVA 384

Query: 297 TPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           TPGR+ID+VKM AT L RVTFLVLDEADRMFDMG
Sbjct: 385 TPGRMIDLVKMKATNLTRVTFLVLDEADRMFDMG 418

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66522071|ref|XP_624210.1| PREDICTED: ATP-dependent RNA helicase DDX42-like [Apis mellifera]

 Score =  491 bits (1264), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 243/334 (72%), Positives = 272/334 (81%), Gaps = 7/334 (2%)

Query: 4   LEYIPAPGSPSY---KGNNASADTDSDEDPLDAFMKGIDKEVKQ---EAKGVKTKKIEE- 56
           LEYIPAPGSP+Y   K +    D+DS+EDPLDAFM GID EVK+   EA+  + ++ EE 
Sbjct: 85  LEYIPAPGSPTYDWMKKSTPKEDSDSEEDPLDAFMAGIDAEVKKNNYEAQLAEDERKEEK 144

Query: 57  VKGIRDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPP 116
            KG R DID EDDEESYYRYMEENP AGLQ  +SD ++EYDEDGNPIA  K K IDPLPP
Sbjct: 145 SKGFRADIDGEDDEESYYRYMEENPTAGLQQEESDQEIEYDEDGNPIAIPKKKEIDPLPP 204

Query: 117 IDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDE 176
           IDHS I YE  EKNFY  H++IA L  Q+  +LR   GI VSG  PP PV+SFGHFGFD+
Sbjct: 205 IDHSEIQYESFEKNFYNVHDEIANLNKQQVDDLRKTLGIKVSGPSPPNPVTSFGHFGFDD 264

Query: 177 VLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE 236
            L+KA+RK EYT PTPIQAQAVPAALSGRDIIG+AKTGSGKT AFIWPMLVHIMDQ+EL+
Sbjct: 265 ALIKAIRKNEYTQPTPIQAQAVPAALSGRDIIGIAKTGSGKTAAFIWPMLVHIMDQRELK 324

Query: 237 PGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVG 296
            GDGP+GLILAPTRELSQQIY EA++FGK YN+ V CCYGGGSKW+QSKALE GAEIVV 
Sbjct: 325 EGDGPIGLILAPTRELSQQIYQEARKFGKVYNVQVCCCYGGGSKWEQSKALEGGAEIVVA 384

Query: 297 TPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           TPGRIID+VKM AT L RVTFLVLDEADRMFDMG
Sbjct: 385 TPGRIIDLVKMKATNLTRVTFLVLDEADRMFDMG 418

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340723638|ref|XP_003400196.1| PREDICTED: ATP-dependent RNA helicase DDX42-like [Bombus terrestris]

 Score =  491 bits (1263), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 240/334 (71%), Positives = 274/334 (82%), Gaps = 7/334 (2%)

Query: 4   LEYIPAPGSPSY---KGNNASADTDSDEDPLDAFMKGIDKEVKQ---EAKGVKTKKIEE- 56
           LEYIPAPGSP+Y   K + +  D+DS+EDPLDAFM GID EVK+   EA+  + ++ EE 
Sbjct: 85  LEYIPAPGSPTYDWMKKSTSKEDSDSEEDPLDAFMAGIDAEVKRNNYEAQLAEDERKEEK 144

Query: 57  VKGIRDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPP 116
            KG R DID EDDEESYYRYMEENP AGLQ  +SD +++YDEDGNPIAP K K IDPLPP
Sbjct: 145 SKGFRADIDGEDDEESYYRYMEENPTAGLQQEESDQEIDYDEDGNPIAPPKKKDIDPLPP 204

Query: 117 IDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDE 176
           +DHS I YE  EKNFY  H++IA L  Q+  +L+   GI VSG  PP PV+SFGHFGFD+
Sbjct: 205 VDHSEIKYESFEKNFYNVHDEIANLNKQQIDDLKKTLGIKVSGPSPPNPVTSFGHFGFDD 264

Query: 177 VLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE 236
            L+KA+RK EYT PTPIQAQAVPAALSGRDIIG+AKTGSGKT AFIWPMLVHIMDQ+EL+
Sbjct: 265 ALIKAIRKNEYTQPTPIQAQAVPAALSGRDIIGIAKTGSGKTAAFIWPMLVHIMDQRELK 324

Query: 237 PGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVG 296
            GDGP+GLILAPTRELSQQIY EA++FGK YN+ V CCYGGGSKW+QSKALE GAEIVV 
Sbjct: 325 AGDGPIGLILAPTRELSQQIYQEARKFGKVYNIQVCCCYGGGSKWEQSKALEGGAEIVVA 384

Query: 297 TPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           TPGR+ID+VKM AT L RVTFLVLDEADRMFDMG
Sbjct: 385 TPGRMIDLVKMKATNLTRVTFLVLDEADRMFDMG 418

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380022612|ref|XP_003695134.1| PREDICTED: LOW QUALITY PROTEIN: ATP-dependent RNA helicase DDX42-like [Apis florea]

 Score =  490 bits (1261), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 242/334 (72%), Positives = 271/334 (81%), Gaps = 7/334 (2%)

Query: 4   LEYIPAPGSPSY---KGNNASADTDSDEDPLDAFMKGIDKEVKQ---EAKGVKTKKIEE- 56
           LEYIPAPGSP+Y   K +    D+DS+EDPLDAFM GID EVK+   EA+  + ++ EE 
Sbjct: 85  LEYIPAPGSPTYDWMKKSTPKEDSDSEEDPLDAFMAGIDAEVKKNNYEAQLAEDERKEEK 144

Query: 57  VKGIRDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPP 116
            KG R DID EDDEESYYRYMEENP AGLQ  +SD ++EYDEDGNPIA  K K IDPLPP
Sbjct: 145 SKGFRADIDGEDDEESYYRYMEENPTAGLQQEESDQEIEYDEDGNPIAIPKKKEIDPLPP 204

Query: 117 IDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDE 176
           IDHS I YE  EKNFY  H++IA L  Q+  +LR   GI VSG  PP PV+SFGHFGFD+
Sbjct: 205 IDHSEIQYESFEKNFYNVHDEIANLNKQQVDDLRKTLGIKVSGPSPPNPVTSFGHFGFDD 264

Query: 177 VLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE 236
            L+KA+RK EYT PTPIQAQAVPAALSGRDIIG+AKTGSGKT AFIWPMLVHIMDQ+EL+
Sbjct: 265 ALIKAIRKNEYTQPTPIQAQAVPAALSGRDIIGIAKTGSGKTAAFIWPMLVHIMDQRELK 324

Query: 237 PGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVG 296
            GDGP+GLILAPTRELSQQIY EA++FGK YN+ V CCYGGGSKW+Q KALE GAEIVV 
Sbjct: 325 EGDGPIGLILAPTRELSQQIYQEARKFGKVYNVQVCCCYGGGSKWEQXKALEGGAEIVVA 384

Query: 297 TPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           TPGRIID+VKM AT L RVTFLVLDEADRMFDMG
Sbjct: 385 TPGRIIDLVKMKATNLTRVTFLVLDEADRMFDMG 418

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307204462|gb|EFN83169.1| ATP-dependent RNA helicase DDX42 [Harpegnathos saltator]

 Score =  489 bits (1260), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 239/335 (71%), Positives = 269/335 (80%), Gaps = 6/335 (1%)

Query: 2   SKLEYIPAPGSPSY---KGNNASADTDSDEDPLDAFMKGIDKEVKQEAKGVKT---KKIE 55
           S LEYIPAPGSP+Y   K     +++DS+EDPLDAFM GID EVK+     +    +K +
Sbjct: 83  SSLEYIPAPGSPTYDLMKKTATKSESDSEEDPLDAFMAGIDAEVKRNNSLAQCDVDRKED 142

Query: 56  EVKGIRDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLP 115
           + KG R DID EDDEESYYRYMEENP AGLQ  +SD +++YDEDGNPIAP K K IDPLP
Sbjct: 143 KSKGFRADIDGEDDEESYYRYMEENPTAGLQQEESDQEIDYDEDGNPIAPLKKKEIDPLP 202

Query: 116 PIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFD 175
           PI HS I YE  EKNFY  HE+IA L  Q+   LR   GI VSG  PP PV+SFGHFGFD
Sbjct: 203 PIGHSKIDYESFEKNFYNVHEEIANLNKQQVDNLRKTLGIKVSGPSPPNPVTSFGHFGFD 262

Query: 176 EVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL 235
           + LMKA+RK E+T PTPIQAQAVPAAL+GRDIIG+AKTGSGKT AFIWPMLVHIMDQ+EL
Sbjct: 263 DALMKAIRKNEFTQPTPIQAQAVPAALNGRDIIGIAKTGSGKTAAFIWPMLVHIMDQREL 322

Query: 236 EPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVV 295
           + GDGP+GLILAPTRELSQQIY EAK+FGK YN+ V CCYGGGSKW+QSKALE GAEIVV
Sbjct: 323 KAGDGPIGLILAPTRELSQQIYQEAKKFGKVYNIQVCCCYGGGSKWEQSKALESGAEIVV 382

Query: 296 GTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            TPGR+ID+VKM AT L RVTFLVLDEADRMFDMG
Sbjct: 383 ATPGRMIDLVKMKATNLIRVTFLVLDEADRMFDMG 417

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307190551|gb|EFN74538.1| ATP-dependent RNA helicase DDX42 [Camponotus floridanus]

 Score =  489 bits (1259), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 240/335 (71%), Positives = 270/335 (80%), Gaps = 6/335 (1%)

Query: 2   SKLEYIPAPGSPSYKGNNASA---DTDSDEDPLDAFMKGIDKEVKQE---AKGVKTKKIE 55
           S LEYIPAPGSP+Y     SA   ++D +ED LDAFM GID EVK+    A+    +K E
Sbjct: 83  SSLEYIPAPGSPTYDLMKKSAMKEESDGEEDTLDAFMAGIDAEVKRNNYAAQCGDNRKEE 142

Query: 56  EVKGIRDDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLP 115
           + KG R DID EDDEESYYRYMEENP AGLQ  +SD ++EYDEDGNPIAP K K IDPLP
Sbjct: 143 KSKGFRADIDGEDDEESYYRYMEENPTAGLQQEESDQEIEYDEDGNPIAPPKKKEIDPLP 202

Query: 116 PIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFD 175
           P+DHS I YE  +KNFY  HE+IA L+ Q+  +L+   GI VSG  PP PV+SFGHFGFD
Sbjct: 203 PMDHSEIEYETFDKNFYNVHEEIASLSKQQIDDLKKTLGIKVSGPSPPNPVTSFGHFGFD 262

Query: 176 EVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL 235
           + LMK +RK EYT PTPIQAQAVPAALSGRDIIG+AKTGSGKT AFIWPMLVHIMDQ+EL
Sbjct: 263 DALMKTIRKNEYTQPTPIQAQAVPAALSGRDIIGIAKTGSGKTAAFIWPMLVHIMDQREL 322

Query: 236 EPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVV 295
           + GDGP+GLILAPTRELSQQIY EAK+FGK YN+ V CCYGGGSKW+QSKALE GAEIVV
Sbjct: 323 KAGDGPIGLILAPTRELSQQIYQEAKKFGKVYNIQVCCCYGGGSKWEQSKALESGAEIVV 382

Query: 296 GTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            TPGR+ID+VKM AT L RVTFLVLDEADRMFDMG
Sbjct: 383 ATPGRMIDLVKMKATNLTRVTFLVLDEADRMFDMG 417

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157117281|ref|XP_001653010.1| DEAD box ATP-dependent RNA helicase [Aedes aegypti] gi|108883352|gb|EAT47577.1| AAEL001317-PA [Aedes aegypti]

 Score =  476 bits (1224), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 234/329 (71%), Positives = 268/329 (81%), Gaps = 1/329 (0%)

Query: 3   KLEYIPAPGSPSYKGNNA-SADTDSDEDPLDAFMKGIDKEVKQEAKGVKTKKIEEVKGIR 61
           +L+YIPAPGSPS  G+ A S D D ++DPLDAFM GI+ +V++E K +    ++  KG R
Sbjct: 114 QLDYIPAPGSPSASGSQAKSDDEDDEDDPLDAFMAGINAQVEREKKKIPQPNVDPKKGTR 173

Query: 62  DDIDHEDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHST 121
            DID  DDEESYYRYMEENP AGL D+ SD +LEYDEDGNPI P + + IDPLPPIDHS 
Sbjct: 174 GDIDDVDDEESYYRYMEENPMAGLHDDGSDAELEYDEDGNPIPPPRKREIDPLPPIDHSE 233

Query: 122 IVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKA 181
           I Y++ EKNFY PHEDI  L+  +  ELR K G+ VSG  PP PV+SF HFGFDE LMKA
Sbjct: 234 IDYDKFEKNFYNPHEDIVGLSLSKINELRNKLGVKVSGPAPPAPVTSFAHFGFDEQLMKA 293

Query: 182 LRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGP 241
           +RK EYT PTPIQAQ VPAALSGRDIIG+AKTGSGKT AF+WPMLVHIMDQKEL PGDGP
Sbjct: 294 IRKSEYTQPTPIQAQGVPAALSGRDIIGIAKTGSGKTAAFLWPMLVHIMDQKELGPGDGP 353

Query: 242 MGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI 301
           +GLILAPTRELS QIY EAK+FGK YN+SV CCYGGGSKW+QSKALE GAEIVV TPGR+
Sbjct: 354 IGLILAPTRELSLQIYQEAKKFGKIYNISVCCCYGGGSKWEQSKALEQGAEIVVATPGRM 413

Query: 302 IDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           IDMVKM AT L RVT+LVLDEAD+MF++G
Sbjct: 414 IDMVKMKATNLQRVTYLVLDEADKMFNLG 442

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	330
FB|FBgn0036104	791	CG6418 [Drosophila melanogaste	0.978	0.408	0.681	5.4e-118
UNIPROTKB|F1P0H1	703	DDX42 "ATP-dependent RNA helic	0.987	0.463	0.621	3.1e-106
UNIPROTKB|Q5F485	944	DDX42 "ATP-dependent RNA helic	0.987	0.345	0.618	2.2e-105
UNIPROTKB|F1NJ40	946	DDX42 "ATP-dependent RNA helic	0.987	0.344	0.617	7.5e-105
UNIPROTKB|E2RFF1	933	DDX42 "Uncharacterized protein	0.987	0.349	0.615	1.6e-104
MGI|MGI:1919297	929	Ddx42 "DEAD (Asp-Glu-Ala-Asp)	0.987	0.350	0.615	1.6e-104
RGD|1304909	929	Ddx42 "DEAD (Asp-Glu-Ala-Asp)	0.987	0.350	0.615	2e-104
UNIPROTKB|E1BJD2	946	DDX42 "Uncharacterized protein	0.987	0.344	0.612	4.1e-104
UNIPROTKB|Q86XP3	938	DDX42 "ATP-dependent RNA helic	0.987	0.347	0.612	5.3e-104
UNIPROTKB|Q5R7D1	942	DDX42 "ATP-dependent RNA helic	0.987	0.346	0.612	6.7e-104

FB|FBgn0036104 CG6418 [Drosophila melanogaster (taxid:7227)]

 Score = 1162 (414.1 bits), Expect = 5.4e-118, P = 5.4e-118
 Identities = 223/327 (68%), Positives = 258/327 (78%)

Query:     6 YIPAPGSPSYKGNNASA--DTDSDEDPLDAFMKGIDKEVKQEAKGVKTKKIEEVKGIRXX 63
             YIPAPGSP     +A    D+DSDEDPL+ FM GI+++V++E +    K     + +R  
Sbjct:   108 YIPAPGSPGAPPTSAKKQEDSDSDEDPLEQFMAGINQQVEKEKRQQAPKP--PTQAVRGD 165

Query:    64 XXXXXXXXSYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHSTIV 123
                     SYYRYM+ENPNAGL+D  SD ++EYDEDGNPIAP K K IDPLPPI HS I 
Sbjct:   166 IDDEDDEESYYRYMKENPNAGLRDEGSDQEIEYDEDGNPIAPPKKKDIDPLPPIYHSEIE 225

Query:   124 YEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALR 183
             YE  EKNFY  H+DIA L  ++ +ELR   G+ V+G  PP PV+SFGHFGFDE L+KA+R
Sbjct:   226 YEPFEKNFYTQHDDIAALDDEQVRELRRTLGVKVTGPSPPKPVTSFGHFGFDEQLIKAVR 285

Query:   184 KCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMG 243
             K EYT PTPIQAQAVP ALSGRDIIG+AKTGSGKT AFIWPML+H+MDQK+L+PGDGP+G
Sbjct:   286 KAEYTQPTPIQAQAVPTALSGRDIIGIAKTGSGKTAAFIWPMLMHVMDQKQLKPGDGPIG 345

Query:   244 LILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIID 303
             LILAPTRELS QIYNEAK+FGK YNL+VVCCYGGGSKW+QSKALE GAEI+V TPGR+ID
Sbjct:   346 LILAPTRELSLQIYNEAKKFGKVYNLNVVCCYGGGSKWEQSKALEQGAEIIVATPGRMID 405

Query:   304 MVKMGATKLNRVTFLVLDEADRMFDMG 330
             MVKM AT L RVTFLVLDEADRMF MG
Sbjct:   406 MVKMKATNLRRVTFLVLDEADRMFHMG 432

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

GO:0004386 "helicase activity" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1P0H1 DDX42 "ATP-dependent RNA helicase DDX42" [Gallus gallus (taxid:9031)]

 Score = 1051 (375.0 bits), Expect = 3.1e-106, P = 3.1e-106
 Identities = 205/330 (62%), Positives = 243/330 (73%)

Query:     4 LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFMKGIDKEVKQEAKGV--KTKKIEEVKGI 60
             L YIPA  SP+ +  N+ SAD+DSD+DPL+AFM  ++ +  ++ K +  K K+ +  KGI
Sbjct:    83 LPYIPAENSPTRQQFNSKSADSDSDDDPLEAFMAEVEDQAARDMKRLEDKDKEKKNAKGI 142

Query:    61 RXXXXXXXXXXSYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHS 120
             R          +Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPIDHS
Sbjct:   143 RDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPSK-KIIDPLPPIDHS 201

Query:   121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMK 180
              I Y   EKNFY  HE+I  LTPQ+  ELR K  + VSGA PP P SSF HFGFDE LM 
Sbjct:   202 EIEYPPFEKNFYDEHEEITSLTPQQVVELRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMH 261

Query:   181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
              +RK EYT PTPIQ Q VP A+SGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPGDG
Sbjct:   262 QIRKSEYTQPTPIQCQGVPVAMSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDG 321

Query:   241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR 300
             P+ +I+ PTREL QQI++E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR
Sbjct:   322 PIAVIVCPTRELCQQIHSECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGR 381

Query:   301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
             +ID VK  AT L RVT+LV DEADRMFDMG
Sbjct:   382 LIDHVKKKATNLQRVTYLVFDEADRMFDMG 411

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q5F485 DDX42 "ATP-dependent RNA helicase DDX42" [Gallus gallus (taxid:9031)]

 Score = 1043 (372.2 bits), Expect = 2.2e-105, P = 2.2e-105
 Identities = 204/330 (61%), Positives = 242/330 (73%)

Query:     4 LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFMKGIDKEVKQEAKGV--KTKKIEEVKGI 60
             L YIPA  SP+ +  N+ SAD+DSD+DPL+AFM  ++ +  ++ K +  K K+ +  KGI
Sbjct:    88 LPYIPAENSPTRQQFNSKSADSDSDDDPLEAFMAEVEDQAARDMKRLEDKDKEKKNAKGI 147

Query:    61 RXXXXXXXXXXSYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHS 120
             R          +Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPIDHS
Sbjct:   148 RDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPSK-KIIDPLPPIDHS 206

Query:   121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMK 180
              I Y   EKNFY  HE+I  LTPQ+  ELR K  + VSGA PP P SSF  FGFDE LM 
Sbjct:   207 EIEYPPFEKNFYDEHEEITSLTPQQVVELRHKLNLRVSGAAPPRPGSSFARFGFDEQLMH 266

Query:   181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
              +RK EYT PTPIQ Q VP A+SGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPGDG
Sbjct:   267 QIRKSEYTQPTPIQCQGVPVAMSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDG 326

Query:   241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR 300
             P+ +I+ PTREL QQI++E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR
Sbjct:   327 PIAVIVCPTRELCQQIHSECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGR 386

Query:   301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
             +ID VK  AT L RVT+LV DEADRMFDMG
Sbjct:   387 LIDHVKKKATNLQRVTYLVFDEADRMFDMG 416

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008104 "protein localization" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

UNIPROTKB|F1NJ40 DDX42 "ATP-dependent RNA helicase DDX42" [Gallus gallus (taxid:9031)]

 Score = 1038 (370.5 bits), Expect = 7.5e-105, P = 7.5e-105
 Identities = 205/332 (61%), Positives = 244/332 (73%)

Query:     4 LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFM-KGIDKE-VKQEAKGV--KTKKIEEVK 58
             L YIPA  SP+ +  N+ SAD+DSD+DPL+AFM + ++ +   ++ K +  K K+ +  K
Sbjct:    88 LPYIPAENSPTRQQFNSKSADSDSDDDPLEAFMAESVENDQAARDMKRLEDKDKEKKNAK 147

Query:    59 GIRXXXXXXXXXXSYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPID 118
             GIR          +Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPID
Sbjct:   148 GIRDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPSK-KIIDPLPPID 206

Query:   119 HSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVL 178
             HS I Y   EKNFY  HE+I  LTPQ+  ELR K  + VSGA PP P SSF HFGFDE L
Sbjct:   207 HSEIEYPPFEKNFYDEHEEITSLTPQQVVELRHKLNLRVSGAAPPRPGSSFAHFGFDEQL 266

Query:   179 MKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPG 238
             M  +RK EYT PTPIQ Q VP A+SGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPG
Sbjct:   267 MHQIRKSEYTQPTPIQCQGVPVAMSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPG 326

Query:   239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTP 298
             DGP+ +I+ PTREL QQI++E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TP
Sbjct:   327 DGPIAVIVCPTRELCQQIHSECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTP 386

Query:   299 GRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
             GR+ID VK  AT L RVT+LV DEADRMFDMG
Sbjct:   387 GRLIDHVKKKATNLQRVTYLVFDEADRMFDMG 418

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008104 "protein localization" evidence=IEA

UNIPROTKB|E2RFF1 DDX42 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1035 (369.4 bits), Expect = 1.6e-104, P = 1.6e-104
 Identities = 203/330 (61%), Positives = 242/330 (73%)

Query:     4 LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFMKGIDKEVKQEAKGV--KTKKIEEVKGI 60
             L YIPA  SP+ +  ++  AD+DSD+DPL+AFM  ++ +  ++ K +  K K+ + VKGI
Sbjct:    88 LPYIPAENSPTRQQFHSKPADSDSDDDPLEAFMAEVEDQAARDMKRLEEKDKERKNVKGI 147

Query:    61 RXXXXXXXXXXSYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHS 120
             R          +Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPIDHS
Sbjct:   148 RDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPSK-KIIDPLPPIDHS 206

Query:   121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMK 180
              I Y   EKNFY  HE+I  LTPQ+  +LR K  + VSGA PP P SSF HFGFDE LM 
Sbjct:   207 EIDYPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMH 266

Query:   181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
              +RK EYT PTPIQ Q VP ALSGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPGDG
Sbjct:   267 QIRKSEYTQPTPIQCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDG 326

Query:   241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR 300
             P+ +I+ PTREL QQI+ E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR
Sbjct:   327 PIAVIVCPTRELCQQIHAECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGR 386

Query:   301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
             +ID VK  AT L RV++LV DEADRMFDMG
Sbjct:   387 LIDHVKKKATNLQRVSYLVFDEADRMFDMG 416

GO:0008104 "protein localization" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1919297 Ddx42 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 42" [Mus musculus (taxid:10090)]

 Score = 1035 (369.4 bits), Expect = 1.6e-104, P = 1.6e-104
 Identities = 203/330 (61%), Positives = 242/330 (73%)

Query:     4 LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFMKGIDKEVKQEAKGV--KTKKIEEVKGI 60
             L YIPA  SP+ +  ++  AD+DSD+DPL+AFM  ++ +  ++ K +  K K+ + VKGI
Sbjct:    88 LPYIPAENSPTRQQFHSKPADSDSDDDPLEAFMAEVEDQAARDMKRLEEKDKERKNVKGI 147

Query:    61 RXXXXXXXXXXSYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHS 120
             R          +Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPIDHS
Sbjct:   148 RDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPSK-KIIDPLPPIDHS 206

Query:   121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMK 180
              I Y   EKNFY  HE+I  LTPQ+  +LR K  + VSGA PP P SSF HFGFDE LM 
Sbjct:   207 EIDYPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMH 266

Query:   181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
              +RK EYT PTPIQ Q VP ALSGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPGDG
Sbjct:   267 QIRKSEYTQPTPIQCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDG 326

Query:   241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR 300
             P+ +I+ PTREL QQI+ E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR
Sbjct:   327 PIAVIVCPTRELCQQIHAECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGR 386

Query:   301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
             +ID VK  AT L RV++LV DEADRMFDMG
Sbjct:   387 LIDHVKKKATNLQRVSYLVFDEADRMFDMG 416

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

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

GO:0008104 "protein localization" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

RGD|1304909 Ddx42 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 42" [Rattus norvegicus (taxid:10116)]

 Score = 1034 (369.0 bits), Expect = 2.0e-104, P = 2.0e-104
 Identities = 203/330 (61%), Positives = 241/330 (73%)

Query:     4 LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFMKGIDKEVKQEAKGV--KTKKIEEVKGI 60
             L YIPA  SP+ +   +  AD+DSD+DPL+AFM  ++ +  ++ K +  K K+ + VKGI
Sbjct:    88 LPYIPAENSPTRQQFRSKPADSDSDDDPLEAFMAEVEDQAARDMKRLEEKDKERKNVKGI 147

Query:    61 RXXXXXXXXXXSYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHS 120
             R          +Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPIDHS
Sbjct:   148 RDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPSK-KIIDPLPPIDHS 206

Query:   121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMK 180
              I Y   EKNFY  HE+I  LTPQ+  +LR K  + VSGA PP P SSF HFGFDE LM 
Sbjct:   207 EIDYPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMH 266

Query:   181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
              +RK EYT PTPIQ Q VP ALSGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPGDG
Sbjct:   267 QIRKSEYTQPTPIQCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDG 326

Query:   241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR 300
             P+ +I+ PTREL QQI+ E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR
Sbjct:   327 PIAVIVCPTRELCQQIHAECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGR 386

Query:   301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
             +ID VK  AT L RV++LV DEADRMFDMG
Sbjct:   387 LIDHVKKKATNLQRVSYLVFDEADRMFDMG 416

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

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

GO:0008104 "protein localization" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|E1BJD2 DDX42 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 1031 (368.0 bits), Expect = 4.1e-104, P = 4.1e-104
 Identities = 202/330 (61%), Positives = 241/330 (73%)

Query:     4 LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFMKGIDKEVKQEAKGV--KTKKIEEVKGI 60
             L YIPA  SP+ +  ++   D+DSD+DPL+AFM  ++ +  ++ K +  K K+ + VKGI
Sbjct:    88 LPYIPAENSPTRQQFHSKPVDSDSDDDPLEAFMAEVEDQAARDMKRLEEKDKERKNVKGI 147

Query:    61 RXXXXXXXXXXSYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHS 120
             R          +Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPIDHS
Sbjct:   148 RDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPSK-KIIDPLPPIDHS 206

Query:   121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMK 180
              I Y   EKNFY  HE+I  LTPQ+  +LR K  + VSGA PP P SSF HFGFDE LM 
Sbjct:   207 EIDYPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMH 266

Query:   181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
              +RK EYT PTPIQ Q VP ALSGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPGDG
Sbjct:   267 QIRKSEYTQPTPIQCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDG 326

Query:   241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR 300
             P+ +I+ PTREL QQI+ E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR
Sbjct:   327 PIAVIVCPTRELCQQIHAECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGR 386

Query:   301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
             +ID VK  AT L RV++LV DEADRMFDMG
Sbjct:   387 LIDHVKKKATNLQRVSYLVFDEADRMFDMG 416

GO:0008104 "protein localization" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q86XP3 DDX42 "ATP-dependent RNA helicase DDX42" [Homo sapiens (taxid:9606)]

 Score = 1030 (367.6 bits), Expect = 5.3e-104, P = 5.3e-104
 Identities = 202/330 (61%), Positives = 241/330 (73%)

Query:     4 LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFMKGIDKEVKQEAKGV--KTKKIEEVKGI 60
             L YIPA  SP+ +  ++   D+DSD+DPL+AFM  ++ +  ++ K +  K K+ + VKGI
Sbjct:    88 LPYIPAENSPTRQQFHSKPVDSDSDDDPLEAFMAEVEDQAARDMKRLEEKDKERKNVKGI 147

Query:    61 RXXXXXXXXXXSYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHS 120
             R          +Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPIDHS
Sbjct:   148 RDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPTK-KIIDPLPPIDHS 206

Query:   121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMK 180
              I Y   EKNFY  HE+I  LTPQ+  +LR K  + VSGA PP P SSF HFGFDE LM 
Sbjct:   207 EIDYPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMH 266

Query:   181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
              +RK EYT PTPIQ Q VP ALSGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPGDG
Sbjct:   267 QIRKSEYTQPTPIQCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDG 326

Query:   241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR 300
             P+ +I+ PTREL QQI+ E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR
Sbjct:   327 PIAVIVCPTRELCQQIHAECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGR 386

Query:   301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
             +ID VK  AT L RV++LV DEADRMFDMG
Sbjct:   387 LIDHVKKKATNLQRVSYLVFDEADRMFDMG 416

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0015030 "Cajal body" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0008104 "protein localization" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q5R7D1 DDX42 "ATP-dependent RNA helicase DDX42" [Pongo abelii (taxid:9601)]

 Score = 1029 (367.3 bits), Expect = 6.7e-104, P = 6.7e-104
 Identities = 202/330 (61%), Positives = 241/330 (73%)

Query:     4 LEYIPAPGSPSYKG-NNASADTDSDEDPLDAFMKGIDKEVKQEAKGV--KTKKIEEVKGI 60
             L YIPA  SP+ +  ++   D+DSD+DPL+AFM  ++ +  ++ K +  K K+ + VKGI
Sbjct:    88 LPYIPAENSPTRQQFHSKPIDSDSDDDPLEAFMAEVEDQAARDMKRLEEKDKERKNVKGI 147

Query:    61 RXXXXXXXXXXSYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHS 120
             R          +Y+RYM ENP AG+   + + +LEYD DGNPIAP K K IDPLPPIDHS
Sbjct:   148 RDDIEEEDDQETYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPTK-KIIDPLPPIDHS 206

Query:   121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMK 180
              I Y   EKNFY  HE+I  LTPQ+  +LR K  + VSGA PP P SSF HFGFDE LM 
Sbjct:   207 EIDYPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMH 266

Query:   181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
              +RK EYT PTPIQ Q VP ALSGRD+IG+AKTGSGKT AFIWPML+HIMDQKELEPGDG
Sbjct:   267 QIRKSEYTQPTPIQCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDG 326

Query:   241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR 300
             P+ +I+ PTREL QQI+ E KRFGK YNL  V  YGGGS W+Q+KAL+ GAEIVV TPGR
Sbjct:   327 PIAVIVCPTRELCQQIHAEGKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGR 386

Query:   301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
             +ID VK  AT L RV++LV DEADRMFDMG
Sbjct:   387 LIDHVKKKATNLQRVSYLVFDEADRMFDMG 416

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0008104 "protein localization" evidence=ISS

---

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)
Q6CIV2	DBP2_KLULA	3, ., 6, ., 4, ., 1, 3	0.5073	0.6151	0.3664	yes	N/A
Q9P7C7	PRP11_SCHPO	3, ., 6, ., 4, ., 1, 3	0.5065	0.6787	0.2209	yes	N/A
Q5F485	DDX42_CHICK	3, ., 6, ., 4, ., 1, 3	0.6393	0.9878	0.3453	yes	N/A
Q86XP3	DDX42_HUMAN	3, ., 6, ., 4, ., 1, 3	0.6333	0.9878	0.3475	yes	N/A
A3LQ55	PRP5_PICST	3, ., 6, ., 4, ., 1, 3	0.5045	0.6575	0.248	yes	N/A
Q10MH8	RH24_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.5031	0.8969	0.3844	yes	N/A
Q5R7D1	DDX42_PONAB	3, ., 6, ., 4, ., 1, 3	0.6333	0.9878	0.3460	yes	N/A
Q810A7	DDX42_MOUSE	3, ., 6, ., 4, ., 1, 3	0.6363	0.9878	0.3509	yes	N/A
Q5BDW4	PRP5_EMENI	3, ., 6, ., 4, ., 1, 3	0.5022	0.6575	0.1849	yes	N/A
Q2U2J6	PRP5_ASPOR	3, ., 6, ., 4, ., 1, 3	0.5067	0.6575	0.1829	yes	N/A

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	330
cd00268	203	cd00268, DEADc, DEAD-box helicases	9e-78
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	2e-77
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-66
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	3e-54
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	2e-42
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	4e-42
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	7e-42
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	3e-41
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	9e-41
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	7e-38
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	3e-36
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	4e-36
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	2e-33
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	2e-31
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	3e-26
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	7e-09
COG1205	851	COG1205, COG1205, Distinct helicase family with a	5e-08
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	4e-07
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	5e-05
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	2e-04
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	0.004

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

 Score =  236 bits (604), Expect = 9e-78
 Identities = 80/162 (49%), Positives = 105/162 (64%), Gaps = 3/162 (1%)

Query: 169 FGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVH 228
           F   G    L++ +    +  PTPIQA+A+P  LSGRD+IG A+TGSGKT AF+ P+L  
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 229 IMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE 288
           +    +    DGP  LILAPTREL+ QI   A++ GK  NL VV  YGG S   Q + L+
Sbjct: 61  LDPSPKK---DGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLK 117

Query: 289 LGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            G  IVV TPGR++D+++ G   L++V +LVLDEADRM DMG
Sbjct: 118 RGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMG 159

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|240273 PTZ00110, PTZ00110, helicase; Provisional

 Score =  246 bits (629), Expect = 2e-77
 Identities = 105/220 (47%), Positives = 142/220 (64%), Gaps = 1/220 (0%)

Query: 112 DPLPPIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGIT-VSGADPPYPVSSFG 170
             L PID  +I     EKNFY+ H +++ L+ +E  E+R +  IT ++G + P PV SF 
Sbjct: 74  KRLQPIDWKSINLVPFEKNFYKEHPEVSALSSKEVDEIRKEKEITIIAGENVPKPVVSFE 133

Query: 171 HFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIM 230
           +  F + ++K+L+   +T PTPIQ Q  P ALSGRD+IG+A+TGSGKT AF+ P +VHI 
Sbjct: 134 YTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHIN 193

Query: 231 DQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELG 290
            Q  L  GDGP+ L+LAPTREL++QI  +  +FG    +     YGG  K  Q  AL  G
Sbjct: 194 AQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRG 253

Query: 291 AEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            EI++  PGR+ID ++   T L RVT+LVLDEADRM DMG
Sbjct: 254 VEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMG 293

Length = 545

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

 Score =  216 bits (553), Expect = 1e-66
 Identities = 77/177 (43%), Positives = 102/177 (57%), Gaps = 4/177 (2%)

Query: 155 ITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTG 214
                         F   G    L++AL+   +  PTPIQ  A+P  L+GRD++G A+TG
Sbjct: 17  NVALSRGEEKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTG 76

Query: 215 SGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG-YNLSVVC 273
           +GKT AF+ P+L  I+   E +       LILAPTREL+ QI  E ++ GK    L V  
Sbjct: 77  TGKTAAFLLPLLQKILKSVERK---YVSALILAPTRELAVQIAEELRKLGKNLGGLRVAV 133

Query: 274 CYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            YGG S   Q +AL+ G +IVV TPGR++D++K G   L+ V  LVLDEADRM DMG
Sbjct: 134 VYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMG 190

Length = 513

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

 Score =  174 bits (444), Expect = 3e-54
 Identities = 71/142 (50%), Positives = 97/142 (68%), Gaps = 7/142 (4%)

Query: 191 TPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR 250
           TPIQAQA+PA LSG+D++  A TGSGKT AF+ P+L  ++ +K      GP  L+LAPTR
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKK-----GGPQALVLAPTR 55

Query: 251 ELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELG-AEIVVGTPGRIIDMVKMGA 309
           EL++QIY E K+  K   L V    GG S  +Q++ L+ G A+I+VGTPGR++D+++ G 
Sbjct: 56  ELAEQIYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGK 115

Query: 310 TKL-NRVTFLVLDEADRMFDMG 330
            KL   +  LVLDEA R+ DMG
Sbjct: 116 LKLLKNLKLLVLDEAHRLLDMG 137

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 =  153 bits (387), Expect = 2e-42
 Identities = 76/193 (39%), Positives = 108/193 (55%), Gaps = 2/193 (1%)

Query: 140 RLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVP 199
            L+  +A+ LR K  I V G   P P+ SF   G    L+  L    Y  PTPIQ QA+P
Sbjct: 94  GLSSSQAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIP 153

Query: 200 AALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGD--GPMGLILAPTRELSQQIY 257
           AALSGR ++  A TGSGKT +F+ P++      +   P +   P+ ++L PTREL  Q+ 
Sbjct: 154 AALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVE 213

Query: 258 NEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTF 317
           ++AK  GKG         GG +   Q   ++ G E++VGTPGR+ID++     +L+ V+ 
Sbjct: 214 DQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSV 273

Query: 318 LVLDEADRMFDMG 330
           LVLDE D M + G
Sbjct: 274 LVLDEVDCMLERG 286

Length = 518

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

 Score =  150 bits (382), Expect = 4e-42
 Identities = 69/162 (42%), Positives = 97/162 (59%), Gaps = 1/162 (0%)

Query: 169 FGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVH 228
           F     DE L++AL+   YT PT IQA+A+P AL GRD++G A TG+GKT AF+ P L H
Sbjct: 3   FSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQH 62

Query: 229 IMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE 288
           ++D    + G  P  LIL PTREL+ Q+ ++A+   K  +L +    GG +  + ++   
Sbjct: 63  LLDFPRRKSGP-PRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFS 121

Query: 289 LGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
              +IVV TPGR++  +K        V  L+LDEADRM DMG
Sbjct: 122 ENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMG 163

Length = 434

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

 Score =  143 bits (363), Expect = 7e-42
 Identities = 62/151 (41%), Positives = 86/151 (56%), Gaps = 8/151 (5%)

Query: 182 LRKCEYTSPTPIQAQAVPAALSG-RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG 240
           + K  +    P Q +A+ A LSG RD+I  A TGSGKT A + P L  +        G G
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALK------RGKG 54

Query: 241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELG-AEIVVGTPG 299
              L+L PTREL++Q   E K+ G    L VV  YGG SK +Q + LE G  +I+V TPG
Sbjct: 55  GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPG 114

Query: 300 RIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           R++D+++     L+ V  ++LDEA R+ D G
Sbjct: 115 RLLDLLENDKLSLSNVDLVILDEAHRLLDGG 145

Length = 201

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

 Score =  148 bits (377), Expect = 3e-41
 Identities = 69/145 (47%), Positives = 90/145 (62%), Gaps = 6/145 (4%)

Query: 187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL 246
           YT  TPIQAQ++PA L+G+D+I  AKTGSGKT AF   +L  + D K          L+L
Sbjct: 24  YTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKL-DVKRF----RVQALVL 78

Query: 247 APTRELSQQIYNEAKRFGKG-YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMV 305
            PTREL+ Q+  E +R  +   N+ V+   GG     Q  +LE GA I+VGTPGRI+D +
Sbjct: 79  CPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHL 138

Query: 306 KMGATKLNRVTFLVLDEADRMFDMG 330
           + G   L+ +  LVLDEADRM DMG
Sbjct: 139 RKGTLDLDALNTLVLDEADRMLDMG 163

Length = 460

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

 Score =  147 bits (372), Expect = 9e-41
 Identities = 67/164 (40%), Positives = 96/164 (58%), Gaps = 2/164 (1%)

Query: 169 FGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVH 228
           F  F     +++AL K  + + TPIQA A+P  L+GRD+ G A+TG+GKT AF+     +
Sbjct: 10  FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69

Query: 229 IMDQKELEPG--DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA 286
           ++     E    + P  LI+APTREL+ QI+ +A+   +   L +   YGG     Q K 
Sbjct: 70  LLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKV 129

Query: 287 LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           LE G +I++GT GR+ID  K     L  +  +VLDEADRMFD+G
Sbjct: 130 LESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLG 173

Length = 423

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

 Score =  139 bits (353), Expect = 7e-38
 Identities = 70/164 (42%), Positives = 100/164 (60%), Gaps = 1/164 (0%)

Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLV 227
           SF   G    +++A+ +  Y  PTPIQ QA+PA L GRD++  A+TG+GKT  F  P+L 
Sbjct: 2   SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61

Query: 228 HIMDQKELEPGDGPM-GLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA 286
           H++ ++    G  P+  LIL PTREL+ QI    + + K  N+  +  +GG S   Q   
Sbjct: 62  HLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK 121

Query: 287 LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           L  G +++V TPGR++D+    A KL++V  LVLDEADRM DMG
Sbjct: 122 LRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMG 165

Length = 456

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

 Score =  127 bits (321), Expect = 3e-36
 Identities = 48/126 (38%), Positives = 67/126 (53%), Gaps = 7/126 (5%)

Query: 205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG 264
           RD++  A TGSGKT A + P+L        L+   G   L+LAPTREL+ Q+    K   
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILEL------LDSLKGGQVLVLAPTRELANQVAERLKELF 54

Query: 265 KGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD 324
               + V    GG S   Q K L    +IVVGTPGR++D ++     L ++  L+LDEA 
Sbjct: 55  G-EGIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAH 113

Query: 325 RMFDMG 330
           R+ + G
Sbjct: 114 RLLNQG 119

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

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

 Score =  136 bits (345), Expect = 4e-36
 Identities = 73/166 (43%), Positives = 106/166 (63%), Gaps = 8/166 (4%)

Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           ++F   G    +++AL    Y  P+PIQA+ +P  L+GRD++G+A+TGSGKT AF  P+L
Sbjct: 6   TTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLL 65

Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG-YNLSVVCCYGGGSKWD-QS 284
            ++    EL+    P  L+LAPTREL+ Q+      F K    ++VV  Y GG ++D Q 
Sbjct: 66  HNL--DPELK---APQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALY-GGQRYDVQL 119

Query: 285 KALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           +AL  G +IVVGTPGR++D +K G   L++++ LVLDEAD M  MG
Sbjct: 120 RALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMG 165

Length = 629

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

 Score =  129 bits (325), Expect = 2e-33
 Identities = 72/178 (40%), Positives = 97/178 (54%), Gaps = 11/178 (6%)

Query: 160 ADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTG 219
           +D P    +F  F     L+  L    +T  TPIQA  +P AL G D+ G A+TG+GKT 
Sbjct: 2   SDKPLTDLTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTL 61

Query: 220 AFIWPMLVHIMDQKELEPG------DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVC 273
           AF    LV +M++    P       + P  LILAPTREL+ QI+ +A +FG    L    
Sbjct: 62  AF----LVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFAL 117

Query: 274 CYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKM-GATKLNRVTFLVLDEADRMFDMG 330
            YGG     Q + L+ G ++++ TPGR+ID VK      L+     VLDEADRMFD+G
Sbjct: 118 VYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLG 175

Length = 572

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

 Score =  122 bits (308), Expect = 2e-31
 Identities = 72/174 (41%), Positives = 93/174 (53%), Gaps = 5/174 (2%)

Query: 161 DPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGA 220
           +P    + F  F     LM A+    +   TPIQAQ +   L+G D IG A+TG+GKT A
Sbjct: 81  EPQEGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAA 140

Query: 221 F---IWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGG 277
           F   I   L+     KE   G+ P  LI+APTREL  QI  +A    K   L+V+   GG
Sbjct: 141 FLISIINQLLQTPPPKERYMGE-PRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGG 199

Query: 278 GSKWDQSKALELG-AEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
                Q K LE    +I+V TPGR++D  + G   L+ V  +VLDEADRM DMG
Sbjct: 200 MDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMG 253

Length = 475

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

 Score =  107 bits (268), Expect = 3e-26
 Identities = 56/165 (33%), Positives = 82/165 (49%), Gaps = 5/165 (3%)

Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           V SF     +E L++ +    +  P+ IQ + +   L G D IG A++G+GKT  F+   
Sbjct: 27  VDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAA 86

Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
           L  ++D       +    LILAPTREL+QQI       G    +    C GG    D   
Sbjct: 87  L-QLIDYDL----NACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDIN 141

Query: 286 ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L+ G  +VVGTPGR+ DM+     +++ +   +LDEAD M   G
Sbjct: 142 KLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRG 186

Length = 401

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

 Score = 56.9 bits (138), Expect = 7e-09
 Identities = 26/98 (26%), Positives = 50/98 (51%), Gaps = 1/98 (1%)

Query: 174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQK 233
            D  + +  ++ ++TS TP Q  A+P   SG +++ +A TGSGKT A   P++  ++   
Sbjct: 8   LDPRVREWFKR-KFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLG 66

Query: 234 ELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSV 271
           + +  DG   L ++P + L+  I    +   +   + V
Sbjct: 67  KGKLEDGIYALYISPLKALNNDIRRRLEEPLRELGIEV 104

Length = 814

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

 Score = 54.3 bits (131), Expect = 5e-08
 Identities = 31/143 (21%), Positives = 57/143 (39%), Gaps = 26/143 (18%)

Query: 194 QAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELS 253
           Q  A+     GR+++    TGSGKT +F+ P+L H++             L+L PT  L+
Sbjct: 75  QVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSAR------ALLLYPTNALA 128

Query: 254 Q----QIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL-ELGAEIVVGTPGRIIDMVKMG 308
                ++                  Y G +  ++ +A+     +I++  P    DM+   
Sbjct: 129 NDQAERLRELISDLPGKVTFGR---YTGDTPPEERRAIIRNPPDILLTNP----DMLHYL 181

Query: 309 ATK--------LNRVTFLVLDEA 323
             +        L  + +LV+DE 
Sbjct: 182 LLRNHDAWLWLLRNLKYLVVDEL 204

Length = 851

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

 Score = 51.2 bits (123), Expect = 4e-07
 Identities = 31/133 (23%), Positives = 56/133 (42%), Gaps = 12/133 (9%)

Query: 192 PIQAQAVPA-ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR 250
             Q +AV    LS  +++  A TGSGKT      ++  +     L  G G +  I  P +
Sbjct: 34  NPQQEAVEKGLLSDENVLISAPTGSGKT------LIALLAILSTLLEGGGKVVYI-VPLK 86

Query: 251 ELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT 310
            L+++ Y E  R  +   + V     G    D         +++V TP ++  + +   +
Sbjct: 87  ALAEEKYEEFSRL-EELGIRVG-ISTGDY--DLDDERLARYDVIVTTPEKLDSLTRKRPS 142

Query: 311 KLNRVTFLVLDEA 323
            +  V  +V+DE 
Sbjct: 143 WIEEVDLVVIDEI 155

Length = 766

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

 Score = 44.4 bits (105), Expect = 5e-05
 Identities = 33/146 (22%), Positives = 51/146 (34%), Gaps = 31/146 (21%)

Query: 186 EYTSPTPIQAQAVPAALS----GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGP 241
                 P Q +A+ A +      R  + V  TG+GKT           +   EL      
Sbjct: 33  FEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAA-----EAI--AEL----KR 81

Query: 242 MGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI 301
             L+L PT+EL  Q     K+F    +   +  YGGG K          A++ V T    
Sbjct: 82  STLVLVPTKELLDQWAEALKKFLLLNDEIGI--YGGGEKE------LEPAKVTVAT---- 129

Query: 302 IDMV-KMGATKL---NRVTFLVLDEA 323
           +  + +         N    ++ DE 
Sbjct: 130 VQTLARRQLLDEFLGNEFGLIIFDEV 155

Length = 442

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

 Score = 42.5 bits (101), Expect = 2e-04
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP 248
           +P P Q +   AAL GR  + +A TGSGKT A   P L+ +   +  +P  G   L + P
Sbjct: 13  TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPE--KPKKGLHTLYITP 70

Query: 249 TRELSQQIYNEAKR 262
            R L+  I    + 
Sbjct: 71  LRALAVDIARNLQA 84

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

>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase

 Score = 38.6 bits (90), Expect = 0.004
 Identities = 40/160 (25%), Positives = 64/160 (40%), Gaps = 24/160 (15%)

Query: 174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQK 233
               ++ AL       P   QA+A   A +GR ++    T SGK+ A+  P+L  + D  
Sbjct: 21  AHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD- 79

Query: 234 ELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVV--CCYGGGSKWDQSKALELGA 291
                     L LAPT+ L+     +  R  +   L  V    Y G +  ++ +     A
Sbjct: 80  -----PRATALYLAPTKALAA----DQLRAVRELTLRGVRPATYDGDTPTEERRWAREHA 130

Query: 292 EIVVGTPGRIIDMVKMG--------ATKLNRVTFLVLDEA 323
             V+  P    DM+  G        A  L R+ ++V+DE 
Sbjct: 131 RYVLTNP----DMLHRGILPSHARWARFLRRLRYVVIDEC 166

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. Length = 742

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	330
KOG0339|consensus	731		100.0
KOG0334|consensus	997		100.0
PTZ00110	545	helicase; Provisional	100.0
KOG0331|consensus	519		100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
KOG0336|consensus	629		100.0
KOG0338|consensus	691		100.0
KOG0333|consensus	673		100.0
KOG0341|consensus	610		100.0
KOG0330|consensus	476		100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0335|consensus	482		100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0348|consensus	708		100.0
KOG0345|consensus	567		100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0343|consensus	758		100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
KOG0342|consensus	543		100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.98
KOG0347|consensus	731		99.98
KOG0340|consensus	442		99.97
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.97
KOG0346|consensus	569		99.97
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.97
KOG0337|consensus	529		99.97
PTZ00424	401	helicase 45; Provisional	99.96
KOG0328|consensus	400		99.96
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.96
KOG0326|consensus	459		99.96
KOG0350|consensus	620		99.95
KOG0329|consensus	387		99.94
KOG0344|consensus	593		99.94
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.94
KOG4284|consensus	980		99.93
PRK02362	737	ski2-like helicase; Provisional	99.93
KOG0327|consensus	397		99.93
PRK00254	720	ski2-like helicase; Provisional	99.92
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.92
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.91
PRK13767	876	ATP-dependent helicase; Provisional	99.91
PRK01172	674	ski2-like helicase; Provisional	99.9
KOG0332|consensus	477		99.9
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.89
PRK09401	1176	reverse gyrase; Reviewed	99.89
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.88
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.88
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.88
PRK14701	1638	reverse gyrase; Provisional	99.87
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.86
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.85
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.85
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.84
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.83
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.83
COG1205	851	Distinct helicase family with a unique C-terminal	99.83
PRK10689	1147	transcription-repair coupling factor; Provisional	99.81
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.8
KOG0349|consensus	725		99.79
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.79
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.78
COG1204	766	Superfamily II helicase [General function predicti	99.78
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.77
PHA02558	501	uvsW UvsW helicase; Provisional	99.76
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.76
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.75
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.75
KOG0952|consensus	1230		99.71
KOG2340|consensus	698		99.71
PRK13766	773	Hef nuclease; Provisional	99.7
COG1202	830	Superfamily II helicase, archaea-specific [General	99.67
PHA02653	675	RNA helicase NPH-II; Provisional	99.66
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.65
PRK05580	679	primosome assembly protein PriA; Validated	99.63
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.63
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.62
KOG0354|consensus	746		99.62
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.6
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.6
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.59
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.58
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.57
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.57
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.57
KOG0352|consensus	641		99.49
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.48
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.48
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.44
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.42
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.4
KOG0351|consensus	941		99.4
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.39
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.37
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.37
KOG0353|consensus	695		99.37
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.33
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.33
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.33
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.32
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.31
KOG0951|consensus	1674		99.28
PRK09694	878	helicase Cas3; Provisional	99.26
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.22
KOG0947|consensus	1248		99.17
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.16
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.15
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.15
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.13
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.1
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.05
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.03
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.01
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.97
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	98.97
KOG0948|consensus	1041		98.93
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.92
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.92
KOG0949|consensus	1330		98.92
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	98.9
COG4096	875	HsdR Type I site-specific restriction-modification	98.87
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	98.84
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	98.84
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	98.82
KOG1002|consensus	791		98.8
KOG0950|consensus	1008		98.78
KOG0385|consensus	971		98.78
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.74
PRK04914	956	ATP-dependent helicase HepA; Validated	98.71
KOG0951|consensus	1674		98.68
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.66
COG4889	1518	Predicted helicase [General function prediction on	98.65
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.59
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.58
KOG0387|consensus	923		98.49
KOG0391|consensus	1958		98.48
KOG1132|consensus	945		98.35
KOG0389|consensus	941		98.32
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.32
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	98.28
KOG1123|consensus	776		98.28
KOG4439|consensus	901		98.27
KOG0952|consensus	1230		98.24
KOG0390|consensus	776		98.2
PRK14873	665	primosome assembly protein PriA; Provisional	98.2
COG0610	962	Type I site-specific restriction-modification syst	98.15
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.11
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.09
KOG0392|consensus	1549		98.09
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	98.09
KOG1803|consensus	649		98.03
KOG0384|consensus	1373		97.99
PRK15483	986	type III restriction-modification system StyLTI en	97.99
TIGR00376	637	DNA helicase, putative. The gene product may repre	97.98
KOG0920|consensus	924		97.93
KOG1802|consensus	935		97.92
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.92
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	97.89
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.83
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.75
KOG0388|consensus	1185		97.71
KOG0386|consensus	1157		97.66
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.62
PF13245	76	AAA_19: Part of AAA domain	97.61
KOG0926|consensus	1172		97.59
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.52
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.51
KOG1805|consensus	1100		97.5
KOG1000|consensus	689		97.5
PRK10536	262	hypothetical protein; Provisional	97.5
KOG0922|consensus	674		97.43
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.39
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.39
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.34
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	97.34
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.32
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	97.29
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	97.29
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	97.26
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.25
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.23
KOG1131|consensus	755		97.2
KOG1133|consensus	821		97.16
KOG0925|consensus	699		96.97
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.97
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	96.94
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.8
PHA02533	534	17 large terminase protein; Provisional	96.72
KOG0923|consensus	902		96.7
PRK04296	190	thymidine kinase; Provisional	96.65
COG3587	985	Restriction endonuclease [Defense mechanisms]	96.63
smart00382	148	AAA ATPases associated with a variety of cellular	96.58
KOG0924|consensus	1042		96.57
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.52
PRK13826	1102	Dtr system oriT relaxase; Provisional	96.49
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.47
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.46
PRK11054	684	helD DNA helicase IV; Provisional	96.41
KOG0953|consensus	700		96.37
PRK05298	652	excinuclease ABC subunit B; Provisional	96.34
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.3
KOG1001|consensus	674		96.25
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.18
KOG4150|consensus	1034		96.16
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	96.14
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	96.09
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	95.99
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	95.99
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	95.93
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.81
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	95.8
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	95.75
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	95.68
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.68
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	95.61
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	95.59
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	95.58
KOG0298|consensus	1394		95.51
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.51
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.5
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	95.48
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.34
KOG1015|consensus	1567		95.31
PRK08727	233	hypothetical protein; Validated	95.27
PRK07952	244	DNA replication protein DnaC; Validated	95.26
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	95.24
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	95.24
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	95.2
PRK14087	450	dnaA chromosomal replication initiation protein; P	95.11
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	95.11
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.01
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	94.91
PTZ00112	1164	origin recognition complex 1 protein; Provisional	94.9
PRK05973	237	replicative DNA helicase; Provisional	94.89
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	94.86
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	94.83
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	94.83
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	94.81
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	94.81
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	94.8
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	94.8
PHA03333	752	putative ATPase subunit of terminase; Provisional	94.7
PRK11823	446	DNA repair protein RadA; Provisional	94.63
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	94.44
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	94.39
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	94.38
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	94.36
COG3973	747	Superfamily I DNA and RNA helicases [General funct	94.35
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	94.33
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	94.3
PRK08506	472	replicative DNA helicase; Provisional	94.26
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	94.2
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	94.09
PRK00411	394	cdc6 cell division control protein 6; Reviewed	94.07
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.04
PRK05748	448	replicative DNA helicase; Provisional	93.99
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	93.97
PRK08181	269	transposase; Validated	93.96
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	93.93
PRK07004	460	replicative DNA helicase; Provisional	93.9
PRK08006	471	replicative DNA helicase; Provisional	93.88
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	93.85
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	93.82
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	93.81
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	93.74
COG1484	254	DnaC DNA replication protein [DNA replication, rec	93.67
PRK13851	344	type IV secretion system protein VirB11; Provision	93.66
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	93.66
COG4626	546	Phage terminase-like protein, large subunit [Gener	93.64
PRK13764	602	ATPase; Provisional	93.62
TIGR02237	209	recomb_radB DNA repair and recombination protein R	93.62
PRK00771	437	signal recognition particle protein Srp54; Provisi	93.53
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	93.53
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	93.53
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	93.51
PRK06904	472	replicative DNA helicase; Validated	93.47
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	93.44
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	93.44
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	93.43
PRK14974	336	cell division protein FtsY; Provisional	93.43
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	93.42
PRK08903	227	DnaA regulatory inactivator Hda; Validated	93.37
PRK10689	1147	transcription-repair coupling factor; Provisional	93.35
PRK06921	266	hypothetical protein; Provisional	93.35
TIGR00665	434	DnaB replicative DNA helicase. This model describe	93.34
PRK06835	329	DNA replication protein DnaC; Validated	93.34
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	93.28
KOG0989|consensus	346		93.28
PRK08116	268	hypothetical protein; Validated	93.28
PRK05595	444	replicative DNA helicase; Provisional	93.18
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	93.17
PRK12402	337	replication factor C small subunit 2; Reviewed	93.16
PRK10416	318	signal recognition particle-docking protein FtsY;	93.12
PRK13897	606	type IV secretion system component VirD4; Provisio	93.07
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	93.04
PRK00149	450	dnaA chromosomal replication initiation protein; R	92.99
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	92.99
PRK08840	464	replicative DNA helicase; Provisional	92.92
PRK08760	476	replicative DNA helicase; Provisional	92.75
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	92.68
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	92.66
PRK12377	248	putative replication protein; Provisional	92.64
PF12846	304	AAA_10: AAA-like domain	92.61
KOG0344|consensus	593		92.6
TIGR00959	428	ffh signal recognition particle protein. This mode	92.5
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	92.49
KOG0331|consensus	519		92.48
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	92.47
PRK09165	497	replicative DNA helicase; Provisional	92.42
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	92.4
PRK05636	505	replicative DNA helicase; Provisional	92.37
PRK08769	319	DNA polymerase III subunit delta'; Validated	92.34
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	92.33
PRK08533	230	flagellar accessory protein FlaH; Reviewed	92.29
PRK06526	254	transposase; Provisional	92.22
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	92.18
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	92.05
COG3972	660	Superfamily I DNA and RNA helicases [General funct	91.99
PRK10867	433	signal recognition particle protein; Provisional	91.94
PRK04328	249	hypothetical protein; Provisional	91.92
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	91.91
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	91.86
PRK06321	472	replicative DNA helicase; Provisional	91.73
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	91.64
PTZ00110	545	helicase; Provisional	91.64
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	91.63
KOG3089|consensus	271		91.55
PHA02535	581	P terminase ATPase subunit; Provisional	91.52
KOG0333|consensus	673		91.46
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	91.43
PRK13850	670	type IV secretion system protein VirD4; Provisiona	91.4
PRK09183	259	transposase/IS protein; Provisional	91.33
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	91.33
cd03115	173	SRP The signal recognition particle (SRP) mediates	91.17
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	91.15
PRK09376	416	rho transcription termination factor Rho; Provisio	91.09
PRK10436	462	hypothetical protein; Provisional	91.03
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	90.99
PTZ00293	211	thymidine kinase; Provisional	90.98
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	90.91
PRK09112	351	DNA polymerase III subunit delta'; Validated	90.86
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	90.83
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	90.79
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	90.77
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	90.75
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	90.74
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	90.69
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	90.65
PF13173	128	AAA_14: AAA domain	90.5
PHA00729	226	NTP-binding motif containing protein	90.42
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	90.41
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	90.4
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	90.35
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	90.23
TIGR00767	415	rho transcription termination factor Rho. Members	90.19
cd01128	249	rho_factor Transcription termination factor rho is	90.09
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	90.07
PRK13822	641	conjugal transfer coupling protein TraG; Provision	90.01
PHA03368	738	DNA packaging terminase subunit 1; Provisional	89.98
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	89.84
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	89.83
PRK13876	663	conjugal transfer coupling protein TraG; Provision	89.73
PRK13700	732	conjugal transfer protein TraD; Provisional	89.72
KOG2004|consensus	906		89.71
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	89.69
KOG1806|consensus	1320		89.58
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	89.54
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	89.53
cd03114	148	ArgK-like The function of this protein family is u	89.52
TIGR02533	486	type_II_gspE general secretory pathway protein E.	89.48
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	89.47
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	89.42
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	89.4
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	89.39
PRK13880	636	conjugal transfer coupling protein TraG; Provision	89.34
PRK07471	365	DNA polymerase III subunit delta'; Validated	89.34
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	89.3
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	89.28
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	89.25
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	89.23
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	89.22
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	89.16
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	89.14
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	89.11
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	89.06
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	88.98
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	88.98
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	88.9
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	88.89
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	88.87
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	88.84
PRK08939	306	primosomal protein DnaI; Reviewed	88.8
PRK13767	876	ATP-dependent helicase; Provisional	88.79
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	88.74
KOG0991|consensus	333		88.72
KOG0744|consensus	423		88.72
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	88.53
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	88.52
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	88.52
PRK06871	325	DNA polymerase III subunit delta'; Validated	88.5
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	88.45
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	88.4
COG2256	436	MGS1 ATPase related to the helicase subunit of the	88.34
PRK08699	325	DNA polymerase III subunit delta'; Validated	88.18
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	88.12
PRK05642	234	DNA replication initiation factor; Validated	88.08
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	88.03
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	87.96
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	87.95
PHA03372	668	DNA packaging terminase subunit 1; Provisional	87.92
PRK05707	328	DNA polymerase III subunit delta'; Validated	87.89
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	87.79
PF14516	331	AAA_35: AAA-like domain	87.64
KOG1016|consensus	1387		87.63
PHA02544	316	44 clamp loader, small subunit; Provisional	87.63
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	87.53
PRK04301	317	radA DNA repair and recombination protein RadA; Va	87.53
PHA02542	473	41 41 helicase; Provisional	87.49
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	87.49
cd01394	218	radB RadB. The archaeal protein radB shares simila	87.44
KOG1533|consensus	290		87.34
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	87.33
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	87.3
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	87.22
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	87.2
PRK07773	886	replicative DNA helicase; Validated	87.14
PRK06749	428	replicative DNA helicase; Provisional	87.07
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	87.02
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	87.01
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	87.0
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	86.86
PF13555	62	AAA_29: P-loop containing region of AAA domain	86.79
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	86.75
COG1086	588	Predicted nucleoside-diphosphate sugar epimerases	86.59
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	86.55
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	86.42
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	86.36
KOG0741|consensus	744		86.34
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	86.1
PRK04195	482	replication factor C large subunit; Provisional	86.04
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	86.0
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	85.95
PTZ00424	401	helicase 45; Provisional	85.89
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	85.78
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	85.76
PRK00440	319	rfc replication factor C small subunit; Reviewed	85.66
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	85.62
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	85.48
KOG0741|consensus	744		85.46
PRK06067	234	flagellar accessory protein FlaH; Validated	85.41
PRK09694	878	helicase Cas3; Provisional	85.38
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	85.28
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	85.19
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	85.15
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	85.03
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	84.99
KOG0330|consensus	476		84.97
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	84.87
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	84.74
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	84.62
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	84.49
COG0305	435	DnaB Replicative DNA helicase [DNA replication, re	84.44
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	84.38
PRK08084	235	DNA replication initiation factor; Provisional	84.35
PRK04914	956	ATP-dependent helicase HepA; Validated	84.24
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	84.19
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	83.92
PRK09302	509	circadian clock protein KaiC; Reviewed	83.72
cd00983	325	recA RecA is a bacterial enzyme which has roles in	83.59
KOG0341|consensus	610		83.5
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	83.48
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	83.32
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	83.22
PRK06893	229	DNA replication initiation factor; Validated	83.19
KOG0780|consensus	483		83.08
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	82.95
PHA00350	399	putative assembly protein	82.93
PRK09302	509	circadian clock protein KaiC; Reviewed	82.87
TIGR02746	797	TraC-F-type type-IV secretion system protein TraC.	82.68
COG0593	408	DnaA ATPase involved in DNA replication initiation	82.65
PF05729	166	NACHT: NACHT domain	82.6
KOG2227|consensus	529		82.5
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	82.48
PF02302	90	PTS_IIB: PTS system, Lactose/Cellobiose specific I	82.43
PRK09354	349	recA recombinase A; Provisional	82.35
PF09439	181	SRPRB: Signal recognition particle receptor beta s	82.33
COG3451	796	VirB4 Type IV secretory pathway, VirB4 components	82.29
PRK07993	334	DNA polymerase III subunit delta'; Validated	82.18
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	82.07
PRK06090	319	DNA polymerase III subunit delta'; Validated	81.9
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	81.66
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	81.55
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	81.47
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	81.3
PHA00012	361	I assembly protein	81.28
PRK06964	342	DNA polymerase III subunit delta'; Validated	81.26
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	81.03
TIGR02236	310	recomb_radA DNA repair and recombination protein R	80.89
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	80.79
PRK05298	652	excinuclease ABC subunit B; Provisional	80.52

>KOG0339|consensus

Probab=100.00  E-value=1.5e-61  Score=452.50  Aligned_cols=325  Identities=59%  Similarity=0.986  Sum_probs=292.4

Q ss_pred             CCCCCCCCCCccCCCCCCCCCCCCChHHHHHhhhhHHHHHhhhccccccccc--------ccCccCCCCCccchHHHHhh
Q psy17644          5 EYIPAPGSPSYKGNNASADTDSDEDPLDAFMKGIDKEVKQEAKGVKTKKIEE--------VKGIRDDIDHEDDEESYYRY   76 (330)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~d~~d~~~~~l~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~e~~~~~~~~~   76 (330)
                      +|-..+..|..........+.++.||+|+||+.+....+++++...+++.+.        ....+.+++++++.+.++.+
T Consensus        54 ey~eddd~p~~~s~~~a~~~~de~d~ldafMA~~~d~~~sd~~~~e~kk~eRkn~dd~~p~~~vr~dI~~e~aae~~~ky  133 (731)
T KOG0339|consen   54 EYEEDDDIPEGGSAAAAGGEVDEIDPLDAFMAKIEDQAQSDKKPLEQKKKERKNDDDDDPTATVRADIDEEDAAEALFKY  133 (731)
T ss_pred             ccccccccccccchhhccCCCCCCCCcchhhhhhhhhhhccCCccchHHHhhhccCCCccchhhhcchhhHHhHHHHHHH
Confidence            4444444443333334455677889999999999998877766542222111        22456788889999999999


Q ss_pred             hhcCCCCCCCCCCCccccccccCCCCCCCccccCCCCCCCCCCCccchhhhhhhcCCCChhhhccCHHHHHHHHHHcCcE
Q psy17644         77 MEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGIT  156 (330)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~r~~~~i~  156 (330)
                      +.++...+...+.++...++++|++++.+ .++.++|+++++|+++.|.||+++||..|+.+..++..++..+|..++++
T Consensus       134 m~e~k~~~~~~e~~~~~leydsd~nPi~~-~kr~idpl~~idhs~i~y~p~~kdfy~e~esI~gl~~~d~~~~r~~Lnlr  212 (731)
T KOG0339|consen  134 MSENKRAGAAKECDDMCLEYDSDGNPIAP-DKRQIDPLPPIDHSEIDYEPFNKDFYEEHESIEGLTKMDVIDLRLTLNLR  212 (731)
T ss_pred             hhhcccchhhhhcccceeecCCCCCccCc-ccccCCCCCCcchhhccccccccccccChhhhhccccccchhhHhhhcce
Confidence            99988776666677777899999999987 66789999999999999999999999999999999999999999999999


Q ss_pred             eeCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCC
Q psy17644        157 VSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE  236 (330)
Q Consensus       157 ~~g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~  236 (330)
                      +.|..+|+|+++|.+++|+..|+.++++..|++|||+|++++|..++|||++.+|.||||||.||++|++.|++.++.+.
T Consensus       213 v~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~  292 (731)
T KOG0339|consen  213 VSGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELK  292 (731)
T ss_pred             eccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCcc
Q psy17644        237 PGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVT  316 (330)
Q Consensus       237 ~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~  316 (330)
                      .+++|..|||||||+||.||+.++++|++.+|++++++|||.+.++|.+.|+.++.||||||+||++++..+..+++++.
T Consensus       293 ~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS  372 (731)
T KOG0339|consen  293 PGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVS  372 (731)
T ss_pred             CCCCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeee
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeecccccCcCC
Q psy17644        317 FLVLDEADRMFDMG  330 (330)
Q Consensus       317 ~lVvDEad~lld~G  330 (330)
                      ||||||||+|++||
T Consensus       373 ~LV~DEadrmfdmG  386 (731)
T KOG0339|consen  373 YLVLDEADRMFDMG  386 (731)
T ss_pred             EEEEechhhhhccc
Confidence            99999999999998

>KOG0334|consensus

Probab=100.00  E-value=2.6e-45  Score=369.10  Aligned_cols=218  Identities=55%  Similarity=0.859  Sum_probs=209.1

Q ss_pred             CCCCCCCCccchhhhhhhcCCCChhhhccCHHHHHHHHHHcC-cEeeCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCC
Q psy17644        113 PLPPIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSG-ITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPT  191 (330)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~r~~~~-i~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt  191 (330)
                      -+..++||++.|.||.++||.+..++..|+..++..+|...- |.+.|..+|.|+.+|.++|+...++..++++||.+||
T Consensus       310 ~~~~~~~S~~~~epFRknfy~e~~di~~ms~~eV~~yr~~l~~i~v~g~~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~  389 (997)
T KOG0334|consen  310 NLIQVDHSKISYEPFRKNFYIEVRDIKRMSAAEVDEYRCELDGIKVKGKECPKPVTSWTQCGLSSKILETLKKLGYEKPT  389 (997)
T ss_pred             ceeecccccccchhhhhcccccchhHHHHHHHHHHHhhcCccceeeccCCCCcccchHhhCCchHHHHHHHHHhcCCCCc
Confidence            567899999999999999999999999999999999998884 9999999999999999999999999999999999999


Q ss_pred             HHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceE
Q psy17644        192 PIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSV  271 (330)
Q Consensus       192 ~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~  271 (330)
                      |||.+|||++++|||+|++|.||||||++|+||++.|+..++....+.||.+|||+|||+||.||++++++|++.+++++
T Consensus       390 ~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~  469 (997)
T KOG0334|consen  390 PIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKLLGIRV  469 (997)
T ss_pred             chhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceE
Confidence            99999999999999999999999999999999999999999999888999999999999999999999999999999999


Q ss_pred             EEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcC---CCCCCCccEEEeecccccCcCC
Q psy17644        272 VCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG---ATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       272 ~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~---~~~l~~i~~lVvDEad~lld~G  330 (330)
                      +++|||....+++..+++++.|+||||+++++++-.+   ..++.++.+||+||||+|+|||
T Consensus       470 v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrmfdmg  531 (997)
T KOG0334|consen  470 VCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRMFDMG  531 (997)
T ss_pred             EEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccccceeeechhhhhheec
Confidence            9999999999999999999999999999999998654   3457788899999999999998

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=4.3e-42  Score=342.60  Aligned_cols=220  Identities=48%  Similarity=0.783  Sum_probs=206.7

Q ss_pred             CCCCCCCCCCccchhhhhhhcCCCChhhhccCHHHHHHHHHHcCcEe-eCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCC
Q psy17644        111 IDPLPPIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITV-SGADPPYPVSSFGHFGFDEVLMKALRKCEYTS  189 (330)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~r~~~~i~~-~g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~  189 (330)
                      ...++.++|+...+.||+++||.+++.+..++..++..+|...++.+ .|..+|.|+.+|.+++|++.|+++|.++||.+
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~g~~~  152 (545)
T PTZ00110         73 GKRLQPIDWKSINLVPFEKNFYKEHPEVSALSSKEVDEIRKEKEITIIAGENVPKPVVSFEYTSFPDYILKSLKNAGFTE  152 (545)
T ss_pred             ccccCCCCCccccccchhhhcccCChhhhcCCHHHHHHHHHhcCcEEecCCCCCcccCCHhhcCCCHHHHHHHHHCCCCC
Confidence            34577889988889999999999999999999999999999999886 68999999999999999999999999999999


Q ss_pred             CCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCc
Q psy17644        190 PTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNL  269 (330)
Q Consensus       190 pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~  269 (330)
                      |||+|.++||.+++|+|+|++|+||||||++|+||++.+++.++......+|.+|||+|||+||.|++..+++|+...++
T Consensus       153 pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i  232 (545)
T PTZ00110        153 PTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKI  232 (545)
T ss_pred             CCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHHHHHHHhcccCc
Confidence            99999999999999999999999999999999999999998765544556899999999999999999999999998899


Q ss_pred             eEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        270 SVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       270 ~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      ++.+++||.....+...+..+++|||+||++|.+++.++...++++++|||||||+|++||
T Consensus       233 ~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~lViDEAd~mld~g  293 (545)
T PTZ00110        233 RNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMG  293 (545)
T ss_pred             cEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEEEeehHHhhhhcc
Confidence            9999999999988888899999999999999999999888889999999999999999987

>KOG0331|consensus

Probab=100.00  E-value=6.9e-42  Score=329.06  Aligned_cols=209  Identities=50%  Similarity=0.851  Sum_probs=187.9

Q ss_pred             cchhhhhhhcCCCChhhhccCHHHHHHHHHHcCcEeeCCC-CCCCCCCC-----------------------------CC
Q psy17644        122 IVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGAD-PPYPVSSF-----------------------------GH  171 (330)
Q Consensus       122 ~~~~~~~~~f~~~~~~~~~~~~~~~~~~r~~~~i~~~g~~-~p~p~~~f-----------------------------~~  171 (330)
                      ..+.+|.++||.+++....+...+....+.+..+.+.+.. +|.|+.+|                             ..
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~v~~~~~~p~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~   95 (519)
T KOG0331|consen   16 LDLSPFDKNFYKEHPSVKKRGSAEVERKRKKNEITVKGGDSVPKPVKSFEESGFPAKVLEEIPKLSRSSGESDSSAAFQE   95 (519)
T ss_pred             cccCcccccccccccccccccccccccccCcceeeccCCCCCCCCccchhcccCCccccccccccccccccCCcchhhhc
Confidence            3457788899988888777777777777777777777765 66665554                             44


Q ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHh-cCCCCCCCCCeEEEEcccH
Q psy17644        172 FGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMD-QKELEPGDGPMGLILAPTR  250 (330)
Q Consensus       172 ~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~-~~~~~~~~~~~vLil~Ptr  250 (330)
                      ++|++.+..+++..||..|||||+++||+++.|||++++|.||||||++|+||++.|+.. +.......+|++|||+|||
T Consensus        96 ~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTR  175 (519)
T KOG0331|consen   96 LGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTR  175 (519)
T ss_pred             ccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcH
Confidence            566777777788999999999999999999999999999999999999999999999998 5666677899999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        251 ELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       251 ~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      |||.|+...+..++....++++|+|||.....|...++++++|+||||+||+++++.+..+|++|.|||+||||+|||||
T Consensus       176 ELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrMldmG  255 (519)
T KOG0331|consen  176 ELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRMLDMG  255 (519)
T ss_pred             HHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHhhhccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998

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

Probab=100.00  E-value=2.3e-39  Score=321.71  Aligned_cols=216  Identities=36%  Similarity=0.573  Sum_probs=196.0

Q ss_pred             CCCCCCccch-hhhhhhcCCCChhhh-ccCHHHHHHHHHHcCcEeeCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCH
Q psy17644        115 PPIDHSTIVY-EEVEKNFYQPHEDIA-RLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTP  192 (330)
Q Consensus       115 ~~~~~~~~~~-~~~~~~f~~~~~~~~-~~~~~~~~~~r~~~~i~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~  192 (330)
                      ..++++...+ .+++++||..+.... +++..++..+|..++|.+.|..+|.|+.+|.+++|++.++++|.+.||..|||
T Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~i~~~g~~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptp  146 (518)
T PLN00206         67 VAVGAPKPKRLPATDECFYVRDPGSTSGLSSSQAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTP  146 (518)
T ss_pred             CCcCCCchhhcCCcCCcCCccCcchhccCCHHHHHHHHHHCCCEecCCCCCchhcCHHhCCCCHHHHHHHHHcCCCCCCH
Confidence            3445555554 678899999888765 49999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCC--CCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCce
Q psy17644        193 IQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL--EPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLS  270 (330)
Q Consensus       193 iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~--~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~  270 (330)
                      +|.++||.+++|+|++++|+||||||++|++|++.+++..+..  ....+|++|||+|||+||.|++..++.+++..+++
T Consensus       147 iQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~  226 (518)
T PLN00206        147 IQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFK  226 (518)
T ss_pred             HHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCce
Confidence            9999999999999999999999999999999999998764321  12367999999999999999999999999988999


Q ss_pred             EEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        271 VVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       271 ~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      +.+++||.....+...+..+++|||+||++|.+++.+....++++.+|||||||+|+++|
T Consensus       227 ~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~~lViDEad~ml~~g  286 (518)
T PLN00206        227 TALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERG  286 (518)
T ss_pred             EEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchheeEEEeecHHHHhhcc
Confidence            999999999888888888899999999999999999888889999999999999999987

>KOG0336|consensus

Probab=100.00  E-value=6.3e-40  Score=300.88  Aligned_cols=206  Identities=43%  Similarity=0.721  Sum_probs=189.0

Q ss_pred             hhhhhhhcCCCChhhhccCHHHHHHHHHHc-CcEee----C--CCCCCCCCCCCC-CCCCHHHHHHHHHCCCCCCCHHHH
Q psy17644        124 YEEVEKNFYQPHEDIARLTPQEAQELRAKS-GITVS----G--ADPPYPVSSFGH-FGFDEVLMKALRKCEYTSPTPIQA  195 (330)
Q Consensus       124 ~~~~~~~f~~~~~~~~~~~~~~~~~~r~~~-~i~~~----g--~~~p~p~~~f~~-~~l~~~l~~~l~~~~~~~pt~iQ~  195 (330)
                      ++|..+|||....+.+.|+..++..+|... +|.+.    |  ..+|+|+.+|++ |.-.+.+++++++.||.+|||||.
T Consensus       169 lpPi~knfYke~~e~s~ls~~q~~~~r~en~~it~dd~K~gekrpIPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqS  248 (629)
T KOG0336|consen  169 LPPIKKNFYKESNETSNLSKEQLQEWRKENFNITCDDLKEGEKRPIPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQS  248 (629)
T ss_pred             CCchhhhhhhcCchhccCCHHHHHHHHHcCCcEEecccccCCcccCCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchh
Confidence            468999999999999999999999999877 45543    2  347899999987 678899999999999999999999


Q ss_pred             HhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCC-CCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEE
Q psy17644        196 QAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL-EPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCC  274 (330)
Q Consensus       196 ~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~-~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~  274 (330)
                      |+||++++|+|++++|+||+|||++||+|.+.|+..++.+ ...++|.+|+++|||+||.|+.-+++++. +.+.+.+|+
T Consensus       249 QaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqie~e~~kys-yng~ksvc~  327 (629)
T KOG0336|consen  249 QAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIEGEVKKYS-YNGLKSVCV  327 (629)
T ss_pred             cccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHHHHHHhHHhHhh-hcCcceEEE
Confidence            9999999999999999999999999999999999887643 34578999999999999999999999885 458899999


Q ss_pred             ECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        275 YGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       275 ~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      |||.+..+|+..++++.+||||||++|.++...+.++|.+|.|||+||||+|||||
T Consensus       328 ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDMg  383 (629)
T KOG0336|consen  328 YGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLDMG  383 (629)
T ss_pred             ecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhccc
Confidence            99999999999999999999999999999999999999999999999999999998

>KOG0338|consensus

Probab=100.00  E-value=7.6e-38  Score=293.75  Aligned_cols=162  Identities=38%  Similarity=0.573  Sum_probs=152.4

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      .+|.+++|+..|++++..+||..|||||..+||..+-|+|+++||.||||||+||.||+|.+++..+..  ....+||||
T Consensus       181 ~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~--~~~TRVLVL  258 (691)
T KOG0338|consen  181 ESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKK--VAATRVLVL  258 (691)
T ss_pred             hhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCccc--CcceeEEEE
Confidence            569999999999999999999999999999999999999999999999999999999999999987654  346799999


Q ss_pred             cccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcC-CCCCCCccEEEeecccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG-ATKLNRVTFLVLDEADR  325 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~-~~~l~~i~~lVvDEad~  325 (330)
                      ||||+||.|++...++++..+.+.+++++||.+...|...|+.++||||||||||++++.+. .+++++|.+||+||||+
T Consensus       259 ~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADR  338 (691)
T KOG0338|consen  259 VPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADR  338 (691)
T ss_pred             eccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHH
Confidence            99999999999999999999999999999999999999999999999999999999999765 56799999999999999


Q ss_pred             cCcCC
Q psy17644        326 MFDMG  330 (330)
Q Consensus       326 lld~G  330 (330)
                      ||+-|
T Consensus       339 MLeeg  343 (691)
T KOG0338|consen  339 MLEEG  343 (691)
T ss_pred             HHHHH
Confidence            99754

>KOG0333|consensus

Probab=100.00  E-value=5.4e-38  Score=295.68  Aligned_cols=194  Identities=44%  Similarity=0.697  Sum_probs=184.9

Q ss_pred             hhhccCHHHHHHHHHHcCcEeeCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCCh
Q psy17644        137 DIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSG  216 (330)
Q Consensus       137 ~~~~~~~~~~~~~r~~~~i~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsG  216 (330)
                      .+..|+...|..||..++|.++|..+|+|+++|++.+|+..++..+.+.||..|||||+++||.+++.+|+|++|.||||
T Consensus       215 ~l~Em~~rdwri~redynis~kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsG  294 (673)
T KOG0333|consen  215 VLAEMTERDWRIFREDYNISIKGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSG  294 (673)
T ss_pred             hHHhcCCccceeeecceeeeecCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCC
Confidence            47778889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHhcCCCC----CCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCe
Q psy17644        217 KTGAFIWPMLVHIMDQKELE----PGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAE  292 (330)
Q Consensus       217 KT~a~llp~l~~i~~~~~~~----~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~d  292 (330)
                      ||++|++|+|..+...++..    .-.||+++||+|||+|++||..+..+|++.++++++.++||.+..++...++.+|+
T Consensus       295 ktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gce  374 (673)
T KOG0333|consen  295 KTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCE  374 (673)
T ss_pred             ccccchhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccce
Confidence            99999999999998876443    23589999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        293 IVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       293 IiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      |+||||++|++.+.+..+-++.+.+||+||||+|+|||
T Consensus       375 iviatPgrLid~Lenr~lvl~qctyvvldeadrmiDmg  412 (673)
T KOG0333|consen  375 IVIATPGRLIDSLENRYLVLNQCTYVVLDEADRMIDMG  412 (673)
T ss_pred             eeecCchHHHHHHHHHHHHhccCceEeccchhhhhccc
Confidence            99999999999999988889999999999999999998

>KOG0341|consensus

Probab=100.00  E-value=2.1e-38  Score=289.21  Aligned_cols=210  Identities=39%  Similarity=0.691  Sum_probs=194.2

Q ss_pred             ccchhhhhhhcCCCChhhhccCHHHHHHHHHHcCcEeeCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhh
Q psy17644        121 TIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPA  200 (330)
Q Consensus       121 ~~~~~~~~~~f~~~~~~~~~~~~~~~~~~r~~~~i~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~  200 (330)
                      .+.|+.--+..|.|+--+..|+.++....|++++|.+.|..+|+|+.+|.++.|+..+++.|++.|+..|||||.+.+|.
T Consensus       124 Gi~Y~ePi~T~WkPP~hir~mS~e~~e~vRk~~~I~veGd~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPv  203 (610)
T KOG0341|consen  124 GITYEEPIKTAWKPPRHIRKMSEEQRELVRKQLHILVEGDDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPV  203 (610)
T ss_pred             CCcccCcchhccCCcHHHHHhhHHHHHHHHHhheEEeeCCCCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcce
Confidence            34566666777888889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcC---CCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC------CceE
Q psy17644        201 ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQK---ELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY------NLSV  271 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~---~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~------~~~~  271 (330)
                      +++|||+|++|-||||||++|.||++...+.+.   +...+.||..|||||+|+||.|++..+..++..+      .++.
T Consensus       204 vLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs  283 (610)
T KOG0341|consen  204 VLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRS  283 (610)
T ss_pred             EeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhh
Confidence            999999999999999999999999999888763   3345689999999999999999999998886532      4688


Q ss_pred             EEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        272 VCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       272 ~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      .+|.||.....|...++.|.+|+|+||+||.+++.++..+|.-++||++||||+|+|||
T Consensus       284 ~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~KK~~sLd~CRyL~lDEADRmiDmG  342 (610)
T KOG0341|consen  284 LLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAKKIMSLDACRYLTLDEADRMIDMG  342 (610)
T ss_pred             hhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHHhhccHHHHHHhhhhhHHHHhhcc
Confidence            89999999999999999999999999999999999999999999999999999999998

>KOG0330|consensus

Probab=100.00  E-value=9.4e-37  Score=278.65  Aligned_cols=159  Identities=42%  Similarity=0.687  Sum_probs=152.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       166 ~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      ..+|.++++.+.|++++...++..||+||+++||.++.|+|+|+.|.||||||.+|+||++++++.++.     .+.+||
T Consensus        60 ~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~-----~~~~lV  134 (476)
T KOG0330|consen   60 FKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPK-----LFFALV  134 (476)
T ss_pred             hcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCC-----CceEEE
Confidence            567999999999999999999999999999999999999999999999999999999999999998754     499999


Q ss_pred             EcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHH-cCCCCCCCccEEEeeccc
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVK-MGATKLNRVTFLVLDEAD  324 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~-~~~~~l~~i~~lVvDEad  324 (330)
                      |+||||||.||...+..++...|+++.++.||.+...|...+.+.+||||||||+|.+++. .+.+++..+++||+||||
T Consensus       135 LtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEAD  214 (476)
T KOG0330|consen  135 LTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEAD  214 (476)
T ss_pred             ecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHH
Confidence            9999999999999999999999999999999999999999999999999999999999998 567789999999999999


Q ss_pred             ccCcC
Q psy17644        325 RMFDM  329 (330)
Q Consensus       325 ~lld~  329 (330)
                      ++|||
T Consensus       215 rlLd~  219 (476)
T KOG0330|consen  215 RLLDM  219 (476)
T ss_pred             hhhhh
Confidence            99987

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

Probab=100.00  E-value=1.6e-35  Score=293.12  Aligned_cols=161  Identities=48%  Similarity=0.777  Sum_probs=149.7

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      ..|.+++|++.+++++.+.||..|||||.++||.++.|+|++++|+||||||+||++|+|+++.....   ...+.+|||
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~---~~~~~aLil  105 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVE---RKYVSALIL  105 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccc---cCCCceEEE
Confidence            67999999999999999999999999999999999999999999999999999999999999764211   111129999


Q ss_pred             cccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      +|||+||.|+++.+..++... ++++.+++||.+...+...++.+++||||||+||++++.++.++++.+++||+||||+
T Consensus       106 ~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADr  185 (513)
T COG0513         106 APTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADR  185 (513)
T ss_pred             CCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccHhh
Confidence            999999999999999999998 7999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcCC
Q psy17644        326 MFDMG  330 (330)
Q Consensus       326 lld~G  330 (330)
                      |||||
T Consensus       186 mLd~G  190 (513)
T COG0513         186 MLDMG  190 (513)
T ss_pred             hhcCC
Confidence            99998

>KOG0335|consensus

Probab=100.00  E-value=4.1e-35  Score=278.16  Aligned_cols=176  Identities=43%  Similarity=0.722  Sum_probs=164.6

Q ss_pred             cEeeCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCC
Q psy17644        155 ITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKE  234 (330)
Q Consensus       155 i~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~  234 (330)
                      +.+.|.+.|.++.+|.+..+.+.++.++...+|..|||+|+.+||.+..|+|+++||+||||||.|||+|++.+++..+.
T Consensus        62 v~~~G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~  141 (482)
T KOG0335|consen   62 VKVSGRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGP  141 (482)
T ss_pred             eeccCCccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCc
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999998754


Q ss_pred             CC---C--CCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCC
Q psy17644        235 LE---P--GDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA  309 (330)
Q Consensus       235 ~~---~--~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~  309 (330)
                      ..   .  ...|.+|||+|||+||.|++++.++|.-..+++++..|||.+...+...+.++|+|+||||+||.++++.+.
T Consensus       142 ~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~  221 (482)
T KOG0335|consen  142 EDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGK  221 (482)
T ss_pred             ccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcce
Confidence            21   1  135999999999999999999999999888999999999999999999999999999999999999999999


Q ss_pred             CCCCCccEEEeecccccCc-CC
Q psy17644        310 TKLNRVTFLVLDEADRMFD-MG  330 (330)
Q Consensus       310 ~~l~~i~~lVvDEad~lld-~G  330 (330)
                      +.|..++||||||||+|+| ||
T Consensus       222 i~l~~~k~~vLDEADrMlD~mg  243 (482)
T KOG0335|consen  222 ISLDNCKFLVLDEADRMLDEMG  243 (482)
T ss_pred             eehhhCcEEEecchHHhhhhcc
Confidence            9999999999999999999 87

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=7.8e-34  Score=276.06  Aligned_cols=165  Identities=41%  Similarity=0.634  Sum_probs=152.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCC--CCCCCeE
Q psy17644        166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE--PGDGPMG  243 (330)
Q Consensus       166 ~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~--~~~~~~v  243 (330)
                      ..+|.+++|++.+++++.+.||..|||+|.++||.+++|+|++++||||||||++|++|++++++..+...  ..+++++
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            36799999999999999999999999999999999999999999999999999999999999998654321  1357899


Q ss_pred             EEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecc
Q psy17644        244 LILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEA  323 (330)
Q Consensus       244 Lil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEa  323 (330)
                      |||+|||+||.|+++.+..++...++++..++||.....+...+..+++||||||++|.+++.+....++++.+||||||
T Consensus        87 lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEa  166 (423)
T PRK04837         87 LIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEA  166 (423)
T ss_pred             EEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecH
Confidence            99999999999999999999999999999999999888888888888999999999999999988889999999999999


Q ss_pred             cccCcCC
Q psy17644        324 DRMFDMG  330 (330)
Q Consensus       324 d~lld~G  330 (330)
                      |+|+++|
T Consensus       167 d~l~~~~  173 (423)
T PRK04837        167 DRMFDLG  173 (423)
T ss_pred             HHHhhcc
Confidence            9999987

>KOG0348|consensus

Probab=100.00  E-value=2.8e-34  Score=271.10  Aligned_cols=170  Identities=36%  Similarity=0.667  Sum_probs=152.0

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHH-HCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCC-CCC
Q psy17644        161 DPPYPVSSFGHFGFDEVLMKALR-KCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL-EPG  238 (330)
Q Consensus       161 ~~p~p~~~f~~~~l~~~l~~~l~-~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~-~~~  238 (330)
                      +.|..-..|..+||++.+...|. .+++..||.+|+++||.+++|||+++.++||||||++||+|+++++...... ...
T Consensus       130 e~~fts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs  209 (708)
T KOG0348|consen  130 EAPFTSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRS  209 (708)
T ss_pred             ccccccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCcccccc
Confidence            44555677999999999999995 4699999999999999999999999999999999999999999999876433 456


Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcC-CCCCCCcc
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG-ATKLNRVT  316 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~-~~~l~~i~  316 (330)
                      .|+.+|||+||||||.|+|+.+.++.+.+ -+....+.||.........+++|+.|||+|||||.+.+.+. .+.+++++
T Consensus       210 ~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LR  289 (708)
T KOG0348|consen  210 DGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLR  289 (708)
T ss_pred             CCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeee
Confidence            89999999999999999999999998764 34556788999988888999999999999999999998764 56799999


Q ss_pred             EEEeecccccCcCC
Q psy17644        317 FLVLDEADRMFDMG  330 (330)
Q Consensus       317 ~lVvDEad~lld~G  330 (330)
                      +||+||||+|+|+|
T Consensus       290 wlVlDEaDrlleLG  303 (708)
T KOG0348|consen  290 WLVLDEADRLLELG  303 (708)
T ss_pred             EEEecchhHHHhcc
Confidence            99999999999998

>KOG0345|consensus

Probab=100.00  E-value=3.4e-33  Score=260.51  Aligned_cols=164  Identities=39%  Similarity=0.598  Sum_probs=143.5

Q ss_pred             CCCCCCC--CCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEE
Q psy17644        167 SSFGHFG--FDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGL  244 (330)
Q Consensus       167 ~~f~~~~--l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vL  244 (330)
                      .+|+.++  |.+.|++++...||...||+|..+||.+++++|+++.|+||||||+||++|++..+..+..........+|
T Consensus         4 ~~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgal   83 (567)
T KOG0345|consen    4 KSFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGAL   83 (567)
T ss_pred             cchhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEE
Confidence            3577765  55999999999999999999999999999999999999999999999999999998765433222235789


Q ss_pred             EEcccHHHHHHHHHHHHHhccC-CCceEEEEECCCchHHHHHHHhC-CCeEEEEChHHHHHHHHcCCC--CCCCccEEEe
Q psy17644        245 ILAPTRELSQQIYNEAKRFGKG-YNLSVVCCYGGGSKWDQSKALEL-GAEIVVGTPGRIIDMVKMGAT--KLNRVTFLVL  320 (330)
Q Consensus       245 il~Ptr~La~Qi~~~~~~l~~~-~~~~~~~~~gg~~~~~~~~~l~~-~~dIiV~TP~~L~~~l~~~~~--~l~~i~~lVv  320 (330)
                      ||+||||||.||++.+..|... .++.+.+++||.+.....+.+++ ++.|+|||||||.+++.+...  +++++++||+
T Consensus        84 IIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVL  163 (567)
T KOG0345|consen   84 IISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVL  163 (567)
T ss_pred             EecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEe
Confidence            9999999999999999999877 68899999999998888777664 789999999999999988544  4569999999


Q ss_pred             ecccccCcCC
Q psy17644        321 DEADRMFDMG  330 (330)
Q Consensus       321 DEad~lld~G  330 (330)
                      ||||+|+|||
T Consensus       164 DEADrLldmg  173 (567)
T KOG0345|consen  164 DEADRLLDMG  173 (567)
T ss_pred             cchHhHhccc
Confidence            9999999998

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=1.5e-32  Score=269.31  Aligned_cols=163  Identities=42%  Similarity=0.695  Sum_probs=149.5

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCC-CCCCCeEEEE
Q psy17644        168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE-PGDGPMGLIL  246 (330)
Q Consensus       168 ~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~-~~~~~~vLil  246 (330)
                      +|++++|++.++++|.+.||..|||+|.++||.+++|+|++++||||||||++|++|+++++....... ....+++|||
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            689999999999999999999999999999999999999999999999999999999999987643221 1234689999


Q ss_pred             cccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      +|||+||.|+++.++.++...++++..++||.....+...+..+++||||||++|.+++.+....++++.+|||||||+|
T Consensus        82 ~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~l  161 (456)
T PRK10590         82 TPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRM  161 (456)
T ss_pred             eCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHHH
Confidence            99999999999999999999999999999999988888888888999999999999999888888999999999999999


Q ss_pred             CcCC
Q psy17644        327 FDMG  330 (330)
Q Consensus       327 ld~G  330 (330)
                      +++|
T Consensus       162 l~~~  165 (456)
T PRK10590        162 LDMG  165 (456)
T ss_pred             hccc
Confidence            9986

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.9e-32  Score=274.46  Aligned_cols=164  Identities=41%  Similarity=0.673  Sum_probs=149.6

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCC--CCCCCeEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE--PGDGPMGL  244 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~--~~~~~~vL  244 (330)
                      .+|.+|+|++.|+++|.+.||..|||+|.++||.+++|+|++++|+||||||++|++|++++++......  ...++++|
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            4699999999999999999999999999999999999999999999999999999999999987643211  12368999


Q ss_pred             EEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcC-CCCCCCccEEEeecc
Q psy17644        245 ILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG-ATKLNRVTFLVLDEA  323 (330)
Q Consensus       245 il~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~-~~~l~~i~~lVvDEa  323 (330)
                      ||+|||+||.|+++.+.+|+...++++..++||.....+...+..+++|||+||++|.+++.+. ...++.+++||||||
T Consensus        89 Il~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEA  168 (572)
T PRK04537         89 ILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEA  168 (572)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCH
Confidence            9999999999999999999999999999999999998888888888999999999999998765 467899999999999


Q ss_pred             cccCcCC
Q psy17644        324 DRMFDMG  330 (330)
Q Consensus       324 d~lld~G  330 (330)
                      |+|+++|
T Consensus       169 h~lld~g  175 (572)
T PRK04537        169 DRMFDLG  175 (572)
T ss_pred             HHHhhcc
Confidence            9999886

>KOG0343|consensus

Probab=100.00  E-value=2.5e-33  Score=265.55  Aligned_cols=164  Identities=35%  Similarity=0.577  Sum_probs=150.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEE
Q psy17644        165 PVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGL  244 (330)
Q Consensus       165 p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vL  244 (330)
                      .+..|.+|+|+...+++|+..+|..||.+|+++||..+.|+|+++.|.||||||+||++|+|.+++.. .+....|.-+|
T Consensus        67 ~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~-kWs~~DGlGal  145 (758)
T KOG0343|consen   67 TIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRL-KWSPTDGLGAL  145 (758)
T ss_pred             hhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHc-CCCCCCCceeE
Confidence            45679999999999999999999999999999999999999999999999999999999999998764 46667889999


Q ss_pred             EEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcC-CCCCCCccEEEeecc
Q psy17644        245 ILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG-ATKLNRVTFLVLDEA  323 (330)
Q Consensus       245 il~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~-~~~l~~i~~lVvDEa  323 (330)
                      ||.|||+||.|++..+.+.+++..+++.++.||.........+. ++.|+|||||||+.++... .++.+++.+||+|||
T Consensus       146 IISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi~-~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEA  224 (758)
T KOG0343|consen  146 IISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERIS-QMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEA  224 (758)
T ss_pred             EecchHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhhh-cCCeEEechHHHHHHhhhcCCCCCCcceEEEeccH
Confidence            99999999999999999999999999999999999766555554 4899999999999988654 567899999999999


Q ss_pred             cccCcCC
Q psy17644        324 DRMFDMG  330 (330)
Q Consensus       324 d~lld~G  330 (330)
                      |+|||||
T Consensus       225 DR~LDMG  231 (758)
T KOG0343|consen  225 DRMLDMG  231 (758)
T ss_pred             HHHHHHh
Confidence            9999998

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=5.2e-32  Score=264.07  Aligned_cols=162  Identities=42%  Similarity=0.692  Sum_probs=150.3

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc
Q psy17644        168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA  247 (330)
Q Consensus       168 ~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~  247 (330)
                      +|++++|++.++++|.+.||..||++|.++||.+++|+|++++||||+|||++|++|++++++.... ....++++|||+
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~-~~~~~~~~lil~   80 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPR-RKSGPPRILILT   80 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccc-cCCCCceEEEEC
Confidence            5999999999999999999999999999999999999999999999999999999999999976422 122457999999


Q ss_pred             ccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        248 PTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       248 Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ||++||.|+++.+..++...++++..++||.....+...+..+++||||||++|++++.+..+.+.++.+|||||||+|+
T Consensus        81 Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l  160 (434)
T PRK11192         81 PTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRML  160 (434)
T ss_pred             CcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHh
Confidence            99999999999999999999999999999999888888888889999999999999999888889999999999999999


Q ss_pred             cCC
Q psy17644        328 DMG  330 (330)
Q Consensus       328 d~G  330 (330)
                      +||
T Consensus       161 ~~~  163 (434)
T PRK11192        161 DMG  163 (434)
T ss_pred             CCC
Confidence            987

>KOG0342|consensus

Probab=100.00  E-value=1.2e-32  Score=258.30  Aligned_cols=164  Identities=35%  Similarity=0.565  Sum_probs=150.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       166 ~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      ...|.++.|++..++++..+||..+|++|..+||.++.|+|+++.|.||||||+||++|++.++++.+.. ..++-.|||
T Consensus        81 ~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~-~r~~~~vlI  159 (543)
T KOG0342|consen   81 TFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFK-PRNGTGVLI  159 (543)
T ss_pred             hhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccC-CCCCeeEEE
Confidence            4558889999999999999999999999999999999999999999999999999999999999987543 347889999


Q ss_pred             EcccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCC-CCCccEEEeecc
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATK-LNRVTFLVLDEA  323 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~-l~~i~~lVvDEa  323 (330)
                      |||||+||.|++.+++.+..+. +..+..+.||+........+.++|.|+|||||||.+++++...+ ++.++++|+|||
T Consensus       160 i~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEA  239 (543)
T KOG0342|consen  160 ICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEA  239 (543)
T ss_pred             ecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecc
Confidence            9999999999999999999887 88999999999988777888889999999999999999876554 567789999999


Q ss_pred             cccCcCC
Q psy17644        324 DRMFDMG  330 (330)
Q Consensus       324 d~lld~G  330 (330)
                      |++||||
T Consensus       240 DrlLd~G  246 (543)
T KOG0342|consen  240 DRLLDIG  246 (543)
T ss_pred             hhhhhcc
Confidence            9999998

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.98  E-value=6.2e-32  Score=265.40  Aligned_cols=159  Identities=44%  Similarity=0.666  Sum_probs=147.8

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      .+|..++|++.++++|.+.||..|||+|.++||.+++|+|++++||||||||++|++|+++++....     .++++|||
T Consensus         4 ~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~-----~~~~~lil   78 (460)
T PRK11776          4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKR-----FRVQALVL   78 (460)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhcc-----CCceEEEE
Confidence            5799999999999999999999999999999999999999999999999999999999999875422     35789999


Q ss_pred             cccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      +|||+||.|+.+.++.++... ++++..++||.+...+...+..+++|+||||++|.+++.++...++++++|||||||+
T Consensus        79 ~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~  158 (460)
T PRK11776         79 CPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADR  158 (460)
T ss_pred             eCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHH
Confidence            999999999999999988754 7889999999999888888889999999999999999998888899999999999999


Q ss_pred             cCcCC
Q psy17644        326 MFDMG  330 (330)
Q Consensus       326 lld~G  330 (330)
                      |++||
T Consensus       159 ~l~~g  163 (460)
T PRK11776        159 MLDMG  163 (460)
T ss_pred             HhCcC
Confidence            99987

>KOG0347|consensus

Probab=99.98  E-value=2.2e-32  Score=259.06  Aligned_cols=167  Identities=34%  Similarity=0.552  Sum_probs=149.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCC-CcEEEEcCCCChhHHHHHHHHHHHHHhcCCC------C
Q psy17644        164 YPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG-RDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL------E  236 (330)
Q Consensus       164 ~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g-~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~------~  236 (330)
                      ..++.|.+|+|+..++++|..+||..||+||..+||+++.| .|+++.|.||||||+||-+|++..+......      .
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            34667999999999999999999999999999999999999 7999999999999999999999965543211      1


Q ss_pred             CCCCC--eEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC---C
Q psy17644        237 PGDGP--MGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT---K  311 (330)
Q Consensus       237 ~~~~~--~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~---~  311 (330)
                      ...++  .+|||+|||+||.|+.+.+..++...++++..++||.....|.+.++..++|||||||||+.++.....   +
T Consensus       258 ~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~  337 (731)
T KOG0347|consen  258 SAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGN  337 (731)
T ss_pred             HhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhh
Confidence            11234  599999999999999999999999999999999999999999999999999999999999999986644   5


Q ss_pred             CCCccEEEeecccccCcCC
Q psy17644        312 LNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       312 l~~i~~lVvDEad~lld~G  330 (330)
                      ++.+.+|||||||||++-|
T Consensus       338 ~k~vkcLVlDEaDRmvekg  356 (731)
T KOG0347|consen  338 FKKVKCLVLDEADRMVEKG  356 (731)
T ss_pred             hhhceEEEEccHHHHhhhc
Confidence            8899999999999999866

>KOG0340|consensus

Probab=99.97  E-value=2.4e-32  Score=247.23  Aligned_cols=159  Identities=40%  Similarity=0.597  Sum_probs=149.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       166 ~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      ...|..+||++++.+.++.+|+.+|||+|..|||.++.|||+|++|.||||||++|.+|+|+.+.+.+     .|-.+||
T Consensus         6 ~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP-----~giFalv   80 (442)
T KOG0340|consen    6 AKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDP-----YGIFALV   80 (442)
T ss_pred             cCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCC-----CcceEEE
Confidence            46799999999999999999999999999999999999999999999999999999999999988764     5889999


Q ss_pred             EcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCC----CCCCCccEEEee
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA----TKLNRVTFLVLD  321 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~----~~l~~i~~lVvD  321 (330)
                      ++|||+||.|+.+.+..+++..++++.+++||.+.-.+...|..++||||+||+||.+++..+.    ..+++++++|+|
T Consensus        81 lTPTrELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlD  160 (442)
T KOG0340|consen   81 LTPTRELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLD  160 (442)
T ss_pred             ecchHHHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEec
Confidence            9999999999999999999999999999999999999999999999999999999999998652    238899999999


Q ss_pred             cccccCcC
Q psy17644        322 EADRMFDM  329 (330)
Q Consensus       322 Ead~lld~  329 (330)
                      |||+|++-
T Consensus       161 EADrvL~~  168 (442)
T KOG0340|consen  161 EADRVLAG  168 (442)
T ss_pred             chhhhhcc
Confidence            99999863

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.97  E-value=2e-31  Score=268.95  Aligned_cols=160  Identities=44%  Similarity=0.726  Sum_probs=148.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       166 ~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      ..+|.+++|++.++++|.++||..|||+|.++||.++.|+|+|++||||||||++|++|++..+...     ..++++||
T Consensus         5 ~~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~-----~~~~~~LI   79 (629)
T PRK11634          5 ETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPE-----LKAPQILV   79 (629)
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhc-----cCCCeEEE
Confidence            3469999999999999999999999999999999999999999999999999999999999887543     24689999


Q ss_pred             EcccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccc
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD  324 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad  324 (330)
                      |+|||+||.|++..+..+.+.. ++.++.++||.....+...++.+++|||+||++|++++.+....++++.+|||||||
T Consensus        80 L~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd  159 (629)
T PRK11634         80 LAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEAD  159 (629)
T ss_pred             EeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHH
Confidence            9999999999999999987765 789999999999888888888899999999999999999888889999999999999


Q ss_pred             ccCcCC
Q psy17644        325 RMFDMG  330 (330)
Q Consensus       325 ~lld~G  330 (330)
                      .|++||
T Consensus       160 ~ml~~g  165 (629)
T PRK11634        160 EMLRMG  165 (629)
T ss_pred             HHhhcc
Confidence            999987

>KOG0346|consensus

Probab=99.97  E-value=6.7e-32  Score=250.06  Aligned_cols=164  Identities=37%  Similarity=0.616  Sum_probs=144.9

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCC-CCCCCCeEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL-EPGDGPMGLI  245 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~-~~~~~~~vLi  245 (330)
                      .+|++|+|+++|++++.+.||.+||-||..+||.++.|+|+++.|.||||||+||++|+++.++..... ....+|.++|
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            579999999999999999999999999999999999999999999999999999999999999986544 4567899999


Q ss_pred             EcccHHHHHHHHHHHHHhccCCC--ceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCC-CCCCCccEEEeec
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYN--LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA-TKLNRVTFLVLDE  322 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~--~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~-~~l~~i~~lVvDE  322 (330)
                      |+|||+||.|++..+.++...++  ++++-+....+.......+...++|||+||++|..++..+. ..+..+.+||+||
T Consensus        99 LvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDE  178 (569)
T KOG0346|consen   99 LVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDE  178 (569)
T ss_pred             EechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEech
Confidence            99999999999999999877654  45555554455555557777789999999999999998876 6689999999999


Q ss_pred             ccccCcCC
Q psy17644        323 ADRMFDMG  330 (330)
Q Consensus       323 ad~lld~G  330 (330)
                      ||.||..|
T Consensus       179 ADLllsfG  186 (569)
T KOG0346|consen  179 ADLLLSFG  186 (569)
T ss_pred             hhhhhhcc
Confidence            99999887

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.97  E-value=2.5e-30  Score=255.00  Aligned_cols=166  Identities=40%  Similarity=0.564  Sum_probs=149.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCC--CCCCCe
Q psy17644        165 PVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE--PGDGPM  242 (330)
Q Consensus       165 p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~--~~~~~~  242 (330)
                      ....|..++|++.|+++|.+.||..||++|.++|+.+++|+|+|++++||||||++|++|++.+++..+...  ....++
T Consensus        85 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~  164 (475)
T PRK01297         85 GKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPR  164 (475)
T ss_pred             CCCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCce
Confidence            356789999999999999999999999999999999999999999999999999999999999998754221  123689


Q ss_pred             EEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh-CCCeEEEEChHHHHHHHHcCCCCCCCccEEEee
Q psy17644        243 GLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE-LGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLD  321 (330)
Q Consensus       243 vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~-~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvD  321 (330)
                      +|||+|||+||.|+++.++.+++..++.+..++||.....+...+. ..++|||+||++|..++.++...++++++||||
T Consensus       165 aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViD  244 (475)
T PRK01297        165 ALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLD  244 (475)
T ss_pred             EEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEec
Confidence            9999999999999999999999988999999999988777766664 468999999999999999888889999999999


Q ss_pred             cccccCcCC
Q psy17644        322 EADRMFDMG  330 (330)
Q Consensus       322 Ead~lld~G  330 (330)
                      |||+++++|
T Consensus       245 Eah~l~~~~  253 (475)
T PRK01297        245 EADRMLDMG  253 (475)
T ss_pred             hHHHHHhcc
Confidence            999999875

>KOG0337|consensus

Probab=99.97  E-value=1e-30  Score=241.17  Aligned_cols=161  Identities=39%  Similarity=0.671  Sum_probs=151.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       166 ~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      ..+|..+||+..++++|.+.||..|||||+.+||.++.|+|++..|.||||||.||++||+.++....    ..|.++||
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s----~~g~Rali   95 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS----QTGLRALI   95 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhcc----ccccceee
Confidence            46799999999999999999999999999999999999999999999999999999999999986542    35789999


Q ss_pred             EcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      +.|||+|+.|+.+..+.+++.+++++.+++||....++...+..++|||+|||+++..+.-.-...|++|+|||+||||+
T Consensus        96 lsptreLa~qtlkvvkdlgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadr  175 (529)
T KOG0337|consen   96 LSPTRELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADR  175 (529)
T ss_pred             ccCcHHHHHHHHHHHHHhccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhH
Confidence            99999999999999999999999999999999999999999998999999999999988766668899999999999999


Q ss_pred             cCcCC
Q psy17644        326 MFDMG  330 (330)
Q Consensus       326 lld~G  330 (330)
                      |++||
T Consensus       176 lfemg  180 (529)
T KOG0337|consen  176 LFEMG  180 (529)
T ss_pred             HHhhh
Confidence            99997

>PTZ00424 helicase 45; Provisional

Probab=99.96  E-value=4.1e-29  Score=241.06  Aligned_cols=160  Identities=35%  Similarity=0.586  Sum_probs=146.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       166 ~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      +.+|..++|++.+.+++.+.||..|+|+|.++|+.+++|+|++++||||||||++|++|++.++...     .+++++||
T Consensus        27 ~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~-----~~~~~~li  101 (401)
T PTZ00424         27 VDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYD-----LNACQALI  101 (401)
T ss_pred             cCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCC-----CCCceEEE
Confidence            5779999999999999999999999999999999999999999999999999999999999887432     24688999


Q ss_pred             EcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      |+||++||.|+...+..++...+..+..++||.....+...+..+++|+|+||++|..++.++...++++++|||||||+
T Consensus       102 l~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~  181 (401)
T PTZ00424        102 LAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADE  181 (401)
T ss_pred             ECCCHHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHH
Confidence            99999999999999999988888888889999888777778888899999999999999988888899999999999999


Q ss_pred             cCcCC
Q psy17644        326 MFDMG  330 (330)
Q Consensus       326 lld~G  330 (330)
                      ++++|
T Consensus       182 ~~~~~  186 (401)
T PTZ00424        182 MLSRG  186 (401)
T ss_pred             HHhcc
Confidence            98764

>KOG0328|consensus

Probab=99.96  E-value=2.6e-30  Score=227.91  Aligned_cols=165  Identities=35%  Similarity=0.598  Sum_probs=152.8

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCC
Q psy17644        161 DPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG  240 (330)
Q Consensus       161 ~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~  240 (330)
                      .-..++.+|+++||+..+++++...||.+|+.+|+.|||.++.|||+|++|++|+|||.+|.+.+|+.+--.     ...
T Consensus        21 ~~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~-----~r~   95 (400)
T KOG0328|consen   21 EKVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDIS-----VRE   95 (400)
T ss_pred             cCcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccc-----cce
Confidence            345578899999999999999999999999999999999999999999999999999999999888765332     235


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEe
Q psy17644        241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVL  320 (330)
Q Consensus       241 ~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVv  320 (330)
                      .++|||+|||+||.|+.+.+..++..+++.+..|.||.+..+.++.+..|++++.+||+++++|++++....+.+++||+
T Consensus        96 tQ~lilsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVL  175 (400)
T KOG0328|consen   96 TQALILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVL  175 (400)
T ss_pred             eeEEEecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhccccccceeEEEe
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccccCcCC
Q psy17644        321 DEADRMFDMG  330 (330)
Q Consensus       321 DEad~lld~G  330 (330)
                      ||||.||+-|
T Consensus       176 DEaDemL~kg  185 (400)
T KOG0328|consen  176 DEADEMLNKG  185 (400)
T ss_pred             ccHHHHHHhh
Confidence            9999999755

>cd00268 DEADc DEAD-box helicases

Probab=99.96  E-value=6e-28  Score=211.57  Aligned_cols=159  Identities=50%  Similarity=0.819  Sum_probs=145.2

Q ss_pred             CCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q psy17644        169 FGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP  248 (330)
Q Consensus       169 f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P  248 (330)
                      |+++++++.+.+.+.+.|+..|+++|.++++.+++|++++++++||+|||++|++|++.++...+   ..+++++||++|
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~---~~~~~~viii~p   77 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSP---KKDGPQALILAP   77 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhc---ccCCceEEEEcC
Confidence            78899999999999999999999999999999999999999999999999999999999988753   125799999999


Q ss_pred             cHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        249 TRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       249 tr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      |++|+.|+...++.+....++.+..++|+.........+..+++|+|+||.+|..++.+....+.++.++|+||||.+.+
T Consensus        78 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~  157 (203)
T cd00268          78 TRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLD  157 (203)
T ss_pred             CHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhc
Confidence            99999999999999988888899999999988777777777899999999999999988888889999999999999876


Q ss_pred             CC
Q psy17644        329 MG  330 (330)
Q Consensus       329 ~G  330 (330)
                      +|
T Consensus       158 ~~  159 (203)
T cd00268         158 MG  159 (203)
T ss_pred             cC
Confidence            53

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.

>KOG0326|consensus

Probab=99.96  E-value=3.6e-30  Score=230.33  Aligned_cols=157  Identities=36%  Similarity=0.610  Sum_probs=148.7

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      ..|+++.|++.|+..+...||.+|+|+|.++||+++.|||+++.|..|+|||.||++|+|..+-..     .+.-+++|+
T Consensus        85 ~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~-----~~~IQ~~il  159 (459)
T KOG0326|consen   85 NEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPK-----KNVIQAIIL  159 (459)
T ss_pred             ccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCcc-----ccceeEEEE
Confidence            459999999999999999999999999999999999999999999999999999999999987543     356789999


Q ss_pred             cccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      +|||+||.|+.+.++.+++.+++++....||.+.+..+..+....+++|+||+|+++++.++...++.+.++|+||||.|
T Consensus       160 VPtrelALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKl  239 (459)
T KOG0326|consen  160 VPTRELALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKL  239 (459)
T ss_pred             eecchhhHHHHHHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhh
Confidence            99999999999999999999999999999999999888888889999999999999999999999999999999999999


Q ss_pred             Cc
Q psy17644        327 FD  328 (330)
Q Consensus       327 ld  328 (330)
                      |+
T Consensus       240 Ls  241 (459)
T KOG0326|consen  240 LS  241 (459)
T ss_pred             hc
Confidence            85

>KOG0350|consensus

Probab=99.95  E-value=3.6e-28  Score=228.37  Aligned_cols=149  Identities=34%  Similarity=0.536  Sum_probs=129.9

Q ss_pred             HHHHHHHHHCCCCCCCHHHHHhhhhhc---------CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        176 EVLMKALRKCEYTSPTPIQAQAVPAAL---------SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       176 ~~l~~~l~~~~~~~pt~iQ~~~i~~~~---------~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      ..+.+++.++++....|+|.+++|.++         .++|+++.||||||||++|.||+++.+..++.    +.-++|||
T Consensus       146 a~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v----~~LRavVi  221 (620)
T KOG0350|consen  146 ATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPV----KRLRAVVI  221 (620)
T ss_pred             HHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCc----cceEEEEE
Confidence            345566899999999999999999985         47899999999999999999999998876532    34799999


Q ss_pred             cccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCC-----CeEEEEChHHHHHHHH-cCCCCCCCccEEEe
Q psy17644        247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELG-----AEIVVGTPGRIIDMVK-MGATKLNRVTFLVL  320 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~-----~dIiV~TP~~L~~~l~-~~~~~l~~i~~lVv  320 (330)
                      +|||+|+.|++..+.+++...|+.++.+.|-++.....+.|...     .||||+|||||.++++ .+.++|++++||||
T Consensus       222 vPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVI  301 (620)
T KOG0350|consen  222 VPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVI  301 (620)
T ss_pred             eeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhhceEEEe
Confidence            99999999999999999999999988888877777666666552     4999999999999998 46778999999999


Q ss_pred             ecccccCc
Q psy17644        321 DEADRMFD  328 (330)
Q Consensus       321 DEad~lld  328 (330)
                      ||||||++
T Consensus       302 DEADRll~  309 (620)
T KOG0350|consen  302 DEADRLLD  309 (620)
T ss_pred             chHHHHHH
Confidence            99999985

>KOG0329|consensus

Probab=99.94  E-value=1.8e-27  Score=207.45  Aligned_cols=166  Identities=33%  Similarity=0.527  Sum_probs=149.8

Q ss_pred             eCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCC
Q psy17644        158 SGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEP  237 (330)
Q Consensus       158 ~g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~  237 (330)
                      +|+.+....+.|.+|-|+++|++++..+||..|+.+|..+||..+-|.|++.+|.+|.|||++|+|..|+.+---     
T Consensus        33 kgsyv~ihssgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv-----  107 (387)
T KOG0329|consen   33 KGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPV-----  107 (387)
T ss_pred             cCcEEEEeccchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCC-----
Confidence            444455556779999999999999999999999999999999999999999999999999999999999875321     


Q ss_pred             CCCCeEEEEcccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCcc
Q psy17644        238 GDGPMGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVT  316 (330)
Q Consensus       238 ~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~  316 (330)
                      .....+|++|.||+||.||.++..+|++++ ++++.+.|||.+.......+++.++|+|+||+|++.+.+++.+++++++
T Consensus       108 ~g~vsvlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vk  187 (387)
T KOG0329|consen  108 DGQVSVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVK  187 (387)
T ss_pred             CCeEEEEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcc
Confidence            124678999999999999999999999987 5788899999999988899999999999999999999999999999999


Q ss_pred             EEEeecccccCc
Q psy17644        317 FLVLDEADRMFD  328 (330)
Q Consensus       317 ~lVvDEad~lld  328 (330)
                      .+|+||||.||+
T Consensus       188 hFvlDEcdkmle  199 (387)
T KOG0329|consen  188 HFVLDECDKMLE  199 (387)
T ss_pred             eeehhhHHHHHH
Confidence            999999999985

>KOG0344|consensus

Probab=99.94  E-value=4.5e-27  Score=225.28  Aligned_cols=184  Identities=35%  Similarity=0.572  Sum_probs=154.8

Q ss_pred             HHHHHHHHcCcEeeCCCCCCCCCCCCC----CCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHH
Q psy17644        145 EAQELRAKSGITVSGADPPYPVSSFGH----FGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       145 ~~~~~r~~~~i~~~g~~~p~p~~~f~~----~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a  220 (330)
                      .....|..+++.+.|..+|+|+.+|..    +.+...+++++...+|..|||+|++++|.++.+++++.|||||||||++
T Consensus       110 ~~~~~Rk~~k~~v~G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtla  189 (593)
T KOG0344|consen  110 KLLGIRKSNKINVDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLA  189 (593)
T ss_pred             ccccchhcceeeccCCCCCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhh
Confidence            355678888999999999999999997    6789999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc--cCCCceEEEEECCCc-hHHHHHHHhCCCeEEEEC
Q psy17644        221 FIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG--KGYNLSVVCCYGGGS-KWDQSKALELGAEIVVGT  297 (330)
Q Consensus       221 ~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~--~~~~~~~~~~~gg~~-~~~~~~~l~~~~dIiV~T  297 (330)
                      |++|++.++..........|-+++||.|||+||.|++.++.++.  ...+.+++....... ...+.......++|+|+|
T Consensus       190 f~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~T  269 (593)
T KOG0344|consen  190 FNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILIST  269 (593)
T ss_pred             hhhHHHHHHHHhhcccCccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcC
Confidence            99999999987653334568899999999999999999999998  555555544433222 222222233358999999


Q ss_pred             hHHHHHHHHcCC--CCCCCccEEEeecccccCc
Q psy17644        298 PGRIIDMVKMGA--TKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       298 P~~L~~~l~~~~--~~l~~i~~lVvDEad~lld  328 (330)
                      |.++..++....  +.++.|.++|+||||++++
T Consensus       270 P~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe  302 (593)
T KOG0344|consen  270 PMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFE  302 (593)
T ss_pred             HHHHHHHhcCCCccchhheeeeEeechHHhhhC
Confidence            999999998776  5799999999999999986

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

Probab=99.94  E-value=1e-25  Score=231.54  Aligned_cols=148  Identities=22%  Similarity=0.255  Sum_probs=125.9

Q ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q psy17644        173 GFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL  252 (330)
Q Consensus       173 ~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~L  252 (330)
                      .|++.|.++|.+.||.+||++|.++||.+++|+|+++++|||||||+||++|+|+.+...      .++++|||+|||+|
T Consensus        20 ~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~------~~~~aL~l~PtraL   93 (742)
T TIGR03817        20 WAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD------PRATALYLAPTKAL   93 (742)
T ss_pred             cCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC------CCcEEEEEcChHHH
Confidence            388999999999999999999999999999999999999999999999999999998753      36899999999999


Q ss_pred             HHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHc----CCCCCCCccEEEeecccccCc
Q psy17644        253 SQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKM----GATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       253 a~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~----~~~~l~~i~~lVvDEad~lld  328 (330)
                      |.|++..++.++ ..++++..+.|+.. ..+...++.+++|||+||++|...+-.    +...++++++|||||||.|.+
T Consensus        94 a~q~~~~l~~l~-~~~i~v~~~~Gdt~-~~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g  171 (742)
T TIGR03817        94 AADQLRAVRELT-LRGVRPATYDGDTP-TEERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRG  171 (742)
T ss_pred             HHHHHHHHHHhc-cCCeEEEEEeCCCC-HHHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccC
Confidence            999999999997 44677665555554 455666777899999999999753321    122378999999999999865

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.

>KOG4284|consensus

Probab=99.93  E-value=6.9e-27  Score=225.15  Aligned_cols=165  Identities=30%  Similarity=0.453  Sum_probs=149.1

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCC
Q psy17644        160 ADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGD  239 (330)
Q Consensus       160 ~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~  239 (330)
                      ...|.-...|+++-|...++..|+..+|..||++|..|||+++.+.|+|++|..|+|||++|.+.++..+...     ..
T Consensus        18 DV~~~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~-----~~   92 (980)
T KOG4284|consen   18 DVQSNCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSR-----SS   92 (980)
T ss_pred             ccccCCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcc-----cC
Confidence            3445566779999999999999999999999999999999999999999999999999999998888776432     25


Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccC-CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEE
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKG-YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFL  318 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~-~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~l  318 (330)
                      .+.++||+|||++|.||...+.++|.. .|++|.+..||.........++. |+|+|+||||+..+++.+..+.++|+++
T Consensus        93 ~~q~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~-~rIvIGtPGRi~qL~el~~~n~s~vrlf  171 (980)
T KOG4284|consen   93 HIQKVIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQ-TRIVIGTPGRIAQLVELGAMNMSHVRLF  171 (980)
T ss_pred             cceeEEEecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhh-ceEEecCchHHHHHHHhcCCCccceeEE
Confidence            789999999999999999999999975 58999999999998887777776 7999999999999999999999999999


Q ss_pred             EeecccccCcCC
Q psy17644        319 VLDEADRMFDMG  330 (330)
Q Consensus       319 VvDEad~lld~G  330 (330)
                      ||||||.|++-|
T Consensus       172 VLDEADkL~~t~  183 (980)
T KOG4284|consen  172 VLDEADKLMDTE  183 (980)
T ss_pred             EeccHHhhhchh
Confidence            999999999743

>PRK02362 ski2-like helicase; Provisional

Probab=99.93  E-value=4.9e-25  Score=227.74  Aligned_cols=150  Identities=25%  Similarity=0.329  Sum_probs=131.1

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhh-hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPA-ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       168 ~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~-~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      .|++++|++.+++++.+.|+.+|+|+|.++++. ++.|+|++++||||||||++|.+|+++++.        ++.++|||
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~--------~~~kal~i   73 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIA--------RGGKALYI   73 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHh--------cCCcEEEE
Confidence            478899999999999999999999999999998 779999999999999999999999999884        36789999


Q ss_pred             cccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      +|||+||.|++..++++.. .++++..+.|+......  . ...++||||||+++..+++++...++++++|||||||.|
T Consensus        74 ~P~raLa~q~~~~~~~~~~-~g~~v~~~tGd~~~~~~--~-l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l  149 (737)
T PRK02362         74 VPLRALASEKFEEFERFEE-LGVRVGISTGDYDSRDE--W-LGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLI  149 (737)
T ss_pred             eChHHHHHHHHHHHHHhhc-CCCEEEEEeCCcCcccc--c-cCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECcccc
Confidence            9999999999999998754 47888888887654331  2 234799999999999999876666889999999999999


Q ss_pred             CcC
Q psy17644        327 FDM  329 (330)
Q Consensus       327 ld~  329 (330)
                      .+.
T Consensus       150 ~d~  152 (737)
T PRK02362        150 DSA  152 (737)
T ss_pred             CCC
Confidence            863

>KOG0327|consensus

Probab=99.93  E-value=6e-26  Score=208.06  Aligned_cols=160  Identities=37%  Similarity=0.624  Sum_probs=144.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       166 ~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      +.+|++++|++.|++.+...||.+|+.||+.||..+..|+|+++.+++|+|||.+|++++++++-..     .....||+
T Consensus        25 vdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~-----~ke~qali   99 (397)
T KOG0327|consen   25 VDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMS-----VKETQALI   99 (397)
T ss_pred             hhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcc-----hHHHHHHH
Confidence            4579999999999999999999999999999999999999999999999999999999999987322     13578999


Q ss_pred             EcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHH-HHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccc
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ-SKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD  324 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~-~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad  324 (330)
                      ++|||+||.|+......++...+.++..+.||...... ....+..++|+|+||+++.++++...+....++++|+||||
T Consensus       100 laPtreLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaD  179 (397)
T KOG0327|consen  100 LAPTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEAD  179 (397)
T ss_pred             hcchHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeecchH
Confidence            99999999999999999999999999999998887633 34445568999999999999999888888899999999999


Q ss_pred             ccCcCC
Q psy17644        325 RMFDMG  330 (330)
Q Consensus       325 ~lld~G  330 (330)
                      .|+..|
T Consensus       180 EmLs~g  185 (397)
T KOG0327|consen  180 EMLSRG  185 (397)
T ss_pred             hhhccc
Confidence            999766

>PRK00254 ski2-like helicase; Provisional

Probab=99.92  E-value=1.5e-24  Score=223.55  Aligned_cols=151  Identities=22%  Similarity=0.312  Sum_probs=132.5

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhh-hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPA-ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       168 ~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~-~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      .|.++++++.+.+.+.+.|+..|+|+|.++++. +++|+|+++++|||||||++|.+|++.+++.       .+.++|||
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~-------~~~~~l~l   74 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLR-------EGGKAVYL   74 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHh-------cCCeEEEE
Confidence            477889999999999999999999999999986 7899999999999999999999999998875       36799999


Q ss_pred             cccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      +||++||.|++..++.+. ..++++..+.|+......  . ...++|||+||+++..++++....++++++|||||+|.|
T Consensus        75 ~P~~aLa~q~~~~~~~~~-~~g~~v~~~~Gd~~~~~~--~-~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l  150 (720)
T PRK00254         75 VPLKALAEEKYREFKDWE-KLGLRVAMTTGDYDSTDE--W-LGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLI  150 (720)
T ss_pred             eChHHHHHHHHHHHHHHh-hcCCEEEEEeCCCCCchh--h-hccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCcc
Confidence            999999999999999874 458888888887764322  2 245899999999999999876667899999999999999


Q ss_pred             CcC
Q psy17644        327 FDM  329 (330)
Q Consensus       327 ld~  329 (330)
                      .++
T Consensus       151 ~~~  153 (720)
T PRK00254        151 GSY  153 (720)
T ss_pred             CCc
Confidence            865

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

Probab=99.92  E-value=4.9e-24  Score=180.82  Aligned_cols=133  Identities=36%  Similarity=0.581  Sum_probs=117.0

Q ss_pred             CHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCce
Q psy17644        191 TPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLS  270 (330)
Q Consensus       191 t~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~  270 (330)
                      ||+|.++++.+.+|+++++.||||+|||++|++++++++...      ...++||++|+++|+.|++..+..++...+.+
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~------~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~   74 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG------KDARVLIIVPTRALAEQQFERLRKFFSNTNVR   74 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT------SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSS
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC------CCceEEEEeecccccccccccccccccccccc
Confidence            799999999999999999999999999999999999988764      13599999999999999999999999888889


Q ss_pred             EEEEECCCchH-HHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcC
Q psy17644        271 VVCCYGGGSKW-DQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       271 ~~~~~gg~~~~-~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~  329 (330)
                      +..++|+.... .....+..+++|+|+||.+|..++..+..++.++.+|||||+|.+..+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~  134 (169)
T PF00270_consen   75 VVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDE  134 (169)
T ss_dssp             EEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHT
T ss_pred             cccccccccccccccccccccccccccCcchhhccccccccccccceeeccCcccccccc
Confidence            99999988755 444555667999999999999999886667778999999999998764

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 ....

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.91  E-value=2e-24  Score=219.40  Aligned_cols=148  Identities=17%  Similarity=0.240  Sum_probs=132.5

Q ss_pred             CCCCCCHHHHHHHH-----HCCCCCC---CHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCC
Q psy17644        170 GHFGFDEVLMKALR-----KCEYTSP---TPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGP  241 (330)
Q Consensus       170 ~~~~l~~~l~~~l~-----~~~~~~p---t~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~  241 (330)
                      +.|++.+.+.+++.     .+||..|   ||+|.+++|.++.++++++.++||+|||++|++|++.+++..        .
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g--------~  136 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTG--------K  136 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhc--------C
Confidence            46788888888876     6789988   999999999999999999999999999999999999888742        2


Q ss_pred             eEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcCCCCCC-------
Q psy17644        242 MGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMGATKLN-------  313 (330)
Q Consensus       242 ~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~~~~l~-------  313 (330)
                      .++||+|||+||.|+++.+..+++.+++++.+++||.+...+...+  +|||+||||++| +++++.+...++       
T Consensus       137 ~v~IVTpTrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDyLrd~~~~~~~~~~vqr  214 (970)
T PRK12899        137 PVHLVTVNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDYLRDNSIATRKEEQVGR  214 (970)
T ss_pred             CeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHHhhCCCCCcCHHHhhcc
Confidence            4899999999999999999999999999999999999988877665  589999999999 999998766655       


Q ss_pred             CccEEEeecccccC
Q psy17644        314 RVTFLVLDEADRMF  327 (330)
Q Consensus       314 ~i~~lVvDEad~ll  327 (330)
                      .+.++||||||.||
T Consensus       215 ~~~~~IIDEADsmL  228 (970)
T PRK12899        215 GFYFAIIDEVDSIL  228 (970)
T ss_pred             cccEEEEechhhhh
Confidence            45899999999998

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.91  E-value=3.9e-24  Score=223.76  Aligned_cols=155  Identities=21%  Similarity=0.334  Sum_probs=127.1

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCC-CCCCCCeEEEEcccHHH
Q psy17644        174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL-EPGDGPMGLILAPTREL  252 (330)
Q Consensus       174 l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~-~~~~~~~vLil~Ptr~L  252 (330)
                      |++.+.+.+.+ +|..|||+|.++||.+++|+|++++||||||||++|++|++.+++..... ...+++++|||+|||+|
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            56666666555 78999999999999999999999999999999999999999998864321 11357899999999999


Q ss_pred             HHHHHHHHHH-------hc----cCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC--CCCCccEE
Q psy17644        253 SQQIYNEAKR-------FG----KGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT--KLNRVTFL  318 (330)
Q Consensus       253 a~Qi~~~~~~-------l~----~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~--~l~~i~~l  318 (330)
                      |.|++..+..       ++    ... ++++...+|+.......+.+++.++|+||||++|..++.+...  .++++++|
T Consensus        97 a~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~V  176 (876)
T PRK13767         97 NNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKWV  176 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCEE
Confidence            9999886542       22    233 6677888898888777777888899999999999988865433  47899999


Q ss_pred             EeecccccCcC
Q psy17644        319 VLDEADRMFDM  329 (330)
Q Consensus       319 VvDEad~lld~  329 (330)
                      ||||||.|++.
T Consensus       177 VIDE~H~l~~~  187 (876)
T PRK13767        177 IVDEIHSLAEN  187 (876)
T ss_pred             EEechhhhccC
Confidence            99999999853

>PRK01172 ski2-like helicase; Provisional

Probab=99.90  E-value=4.3e-23  Score=211.60  Aligned_cols=149  Identities=18%  Similarity=0.261  Sum_probs=129.2

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc
Q psy17644        168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA  247 (330)
Q Consensus       168 ~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~  247 (330)
                      .|++++|++.+++.+.+.+|. ++++|.++++.+.+|++++++||||||||+++.++++.++..        +.++|||+
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~--------~~k~v~i~   72 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA--------GLKSIYIV   72 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh--------CCcEEEEe
Confidence            477889999999999998886 999999999999999999999999999999999999988753        56899999


Q ss_pred             ccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        248 PTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       248 Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      |||+||.|+++.++++. ..+.++...+|+......   ....++|+|+||+++..++.++...++++.+|||||||++.
T Consensus        73 P~raLa~q~~~~~~~l~-~~g~~v~~~~G~~~~~~~---~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~  148 (674)
T PRK01172         73 PLRSLAMEKYEELSRLR-SLGMRVKISIGDYDDPPD---FIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIG  148 (674)
T ss_pred             chHHHHHHHHHHHHHHh-hcCCeEEEEeCCCCCChh---hhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhcc
Confidence            99999999999999874 457888888887654321   22357999999999999998877778999999999999997


Q ss_pred             cC
Q psy17644        328 DM  329 (330)
Q Consensus       328 d~  329 (330)
                      +.
T Consensus       149 d~  150 (674)
T PRK01172        149 DE  150 (674)
T ss_pred             CC
Confidence            63

>KOG0332|consensus

Probab=99.90  E-value=4.8e-24  Score=194.62  Aligned_cols=162  Identities=32%  Similarity=0.530  Sum_probs=140.3

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcC--CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCC
Q psy17644        159 GADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALS--GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE  236 (330)
Q Consensus       159 g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~--g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~  236 (330)
                      +..+...+++|++|+|+++|++++..++|.+|+.||..++|.++.  .+++|.++++|+|||.||.|.||.++--.    
T Consensus        82 pnsPlyS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~----  157 (477)
T KOG0332|consen   82 PNSPLYSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPD----  157 (477)
T ss_pred             CCCCccccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCcc----
Confidence            455667899999999999999999999999999999999999995  48999999999999999999999886432    


Q ss_pred             CCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHc-CCCCCCCc
Q psy17644        237 PGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKM-GATKLNRV  315 (330)
Q Consensus       237 ~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~-~~~~l~~i  315 (330)
                       ...|.++.|+|||+||.|+.+.+.+.++..++...+.+-|...   .+.-.-..+|+|+||+.+.+++.+ +.+.+..+
T Consensus       158 -~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~ita~yair~sk~---~rG~~i~eqIviGTPGtv~Dlm~klk~id~~ki  233 (477)
T KOG0332|consen  158 -VVVPQCICLAPTRELAPQTGEVVEEMGKFTELTASYAIRGSKA---KRGNKLTEQIVIGTPGTVLDLMLKLKCIDLEKI  233 (477)
T ss_pred             -ccCCCceeeCchHHHHHHHHHHHHHhcCceeeeEEEEecCccc---ccCCcchhheeeCCCccHHHHHHHHHhhChhhc
Confidence             2368999999999999999999999999988888877776621   111112368999999999999987 88899999


Q ss_pred             cEEEeecccccCc
Q psy17644        316 TFLVLDEADRMFD  328 (330)
Q Consensus       316 ~~lVvDEad~lld  328 (330)
                      +++|+||||.|++
T Consensus       234 kvfVlDEAD~Mi~  246 (477)
T KOG0332|consen  234 KVFVLDEADVMID  246 (477)
T ss_pred             eEEEecchhhhhh
Confidence            9999999999985

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

Probab=99.89  E-value=3.2e-23  Score=210.16  Aligned_cols=154  Identities=23%  Similarity=0.364  Sum_probs=138.6

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q psy17644        174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELS  253 (330)
Q Consensus       174 l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La  253 (330)
                      |++.+.+.++.. |..|||.|.++||.+.+|++++++||||||||.|.+||+++.+++........+-.+|||+|.|+|.
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            678888988887 9999999999999999999999999999999999999999999987433344678999999999999


Q ss_pred             HHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC--CCCCccEEEeecccccCc
Q psy17644        254 QQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT--KLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       254 ~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~--~l~~i~~lVvDEad~lld  328 (330)
                      ..+...+..++..+|+.+...+|..+..+..+..++.+||+|+||+.|.-++.....  .|++++++||||+|.|.+
T Consensus        87 ~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~  163 (814)
T COG1201          87 NDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAE  163 (814)
T ss_pred             HHHHHHHHHHHHHcCCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhc
Confidence            999999999999999999888888888887888888999999999999998875433  489999999999999863

>PRK09401 reverse gyrase; Reviewed

Probab=99.89  E-value=1.5e-22  Score=215.30  Aligned_cols=138  Identities=24%  Similarity=0.295  Sum_probs=113.1

Q ss_pred             HHHHC-CCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q psy17644        181 ALRKC-EYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE  259 (330)
Q Consensus       181 ~l~~~-~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~  259 (330)
                      .+.+. |+ .||++|+.++|.++.|+|++++||||||||+ |+++++.++..       +++++|||+|||+||.|++..
T Consensus        72 ~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~-------~g~~alIL~PTreLa~Qi~~~  142 (1176)
T PRK09401         72 FFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK-------KGKKSYIIFPTRLLVEQVVEK  142 (1176)
T ss_pred             HHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh-------cCCeEEEEeccHHHHHHHHHH
Confidence            34444 55 8999999999999999999999999999995 66666655432       478999999999999999999


Q ss_pred             HHHhccCCCceEEEEECCCc-----hHHHHHHHhC-CCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcC
Q psy17644        260 AKRFGKGYNLSVVCCYGGGS-----KWDQSKALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       260 ~~~l~~~~~~~~~~~~gg~~-----~~~~~~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~  329 (330)
                      +++++...++.+..++||..     ...+...+.. .++|+||||++|.+++.  .....++++|||||||+|+++
T Consensus       143 l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~~~lVvDEaD~~L~~  216 (1176)
T PRK09401        143 LEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKFDFVFVDDVDAVLKS  216 (1176)
T ss_pred             HHHHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH--hccccccCEEEEEChHHhhhc
Confidence            99999988888888877764     2333344443 58999999999999886  345667999999999999974

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.88  E-value=2.6e-22  Score=197.67  Aligned_cols=131  Identities=23%  Similarity=0.299  Sum_probs=105.9

Q ss_pred             HCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        184 KCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       184 ~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..||..|+|+|.++|+.+++|+|+++++|||+|||++|++|++..           ++.+|||+|||+|+.|++..+..+
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~-----------~~~~lVi~P~~~L~~dq~~~l~~~   74 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS-----------DGITLVISPLISLMEDQVLQLKAS   74 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc-----------CCcEEEEecHHHHHHHHHHHHHHc
Confidence            459999999999999999999999999999999999999999842           467999999999999999988765


Q ss_pred             ccCCCceEEEEECCCchHHHHH---HHh-CCCeEEEEChHHHHHH---HHcCCCCCCCccEEEeecccccCcCC
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQSK---ALE-LGAEIVVGTPGRIIDM---VKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~~~---~l~-~~~dIiV~TP~~L~~~---l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                          ++.+..+.++.....+..   .+. ...+||++||+++...   +.. ...+.++.+|||||||++++||
T Consensus        75 ----gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~-l~~~~~i~~iViDEaH~i~~~g  143 (470)
T TIGR00614        75 ----GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQT-LEERKGITLIAVDEAHCISQWG  143 (470)
T ss_pred             ----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHH-HHhcCCcCEEEEeCCcccCccc
Confidence                566777777666543322   222 3479999999997542   211 1146789999999999999998

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

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

Probab=99.88  E-value=4.5e-22  Score=206.07  Aligned_cols=148  Identities=21%  Similarity=0.287  Sum_probs=116.2

Q ss_pred             CCCC--CCCCHHHHHHHHH-CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEE
Q psy17644        168 SFGH--FGFDEVLMKALRK-CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGL  244 (330)
Q Consensus       168 ~f~~--~~l~~~l~~~l~~-~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vL  244 (330)
                      .|..  |.....+...+++ .||..++|+|.++|++++.|+|+++++|||+|||+||+||+|..           ++.+|
T Consensus       436 ~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~-----------~GiTL  504 (1195)
T PLN03137        436 KWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC-----------PGITL  504 (1195)
T ss_pred             cccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc-----------CCcEE
Confidence            3553  4555566666554 58999999999999999999999999999999999999999853           46799


Q ss_pred             EEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh------CCCeEEEEChHHHHH---HHHc--CCCCCC
Q psy17644        245 ILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE------LGAEIVVGTPGRIID---MVKM--GATKLN  313 (330)
Q Consensus       245 il~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~------~~~dIiV~TP~~L~~---~l~~--~~~~l~  313 (330)
                      ||+|+++|+.+++..+...    ++....+.++.....+...+.      ..++||++||++|..   ++..  ......
T Consensus       505 VISPLiSLmqDQV~~L~~~----GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~  580 (1195)
T PLN03137        505 VISPLVSLIQDQIMNLLQA----NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRG  580 (1195)
T ss_pred             EEeCHHHHHHHHHHHHHhC----CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhcc
Confidence            9999999998766666553    688888999888766654443      357999999999863   2221  111235


Q ss_pred             CccEEEeecccccCcCC
Q psy17644        314 RVTFLVLDEADRMFDMG  330 (330)
Q Consensus       314 ~i~~lVvDEad~lld~G  330 (330)
                      .+.+|||||||+|++||
T Consensus       581 ~LslIVIDEAHcVSqWG  597 (1195)
T PLN03137        581 LLARFVIDEAHCVSQWG  597 (1195)
T ss_pred             ccceeccCcchhhhhcc
Confidence            68999999999999998

>TIGR01054 rgy reverse gyrase

Probab=99.88  E-value=7.6e-22  Score=210.20  Aligned_cols=142  Identities=19%  Similarity=0.233  Sum_probs=114.8

Q ss_pred             HHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHH
Q psy17644        176 EVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQ  255 (330)
Q Consensus       176 ~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Q  255 (330)
                      ..+.+.+.+.....||++|+.++|.++.|+|++++||||||||+ |.+|++.++..       .++++|||+|||+||.|
T Consensus        65 ~~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~-------~g~~vLIL~PTreLa~Q  136 (1171)
T TIGR01054        65 KEFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK-------KGKRCYIILPTTLLVIQ  136 (1171)
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh-------cCCeEEEEeCHHHHHHH
Confidence            34555566656668999999999999999999999999999996 77777766543       37899999999999999


Q ss_pred             HHHHHHHhccCCCceEE---EEECCCchHHHH---HHHhC-CCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        256 IYNEAKRFGKGYNLSVV---CCYGGGSKWDQS---KALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       256 i~~~~~~l~~~~~~~~~---~~~gg~~~~~~~---~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      +++.+++++...++.+.   +++||.+...+.   ..+.+ +++|||+||++|...+.+-.  . +++++||||||+|++
T Consensus       137 i~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~--~-~~~~iVvDEaD~~L~  213 (1171)
T TIGR01054       137 VAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELG--P-KFDFIFVDDVDALLK  213 (1171)
T ss_pred             HHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhc--C-CCCEEEEeChHhhhh
Confidence            99999999987776544   456887765542   33444 48999999999998876521  2 899999999999998

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.

>PRK14701 reverse gyrase; Provisional

Probab=99.87  E-value=8.1e-22  Score=214.15  Aligned_cols=143  Identities=20%  Similarity=0.228  Sum_probs=115.5

Q ss_pred             HHHHHHHH-CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHH
Q psy17644        177 VLMKALRK-CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQ  255 (330)
Q Consensus       177 ~l~~~l~~-~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Q  255 (330)
                      .+.+.+.+ .|| .||++|+.++|.+++|+|++++||||||||++++++++.+..        .++++|||+|||+|+.|
T Consensus        67 ~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~--------~g~~aLVl~PTreLa~Q  137 (1638)
T PRK14701         67 EFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL--------KGKKCYIILPTTLLVKQ  137 (1638)
T ss_pred             HHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh--------cCCeEEEEECHHHHHHH
Confidence            34455555 788 699999999999999999999999999999966666654421        46799999999999999


Q ss_pred             HHHHHHHhccCC--CceEEEEECCCchHHHH---HHHhCC-CeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcC
Q psy17644        256 IYNEAKRFGKGY--NLSVVCCYGGGSKWDQS---KALELG-AEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       256 i~~~~~~l~~~~--~~~~~~~~gg~~~~~~~---~~l~~~-~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~  329 (330)
                      ++..++.++...  ++++..++||.+..++.   ..+..+ ++|||+||++|...+... . ..++.+|||||||+|++|
T Consensus       138 i~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l-~-~~~i~~iVVDEAD~ml~~  215 (1638)
T PRK14701        138 TVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM-K-HLKFDFIFVDDVDAFLKA  215 (1638)
T ss_pred             HHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH-h-hCCCCEEEEECceecccc
Confidence            999999998765  45667788888876653   334444 899999999998876542 1 267999999999999986


Q ss_pred             C
Q psy17644        330 G  330 (330)
Q Consensus       330 G  330 (330)
                      |
T Consensus       216 ~  216 (1638)
T PRK14701        216 S  216 (1638)
T ss_pred             c
Confidence            5

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

Probab=99.86  E-value=2.6e-21  Score=197.27  Aligned_cols=133  Identities=23%  Similarity=0.261  Sum_probs=107.7

Q ss_pred             CCCCCCCHHHHHhhhhhcCCC-cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE-EcccHHHHHHHHHHHHH
Q psy17644        185 CEYTSPTPIQAQAVPAALSGR-DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI-LAPTRELSQQIYNEAKR  262 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g~-d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi-l~Ptr~La~Qi~~~~~~  262 (330)
                      .||. |||||.++||.++.|+ ++++++|||||||.+|.++++.. ..     ....|+.|| ++|||+||.|+++.+.+
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~-----~~~~~~rLv~~vPtReLa~Qi~~~~~~   84 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EI-----GAKVPRRLVYVVNRRTVVDQVTEEAEK   84 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cc-----cccccceEEEeCchHHHHHHHHHHHHH
Confidence            4787 9999999999999998 57777999999999776555522 11     123566666 66999999999999999


Q ss_pred             hccCC-----------------------CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC---------
Q psy17644        263 FGKGY-----------------------NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT---------  310 (330)
Q Consensus       263 l~~~~-----------------------~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~---------  310 (330)
                      +++.+                       ++++.+++||.....+...+..+++|||||+    +++.++.+         
T Consensus        85 ~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~----D~i~sr~L~~gYg~~~~  160 (844)
T TIGR02621        85 IGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTV----DMIGSRLLFSGYGCGFK  160 (844)
T ss_pred             HHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECH----HHHcCCccccccccccc
Confidence            98755                       4888999999999999999999999999995    55544443         


Q ss_pred             -------CCCCccEEEeecccccCcCC
Q psy17644        311 -------KLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       311 -------~l~~i~~lVvDEad~lld~G  330 (330)
                             .++++++|||||||  ++||
T Consensus       161 ~~pi~ag~L~~v~~LVLDEAD--Ld~g  185 (844)
T TIGR02621       161 SRPLHAGFLGQDALIVHDEAH--LEPA  185 (844)
T ss_pred             cccchhhhhccceEEEEehhh--hccc
Confidence                   27889999999999  6665

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.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.85  E-value=8.8e-21  Score=191.95  Aligned_cols=131  Identities=22%  Similarity=0.277  Sum_probs=105.7

Q ss_pred             CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        185 CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .||..|+|+|.++|+.+++|+|+++++|||+|||++|++|++.+           +..+|||+||++|+.|++..++.+ 
T Consensus        21 fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~-----------~g~tlVisPl~sL~~dqv~~l~~~-   88 (607)
T PRK11057         21 FGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL-----------DGLTLVVSPLISLMKDQVDQLLAN-   88 (607)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc-----------CCCEEEEecHHHHHHHHHHHHHHc-
Confidence            59999999999999999999999999999999999999999853           357899999999999999998875 


Q ss_pred             cCCCceEEEEECCCchHHHHHH---Hh-CCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSKA---LE-LGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~~---l~-~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                         ++.+.++.++.........   +. ...+|+++||++|............++.+|||||||+|++||
T Consensus        89 ---gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G  155 (607)
T PRK11057         89 ---GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWG  155 (607)
T ss_pred             ---CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCcccccccc
Confidence               5666777776665543322   22 247899999999874221112334578999999999999998

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.85  E-value=8.9e-21  Score=191.80  Aligned_cols=131  Identities=18%  Similarity=0.268  Sum_probs=108.0

Q ss_pred             CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        185 CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .||..++|+|.++|+.+++|+|+++++|||+|||++|++|++.+           +..+|||+|+++|+.|++..++.+ 
T Consensus         9 fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~-----------~g~~lVisPl~sL~~dq~~~l~~~-   76 (591)
T TIGR01389         9 FGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL-----------KGLTVVISPLISLMKDQVDQLRAA-   76 (591)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc-----------CCcEEEEcCCHHHHHHHHHHHHHc-
Confidence            69999999999999999999999999999999999999999843           356899999999999999988876 


Q ss_pred             cCCCceEEEEECCCchHHHHHH----HhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSKA----LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~~----l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                         ++.+..+.++.........    .....+|+++||++|............++.+|||||||++.+||
T Consensus        77 ---gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g  143 (591)
T TIGR01389        77 ---GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWG  143 (591)
T ss_pred             ---CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCccccccc
Confidence               5677777777765544322    23457999999999965333233446789999999999999998

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.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.84  E-value=2.1e-20  Score=191.31  Aligned_cols=138  Identities=25%  Similarity=0.299  Sum_probs=114.5

Q ss_pred             HHHHHHHHHCCCCCCCHHHHHhhhhhcCC------CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q psy17644        176 EVLMKALRKCEYTSPTPIQAQAVPAALSG------RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT  249 (330)
Q Consensus       176 ~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g------~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt  249 (330)
                      ..+.+.+.+.-...||++|.++++.+.++      ++++++|+||||||++|++|++..+.        ++.+++||+||
T Consensus       248 ~~~~~~~~~~l~f~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~--------~g~q~lilaPT  319 (681)
T PRK10917        248 GELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE--------AGYQAALMAPT  319 (681)
T ss_pred             hHHHHHHHHhCCCCCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHH--------cCCeEEEEecc
Confidence            45555554443347999999999999876      48999999999999999999998763        47899999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEECCCchHHH---HHHHhC-CCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        250 RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ---SKALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       250 r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~---~~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      ++||.|++..+++++...++++.+++|+......   ...+.. .++||||||+.+..     ...++++.+|||||+|+
T Consensus       320 ~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~v~~~~l~lvVIDE~Hr  394 (681)
T PRK10917        320 EILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD-----DVEFHNLGLVIIDEQHR  394 (681)
T ss_pred             HHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc-----cchhcccceEEEechhh
Confidence            9999999999999999889999999999885433   344444 49999999988753     34578999999999998


Q ss_pred             c
Q psy17644        326 M  326 (330)
Q Consensus       326 l  326 (330)
                      +
T Consensus       395 f  395 (681)
T PRK10917        395 F  395 (681)
T ss_pred             h
Confidence            6

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.83  E-value=5.3e-20  Score=187.05  Aligned_cols=135  Identities=25%  Similarity=0.310  Sum_probs=112.8

Q ss_pred             HHHHHHHCCCCCCCHHHHHhhhhhcCC------CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q psy17644        178 LMKALRKCEYTSPTPIQAQAVPAALSG------RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE  251 (330)
Q Consensus       178 l~~~l~~~~~~~pt~iQ~~~i~~~~~g------~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~  251 (330)
                      +.+.+...+| .||++|..+|+.++++      .+.+++|+||||||++|++|++..+.        ++.+++||+||++
T Consensus       225 ~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~--------~g~qvlilaPT~~  295 (630)
T TIGR00643       225 LTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIE--------AGYQVALMAPTEI  295 (630)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHH--------cCCcEEEECCHHH
Confidence            4445566677 7999999999999865      36899999999999999999998764        4789999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEECCCchHHH---HHHHhC-CCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        252 LSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ---SKALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       252 La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~---~~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      ||.|+++.+++++...++++.+++|+......   ...+.. .++|||+||+.+..     ...+.++.+|||||+|++
T Consensus       296 LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~f  369 (630)
T TIGR00643       296 LAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRF  369 (630)
T ss_pred             HHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhc
Confidence            99999999999998889999999999876543   333433 47999999998753     345789999999999985

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.83  E-value=7e-20  Score=190.99  Aligned_cols=140  Identities=22%  Similarity=0.266  Sum_probs=113.9

Q ss_pred             CCCHHHHHHHHH-CCCCCCCHHHHHhhhhhcCC------CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        173 GFDEVLMKALRK-CEYTSPTPIQAQAVPAALSG------RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       173 ~l~~~l~~~l~~-~~~~~pt~iQ~~~i~~~~~g------~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      ..+..+...+.+ .+| .|||+|.++|+.++++      +|++++|+||||||.+|++|++..+..        +++++|
T Consensus       435 ~~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~--------g~qvlv  505 (926)
T TIGR00580       435 PPDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD--------GKQVAV  505 (926)
T ss_pred             CCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh--------CCeEEE
Confidence            344556666655 466 5999999999999875      799999999999999999999987643        689999


Q ss_pred             EcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHH---HHHHhC-CCeEEEEChHHHHHHHHcCCCCCCCccEEEee
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ---SKALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLD  321 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~---~~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvD  321 (330)
                      |+||++||.|++..+++++...++++..+.|+.....+   ...+.. .++||||||..    + .+...++++.+||||
T Consensus       506 LvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~l----l-~~~v~f~~L~llVID  580 (926)
T TIGR00580       506 LVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKL----L-QKDVKFKDLGLLIID  580 (926)
T ss_pred             EeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHH----h-hCCCCcccCCEEEee
Confidence            99999999999999999888888898888887765443   333444 48999999942    2 244568999999999


Q ss_pred             ccccc
Q psy17644        322 EADRM  326 (330)
Q Consensus       322 Ead~l  326 (330)
                      |+|++
T Consensus       581 Eahrf  585 (926)
T TIGR00580       581 EEQRF  585 (926)
T ss_pred             ccccc
Confidence            99986

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.

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

Probab=99.83  E-value=5.4e-20  Score=190.60  Aligned_cols=146  Identities=23%  Similarity=0.323  Sum_probs=122.6

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q psy17644        174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELS  253 (330)
Q Consensus       174 l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La  253 (330)
                      ....+..++.+.|...++++|.+|+..+.+|||+|++.+||||||.+|++|++.+++..+.      .++|+|.||++||
T Consensus        55 ~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~------a~AL~lYPtnALa  128 (851)
T COG1205          55 RDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPS------ARALLLYPTNALA  128 (851)
T ss_pred             hhhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcC------ccEEEEechhhhH
Confidence            3445678888899999999999999999999999999999999999999999999998643      3889999999999


Q ss_pred             HHHHHHHHHhccCCC--ceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC----CCCCccEEEeecccc
Q psy17644        254 QQIYNEAKRFGKGYN--LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT----KLNRVTFLVLDEADR  325 (330)
Q Consensus       254 ~Qi~~~~~~l~~~~~--~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~----~l~~i~~lVvDEad~  325 (330)
                      +.+.+.++++....+  +.+....|..........+.+.++||++||.+|..++-+...    .+++++||||||+|-
T Consensus       129 ~DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHt  206 (851)
T COG1205         129 NDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHT  206 (851)
T ss_pred             hhHHHHHHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEeccee
Confidence            999999999988877  454444454444444466778899999999999996654332    378899999999994

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.81  E-value=4.9e-19  Score=188.33  Aligned_cols=136  Identities=24%  Similarity=0.272  Sum_probs=111.5

Q ss_pred             HHHHH-HHHCCCCCCCHHHHHhhhhhcCC------CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q psy17644        177 VLMKA-LRKCEYTSPTPIQAQAVPAALSG------RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT  249 (330)
Q Consensus       177 ~l~~~-l~~~~~~~pt~iQ~~~i~~~~~g------~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt  249 (330)
                      ..... .....| .||++|.++|+.++++      +|++++|+||+|||.+|+.+++..+.        ++++||||+||
T Consensus       588 ~~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~--------~g~qvlvLvPT  658 (1147)
T PRK10689        588 EQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE--------NHKQVAVLVPT  658 (1147)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH--------cCCeEEEEeCc
Confidence            34444 455566 7999999999999987      89999999999999999988876643        47899999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh----CCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        250 RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE----LGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       250 r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~----~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      ++||.|++..+++++...++++.++.|+.+..++...+.    ..++||||||..|.     ....++++.+|||||+|+
T Consensus       659 ~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~-----~~v~~~~L~lLVIDEahr  733 (1147)
T PRK10689        659 TLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQ-----SDVKWKDLGLLIVDEEHR  733 (1147)
T ss_pred             HHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHh-----CCCCHhhCCEEEEechhh
Confidence            999999999999887777888888888888766654432    35899999996432     345678999999999999


Q ss_pred             c
Q psy17644        326 M  326 (330)
Q Consensus       326 l  326 (330)
                      +
T Consensus       734 f  734 (1147)
T PRK10689        734 F  734 (1147)
T ss_pred             c
Confidence            7

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.80  E-value=3.9e-19  Score=178.88  Aligned_cols=129  Identities=22%  Similarity=0.240  Sum_probs=111.9

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG  266 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~  266 (330)
                      ...|+++|..+.+.+..|+  |+.++||+|||++|++|++...+.        |..|+||+||+.||.|.++.+.++.+.
T Consensus        54 g~~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~--------G~~V~VvTpt~~LA~qdae~~~~l~~~  123 (745)
T TIGR00963        54 GMRPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT--------GKGVHVVTVNDYLAQRDAEWMGQVYRF  123 (745)
T ss_pred             CCCccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh--------CCCEEEEcCCHHHHHHHHHHHHHHhcc
Confidence            3579999999999988887  899999999999999999755553        456999999999999999999999999


Q ss_pred             CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcC------CCCCCCccEEEeecccccC
Q psy17644        267 YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMG------ATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       267 ~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~------~~~l~~i~~lVvDEad~ll  327 (330)
                      +|+++.+++||.+...+...+  .++|++|||++| +++++.+      ...++.+.++||||||+|+
T Consensus       124 LGLsv~~i~g~~~~~~r~~~y--~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~L  189 (745)
T TIGR00963       124 LGLSVGLILSGMSPEERREAY--ACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSIL  189 (745)
T ss_pred             CCCeEEEEeCCCCHHHHHHhc--CCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHh
Confidence            999999999998876544444  479999999999 9988765      2357899999999999987

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.

>KOG0349|consensus

Probab=99.79  E-value=7.6e-20  Score=169.97  Aligned_cols=90  Identities=39%  Similarity=0.618  Sum_probs=81.0

Q ss_pred             CeEEEEcccHHHHHHHHHHHHHhccCC---CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccE
Q psy17644        241 PMGLILAPTRELSQQIYNEAKRFGKGY---NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTF  317 (330)
Q Consensus       241 ~~vLil~Ptr~La~Qi~~~~~~l~~~~---~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~  317 (330)
                      |.+||+-|+|+|+.|+++.+++|-.++   .++..++.||.-.+.|.+.++.+.+|+|+||+||.+++.++...++.+++
T Consensus       287 p~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~crF  366 (725)
T KOG0349|consen  287 PEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCRF  366 (725)
T ss_pred             cceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeeeeEE
Confidence            899999999999999999888775443   34666889999999999999999999999999999999999999999999


Q ss_pred             EEeecccccCcCC
Q psy17644        318 LVLDEADRMFDMG  330 (330)
Q Consensus       318 lVvDEad~lld~G  330 (330)
                      ||+||||.+|-.|
T Consensus       367 lvlDead~lL~qg  379 (725)
T KOG0349|consen  367 LVLDEADLLLGQG  379 (725)
T ss_pred             EEecchhhhhhcc
Confidence            9999999998654

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.79  E-value=1.2e-18  Score=177.62  Aligned_cols=130  Identities=18%  Similarity=0.256  Sum_probs=111.2

Q ss_pred             CCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        186 EYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      |. .|+++|..+++++..|+  |+.++||+|||++|++|++...+        .|+.|+||+||+.||.|.+..+..+..
T Consensus        76 g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al--------~G~~v~VvTpt~~LA~qd~e~~~~l~~  144 (790)
T PRK09200         76 GM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNAL--------EGKGVHLITVNDYLAKRDAEEMGQVYE  144 (790)
T ss_pred             CC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHH--------cCCCeEEEeCCHHHHHHHHHHHHHHHh
Confidence            44 79999999999999887  99999999999999999997766        378999999999999999999999999


Q ss_pred             CCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcCC------CCCCCccEEEeecccccC
Q psy17644        266 GYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMGA------TKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       266 ~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~~------~~l~~i~~lVvDEad~ll  327 (330)
                      .+|+++.++.||.....+.+.. .+++|++|||++| .+++....      ..++.+.++||||||+||
T Consensus       145 ~lGl~v~~i~g~~~~~~~r~~~-y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiL  212 (790)
T PRK09200        145 FLGLTVGLNFSDIDDASEKKAI-YEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSIL  212 (790)
T ss_pred             hcCCeEEEEeCCCCcHHHHHHh-cCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccce
Confidence            9999999999998833333333 4589999999999 66665432      246889999999999997

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.78  E-value=1.3e-18  Score=174.11  Aligned_cols=129  Identities=22%  Similarity=0.242  Sum_probs=109.6

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG  266 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~  266 (330)
                      ...|+++|..++|.++.|+  |+.++||+|||++|++|++.+.+        .|+.|+||+||++||.|.+..+..++..
T Consensus       101 g~~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al--------~G~~v~VvTptreLA~qdae~~~~l~~~  170 (656)
T PRK12898        101 GQRHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAAL--------AGLPVHVITVNDYLAERDAELMRPLYEA  170 (656)
T ss_pred             CCCCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhh--------cCCeEEEEcCcHHHHHHHHHHHHHHHhh
Confidence            3579999999999999999  99999999999999999998865        3789999999999999999999999999


Q ss_pred             CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcCC-------------------------CCCCCccEEEe
Q psy17644        267 YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMGA-------------------------TKLNRVTFLVL  320 (330)
Q Consensus       267 ~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~~-------------------------~~l~~i~~lVv  320 (330)
                      +++++.+++||.+..  .+....++||+++|...| .++++.+.                         .-...+.+.||
T Consensus       171 lGlsv~~i~gg~~~~--~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~aIv  248 (656)
T PRK12898        171 LGLTVGCVVEDQSPD--ERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHFAIV  248 (656)
T ss_pred             cCCEEEEEeCCCCHH--HHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhcccccceeEe
Confidence            999999999998653  344456799999999887 55554321                         11356889999


Q ss_pred             ecccccC
Q psy17644        321 DEADRMF  327 (330)
Q Consensus       321 DEad~ll  327 (330)
                      ||+|.||
T Consensus       249 DEvDSiL  255 (656)
T PRK12898        249 DEADSVL  255 (656)
T ss_pred             eccccee
Confidence            9999987

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.78  E-value=1.8e-18  Score=177.21  Aligned_cols=145  Identities=23%  Similarity=0.328  Sum_probs=121.0

Q ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHhhhh-hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q psy17644        173 GFDEVLMKALRKCEYTSPTPIQAQAVPA-ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE  251 (330)
Q Consensus       173 ~l~~~l~~~l~~~~~~~pt~iQ~~~i~~-~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~  251 (330)
                      .+...+...+...++..+.+-|+.++.. ++.++|+++|+|||||||+.+++.+++.+.+.       +.++|+|||+|+
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~-------~~k~vYivPlkA   87 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG-------GGKVVYIVPLKA   87 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc-------CCcEEEEeChHH
Confidence            4667777777777886666666666655 45679999999999999999999999998873       678999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        252 LSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       252 La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      ||.+++.++++| ..+|+++....|......  ..+ .+++|||+||++|..++++....+..|++|||||+|.+.|
T Consensus        88 La~Ek~~~~~~~-~~~GirV~~~TgD~~~~~--~~l-~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d  160 (766)
T COG1204          88 LAEEKYEEFSRL-EELGIRVGISTGDYDLDD--ERL-ARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGD  160 (766)
T ss_pred             HHHHHHHHhhhH-HhcCCEEEEecCCcccch--hhh-ccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCC
Confidence            999999999954 456999999999877443  122 3479999999999999998877788999999999999875

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.77  E-value=3.8e-18  Score=172.64  Aligned_cols=129  Identities=19%  Similarity=0.198  Sum_probs=100.4

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCC
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN  268 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~  268 (330)
                      .|+++|...+..+..  ..|+.++||+|||++|++|++.+.+.        ++.|+||+||++||.|+++++..+.+.+|
T Consensus        70 rpydVQlig~l~l~~--G~Iaem~TGeGKTLta~Lpa~l~aL~--------g~~V~VVTpn~yLA~Rdae~m~~l~~~LG  139 (762)
T TIGR03714        70 FPYDVQVLGAIVLHQ--GNIAEMKTGEGKTLTATMPLYLNALT--------GKGAMLVTTNDYLAKRDAEEMGPVYEWLG  139 (762)
T ss_pred             CccHHHHHHHHHhcC--CceeEecCCcchHHHHHHHHHHHhhc--------CCceEEeCCCHHHHHHHHHHHHHHHhhcC
Confidence            455555554444444  47999999999999999999877654        56799999999999999999999999999


Q ss_pred             ceEEEEECCCc---hHHHHHHHhCCCeEEEEChHHH-HHHHHc------CCCCCCCccEEEeecccccC
Q psy17644        269 LSVVCCYGGGS---KWDQSKALELGAEIVVGTPGRI-IDMVKM------GATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       269 ~~~~~~~gg~~---~~~~~~~l~~~~dIiV~TP~~L-~~~l~~------~~~~l~~i~~lVvDEad~ll  327 (330)
                      +++.+++++..   .....+....+|+|++|||++| .+++..      ....++.+.++||||||.||
T Consensus       140 Lsv~~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsIL  208 (762)
T TIGR03714       140 LTVSLGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVL  208 (762)
T ss_pred             CcEEEEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHh
Confidence            99998887632   1222333445799999999999 565532      23347889999999999997

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.76  E-value=9.1e-18  Score=166.57  Aligned_cols=125  Identities=20%  Similarity=0.137  Sum_probs=98.1

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG  266 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~  266 (330)
                      ...|+++|.++++.++.+++.+++++||+|||+++++. ...++..      ...++|||+||++|+.|+.+.+++++..
T Consensus       112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l-~~~~~~~------~~~~vLilvpt~eL~~Q~~~~l~~~~~~  184 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLL-SRYYLEN------YEGKVLIIVPTTSLVTQMIDDFVDYRLF  184 (501)
T ss_pred             cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHH-HHHHHhc------CCCeEEEEECcHHHHHHHHHHHHHhccc
Confidence            45799999999999999999999999999999876542 2222332      2348999999999999999999998755


Q ss_pred             CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        267 YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       267 ~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      ....+..+++|....       .+.+|+|+||++|.....   ..+.++.+|||||||++..
T Consensus       185 ~~~~~~~i~~g~~~~-------~~~~I~VaT~qsl~~~~~---~~~~~~~~iIvDEaH~~~~  236 (501)
T PHA02558        185 PREAMHKIYSGTAKD-------TDAPIVVSTWQSAVKQPK---EWFDQFGMVIVDECHLFTG  236 (501)
T ss_pred             cccceeEEecCcccC-------CCCCEEEeeHHHHhhchh---hhccccCEEEEEchhcccc
Confidence            445566677776543       347999999999876442   2467899999999999863

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.76  E-value=3.7e-18  Score=183.25  Aligned_cols=120  Identities=23%  Similarity=0.217  Sum_probs=99.4

Q ss_pred             EEcCCCChhHHHHHHHHHHHHHhcCCC-----CCCCCCeEEEEcccHHHHHHHHHHHHHhc------------cCCCceE
Q psy17644        209 GVAKTGSGKTGAFIWPMLVHIMDQKEL-----EPGDGPMGLILAPTRELSQQIYNEAKRFG------------KGYNLSV  271 (330)
Q Consensus       209 ~~a~TGsGKT~a~llp~l~~i~~~~~~-----~~~~~~~vLil~Ptr~La~Qi~~~~~~l~------------~~~~~~~  271 (330)
                      ++||||||||++|+||+|..++.+...     ...++.++|||+|||+|+.|+++.++...            ...++++
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            479999999999999999999865311     12346899999999999999999987521            1246888


Q ss_pred             EEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCC-CCCCCccEEEeecccccCc
Q psy17644        272 VCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA-TKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       272 ~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~-~~l~~i~~lVvDEad~lld  328 (330)
                      ..++|+.+..++.+.+++.++|||+||++|..++.++. ..+++|++|||||+|.|++
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g  138 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAG  138 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcc
Confidence            88999998888777788889999999999999886543 4689999999999999985

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.75  E-value=9.2e-18  Score=171.32  Aligned_cols=128  Identities=23%  Similarity=0.226  Sum_probs=106.7

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      -.|.++|...--++.  +--|+.++||+|||++|++|++.+++.        +..|+||+||++||.|.++++..+...+
T Consensus        81 ~~~ydvQliGg~~Lh--~G~Iaem~TGeGKTL~a~Lpa~~~al~--------G~~V~VvTpn~yLA~qd~e~m~~l~~~l  150 (896)
T PRK13104         81 LRHFDVQLIGGMVLH--EGNIAEMRTGEGKTLVATLPAYLNAIS--------GRGVHIVTVNDYLAKRDSQWMKPIYEFL  150 (896)
T ss_pred             CCcchHHHhhhhhhc--cCccccccCCCCchHHHHHHHHHHHhc--------CCCEEEEcCCHHHHHHHHHHHHHHhccc
Confidence            356666655444444  445899999999999999999988764        4569999999999999999999999999


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcC-CCCC-----CCccEEEeecccccC
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMG-ATKL-----NRVTFLVLDEADRMF  327 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~-~~~l-----~~i~~lVvDEad~ll  327 (330)
                      |+++.+++||.....+...+  .+||++|||++| +++++.+ ...+     +.+.++||||||+||
T Consensus       151 GLtv~~i~gg~~~~~r~~~y--~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiL  215 (896)
T PRK13104        151 GLTVGVIYPDMSHKEKQEAY--KADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSIL  215 (896)
T ss_pred             CceEEEEeCCCCHHHHHHHh--CCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhh
Confidence            99999999998877665554  589999999999 9999876 3334     589999999999997

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.75  E-value=2.5e-17  Score=141.48  Aligned_cols=138  Identities=43%  Similarity=0.650  Sum_probs=115.4

Q ss_pred             CCCCCCCHHHHHhhhhhcCC-CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        185 CEYTSPTPIQAQAVPAALSG-RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g-~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .++..|+++|.+++..+... +.++++++||+|||.+++.+++.++...      ...++||++||+.++.|+...+..+
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~------~~~~~l~~~p~~~~~~~~~~~~~~~   77 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRG------KGKRVLVLVPTRELAEQWAEELKKL   77 (201)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhccc------CCCcEEEEeCCHHHHHHHHHHHHHH
Confidence            46778999999999999998 9999999999999999999988887543      2468999999999999999999998


Q ss_pred             ccCCCceEEEEECCCchHHHHHHHhCCC-eEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQSKALELGA-EIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~-dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      +..........+++.........+..+. +|+++|++.+...+........++.++||||||.+..
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~  143 (201)
T smart00487       78 GPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLD  143 (201)
T ss_pred             hccCCeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhc
Confidence            7665545566677766555555556655 9999999999999988776778899999999999863

>KOG0952|consensus

Probab=99.71  E-value=2.6e-17  Score=166.62  Aligned_cols=141  Identities=21%  Similarity=0.244  Sum_probs=115.5

Q ss_pred             CCCCCCCHHHHHhhhhhc-CCCcEEEEcCCCChhHHHHHHHHHHHHHhcC--CCCCCCCCeEEEEcccHHHHHHHHHHHH
Q psy17644        185 CEYTSPTPIQAQAVPAAL-SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQK--ELEPGDGPMGLILAPTRELSQQIYNEAK  261 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~-~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~--~~~~~~~~~vLil~Ptr~La~Qi~~~~~  261 (330)
                      .+|..+..+|..++|.++ +..|+|+|||||||||..|+|.+|+.+.+..  -...+++.|+++|+|+++||..+++.+.
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            467778899999999998 4569999999999999999999998877521  1233568999999999999999999988


Q ss_pred             HhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC---CCCCccEEEeecccccCc
Q psy17644        262 RFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT---KLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       262 ~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~---~l~~i~~lVvDEad~lld  328 (330)
                      +-....|+++..+.|........  +. .++|||+||+++--..+++..   .++.|++|||||+|.|-|
T Consensus       186 kkl~~~gi~v~ELTGD~ql~~te--i~-~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd  252 (1230)
T KOG0952|consen  186 KKLAPLGISVRELTGDTQLTKTE--IA-DTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHD  252 (1230)
T ss_pred             hhcccccceEEEecCcchhhHHH--HH-hcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcC
Confidence            87788899999999977654432  22 389999999999766665543   267899999999998863

>KOG2340|consensus

Probab=99.71  E-value=4.9e-17  Score=154.60  Aligned_cols=142  Identities=21%  Similarity=0.299  Sum_probs=104.6

Q ss_pred             CCCCCCHHHHHhhhhhcCCCcEEEEcCC-CChh--HHHHHHHHHHHHHhcCCCCCCC-----------------------
Q psy17644        186 EYTSPTPIQAQAVPAALSGRDIIGVAKT-GSGK--TGAFIWPMLVHIMDQKELEPGD-----------------------  239 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~~g~d~i~~a~T-GsGK--T~a~llp~l~~i~~~~~~~~~~-----------------------  239 (330)
                      .-..+|+.|.+++-+++++||+++...| +.|+  +..||||+|+|+++++.++.++                       
T Consensus       213 ~s~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~t  292 (698)
T KOG2340|consen  213 KSEPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFT  292 (698)
T ss_pred             ccCcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCC
Confidence            3456899999999999999999988544 4455  5789999999999887654332                       


Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCc---------eE---------------------EEEECCCchHHHHHHHh-
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNL---------SV---------------------VCCYGGGSKWDQSKALE-  288 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~---------~~---------------------~~~~gg~~~~~~~~~l~-  288 (330)
                      .|+||||||||+.|..+++.+..+..+..-         ++                     ..++.|++...++..++ 
T Consensus       293 RpkVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~f  372 (698)
T KOG2340|consen  293 RPKVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAF  372 (698)
T ss_pred             CceEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHH
Confidence            299999999999999999999887432111         11                     11233443333322221 


Q ss_pred             -----------CCCeEEEEChHHHHHHHHcC------CCCCCCccEEEeecccccC
Q psy17644        289 -----------LGAEIVVGTPGRIIDMVKMG------ATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       289 -----------~~~dIiV~TP~~L~~~l~~~------~~~l~~i~~lVvDEad~ll  327 (330)
                                 ..+|||||+|.+|.+++.+.      ...|++|+++|||.||.|+
T Consensus       373 tkKtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l  428 (698)
T KOG2340|consen  373 TKKTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIML  428 (698)
T ss_pred             HHHHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHH
Confidence                       16899999999999999732      2248999999999999886

>PRK13766 Hef nuclease; Provisional

Probab=99.70  E-value=3.4e-16  Score=163.22  Aligned_cols=133  Identities=27%  Similarity=0.275  Sum_probs=109.7

Q ss_pred             CCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        186 EYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      +...|+++|..++..++.+ +++++++||+|||++++++++.++..       .+.++|||+||++|+.|+...++++..
T Consensus        12 ~~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~-------~~~~vLvl~Pt~~L~~Q~~~~~~~~~~   83 (773)
T PRK13766         12 NTIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHK-------KGGKVLILAPTKPLVEQHAEFFRKFLN   83 (773)
T ss_pred             CcCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHh-------CCCeEEEEeCcHHHHHHHHHHHHHHhC
Confidence            3457899999999888876 99999999999999999988877632       467999999999999999999999865


Q ss_pred             CCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        266 GYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       266 ~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ..+..+..+.|+..... +..+..+++|+|+||..+...+..+...+.++.+|||||||++.
T Consensus        84 ~~~~~v~~~~g~~~~~~-r~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~  144 (773)
T PRK13766         84 IPEEKIVVFTGEVSPEK-RAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAV  144 (773)
T ss_pred             CCCceEEEEeCCCCHHH-HHHHHhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCcccc
Confidence            44456667777666554 34444457999999999988877777788899999999999975

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

Probab=99.67  E-value=2.5e-16  Score=151.27  Aligned_cols=152  Identities=25%  Similarity=0.296  Sum_probs=130.2

Q ss_pred             CCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhh-cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc
Q psy17644        169 FGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAA-LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA  247 (330)
Q Consensus       169 f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~-~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~  247 (330)
                      .+++.+++.+.+.|...|+..+.|+|.-++..- +.|+|++++++|+||||++.-++-+..++.       .|.+.|+|+
T Consensus       196 vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~-------~g~KmlfLv  268 (830)
T COG1202         196 VDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLS-------GGKKMLFLV  268 (830)
T ss_pred             ccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHh-------CCCeEEEEe
Confidence            578899999999999999999999999999885 599999999999999999999999988886       478999999


Q ss_pred             ccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHH----HHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecc
Q psy17644        248 PTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS----KALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEA  323 (330)
Q Consensus       248 Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~----~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEa  323 (330)
                      |..+||+|-+..++.-...+++++..-+|..-.....    -.....+||||+|.+++-.+++.+ ..+.+|..|||||+
T Consensus       269 PLVALANQKy~dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg-~~lgdiGtVVIDEi  347 (830)
T COG1202         269 PLVALANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG-KDLGDIGTVVIDEI  347 (830)
T ss_pred             hhHHhhcchHHHHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC-CcccccceEEeeee
Confidence            9999999999999877777888887777754332221    111235899999999999999876 67899999999999


Q ss_pred             cccCc
Q psy17644        324 DRMFD  328 (330)
Q Consensus       324 d~lld  328 (330)
                      |.|-|
T Consensus       348 HtL~d  352 (830)
T COG1202         348 HTLED  352 (830)
T ss_pred             eeccc
Confidence            99865

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.66  E-value=4.4e-16  Score=157.75  Aligned_cols=129  Identities=15%  Similarity=0.066  Sum_probs=97.3

Q ss_pred             HHHHHhhhhhcCCCcEEEEcCCCChhHHH---------HHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        192 PIQAQAVPAALSGRDIIGVAKTGSGKTGA---------FIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       192 ~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a---------~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      .+|.++++.+++|+++|++|+||||||.+         |++|.+.++..-.  ....+++++|++|||+||.|+...+.+
T Consensus       167 ~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~--~~~~~~~ilvt~PrreLa~qi~~~i~~  244 (675)
T PHA02653        167 DVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKID--PNFIERPIVLSLPRVALVRLHSITLLK  244 (675)
T ss_pred             HHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcc--cccCCcEEEEECcHHHHHHHHHHHHHH
Confidence            58999999999999999999999999976         5555555442110  012357899999999999999999887


Q ss_pred             hccC---CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        263 FGKG---YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       263 l~~~---~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      ..+.   .+..+...+||... .+.....++.+|||+|++.       ....++++++|||||||.+..+|
T Consensus       245 ~vg~~~~~g~~v~v~~Gg~~~-~~~~t~~k~~~Ilv~T~~L-------~l~~L~~v~~VVIDEaHEr~~~~  307 (675)
T PHA02653        245 SLGFDEIDGSPISLKYGSIPD-ELINTNPKPYGLVFSTHKL-------TLNKLFDYGTVIIDEVHEHDQIG  307 (675)
T ss_pred             HhCccccCCceEEEEECCcch-HHhhcccCCCCEEEEeCcc-------cccccccCCEEEccccccCccch
Confidence            6543   35677888999873 2223333467999999752       12357899999999999998765

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.65  E-value=7e-16  Score=157.33  Aligned_cols=128  Identities=20%  Similarity=0.216  Sum_probs=108.4

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      ..|+++|.-..-++..|+  |+.++||+|||+++++|++...+.        |..|-||+||+.||.|.++.+..+...+
T Consensus        80 ~~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~--------G~~V~IvTpn~yLA~rd~e~~~~l~~~L  149 (830)
T PRK12904         80 MRHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALT--------GKGVHVVTVNDYLAKRDAEWMGPLYEFL  149 (830)
T ss_pred             CCCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHc--------CCCEEEEecCHHHHHHHHHHHHHHHhhc
Confidence            467888877776666664  889999999999999999755543        4457799999999999999999999999


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcCCC------CCCCccEEEeecccccC
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMGAT------KLNRVTFLVLDEADRMF  327 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~~~------~l~~i~~lVvDEad~ll  327 (330)
                      |+++.++.||.+...+...+  .++|+++||++| +++++.+..      .++.+.++||||||+||
T Consensus       150 Glsv~~i~~~~~~~er~~~y--~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiL  214 (830)
T PRK12904        150 GLSVGVILSGMSPEERREAY--AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSIL  214 (830)
T ss_pred             CCeEEEEcCCCCHHHHHHhc--CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhhe
Confidence            99999999998887766665  389999999999 999976542      36789999999999997

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.63  E-value=3.1e-15  Score=153.05  Aligned_cols=122  Identities=21%  Similarity=0.269  Sum_probs=98.8

Q ss_pred             CCCCHHHHHhhhhhcCC---CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        188 TSPTPIQAQAVPAALSG---RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g---~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      ..+|+.|.+++..+.++   +++++.++||||||.+|+.++...+.        .|.++|||+||++|+.|+++.+++..
T Consensus       143 ~~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~--------~g~~vLvLvPt~~L~~Q~~~~l~~~f  214 (679)
T PRK05580        143 PTLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLA--------QGKQALVLVPEIALTPQMLARFRARF  214 (679)
T ss_pred             CCCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHH--------cCCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            36899999999999874   78999999999999999887665543        36789999999999999999998753


Q ss_pred             cCCCceEEEEECCCchHHHHH---H-HhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSK---A-LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~---~-l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                         +..+..++|+.+......   . ....++|||+||+.+.       ..++++.+|||||+|...
T Consensus       215 ---g~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-------~p~~~l~liVvDEeh~~s  271 (679)
T PRK05580        215 ---GAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-------LPFKNLGLIIVDEEHDSS  271 (679)
T ss_pred             ---CCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-------ccccCCCEEEEECCCccc
Confidence               567888888877654432   2 2335799999998874       457899999999999764

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

Probab=99.63  E-value=2.9e-15  Score=142.57  Aligned_cols=131  Identities=24%  Similarity=0.223  Sum_probs=109.4

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG  266 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~  266 (330)
                      .-.++-+|..+...++.+ +++++.|||-|||+..++-+.+++...      .+ ++|+|+||+-|+.|....++++..-
T Consensus        13 ~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~------~~-kvlfLAPTKPLV~Qh~~~~~~v~~i   84 (542)
T COG1111          13 TIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWF------GG-KVLFLAPTKPLVLQHAEFCRKVTGI   84 (542)
T ss_pred             cccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhc------CC-eEEEecCCchHHHHHHHHHHHHhCC
Confidence            345777888877776654 999999999999999998888887663      34 8999999999999999999998766


Q ss_pred             CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        267 YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       267 ~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      -...++.+.|............ ...|+|+||..+.+-+..+.+++.++.++|||||||-
T Consensus        85 p~~~i~~ltGev~p~~R~~~w~-~~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRA  143 (542)
T COG1111          85 PEDEIAALTGEVRPEEREELWA-KKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRA  143 (542)
T ss_pred             ChhheeeecCCCChHHHHHHHh-hCCEEEeccHHHHhHHhcCccChHHceEEEechhhhc
Confidence            5567777777777665444444 4699999999999999999999999999999999984

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.62  E-value=4.2e-15  Score=141.47  Aligned_cols=124  Identities=19%  Similarity=0.235  Sum_probs=91.5

Q ss_pred             HHHHhhhhhcCCCc--EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC---
Q psy17644        193 IQAQAVPAALSGRD--IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY---  267 (330)
Q Consensus       193 iQ~~~i~~~~~g~d--~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~---  267 (330)
                      +|.++++.+.++.+  ++++||||||||.+|++|++..           +.+++|++||++|+.|+++.++.+....   
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~-----------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~   69 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG-----------ENDTIALYPTNALIEDQTEAIKEFVDVFKPE   69 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc-----------CCCEEEEeChHHHHHHHHHHHHHHHHhcCCC
Confidence            59999999998875  7788999999999999998842           3468999999999999999999886432   


Q ss_pred             -CceEEEEECCCchHH---H-----------------HHHH-hCCCeEEEEChHHHHHHHHcCCC--------CCCCccE
Q psy17644        268 -NLSVVCCYGGGSKWD---Q-----------------SKAL-ELGAEIVVGTPGRIIDMVKMGAT--------KLNRVTF  317 (330)
Q Consensus       268 -~~~~~~~~gg~~~~~---~-----------------~~~l-~~~~dIiV~TP~~L~~~l~~~~~--------~l~~i~~  317 (330)
                       +..+..+.| .....   .                 +..+ ...++|+++||..|..++.+...        .+.++.+
T Consensus        70 ~~~~v~~~~g-~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~  148 (357)
T TIGR03158        70 RDVNLLHVSK-ATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFST  148 (357)
T ss_pred             CCceEEEecC-CchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCE
Confidence             344444444 32211   0                 0111 23578999999999887754211        2578999


Q ss_pred             EEeecccccCc
Q psy17644        318 LVLDEADRMFD  328 (330)
Q Consensus       318 lVvDEad~lld  328 (330)
                      |||||+|.+-.
T Consensus       149 iV~DE~H~~~~  159 (357)
T TIGR03158       149 VIFDEFHLYDA  159 (357)
T ss_pred             EEEecccccCc
Confidence            99999999753

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.

>KOG0354|consensus

Probab=99.62  E-value=1.7e-15  Score=151.36  Aligned_cols=130  Identities=25%  Similarity=0.223  Sum_probs=106.3

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      ..++.+|..++-.++ |+++|+++|||+|||+++...|++|+-..      ...++|+++||+-|+.|....+..++.. 
T Consensus        61 ~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~------p~~KiVF~aP~~pLv~QQ~a~~~~~~~~-  132 (746)
T KOG0354|consen   61 LELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWR------PKGKVVFLAPTRPLVNQQIACFSIYLIP-  132 (746)
T ss_pred             ccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcC------CcceEEEeeCCchHHHHHHHHHhhccCc-
Confidence            457899999998888 99999999999999999999999998654      3489999999999999999778777654 


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCC-CCCccEEEeeccccc
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATK-LNRVTFLVLDEADRM  326 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~-l~~i~~lVvDEad~l  326 (330)
                       -.+....||......+..+-...+|+|+||..|.+.|...... |+.+.++||||||+-
T Consensus       133 -~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra  191 (746)
T KOG0354|consen  133 -YSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRT  191 (746)
T ss_pred             -ccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccccc
Confidence             4455555664433334455566899999999999998776544 699999999999984

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

Probab=99.60  E-value=1.3e-15  Score=150.05  Aligned_cols=131  Identities=22%  Similarity=0.322  Sum_probs=108.4

Q ss_pred             CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        185 CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .||..++|-|.++|..+++|+|+++..|||.||++||.+|++..           ...+|||.|..+|....+..++.. 
T Consensus        13 fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~-----------~G~TLVVSPLiSLM~DQV~~l~~~-   80 (590)
T COG0514          13 FGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL-----------EGLTLVVSPLISLMKDQVDQLEAA-   80 (590)
T ss_pred             hCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc-----------CCCEEEECchHHHHHHHHHHHHHc-
Confidence            48999999999999999999999999999999999999999854           237899999999999999999886 


Q ss_pred             cCCCceEEEEECCCchHHHHHH---HhCC-CeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSKA---LELG-AEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~~---l~~~-~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                         |+.+.++.+..+..+....   +..+ .+++.-+|++|..--....+.-..+.++||||||++.+||
T Consensus        81 ---Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWG  147 (590)
T COG0514          81 ---GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWG  147 (590)
T ss_pred             ---CceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcC
Confidence               5788888887766555333   3333 7999999999976332222335678999999999999998

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.60  E-value=8.3e-15  Score=151.68  Aligned_cols=121  Identities=21%  Similarity=0.235  Sum_probs=95.8

Q ss_pred             HHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH-HhccCCCceE
Q psy17644        193 IQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK-RFGKGYNLSV  271 (330)
Q Consensus       193 iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~-~l~~~~~~~~  271 (330)
                      +-.+++..+.+++++|++|+||||||.+|.++++.+..        .++++||+.|||++|.|++..+. .++...+..+
T Consensus         6 ~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~--------~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~V   77 (819)
T TIGR01970         6 VLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG--------IGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTV   77 (819)
T ss_pred             HHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc--------cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEE
Confidence            33456666778899999999999999999999997752        35689999999999999999875 4555556666


Q ss_pred             EEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccc-ccCc
Q psy17644        272 VCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD-RMFD  328 (330)
Q Consensus       272 ~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad-~lld  328 (330)
                      ...+++..      ......+|+|+||++|.+++.+ ...++++.+|||||+| ++++
T Consensus        78 Gy~vr~~~------~~s~~t~I~v~T~G~Llr~l~~-d~~L~~v~~VIiDEaHER~L~  128 (819)
T TIGR01970        78 GYRVRGEN------KVSRRTRLEVVTEGILTRMIQD-DPELDGVGALIFDEFHERSLD  128 (819)
T ss_pred             EEEEcccc------ccCCCCcEEEECCcHHHHHHhh-CcccccCCEEEEeccchhhhc
Confidence            65555433      2234579999999999999876 3569999999999999 5665

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.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.59  E-value=3.2e-14  Score=115.15  Aligned_cols=116  Identities=40%  Similarity=0.530  Sum_probs=93.9

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS  284 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~  284 (330)
                      +.+++.++||+|||..++..+......      ....++||++|++.++.|+...+..+... +..+..+.++.......
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~------~~~~~~lv~~p~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   73 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS------LKGGQVLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQE   73 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc------ccCCCEEEEcCcHHHHHHHHHHHHHHhhC-CcEEEEEecCcchhHHH
Confidence            468899999999998888777766544      23578999999999999999999888765 66777777776665555


Q ss_pred             HHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        285 KALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       285 ~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      .....+++|+|+|+..+...+.........+.++||||+|.+.
T Consensus        74 ~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~  116 (144)
T cd00046          74 KLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLL  116 (144)
T ss_pred             HHhcCCCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHh
Confidence            5556678999999999998887665556788999999999875

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

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

Probab=99.58  E-value=3.5e-14  Score=149.16  Aligned_cols=146  Identities=17%  Similarity=0.221  Sum_probs=104.9

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHhhh----hhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q psy17644        174 FDEVLMKALRKCEYTSPTPIQAQAVP----AALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT  249 (330)
Q Consensus       174 l~~~l~~~l~~~~~~~pt~iQ~~~i~----~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt  249 (330)
                      +++.+...+...||. ++|.|.+.+.    .+..|+++++.|+||+|||++|++|++.+..        ++.++||.+||
T Consensus       231 ~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~--------~~~~vvi~t~t  301 (850)
T TIGR01407       231 LSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI--------TEKPVVISTNT  301 (850)
T ss_pred             ccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc--------CCCeEEEEeCc
Confidence            334666777777876 8899998666    5568899999999999999999999988754        24589999999


Q ss_pred             HHHHHHHHH-HHHHhccCCC--ceEEEEECCCch----------------------------------------------
Q psy17644        250 RELSQQIYN-EAKRFGKGYN--LSVVCCYGGGSK----------------------------------------------  280 (330)
Q Consensus       250 r~La~Qi~~-~~~~l~~~~~--~~~~~~~gg~~~----------------------------------------------  280 (330)
                      ++|..|++. .+..+.+.++  ++++.+.|+...                                              
T Consensus       302 ~~Lq~Ql~~~~~~~l~~~~~~~~~~~~~kG~~~ylcl~k~~~~l~~~~~~~~~~~~~~~~~~wl~~T~tGD~~el~~~~~  381 (850)
T TIGR01407       302 KVLQSQLLEKDIPLLNEILNFKINAALIKGKSNYLSLGKFSQILKDNTDNYEFNIFKMQVLVWLTETETGDLDELNLKGG  381 (850)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCceEEEEEcchhhccHHHHHHHHhcCCCcHHHHHHHHHHHHHhccCCccCHhhccCCCc
Confidence            999999976 4555544333  666666653321                                              


Q ss_pred             -------------------------HHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        281 -------------------------WDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       281 -------------------------~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                                               ....+.....++||||+..-|+.-+.....-+....+|||||||+|.+
T Consensus       382 ~~~~~~~i~~~~~l~~~c~~~~~Cf~~~ar~~a~~AdivItNHa~L~~~~~~~~~ilp~~~~lIiDEAH~L~d  454 (850)
T TIGR01407       382 NKMFFAQVRHDGNLSKKDLFYEVDFYNRAQKNAEQAQILITNHAYLITRLVDNPELFPSFRDLIIDEAHHLPD  454 (850)
T ss_pred             chhhHHHhhcCCCCCCCCCCccccHHHHHHHHHhcCCEEEecHHHHHHHhhcccccCCCCCEEEEECcchHHH
Confidence                                     001111122589999999988876644333345557999999999864

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.57  E-value=1.1e-14  Score=150.98  Aligned_cols=117  Identities=21%  Similarity=0.221  Sum_probs=93.9

Q ss_pred             HHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH-HhccCCCceEE
Q psy17644        194 QAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK-RFGKGYNLSVV  272 (330)
Q Consensus       194 Q~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~-~l~~~~~~~~~  272 (330)
                      -.+++..+.++++++++|+||||||.+|.++++....        .++++||+.|||++|.|+++.+. .++...+..+.
T Consensus        10 ~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~--------~~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VG   81 (812)
T PRK11664         10 LPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGG--------INGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVG   81 (812)
T ss_pred             HHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCC--------cCCeEEEECChHHHHHHHHHHHHHHhCcccCceEE
Confidence            3455666778899999999999999999999886531        23589999999999999999985 45556677777


Q ss_pred             EEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        273 CCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       273 ~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      ..+++....      ....+|+|+||++|.+++.+ ...++++.+|||||+|.
T Consensus        82 y~vr~~~~~------~~~t~I~v~T~G~Llr~l~~-d~~L~~v~~IIlDEaHE  127 (812)
T PRK11664         82 YRMRAESKV------GPNTRLEVVTEGILTRMIQR-DPELSGVGLVILDEFHE  127 (812)
T ss_pred             EEecCcccc------CCCCcEEEEChhHHHHHHhh-CCCcCcCcEEEEcCCCc
Confidence            777765432      23468999999999998875 34699999999999996

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.57  E-value=7.6e-15  Score=139.70  Aligned_cols=115  Identities=23%  Similarity=0.172  Sum_probs=81.1

Q ss_pred             cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCch-----
Q psy17644        206 DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSK-----  280 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~-----  280 (330)
                      +++++||||||||.+|++|++..+...      .+.+++|++|||+|+.|+++.+..++..   .+..++|+...     
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~------~~~~ii~v~P~~~L~~q~~~~l~~~f~~---~~~~~~~~~~~~~~~~   71 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ------KADRVIIALPTRATINAMYRRAKELFGS---NLGLLHSSSSFKRIKE   71 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC------CCCeEEEEeehHHHHHHHHHHHHHHhCc---ccEEeeccHHHHHHhc
Confidence            589999999999999999999875432      4679999999999999999999987432   23333332221     


Q ss_pred             ------HHH-HHHH-h-----CCCeEEEEChHHHHHHHHcCCCC----C--CCccEEEeecccccCcC
Q psy17644        281 ------WDQ-SKAL-E-----LGAEIVVGTPGRIIDMVKMGATK----L--NRVTFLVLDEADRMFDM  329 (330)
Q Consensus       281 ------~~~-~~~l-~-----~~~dIiV~TP~~L~~~l~~~~~~----l--~~i~~lVvDEad~lld~  329 (330)
                            ... .... .     ..++|+|+||+++...+......    +  -...+|||||||.++++
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~  139 (358)
T TIGR01587        72 MGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEY  139 (358)
T ss_pred             cCCchhHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHH
Confidence                  000 0001 1     13689999999999877652111    1  12379999999999874

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.

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.57  E-value=1e-14  Score=148.88  Aligned_cols=127  Identities=17%  Similarity=0.211  Sum_probs=104.0

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCC
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN  268 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~  268 (330)
                      .|+++|.-.--++  .+.-|+.++||.|||++|.+|++.+.+.        |..|.||+|++.||.|..+++..+...+|
T Consensus        82 ~~ydVQliGgl~L--~~G~IaEm~TGEGKTL~a~lp~~l~al~--------g~~VhIvT~ndyLA~RD~e~m~~l~~~lG  151 (908)
T PRK13107         82 RHFDVQLLGGMVL--DSNRIAEMRTGEGKTLTATLPAYLNALT--------GKGVHVITVNDYLARRDAENNRPLFEFLG  151 (908)
T ss_pred             CcCchHHhcchHh--cCCccccccCCCCchHHHHHHHHHHHhc--------CCCEEEEeCCHHHHHHHHHHHHHHHHhcC
Confidence            5666775444334  4455889999999999999999988764        45699999999999999999999999999


Q ss_pred             ceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcC-CCC-----CCCccEEEeecccccC
Q psy17644        269 LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMG-ATK-----LNRVTFLVLDEADRMF  327 (330)
Q Consensus       269 ~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~-~~~-----l~~i~~lVvDEad~ll  327 (330)
                      +++.++.+|.+......  .-+|||++|||++| +++++.+ ...     .+.+.++||||||.||
T Consensus       152 lsv~~i~~~~~~~~r~~--~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiL  215 (908)
T PRK13107        152 LTVGINVAGLGQQEKKA--AYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSIL  215 (908)
T ss_pred             CeEEEecCCCCHHHHHh--cCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhc
Confidence            99999999888644322  23689999999999 9988766 333     3788999999999998

>KOG0352|consensus

Probab=99.49  E-value=6e-14  Score=130.84  Aligned_cols=137  Identities=22%  Similarity=0.330  Sum_probs=99.7

Q ss_pred             HHHHHHHC-CCCC-CCHHHHHhhhhhcCC-CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHH
Q psy17644        178 LMKALRKC-EYTS-PTPIQAQAVPAALSG-RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQ  254 (330)
Q Consensus       178 l~~~l~~~-~~~~-pt~iQ~~~i~~~~~g-~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~  254 (330)
                      +..+|++. |+.+ -+++|.+++..+..+ +||+++.|||+||++||.||+|.+           +..+||+.|..+|+.
T Consensus         7 VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~-----------~gITIV~SPLiALIk   75 (641)
T KOG0352|consen    7 VREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH-----------GGITIVISPLIALIK   75 (641)
T ss_pred             HHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh-----------CCeEEEehHHHHHHH
Confidence            44455443 4443 379999999998855 699999999999999999999977           348999999999999


Q ss_pred             HHHHHHHHhccCCCceEEEEECCCchHHHHHH------HhCCCeEEEEChHHHHH-----HHHcCCCCCCCccEEEeecc
Q psy17644        255 QIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA------LELGAEIVVGTPGRIID-----MVKMGATKLNRVTFLVLDEA  323 (330)
Q Consensus       255 Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~------l~~~~dIiV~TP~~L~~-----~l~~~~~~l~~i~~lVvDEa  323 (330)
                      ...+.+.++-    +.+-.+.+-.+..+..+.      .+.+..|+.-||++...     +++ ...+-.-+.|+|||||
T Consensus        76 DQiDHL~~LK----Vp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn-~L~~r~~L~Y~vVDEA  150 (641)
T KOG0352|consen   76 DQIDHLKRLK----VPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLN-GLANRDVLRYIVVDEA  150 (641)
T ss_pred             HHHHHHHhcC----CchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHH-HHhhhceeeeEEechh
Confidence            9999988872    333333333343333222      23357899999987533     332 2233456899999999


Q ss_pred             cccCcCC
Q psy17644        324 DRMFDMG  330 (330)
Q Consensus       324 d~lld~G  330 (330)
                      |++.+||
T Consensus       151 HCVSQWG  157 (641)
T KOG0352|consen  151 HCVSQWG  157 (641)
T ss_pred             hhHhhhc
Confidence            9999998

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

Probab=99.48  E-value=4.4e-13  Score=139.64  Aligned_cols=129  Identities=22%  Similarity=0.269  Sum_probs=97.0

Q ss_pred             CCCHHHHHhhhhh----cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH-HHHHHh
Q psy17644        189 SPTPIQAQAVPAA----LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIY-NEAKRF  263 (330)
Q Consensus       189 ~pt~iQ~~~i~~~----~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~-~~~~~l  263 (330)
                      .+++.|.+....+    ..++.+++.|+||+|||++|++|++.+.         .+.++||++|||+|+.|++ ..+..+
T Consensus       245 e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~---------~~~~vvI~t~T~~Lq~Ql~~~~i~~l  315 (820)
T PRK07246        245 EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS---------DQRQIIVSVPTKILQDQIMAEEVKAI  315 (820)
T ss_pred             ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc---------CCCcEEEEeCcHHHHHHHHHHHHHHH
Confidence            5889999855544    3678899999999999999999988753         3578999999999999995 667777


Q ss_pred             ccCCCceEEEEECCCch---HHHH--------------------------------------------------------
Q psy17644        264 GKGYNLSVVCCYGGGSK---WDQS--------------------------------------------------------  284 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~---~~~~--------------------------------------------------------  284 (330)
                      .+..++++.++.||...   ....                                                        
T Consensus       316 ~~~~~~~~~~~kg~~~ylcl~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~~El~~~~~~~~~w~~i~~~~~~~~~  395 (820)
T PRK07246        316 QEVFHIDCHSLKGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIKQKQRYAAYFDQLKHDGNLSQS  395 (820)
T ss_pred             HHhcCCcEEEEECCcccccHHHHHHHhhccCcchHHHHHHHHHHHHHhcCCCCCHhhccCCccccHHHHHhhccCCCCCC
Confidence            77777777777775531   0000                                                        


Q ss_pred             ------------HHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        285 ------------KALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       285 ------------~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                                  +.....++|||++..-|...+.... .+....+|||||||+|-
T Consensus       396 cp~~~~cf~~~ar~~a~~AdivItNHall~~~~~~~~-~~p~~~~lIiDEAH~l~  449 (820)
T PRK07246        396 SLFYDYDFWKRSYEKAKTARLLITNHAYFLTRVQDDK-DFARNKVLVFDEAQKLM  449 (820)
T ss_pred             CCcchhhHHHHHHHHHHhCCEEEEchHHHHHHHhhcc-CCCCCCEEEEECcchhH
Confidence                        0001157999999998887664432 35678999999999985

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

Probab=99.48  E-value=5.1e-13  Score=134.17  Aligned_cols=125  Identities=22%  Similarity=0.160  Sum_probs=91.2

Q ss_pred             hhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc-cC--CCceEEEE
Q psy17644        198 VPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG-KG--YNLSVVCC  274 (330)
Q Consensus       198 i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~-~~--~~~~~~~~  274 (330)
                      ...+.+++.+++.|+||+|||++|++|++.++...      .+.++||++||++|+.|+++.+..+. +.  .+++++++
T Consensus        10 ~~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~------~~~rvlIstpT~~Lq~Ql~~~l~~l~~~~l~~~i~~~~l   83 (636)
T TIGR03117        10 LTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKER------PDQKIAIAVPTLALMGQLWSELERLTAEGLAGPVQAGFF   83 (636)
T ss_pred             HHHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc------cCceEEEECCcHHHHHHHHHHHHHHHHhhcCCCeeEEEE
Confidence            34455788899999999999999999999887642      35789999999999999999988877 32  24555555


Q ss_pred             ECCCch--------------------------------------------------------------------------
Q psy17644        275 YGGGSK--------------------------------------------------------------------------  280 (330)
Q Consensus       275 ~gg~~~--------------------------------------------------------------------------  280 (330)
                      .|+.+.                                                                          
T Consensus        84 kGr~nYlCl~rl~~~l~~~~~~~~~~i~~W~~~T~~~~~~~~~~~~~~~~~~~~~~~tGD~~el~~~~~~~~~~~~~~~~  163 (636)
T TIGR03117        84 PGSQEFVSPGALQELLDQSGYDKDPAVQLWIGQGGPLIHEAALIRCMSDAPTKMHWMTHDLKAVATLLNRQDDVTLAIRE  163 (636)
T ss_pred             ECCcccccHHHHHHHhcccchhHHHHHHHHHhcCCccccccchhccccchhhccCCCCCCHhhccCCcCcchhhhccccC
Confidence            443210                                                                          


Q ss_pred             ------HHHHHHH---hCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        281 ------WDQSKAL---ELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       281 ------~~~~~~l---~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                            ....+..   ...++|||+++..|...++....-+....+|||||||+|-+
T Consensus       164 ~~~~~~~~~aR~~~~~a~~AdivItNHalL~~~~~~~~~iLP~~~~lIiDEAH~L~d  220 (636)
T TIGR03117       164 DDEDKRLVESREYEAEARRCRILFCTHAMLGLAFRDKWGLLPQPDILIVDEAHLFEQ  220 (636)
T ss_pred             CCcccHHHHHHHHhhccccCCEEEECHHHHHHHhhhhcCCCCCCCEEEEeCCcchHH
Confidence                  0000111   23579999999988876654333466789999999999864

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.

>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=99.44  E-value=7.6e-13  Score=113.05  Aligned_cols=128  Identities=24%  Similarity=0.221  Sum_probs=86.9

Q ss_pred             CCCHHHHHhhhhhcC-------CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH
Q psy17644        189 SPTPIQAQAVPAALS-------GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK  261 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~-------g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~  261 (330)
                      +|++.|.+++..+..       ++.+++.++||||||.+++..+.... .          ++||++|++.|+.|+...+.
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~-~----------~~l~~~p~~~l~~Q~~~~~~   71 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELA-R----------KVLIVAPNISLLEQWYDEFD   71 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHH-C----------EEEEEESSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhccc-c----------ceeEecCHHHHHHHHHHHHH
Confidence            478999999998883       68999999999999988775444332 1          89999999999999999997


Q ss_pred             HhccCCCceEEE-----------EECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCC-----------CCCCCccEEE
Q psy17644        262 RFGKGYNLSVVC-----------CYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA-----------TKLNRVTFLV  319 (330)
Q Consensus       262 ~l~~~~~~~~~~-----------~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~-----------~~l~~i~~lV  319 (330)
                      .+..........           ..................+|+++|...|........           .......+||
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI  151 (184)
T PF04851_consen   72 DFGSEKYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVI  151 (184)
T ss_dssp             HHSTTSEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEE
T ss_pred             HhhhhhhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEE
Confidence            765432111111           111111112223334467999999999998775321           1234678999


Q ss_pred             eecccccC
Q psy17644        320 LDEADRMF  327 (330)
Q Consensus       320 vDEad~ll  327 (330)
                      +||||++.
T Consensus       152 ~DEaH~~~  159 (184)
T PF04851_consen  152 IDEAHHYP  159 (184)
T ss_dssp             EETGGCTH
T ss_pred             EehhhhcC
Confidence            99999874

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 ....

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

Probab=99.42  E-value=7.9e-13  Score=129.23  Aligned_cols=122  Identities=25%  Similarity=0.247  Sum_probs=88.0

Q ss_pred             CCCCHHHHHhhhhhcC----CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        188 TSPTPIQAQAVPAALS----GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~----g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..|+++|.+++..+.+    ++..++++|||+|||++++..+...           +..+||||||++|+.||.+.+.++
T Consensus        35 ~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~-----------~~~~Lvlv~~~~L~~Qw~~~~~~~  103 (442)
T COG1061          35 FELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL-----------KRSTLVLVPTKELLDQWAEALKKF  103 (442)
T ss_pred             CCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHh-----------cCCEEEEECcHHHHHHHHHHHHHh
Confidence            4689999999999998    8999999999999997776544322           233999999999999998777766


Q ss_pred             ccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      ....  .....+||......     . ..|.|+|...+.............+.+|||||||++..
T Consensus       104 ~~~~--~~~g~~~~~~~~~~-----~-~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a  160 (442)
T COG1061         104 LLLN--DEIGIYGGGEKELE-----P-AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPA  160 (442)
T ss_pred             cCCc--cccceecCceeccC-----C-CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCc
Confidence            4321  23445555544321     1 36999998887764211122234799999999999863

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.40  E-value=1.6e-12  Score=132.08  Aligned_cols=123  Identities=18%  Similarity=0.143  Sum_probs=87.4

Q ss_pred             CCCCHHHHHhhhhhc-CC--CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        188 TSPTPIQAQAVPAAL-SG--RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~-~g--~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      ..++|+|.+++..++ +|  +..+++.|||+|||++.+..+. ++          +.++|||||+..|+.||.+++.+|+
T Consensus       254 ~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~-~l----------~k~tLILvps~~Lv~QW~~ef~~~~  322 (732)
T TIGR00603       254 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAAC-TV----------KKSCLVLCTSAVSVEQWKQQFKMWS  322 (732)
T ss_pred             CCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHH-Hh----------CCCEEEEeCcHHHHHHHHHHHHHhc
Confidence            468999999999988 44  4789999999999988765443 22          2458999999999999999999986


Q ss_pred             cCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcC--------CCCCCCccEEEeeccccc
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG--------ATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~--------~~~l~~i~~lVvDEad~l  326 (330)
                      ......+..+.|+... .    ......|+|+|+..+.....+.        .+.-..+.+||+||||++
T Consensus       323 ~l~~~~I~~~tg~~k~-~----~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~l  387 (732)
T TIGR00603       323 TIDDSQICRFTSDAKE-R----FHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVV  387 (732)
T ss_pred             CCCCceEEEEecCccc-c----cccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccc
Confidence            5434444444443221 1    1123689999998775332211        112246789999999987

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).

>KOG0351|consensus

Probab=99.40  E-value=2.8e-13  Score=140.68  Aligned_cols=133  Identities=21%  Similarity=0.267  Sum_probs=106.5

Q ss_pred             HHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        183 RKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       183 ~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      ...|...++|-|.++|..++.|+|+++..|||.||++||.||++..           ++.+|||.|...|+..+...+.+
T Consensus       258 ~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~-----------~gitvVISPL~SLm~DQv~~L~~  326 (941)
T KOG0351|consen  258 EVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL-----------GGVTVVISPLISLMQDQVTHLSK  326 (941)
T ss_pred             HHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc-----------CCceEEeccHHHHHHHHHHhhhh
Confidence            4568899999999999999999999999999999999999999854           56899999999999887777644


Q ss_pred             hccCCCceEEEEECCCchHHHHHH---HhC---CCeEEEEChHHHHHHH--HcCCCCCCC---ccEEEeecccccCcCC
Q psy17644        263 FGKGYNLSVVCCYGGGSKWDQSKA---LEL---GAEIVVGTPGRIIDMV--KMGATKLNR---VTFLVLDEADRMFDMG  330 (330)
Q Consensus       263 l~~~~~~~~~~~~gg~~~~~~~~~---l~~---~~dIiV~TP~~L~~~l--~~~~~~l~~---i~~lVvDEad~lld~G  330 (330)
                      .    ++...++.++....++...   +..   ..+|+..||+++..--  ......+..   +.++||||||+...||
T Consensus       327 ~----~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWg  401 (941)
T KOG0351|consen  327 K----GIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWG  401 (941)
T ss_pred             c----CcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhc
Confidence            3    6788888888877544322   222   4799999999986522  222223444   8999999999999998

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

Probab=99.39  E-value=6.1e-12  Score=128.22  Aligned_cols=142  Identities=21%  Similarity=0.311  Sum_probs=104.3

Q ss_pred             HHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q psy17644        178 LMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIY  257 (330)
Q Consensus       178 l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~  257 (330)
                      +-+.+.+.....|+..|+.+...++.|+..-++||||.||| +|.+.+-..+.+       .|.+++||+||+.|+.|++
T Consensus        71 ~~~fF~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKT-Tfg~~~sl~~a~-------kgkr~yii~PT~~Lv~Q~~  142 (1187)
T COG1110          71 FEEFFKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKT-TFGLLMSLYLAK-------KGKRVYIIVPTTTLVRQVY  142 (1187)
T ss_pred             HHHHHHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchh-HHHHHHHHHHHh-------cCCeEEEEecCHHHHHHHH
Confidence            34445566555999999999999999999999999999999 455444434333       4689999999999999999


Q ss_pred             HHHHHhccCCC-ceEEEEECCC-chH---HHHHHHhC-CCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcC
Q psy17644        258 NEAKRFGKGYN-LSVVCCYGGG-SKW---DQSKALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       258 ~~~~~l~~~~~-~~~~~~~gg~-~~~---~~~~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~  329 (330)
                      +.+.+|+...+ ..+..+|.+. ...   .....+.+ +.||+|+|..-|..-+..-  .--+++++++|.+|.+|-.
T Consensus       143 ~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L--~~~kFdfifVDDVDA~Lka  218 (1187)
T COG1110         143 ERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEEL--SKLKFDFIFVDDVDAILKA  218 (1187)
T ss_pred             HHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHh--cccCCCEEEEccHHHHHhc
Confidence            99999987666 4444435555 322   22334444 5899999987776655421  1136899999999988743

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.37  E-value=9.5e-12  Score=115.04  Aligned_cols=73  Identities=22%  Similarity=0.168  Sum_probs=58.7

Q ss_pred             CCCHHHHHhh----hhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        189 SPTPIQAQAV----PAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       189 ~pt~iQ~~~i----~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .|+|.|.+.+    ..+.+|.++++.||||+|||++|++|++.++......  ..+.+++|+++|..+..|....++++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~--~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER--IQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc--ccccceeEEeccHHHHHHHHHHHHhc
Confidence            4699999954    4455889999999999999999999999887654221  12358999999999999988887765

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.37  E-value=9.5e-12  Score=115.04  Aligned_cols=73  Identities=22%  Similarity=0.168  Sum_probs=58.7

Q ss_pred             CCCHHHHHhh----hhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        189 SPTPIQAQAV----PAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       189 ~pt~iQ~~~i----~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .|+|.|.+.+    ..+.+|.++++.||||+|||++|++|++.++......  ..+.+++|+++|..+..|....++++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~--~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER--IQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc--ccccceeEEeccHHHHHHHHHHHHhc
Confidence            4699999954    4455889999999999999999999999887654221  12358999999999999988887765

>KOG0353|consensus

Probab=99.37  E-value=2.9e-12  Score=118.11  Aligned_cols=145  Identities=19%  Similarity=0.318  Sum_probs=108.9

Q ss_pred             CCCCCHHHHHHHHH-CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q psy17644        171 HFGFDEVLMKALRK-CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT  249 (330)
Q Consensus       171 ~~~l~~~l~~~l~~-~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt  249 (330)
                      .|+.+.+....|+. ....+++|+|..+|.+.+.|.|++++.|||.||++||.||+|-.           ...+|||+|.
T Consensus        75 ~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a-----------dg~alvi~pl  143 (695)
T KOG0353|consen   75 DFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA-----------DGFALVICPL  143 (695)
T ss_pred             CCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc-----------CCceEeechh
Confidence            34555555555543 35678999999999999999999999999999999999999853           5778999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHH---HH-hC--CCeEEEEChHHHHH---HHHc--CCCCCCCccEE
Q psy17644        250 RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK---AL-EL--GAEIVVGTPGRIID---MVKM--GATKLNRVTFL  318 (330)
Q Consensus       250 r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~---~l-~~--~~dIiV~TP~~L~~---~l~~--~~~~l~~i~~l  318 (330)
                      ..|+....-.++.+    |+....+....++.+..+   .+ .+  ...+|..||+.+..   ++++  +......+.++
T Consensus       144 islmedqil~lkql----gi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~i  219 (695)
T KOG0353|consen  144 ISLMEDQILQLKQL----GIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLI  219 (695)
T ss_pred             HHHHHHHHHHHHHh----CcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEE
Confidence            99999988888887    455555544444433211   11 11  35789999999854   3322  34456788999


Q ss_pred             EeecccccCcCC
Q psy17644        319 VLDEADRMFDMG  330 (330)
Q Consensus       319 VvDEad~lld~G  330 (330)
                      -|||+|+..+||
T Consensus       220 aidevhccsqwg  231 (695)
T KOG0353|consen  220 AIDEVHCCSQWG  231 (695)
T ss_pred             eecceeehhhhC
Confidence            999999999998

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

Probab=99.33  E-value=1.2e-11  Score=122.50  Aligned_cols=140  Identities=23%  Similarity=0.288  Sum_probs=113.4

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHhhhhhcCC------CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc
Q psy17644        174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSG------RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA  247 (330)
Q Consensus       174 l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g------~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~  247 (330)
                      ....+++.+.+.=..++|..|++++.-|...      .+-++++--|||||++.++.++..+-        +|.++..++
T Consensus       247 ~~~~l~~~~~~~LPF~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~--------~G~Q~ALMA  318 (677)
T COG1200         247 ANGELLAKFLAALPFKLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIE--------AGYQAALMA  318 (677)
T ss_pred             ccHHHHHHHHHhCCCCccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHH--------cCCeeEEec
Confidence            4445666665555557999999999988732      46788999999999999999988764        588999999


Q ss_pred             ccHHHHHHHHHHHHHhccCCCceEEEEECCCchHH---HHHHHhCC-CeEEEEChHHHHHHHHcCCCCCCCccEEEeecc
Q psy17644        248 PTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWD---QSKALELG-AEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEA  323 (330)
Q Consensus       248 Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~---~~~~l~~~-~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEa  323 (330)
                      ||--||.|.+..+.++....++++..+.|......   ....+.+| .+|||+|..-+.     ....++++.++|+||-
T Consensus       319 PTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQ-----d~V~F~~LgLVIiDEQ  393 (677)
T COG1200         319 PTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQ-----DKVEFHNLGLVIIDEQ  393 (677)
T ss_pred             cHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhh-----cceeecceeEEEEecc
Confidence            99999999999999999999999999998665433   34445555 899999975554     3455899999999999


Q ss_pred             ccc
Q psy17644        324 DRM  326 (330)
Q Consensus       324 d~l  326 (330)
                      ||.
T Consensus       394 HRF  396 (677)
T COG1200         394 HRF  396 (677)
T ss_pred             ccc
Confidence            986

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

Probab=99.33  E-value=8e-12  Score=133.29  Aligned_cols=131  Identities=21%  Similarity=0.192  Sum_probs=89.8

Q ss_pred             CCCCHHHHHhhhhhc----C-CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAAL----S-GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~----~-g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      ..++++|..+|..+.    . .+.++++++||||||.+.+ .++.++++..     ...++|||+|+++|+.|+...++.
T Consensus       412 ~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai-~li~~L~~~~-----~~~rVLfLvDR~~L~~Qa~~~F~~  485 (1123)
T PRK11448        412 LGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAI-ALMYRLLKAK-----RFRRILFLVDRSALGEQAEDAFKD  485 (1123)
T ss_pred             CCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHH-HHHHHHHhcC-----ccCeEEEEecHHHHHHHHHHHHHh
Confidence            358999999998775    2 4689999999999997744 3444555432     346999999999999999999998


Q ss_pred             hccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcC-----CCCCCCccEEEeeccccc
Q psy17644        263 FGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG-----ATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       263 l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~-----~~~l~~i~~lVvDEad~l  326 (330)
                      +....+..+..+++......  ........|+|||...|...+...     ...+..+.+||+||||+-
T Consensus       486 ~~~~~~~~~~~i~~i~~L~~--~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs  552 (1123)
T PRK11448        486 TKIEGDQTFASIYDIKGLED--KFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRG  552 (1123)
T ss_pred             cccccccchhhhhchhhhhh--hcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCC
Confidence            74322212222222111111  111234799999999987765321     134678889999999995

>TIGR00595 priA primosomal protein N'

Probab=99.33  E-value=1.1e-11  Score=122.84  Aligned_cols=102  Identities=21%  Similarity=0.276  Sum_probs=78.0

Q ss_pred             EEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHH---
Q psy17644        208 IGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS---  284 (330)
Q Consensus       208 i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~---  284 (330)
                      ++.|+||||||.+|+.. +.+++.       .+.++|||+|+++|+.|+++.+++..   +..+..++|+.+..+..   
T Consensus         1 LL~g~TGsGKT~v~l~~-i~~~l~-------~g~~vLvlvP~i~L~~Q~~~~l~~~f---~~~v~vlhs~~~~~er~~~~   69 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQA-IEKVLA-------LGKSVLVLVPEIALTPQMIQRFKYRF---GSQVAVLHSGLSDSEKLQAW   69 (505)
T ss_pred             CccCCCCCCHHHHHHHH-HHHHHH-------cCCeEEEEeCcHHHHHHHHHHHHHHh---CCcEEEEECCCCHHHHHHHH
Confidence            46799999999998654 444444       36789999999999999999998753   45677888877654432   


Q ss_pred             HHHh-CCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        285 KALE-LGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       285 ~~l~-~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ..+. ..++|||||+..+.       ..++++.+|||||+|...
T Consensus        70 ~~~~~g~~~IVVGTrsalf-------~p~~~l~lIIVDEeh~~s  106 (505)
T TIGR00595        70 RKVKNGEILVVIGTRSALF-------LPFKNLGLIIVDEEHDSS  106 (505)
T ss_pred             HHHHcCCCCEEECChHHHc-------CcccCCCEEEEECCCccc
Confidence            2233 34799999998774       357899999999999865

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

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

Probab=99.32  E-value=5.2e-12  Score=131.07  Aligned_cols=130  Identities=23%  Similarity=0.256  Sum_probs=101.8

Q ss_pred             HCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        184 KCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       184 ~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..+| .+.++|+.++-++-.|..+++|||||+|||++.-.++...+.        +|.++++.+|.++|..|.+..+...
T Consensus       115 ~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~--------~~qrviYTsPIKALsNQKyrdl~~~  185 (1041)
T COG4581         115 EYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALR--------DGQRVIYTSPIKALSNQKYRDLLAK  185 (1041)
T ss_pred             hCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHH--------cCCceEeccchhhhhhhHHHHHHHH
Confidence            3444 689999999999999999999999999999775544433322        4677999999999999999997765


Q ss_pred             ccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcC
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~  329 (330)
                      .....-.+.++.|..+.       ...+.++|.|-+.|..|+.++...+..+.+||+||+|.|-|+
T Consensus       186 fgdv~~~vGL~TGDv~I-------N~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~  244 (1041)
T COG4581         186 FGDVADMVGLMTGDVSI-------NPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDR  244 (1041)
T ss_pred             hhhhhhhccceecceee-------CCCCceEEeeHHHHHHHhccCcccccccceEEEEeeeecccc
Confidence            43321122344443332       345789999999999999999888999999999999999875

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.31  E-value=2.8e-11  Score=128.14  Aligned_cols=133  Identities=16%  Similarity=0.186  Sum_probs=93.2

Q ss_pred             CCCCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH----
Q psy17644        188 TSPTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE----  259 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~----  259 (330)
                      -.++|-|.+.+..+.    .++.+++.|+||+|||++||+|++.+...       ++.+++|-++|+.|..|++..    
T Consensus       256 ~e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~-------~~~~vvIsT~T~~LQ~Ql~~kDiP~  328 (928)
T PRK08074        256 YEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKK-------KEEPVVISTYTIQLQQQLLEKDIPL  328 (928)
T ss_pred             CcCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhc-------cCCeEEEEcCCHHHHHHHHHhhHHH
Confidence            368999999666544    77889999999999999999999876543       467899999999999999774    


Q ss_pred             HHHhccCCCceEEEEECCCc------------------------------------------------------------
Q psy17644        260 AKRFGKGYNLSVVCCYGGGS------------------------------------------------------------  279 (330)
Q Consensus       260 ~~~l~~~~~~~~~~~~gg~~------------------------------------------------------------  279 (330)
                      ++++.. .+++++++.|...                                                            
T Consensus       329 L~~~~~-~~~~~~~lKGr~nYlcl~k~~~~l~~~~~~~~~~~~~~~ll~Wl~~T~tGD~dEl~~~~~~~~~w~~i~~~~~  407 (928)
T PRK08074        329 LQKIFP-FPVEAALLKGRSHYLCLRKFEQALQEEDDNYDVALTKAQLLVWLTETETGDLDELNLPSGGKLLWNRIASDGE  407 (928)
T ss_pred             HHHHcC-CCceEEEEEcccccccHHHHHHHHhccCCCHHHHHHHHHHHHHHccCCCCCHHHccCCCCCcchHHHhhccCc
Confidence            333321 2334444443221                                                            


Q ss_pred             -------------hHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        280 -------------KWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       280 -------------~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                                   .....+.....++|||++..-|+.-+.....-+....++||||||+|-+
T Consensus       408 ~c~~~~cp~~~~Cf~~~ar~~a~~AdivItNHalLl~dl~~~~~ilp~~~~lViDEAH~l~d  469 (928)
T PRK08074        408 SDGGKQSPWFSRCFYQRAKNRAKFADLVITNHALLLTDLTSEEPLLPSYEHIIIDEAHHFEE  469 (928)
T ss_pred             ccCCCCCCcccccHHHHHHHHHhcCCEEEECHHHHHHHHhhhcccCCCCCeEEEECCchHHH
Confidence                         1111111122589999999988876643333356679999999999864

>KOG0951|consensus

Probab=99.28  E-value=7.9e-12  Score=129.07  Aligned_cols=140  Identities=19%  Similarity=0.226  Sum_probs=111.0

Q ss_pred             CCCCCCCHHHHHhhhhhcCC-CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCC---CCCCCeEEEEcccHHHHHHHHHHH
Q psy17644        185 CEYTSPTPIQAQAVPAALSG-RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE---PGDGPMGLILAPTRELSQQIYNEA  260 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g-~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~---~~~~~~vLil~Ptr~La~Qi~~~~  260 (330)
                      .|...+.++|..+.++++.+ .++++|||||+|||-..++-+|+.+-......   .....++++++|+..||+.++..+
T Consensus       305 ~g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~Vgsf  384 (1674)
T KOG0951|consen  305 FGKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSF  384 (1674)
T ss_pred             ccchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHH
Confidence            35667899999999999866 58999999999999999999999886654322   123569999999999999999999


Q ss_pred             HHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC--CCCCccEEEeecccccC
Q psy17644        261 KRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT--KLNRVTFLVLDEADRMF  327 (330)
Q Consensus       261 ~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~--~l~~i~~lVvDEad~ll  327 (330)
                      .+....+|+++.-..|......+.  + .+.+||||||+.+--+-++...  ..+-++++|+||.|.+-
T Consensus       385 SkRla~~GI~V~ElTgD~~l~~~q--i-eeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLh  450 (1674)
T KOG0951|consen  385 SKRLAPLGITVLELTGDSQLGKEQ--I-EETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLH  450 (1674)
T ss_pred             HhhccccCcEEEEecccccchhhh--h-hcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhcc
Confidence            998899999999999876533221  1 2479999999998655544322  24568999999999884

>PRK09694 helicase Cas3; Provisional

Probab=99.26  E-value=3.4e-11  Score=125.33  Aligned_cols=134  Identities=19%  Similarity=0.145  Sum_probs=89.5

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG  266 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~  266 (330)
                      ...|+|+|..+........-+|+.||||+|||.+.++.+.. ++..     +...+++|.+||++++.|++..++++.+.
T Consensus       284 ~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~-l~~~-----~~~~gi~~aLPT~Atan~m~~Rl~~~~~~  357 (878)
T PRK09694        284 GYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWR-LIDQ-----GLADSIIFALPTQATANAMLSRLEALASK  357 (878)
T ss_pred             CCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHH-HHHh-----CCCCeEEEECcHHHHHHHHHHHHHHHHHH
Confidence            45899999988655445566888899999999988776553 3332     13468999999999999999998875432


Q ss_pred             C--CceEEEEECCCchHHHH---------------------HHHh------CCCeEEEEChHHHHHHHHc-CCCCCCC--
Q psy17644        267 Y--NLSVVCCYGGGSKWDQS---------------------KALE------LGAEIVVGTPGRIIDMVKM-GATKLNR--  314 (330)
Q Consensus       267 ~--~~~~~~~~gg~~~~~~~---------------------~~l~------~~~dIiV~TP~~L~~~l~~-~~~~l~~--  314 (330)
                      .  ...+.+.+|+.......                     ..+.      .-++|+|||...++..+-. +...++.  
T Consensus       358 ~f~~~~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~~lR~~~  437 (878)
T PRK09694        358 LFPSPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIRGFG  437 (878)
T ss_pred             hcCCCceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchHHHHHHh
Confidence            2  24566666654311100                     1111      1269999999998864432 2222222  


Q ss_pred             --ccEEEeeccccc
Q psy17644        315 --VTFLVLDEADRM  326 (330)
Q Consensus       315 --i~~lVvDEad~l  326 (330)
                        -.+|||||+|..
T Consensus       438 La~svvIiDEVHAy  451 (878)
T PRK09694        438 LGRSVLIVDEVHAY  451 (878)
T ss_pred             hccCeEEEechhhC
Confidence              258999999975

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.22  E-value=3.9e-11  Score=127.84  Aligned_cols=119  Identities=18%  Similarity=0.230  Sum_probs=78.5

Q ss_pred             HHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc----cHHHHHHHHHHHHH-hccCCC
Q psy17644        194 QAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP----TRELSQQIYNEAKR-FGKGYN  268 (330)
Q Consensus       194 Q~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P----tr~La~Qi~~~~~~-l~~~~~  268 (330)
                      -.+++.++..++.++++|+||||||.  .+|.+.......     ....+++.-|    +++||.|+..++.. ++...|
T Consensus        79 r~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~lle~g~g-----~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VG  151 (1294)
T PRK11131         79 KQDILEAIRDHQVVIVAGETGSGKTT--QLPKICLELGRG-----VKGLIGHTQPRRLAARTVANRIAEELETELGGCVG  151 (1294)
T ss_pred             HHHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHcCCC-----CCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceec
Confidence            34555666677778888999999996  578543322110     1122223335    67888888888774 444333


Q ss_pred             ceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccc-ccCcCC
Q psy17644        269 LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD-RMFDMG  330 (330)
Q Consensus       269 ~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad-~lld~G  330 (330)
                      ..+    ...      .....+++|+|+|||+|+..+.... .++++++||||||| +++++|
T Consensus       152 Y~v----rf~------~~~s~~t~I~v~TpG~LL~~l~~d~-~Ls~~~~IIIDEAHERsLn~D  203 (1294)
T PRK11131        152 YKV----RFN------DQVSDNTMVKLMTDGILLAEIQQDR-LLMQYDTIIIDEAHERSLNID  203 (1294)
T ss_pred             eee----cCc------cccCCCCCEEEEChHHHHHHHhcCC-ccccCcEEEecCccccccccc
Confidence            322    111      1123468999999999999987643 48999999999999 688764

>KOG0947|consensus

Probab=99.17  E-value=1.2e-10  Score=117.98  Aligned_cols=122  Identities=20%  Similarity=0.199  Sum_probs=100.3

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      ..|.++|++||-++..|-.|++.|+|.+|||+++-.++...   +     .++.+++|-+|-++|.+|-++.++.-....
T Consensus       296 FelD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAiala---q-----~h~TR~iYTSPIKALSNQKfRDFk~tF~Dv  367 (1248)
T KOG0947|consen  296 FELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALA---Q-----KHMTRTIYTSPIKALSNQKFRDFKETFGDV  367 (1248)
T ss_pred             CCccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHH---H-----hhccceEecchhhhhccchHHHHHHhcccc
Confidence            46899999999999999999999999999997744433221   1     157889999999999999999998765543


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      |    .+.|.....       ..+.++|.|-+-|+.|+-++..-++++++||+||+|-+-|
T Consensus       368 g----LlTGDvqin-------PeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND  417 (1248)
T KOG0947|consen  368 G----LLTGDVQIN-------PEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYIND  417 (1248)
T ss_pred             c----eeecceeeC-------CCcceEeehHHHHHHHHhcccchhhccceEEEeeeeeccc
Confidence            4    566654432       3478999999999999999988899999999999998875

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.16  E-value=1.2e-10  Score=119.41  Aligned_cols=128  Identities=19%  Similarity=0.150  Sum_probs=101.1

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      -.|+++|...--++  .+--|+...||+|||+++.+|++...+.        |..|.||+||.-||.|-+.++..+...+
T Consensus        81 m~~ydVQliGg~~L--h~G~iaEM~TGEGKTLvA~l~a~l~al~--------G~~VhvvT~ndyLA~RD~e~m~~l~~~l  150 (913)
T PRK13103         81 MRHFDVQLIGGMTL--HEGKIAEMRTGEGKTLVGTLAVYLNALS--------GKGVHVVTVNDYLARRDANWMRPLYEFL  150 (913)
T ss_pred             CCcchhHHHhhhHh--ccCccccccCCCCChHHHHHHHHHHHHc--------CCCEEEEeCCHHHHHHHHHHHHHHhccc
Confidence            45667776544334  4556889999999999999999877664        7789999999999999999999999999


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcCC------CCCCCccEEEeecccccC
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMGA------TKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~~------~~l~~i~~lVvDEad~ll  327 (330)
                      |+++.++.++.........+.  |+|+++|..-| +++|+.+.      ...+.+.|+||||+|.||
T Consensus       151 Gl~v~~i~~~~~~~err~~Y~--~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        151 GLSVGIVTPFQPPEEKRAAYA--ADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSIL  215 (913)
T ss_pred             CCEEEEECCCCCHHHHHHHhc--CCEEEEcccccccchhhccceechhhhcccccceeEechhhhee
Confidence            999999988777665554444  89999999886 34443221      124789999999999987

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.15  E-value=2.5e-10  Score=114.73  Aligned_cols=129  Identities=16%  Similarity=0.125  Sum_probs=104.0

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG  266 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~  266 (330)
                      ...|++.|.-..-.++.|+  |+...||+|||++..+|++...+.        |..|.|++||.-||.|-++++..+...
T Consensus        76 g~r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~--------G~~VhvvT~NdyLA~RDae~m~~ly~~  145 (764)
T PRK12326         76 GLRPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQ--------GRRVHVITVNDYLARRDAEWMGPLYEA  145 (764)
T ss_pred             CCCcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHc--------CCCeEEEcCCHHHHHHHHHHHHHHHHh
Confidence            3468889988888888774  778999999999999999887764        778999999999999999999999999


Q ss_pred             CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcC------CCCCCCccEEEeecccccC
Q psy17644        267 YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMG------ATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       267 ~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~------~~~l~~i~~lVvDEad~ll  327 (330)
                      +|+++.++.++.+.......+  .|||+.+|..-| +++|+.+      ......+.+.||||+|.||
T Consensus       146 LGLsvg~i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiL  211 (764)
T PRK12326        146 LGLTVGWITEESTPEERRAAY--ACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVL  211 (764)
T ss_pred             cCCEEEEECCCCCHHHHHHHH--cCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhhe
Confidence            999999998887766544444  489999998765 2233221      1124568899999999987

>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=99.15  E-value=1.1e-09  Score=99.53  Aligned_cols=130  Identities=23%  Similarity=0.225  Sum_probs=100.0

Q ss_pred             CCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        186 EYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      -...|++.|..++-.+..|+  |+...||-|||++..+|++.+.+.        |..|-|++....||.+=++++..+..
T Consensus        74 ~g~~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~--------G~~V~vvT~NdyLA~RD~~~~~~~y~  143 (266)
T PF07517_consen   74 LGLRPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQ--------GKGVHVVTSNDYLAKRDAEEMRPFYE  143 (266)
T ss_dssp             TS----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTT--------SS-EEEEESSHHHHHHHHHHHHHHHH
T ss_pred             cCCcccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHh--------cCCcEEEeccHHHhhccHHHHHHHHH
Confidence            34578899988887776666  899999999999999888877764        67889999999999999999999999


Q ss_pred             CCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHH-HHHcCCC------CCCCccEEEeecccccC
Q psy17644        266 GYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIID-MVKMGAT------KLNRVTFLVLDEADRMF  327 (330)
Q Consensus       266 ~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~-~l~~~~~------~l~~i~~lVvDEad~ll  327 (330)
                      .+|+++.++.++.........+.  ++|+.+|...+.- +++....      ....+.++||||||.||
T Consensus       144 ~LGlsv~~~~~~~~~~~r~~~Y~--~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  144 FLGLSVGIITSDMSSEERREAYA--ADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             HTT--EEEEETTTEHHHHHHHHH--SSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             HhhhccccCccccCHHHHHHHHh--CcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            99999999999888655444444  5899999998753 5543211      15688999999999887

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 ....

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.13  E-value=2.8e-10  Score=116.31  Aligned_cols=129  Identities=19%  Similarity=0.196  Sum_probs=103.9

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG  266 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~  266 (330)
                      -..|++.|.-..-++..|+  |+...||+|||++..+|++...+.        |..|-|++||.-||.|-+..+..+...
T Consensus        78 g~~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~--------G~~v~vvT~neyLA~Rd~e~~~~~~~~  147 (796)
T PRK12906         78 GLRPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALT--------GKGVHVVTVNEYLSSRDATEMGELYRW  147 (796)
T ss_pred             CCCCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHc--------CCCeEEEeccHHHHHhhHHHHHHHHHh
Confidence            3468888887776666776  889999999999999999888764        778999999999999999999999999


Q ss_pred             CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHH-HHHHcC------CCCCCCccEEEeecccccC
Q psy17644        267 YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRII-DMVKMG------ATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       267 ~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~-~~l~~~------~~~l~~i~~lVvDEad~ll  327 (330)
                      +|+++.++.++.........+  .|||+.+|...|- ++++.+      ....+.+.+.||||+|.||
T Consensus       148 LGl~vg~i~~~~~~~~r~~~y--~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiL  213 (796)
T PRK12906        148 LGLTVGLNLNSMSPDEKRAAY--NCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSIL  213 (796)
T ss_pred             cCCeEEEeCCCCCHHHHHHHh--cCCCeecCCccccccchhhccccchhhhhccCcceeeeccchhee
Confidence            999999998877666544433  4799999988763 344322      1124578899999999987

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

Probab=99.10  E-value=4.9e-10  Score=114.86  Aligned_cols=125  Identities=22%  Similarity=0.223  Sum_probs=83.5

Q ss_pred             CCHHHHHhhhhhc----C------CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q psy17644        190 PTPIQAQAVPAAL----S------GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE  259 (330)
Q Consensus       190 pt~iQ~~~i~~~~----~------g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~  259 (330)
                      +.+.|..++..++    +      .+..+++.+||||||++.+..+... +..     ...+++|||+|+++|..|+.+.
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l-~~~-----~~~~~vl~lvdR~~L~~Q~~~~  312 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKA-LEL-----LKNPKVFFVVDRRELDYQLMKE  312 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHH-Hhh-----cCCCeEEEEECcHHHHHHHHHH
Confidence            6788988887764    2      3578999999999997765544332 221     2478999999999999999999


Q ss_pred             HHHhccCCCceEEEEECCCchHHHHHHHhC-CCeEEEEChHHHHHHHHcCC--CCCCC-ccEEEeeccccc
Q psy17644        260 AKRFGKGYNLSVVCCYGGGSKWDQSKALEL-GAEIVVGTPGRIIDMVKMGA--TKLNR-VTFLVLDEADRM  326 (330)
Q Consensus       260 ~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~-~~dIiV~TP~~L~~~l~~~~--~~l~~-i~~lVvDEad~l  326 (330)
                      +..++...      ..+..+.......+.. ...|+|+|...|...+....  ....+ --+||+||||+.
T Consensus       313 f~~~~~~~------~~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs  377 (667)
T TIGR00348       313 FQSLQKDC------AERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRS  377 (667)
T ss_pred             HHhhCCCC------CcccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccc
Confidence            99985321      1111223333333333 36899999999986543221  11111 128999999986

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

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

Probab=99.05  E-value=3.8e-09  Score=110.35  Aligned_cols=142  Identities=26%  Similarity=0.297  Sum_probs=112.2

Q ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHhhhhhc----CC--CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        172 FGFDEVLMKALRKCEYTSPTPIQAQAVPAAL----SG--RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       172 ~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~----~g--~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      |..+......+...-...-|+-|..||..+.    ++  .|-++||--|-|||-+.+=++...++        +|.+|.|
T Consensus       577 f~~d~~~q~~F~~~FPyeET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~--------~GKQVAv  648 (1139)
T COG1197         577 FPPDTEWQEEFEASFPYEETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVM--------DGKQVAV  648 (1139)
T ss_pred             CCCChHHHHHHHhcCCCcCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhc--------CCCeEEE
Confidence            3445556666666555568999999999986    34  58999999999999887777766654        5899999


Q ss_pred             EcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCCccEEEee
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLD  321 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvD  321 (330)
                      ||||.-||+|.++.++.-..++++++..+..-.+..++...   ++. ..||||||..-|.     +...++++.+||||
T Consensus       649 LVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~-----kdv~FkdLGLlIID  723 (1139)
T COG1197         649 LVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLS-----KDVKFKDLGLLIID  723 (1139)
T ss_pred             EcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhC-----CCcEEecCCeEEEe
Confidence            99999999999999999889999999888776666665443   444 4899999964333     45668999999999


Q ss_pred             ccccc
Q psy17644        322 EADRM  326 (330)
Q Consensus       322 Ead~l  326 (330)
                      |=|+.
T Consensus       724 EEqRF  728 (1139)
T COG1197         724 EEQRF  728 (1139)
T ss_pred             chhhc
Confidence            99985

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.03  E-value=3e-09  Score=109.52  Aligned_cols=65  Identities=23%  Similarity=0.232  Sum_probs=52.6

Q ss_pred             CCCCHHHHHhhhhhc---C------CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAAL---S------GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~---~------g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      -.+++-|.+.+..+.   +      ++.+++.|+||+|||++||+|++.+...       ++.+|||-+.|+.|-.|+..
T Consensus        24 ~e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~-------~~k~vVIST~T~~LQeQL~~   96 (697)
T PRK11747         24 FIPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARA-------EKKKLVISTATVALQEQLVS   96 (697)
T ss_pred             CCcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHH-------cCCeEEEEcCCHHHHHHHHh
Confidence            368899998665554   3      3667888999999999999999877664       35789999999999999965


Q ss_pred             H
Q psy17644        259 E  259 (330)
Q Consensus       259 ~  259 (330)
                      .
T Consensus        97 k   97 (697)
T PRK11747         97 K   97 (697)
T ss_pred             h
Confidence            4

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=99.01  E-value=2.4e-09  Score=109.95  Aligned_cols=73  Identities=27%  Similarity=0.369  Sum_probs=60.8

Q ss_pred             HCCCCCCCHHHHHhhhhh----cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q psy17644        184 KCEYTSPTPIQAQAVPAA----LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE  259 (330)
Q Consensus       184 ~~~~~~pt~iQ~~~i~~~----~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~  259 (330)
                      ...+..|++.|.+.+..+    .+++.+++.||||+|||++||+|++.+...       .+.+++|.++|+.|-.|+++.
T Consensus        10 ~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~-------~~~~viist~t~~lq~q~~~~   82 (654)
T COG1199          10 AFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYARE-------EGKKVIISTRTKALQEQLLEE   82 (654)
T ss_pred             hCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHH-------cCCcEEEECCCHHHHHHHHHh
Confidence            345668999999988654    366679999999999999999999998766       357899999999999999888


Q ss_pred             HHHh
Q psy17644        260 AKRF  263 (330)
Q Consensus       260 ~~~l  263 (330)
                      ...+
T Consensus        83 ~~~~   86 (654)
T COG1199          83 DLPI   86 (654)
T ss_pred             hcch
Confidence            6554

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.97  E-value=3.8e-09  Score=109.26  Aligned_cols=73  Identities=18%  Similarity=0.175  Sum_probs=61.2

Q ss_pred             CCCCCCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH
Q psy17644        186 EYTSPTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK  261 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~  261 (330)
                      -|..++|.|.+.+..+.    .|.++++.+|||+|||++.|.|+|.++....     ..++++|.+.|..-..|+.++++
T Consensus         7 Py~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~-----~~~kIiy~sRThsQl~q~i~Elk   81 (705)
T TIGR00604         7 PYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP-----EVRKIIYASRTHSQLEQATEELR   81 (705)
T ss_pred             CCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc-----ccccEEEEcccchHHHHHHHHHH
Confidence            35566899998886654    7899999999999999999999998876432     34789999999999999999998


Q ss_pred             Hh
Q psy17644        262 RF  263 (330)
Q Consensus       262 ~l  263 (330)
                      ++
T Consensus        82 ~~   83 (705)
T TIGR00604        82 KL   83 (705)
T ss_pred             hh
Confidence            85

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).

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

Probab=98.97  E-value=4e-09  Score=97.27  Aligned_cols=116  Identities=21%  Similarity=0.178  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWD  282 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~  282 (330)
                      ..+.++++..+|.|||+..+.-+ .++......  .....+|||||. .+..||..++.+++.....++..+.|+.....
T Consensus        24 ~~~g~lL~de~GlGKT~~~i~~~-~~l~~~~~~--~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v~~~~~~~~~~~   99 (299)
T PF00176_consen   24 PPRGGLLADEMGLGKTITAIALI-SYLKNEFPQ--RGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRVIIYDGDSERRR   99 (299)
T ss_dssp             TT-EEEE---TTSSHHHHHHHHH-HHHHHCCTT--SS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-EEEESSSCHHHH
T ss_pred             CCCCEEEEECCCCCchhhhhhhh-hhhhhcccc--ccccceeEeecc-chhhhhhhhhcccccccccccccccccccccc
Confidence            55788899999999996665433 334332210  011248999999 88899999999998654556555555441222


Q ss_pred             HHHHHhCCCeEEEEChHHHH--------HHHHcCCCCCCCccEEEeecccccC
Q psy17644        283 QSKALELGAEIVVGTPGRII--------DMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       283 ~~~~l~~~~dIiV~TP~~L~--------~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      .........+|+|+|...+.        ..+..     -.+.+|||||+|.+-
T Consensus       100 ~~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~-----~~~~~vIvDEaH~~k  147 (299)
T PF00176_consen  100 LSKNQLPKYDVVITTYETLRKARKKKDKEDLKQ-----IKWDRVIVDEAHRLK  147 (299)
T ss_dssp             TTSSSCCCSSEEEEEHHHHH--TSTHTTHHHHT-----SEEEEEEETTGGGGT
T ss_pred             ccccccccceeeecccccccccccccccccccc-----ccceeEEEecccccc
Confidence            22222335799999999998        22222     348999999999983

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.

>KOG0948|consensus

Probab=98.93  E-value=2.7e-09  Score=105.94  Aligned_cols=123  Identities=23%  Similarity=0.252  Sum_probs=100.0

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG  266 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~  266 (330)
                      ...+.|+|..+|-.+-++..+++.|.|.+|||+++-.++...+.        ++.+||+-.|-++|.+|-|+++..=.+.
T Consensus       127 PF~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr--------~kQRVIYTSPIKALSNQKYREl~~EF~D  198 (1041)
T KOG0948|consen  127 PFTLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLR--------EKQRVIYTSPIKALSNQKYRELLEEFKD  198 (1041)
T ss_pred             CcccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHH--------hcCeEEeeChhhhhcchhHHHHHHHhcc
Confidence            34688999999999999999999999999999776555544443        3578999999999999999998764443


Q ss_pred             CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        267 YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       267 ~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                          +.+..|..+.       ...+..+|.|-+-|..|+-++.--++.|.+||+||+|-|=|
T Consensus       199 ----VGLMTGDVTI-------nP~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRD  249 (1041)
T KOG0948|consen  199 ----VGLMTGDVTI-------NPDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRD  249 (1041)
T ss_pred             ----cceeecceee-------CCCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccc
Confidence                3344454443       23467899999999999998888899999999999999865

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.92  E-value=2.6e-09  Score=109.34  Aligned_cols=127  Identities=18%  Similarity=0.141  Sum_probs=98.9

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCC
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN  268 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~  268 (330)
                      .|++.|.-..  +.-.+..|+...||.|||+++.+|++...+.        |..|-||+++..||.+-++++..+...+|
T Consensus        76 r~ydvQlig~--l~L~~G~IaEm~TGEGKTL~a~l~ayl~aL~--------G~~VhVvT~NdyLA~RD~e~m~pvy~~LG  145 (870)
T CHL00122         76 RHFDVQLIGG--LVLNDGKIAEMKTGEGKTLVATLPAYLNALT--------GKGVHIVTVNDYLAKRDQEWMGQIYRFLG  145 (870)
T ss_pred             CCCchHhhhh--HhhcCCccccccCCCCchHHHHHHHHHHHhc--------CCceEEEeCCHHHHHHHHHHHHHHHHHcC
Confidence            4777776544  4445667899999999999999999766553        67889999999999999999999999999


Q ss_pred             ceEEEEECCCchHHHHHHHhCCCeEEEEChHHHH-HHHHcC------CCCCCCccEEEeecccccC
Q psy17644        269 LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRII-DMVKMG------ATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       269 ~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~-~~l~~~------~~~l~~i~~lVvDEad~ll  327 (330)
                      +.+.++.++.+.......+  .|||+.+|..-|- ++++.+      ....+.+.+.||||+|.||
T Consensus       146 Lsvg~i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiL  209 (870)
T CHL00122        146 LTVGLIQEGMSSEERKKNY--LKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSIL  209 (870)
T ss_pred             CceeeeCCCCChHHHHHhc--CCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhhe
Confidence            9999988887776544444  4799999987542 333322      1124678999999999987

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.92  E-value=5.2e-09  Score=107.19  Aligned_cols=128  Identities=18%  Similarity=0.139  Sum_probs=100.3

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      ..|+++|...--++  .+--|+...||.|||+++.+|++...+.        |..|-||+++..||.+-++++..+.+.+
T Consensus        84 ~r~ydVQliGgl~L--h~G~IAEM~TGEGKTL~atlpaylnAL~--------GkgVhVVTvNdYLA~RDae~m~~vy~~L  153 (939)
T PRK12902         84 MRHFDVQLIGGMVL--HEGQIAEMKTGEGKTLVATLPSYLNALT--------GKGVHVVTVNDYLARRDAEWMGQVHRFL  153 (939)
T ss_pred             CCcchhHHHhhhhh--cCCceeeecCCCChhHHHHHHHHHHhhc--------CCCeEEEeCCHHHHHhHHHHHHHHHHHh
Confidence            35666665544444  4556889999999999999999887664        6778999999999999999999999999


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-----HHHHHcC--CCCCCCccEEEeecccccC
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-----IDMVKMG--ATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-----~~~l~~~--~~~l~~i~~lVvDEad~ll  327 (330)
                      |+.+.++.++........  .-.|||+.||+..|     .+.+...  ....+.+.+.||||+|.||
T Consensus       154 GLtvg~i~~~~~~~err~--aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSIL  218 (939)
T PRK12902        154 GLSVGLIQQDMSPEERKK--NYACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSIL  218 (939)
T ss_pred             CCeEEEECCCCChHHHHH--hcCCCeEEecCCcccccchhhhhcccccccccCccceEEEeccccee
Confidence            999999888776654433  33689999999987     4444321  2235788999999999987

>KOG0949|consensus

Probab=98.92  E-value=2.5e-09  Score=108.78  Aligned_cols=132  Identities=16%  Similarity=0.206  Sum_probs=97.5

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc-CC
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK-GY  267 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~-~~  267 (330)
                      .|..||...+..+-.+..++++|||.+|||.+--- ++..++..     .....||+++||++|+.|+...+..... .+
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY-~iEKVLRe-----sD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t  584 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFY-AIEKVLRE-----SDSDVVIYVAPTKALVNQVSANVYARFDTKT  584 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceeccHH-HHHHHHhh-----cCCCEEEEecchHHHhhhhhHHHHHhhccCc
Confidence            58899999999999999999999999999965322 33333332     3568899999999999999988776542 22


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHc---CCCCCCCccEEEeecccccCc
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKM---GATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~---~~~~l~~i~~lVvDEad~lld  328 (330)
                      -.+.+.+.|..+...+..  .-+|+|+|+-|..|..++..   ......+++++|+||+|.+-.
T Consensus       585 ~~rg~sl~g~ltqEYsin--p~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~  646 (1330)
T KOG0949|consen  585 FLRGVSLLGDLTQEYSIN--PWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGN  646 (1330)
T ss_pred             cccchhhHhhhhHHhcCC--chhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccc
Confidence            233344444333333222  22599999999999998876   344578999999999999863

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=98.90  E-value=1.1e-08  Score=109.63  Aligned_cols=120  Identities=18%  Similarity=0.206  Sum_probs=76.7

Q ss_pred             HhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH-hccCCCceEEEE
Q psy17644        196 QAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR-FGKGYNLSVVCC  274 (330)
Q Consensus       196 ~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~-l~~~~~~~~~~~  274 (330)
                      +++..+.+++-+|++|+||||||.  .+|.+..-...     +...++++.-|.|-.|..+...+.. ++...|..+...
T Consensus        74 ~Il~~l~~~~vvii~g~TGSGKTT--qlPq~lle~~~-----~~~~~I~~tQPRRlAA~svA~RvA~elg~~lG~~VGY~  146 (1283)
T TIGR01967        74 DIAEAIAENQVVIIAGETGSGKTT--QLPKICLELGR-----GSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYK  146 (1283)
T ss_pred             HHHHHHHhCceEEEeCCCCCCcHH--HHHHHHHHcCC-----CCCceEecCCccHHHHHHHHHHHHHHhCCCcceEEeeE
Confidence            455555566778888999999996  45655332211     1123555566888777777666544 322233333222


Q ss_pred             ECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccc-ccCcC
Q psy17644        275 YGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD-RMFDM  329 (330)
Q Consensus       275 ~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad-~lld~  329 (330)
                      +.....      ...+..|+|+|+|.|+..+.... .++++.+||||||| +++++
T Consensus       147 vR~~~~------~s~~T~I~~~TdGiLLr~l~~d~-~L~~~~~IIIDEaHERsL~~  195 (1283)
T TIGR01967       147 VRFHDQ------VSSNTLVKLMTDGILLAETQQDR-FLSRYDTIIIDEAHERSLNI  195 (1283)
T ss_pred             EcCCcc------cCCCceeeeccccHHHHHhhhCc-ccccCcEEEEcCcchhhccc
Confidence            221111      23457899999999999886543 48999999999999 67765

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.

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

Probab=98.87  E-value=7.2e-09  Score=104.54  Aligned_cols=123  Identities=21%  Similarity=0.202  Sum_probs=87.8

Q ss_pred             CCCCHHHHHhhhhhc----CC-CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAAL----SG-RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~----~g-~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      ..|+.+|..||..+.    +| +-+++++.||+|||.+.. .++.++++..     .-.+||+|+-++.|+.|.+..+..
T Consensus       164 i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAi-aii~rL~r~~-----~~KRVLFLaDR~~Lv~QA~~af~~  237 (875)
T COG4096         164 IGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAI-AIIDRLIKSG-----WVKRVLFLADRNALVDQAYGAFED  237 (875)
T ss_pred             ccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHH-HHHHHHHhcc-----hhheeeEEechHHHHHHHHHHHHH
Confidence            357899999998765    44 348888999999995543 3444444432     357899999999999999999888


Q ss_pred             hccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcC-----CCCCCCccEEEeecccc
Q psy17644        263 FGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG-----ATKLNRVTFLVLDEADR  325 (330)
Q Consensus       263 l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~-----~~~l~~i~~lVvDEad~  325 (330)
                      +... +..+..+.+-...        ..++|.|+|...+...+...     .+....++++|||||||
T Consensus       238 ~~P~-~~~~n~i~~~~~~--------~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHR  296 (875)
T COG4096         238 FLPF-GTKMNKIEDKKGD--------TSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHR  296 (875)
T ss_pred             hCCC-ccceeeeecccCC--------cceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhh
Confidence            7654 2233333321111        14799999999999988654     22244589999999997

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=98.84  E-value=3.3e-08  Score=104.51  Aligned_cols=129  Identities=21%  Similarity=0.197  Sum_probs=87.6

Q ss_pred             CCCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        189 SPTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .+.++|.+++..++    +|.+.|++-.+|.|||+..+ .++.++...+    +....+|||||. .++.||..++.+|+
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaI-alL~~L~~~~----~~~gp~LIVvP~-SlL~nW~~Ei~kw~  242 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTI-SLLGYLHEYR----GITGPHMVVAPK-STLGNWMNEIRRFC  242 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHH-HHHHHHHHhc----CCCCCEEEEeCh-HHHHHHHHHHHHHC
Confidence            57899999998875    68889999999999997543 3334443321    123457999997 66799999999997


Q ss_pred             cCCCceEEEEECCCchHHHHH--H-HhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSK--A-LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~--~-l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ..  ++++.++|.........  . .....+|||+|+..+.....  .+.--.+.+|||||||+|-
T Consensus       243 p~--l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~--~L~k~~W~~VIvDEAHrIK  304 (1033)
T PLN03142        243 PV--LRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKT--ALKRFSWRYIIIDEAHRIK  304 (1033)
T ss_pred             CC--CceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHH--HhccCCCCEEEEcCccccC
Confidence            53  45555555433222211  1 12357999999998865432  1222357899999999974

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

Probab=98.84  E-value=1.3e-08  Score=83.20  Aligned_cols=105  Identities=17%  Similarity=0.159  Sum_probs=69.2

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWD  282 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~  282 (330)
                      .|+-.++-..+|+|||.-.+.-++...++       .+.++|||.|||.++..+.+.++..    ++++....-+.    
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~-------~~~rvLvL~PTRvva~em~~aL~~~----~~~~~t~~~~~----   67 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIK-------RRLRVLVLAPTRVVAEEMYEALKGL----PVRFHTNARMR----   67 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHH-------TT--EEEEESSHHHHHHHHHHTTTS----SEEEESTTSS-----
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHH-------ccCeEEEecccHHHHHHHHHHHhcC----CcccCceeeec----
Confidence            34556777899999997777667776666       3678999999999999988887654    33333211111    


Q ss_pred             HHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        283 QSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       283 ~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                         ....+.-|-|.|...+..++.+ ...+.+.+++|+||||.+
T Consensus        68 ---~~~g~~~i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~  107 (148)
T PF07652_consen   68 ---THFGSSIIDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFT  107 (148)
T ss_dssp             ------SSSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--
T ss_pred             ---cccCCCcccccccHHHHHHhcC-cccccCccEEEEeccccC
Confidence               1123456778899988887765 555789999999999974

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 ....

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

Probab=98.82  E-value=3.8e-08  Score=90.34  Aligned_cols=115  Identities=23%  Similarity=0.358  Sum_probs=92.2

Q ss_pred             CCCCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        188 TSPTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .++||.|+.+-..+.    +.+++++.|-||+|||-. +.+.+..++.       +|.++.|.+|....|..++..++.-
T Consensus        96 G~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~-------~G~~vciASPRvDVclEl~~Rlk~a  167 (441)
T COG4098          96 GTLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALN-------QGGRVCIASPRVDVCLELYPRLKQA  167 (441)
T ss_pred             cccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHh-------cCCeEEEecCcccchHHHHHHHHHh
Confidence            368899988776654    678999999999999943 3346666666       5889999999999999999999876


Q ss_pred             ccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      ..  +..+.++||+.....+       +.+||||--.|+.+..       .++++||||+|..
T Consensus       168 F~--~~~I~~Lyg~S~~~fr-------~plvVaTtHQLlrFk~-------aFD~liIDEVDAF  214 (441)
T COG4098         168 FS--NCDIDLLYGDSDSYFR-------APLVVATTHQLLRFKQ-------AFDLLIIDEVDAF  214 (441)
T ss_pred             hc--cCCeeeEecCCchhcc-------ccEEEEehHHHHHHHh-------hccEEEEeccccc
Confidence            44  4677889998766543       6899999888887764       6789999999974

>KOG1002|consensus

Probab=98.80  E-value=7.7e-08  Score=91.98  Aligned_cols=127  Identities=26%  Similarity=0.233  Sum_probs=87.8

Q ss_pred             CCCHHHHHhhhhhcCC-----CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        189 SPTPIQAQAVPAALSG-----RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g-----~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .+-|+|++.+-.+...     ...|+.-..|.|||.-.+.-+|.    ..     .+...|||+|+.+| .||.+++.++
T Consensus       184 ~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLlla----e~-----~ra~tLVvaP~VAl-mQW~nEI~~~  253 (791)
T KOG1002|consen  184 PLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLA----EV-----DRAPTLVVAPTVAL-MQWKNEIERH  253 (791)
T ss_pred             cchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHh----cc-----ccCCeeEEccHHHH-HHHHHHHHHh
Confidence            3457888877766532     34567778999999654433333    21     23448999999988 7999999998


Q ss_pred             ccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC-------------CCCC--ccEEEeecccccCc
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT-------------KLNR--VTFLVLDEADRMFD  328 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~-------------~l~~--i~~lVvDEad~lld  328 (330)
                      ..  |...+.+|.|.......+.+.+ .|++++|...+-...++...             -|.+  +..+|+||||.+-+
T Consensus       254 T~--gslkv~~YhG~~R~~nikel~~-YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~IK~  330 (791)
T KOG1002|consen  254 TS--GSLKVYIYHGAKRDKNIKELMN-YDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNIKD  330 (791)
T ss_pred             cc--CceEEEEEecccccCCHHHhhc-CcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhhccccc
Confidence            76  4444556666666555666655 89999999999887764211             1344  45789999998754

>KOG0950|consensus

Probab=98.78  E-value=1.3e-08  Score=103.76  Aligned_cols=146  Identities=16%  Similarity=0.159  Sum_probs=115.4

Q ss_pred             CCHHHHHH-HHHCCCCCCCHHHHHhh--hhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q psy17644        174 FDEVLMKA-LRKCEYTSPTPIQAQAV--PAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR  250 (330)
Q Consensus       174 l~~~l~~~-l~~~~~~~pt~iQ~~~i--~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr  250 (330)
                      +++.+... ....|..++..+|..++  |.++.++++|+.+||+.|||++.-+-++..++..+       ..++.++|..
T Consensus       207 ~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~r-------r~~llilp~v  279 (1008)
T KOG0950|consen  207 LPTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRR-------RNVLLILPYV  279 (1008)
T ss_pred             CchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHh-------hceeEeccee
Confidence            34444433 45568888999999987  56779999999999999999999999999988754       4689999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcC--CCCCCCccEEEeecccccCc
Q psy17644        251 ELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG--ATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       251 ~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~--~~~l~~i~~lVvDEad~lld  328 (330)
                      ..+..-...+..|+...|+.+-+.+|+.......    +.-+|.|||-++-..+++.-  ...+..+.+|||||.|.+.|
T Consensus       280 siv~Ek~~~l~~~~~~~G~~ve~y~g~~~p~~~~----k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d  355 (1008)
T KOG0950|consen  280 SIVQEKISALSPFSIDLGFPVEEYAGRFPPEKRR----KRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGD  355 (1008)
T ss_pred             ehhHHHHhhhhhhccccCCcchhhcccCCCCCcc----cceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeec
Confidence            9988888889999999999887777655543322    23589999999887777542  33577899999999999987


Q ss_pred             CC
Q psy17644        329 MG  330 (330)
Q Consensus       329 ~G  330 (330)
                      -|
T Consensus       356 ~~  357 (1008)
T KOG0950|consen  356 KG  357 (1008)
T ss_pred             cc
Confidence            54

>KOG0385|consensus

Probab=98.78  E-value=4.1e-08  Score=98.01  Aligned_cols=130  Identities=25%  Similarity=0.260  Sum_probs=88.6

Q ss_pred             CCCCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        188 TSPTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..++++|.+.+..+.    +|-+.|+.-.+|-|||+- .+.+|.++...+.   ..||. ||+||...| ..|.+++++|
T Consensus       166 g~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQ-tIs~l~yl~~~~~---~~GPf-LVi~P~StL-~NW~~Ef~rf  239 (971)
T KOG0385|consen  166 GELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQ-TISLLGYLKGRKG---IPGPF-LVIAPKSTL-DNWMNEFKRF  239 (971)
T ss_pred             CccchhhhccHHHHHHHHhcCcccEeehhcccchHHH-HHHHHHHHHHhcC---CCCCe-EEEeeHhhH-HHHHHHHHHh
Confidence            357889999888775    788999999999999943 3334444433211   24564 899998777 6789999999


Q ss_pred             ccCCCceEEEEECCCchHHH--HHHHh-CCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQ--SKALE-LGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~--~~~l~-~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      +..  +.+++++|....+..  ...+. ...+|+|+|.+..+.-  +..+.--.++|+||||||||-
T Consensus       240 ~P~--l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~d--k~~lk~~~W~ylvIDEaHRiK  302 (971)
T KOG0385|consen  240 TPS--LNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKD--KSFLKKFNWRYLVIDEAHRIK  302 (971)
T ss_pred             CCC--cceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhh--HHHHhcCCceEEEechhhhhc
Confidence            874  667777775532221  11122 2579999999877653  112223467999999999984

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

Probab=98.74  E-value=4.7e-08  Score=99.61  Aligned_cols=120  Identities=24%  Similarity=0.310  Sum_probs=94.1

Q ss_pred             CCCCHHHHHhhhhhcCC----CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        188 TSPTPIQAQAVPAALSG----RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g----~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..+++-|..++..+...    +-.++.+.||||||-+|+ .++..++.       .|..||||+|-..|-.|+...++..
T Consensus       197 ~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl-~~i~~~L~-------~GkqvLvLVPEI~Ltpq~~~rf~~r  268 (730)
T COG1198         197 LALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYL-EAIAKVLA-------QGKQVLVLVPEIALTPQLLARFKAR  268 (730)
T ss_pred             cccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHH-HHHHHHHH-------cCCEEEEEeccccchHHHHHHHHHH
Confidence            35678899999988754    677888999999998886 45556665       4789999999999999999998876


Q ss_pred             ccCCCceEEEEECCCchHHH----HHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQ----SKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~----~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      .   +.++..+++|.+..+.    .+.....+.|||||-..|+       ..|+++.++||||=|-
T Consensus       269 F---g~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF-------~Pf~~LGLIIvDEEHD  324 (730)
T COG1198         269 F---GAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALF-------LPFKNLGLIIVDEEHD  324 (730)
T ss_pred             h---CCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhc-------CchhhccEEEEecccc
Confidence            4   4677888887775443    3334456899999976655       4578999999999884

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=98.71  E-value=7.3e-08  Score=101.43  Aligned_cols=130  Identities=18%  Similarity=0.086  Sum_probs=81.7

Q ss_pred             CCCCHHHHHhhhhhcC--CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        188 TSPTPIQAQAVPAALS--GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~--g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      ..|.|+|..++..++.  ...+++.-.+|.|||+-..+.+-..+...      ...++|||||+ .|+.||..++.+.. 
T Consensus       151 ~~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g------~~~rvLIVvP~-sL~~QW~~El~~kF-  222 (956)
T PRK04914        151 ASLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG------RAERVLILVPE-TLQHQWLVEMLRRF-  222 (956)
T ss_pred             CCCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC------CCCcEEEEcCH-HHHHHHHHHHHHHh-
Confidence            3588999998877653  24688889999999977765444333321      23579999998 89999999986542 


Q ss_pred             CCCceEEEEECCCchHHHHH--HHhCCCeEEEEChHHHHHHHH-cCCCCCCCccEEEeecccccC
Q psy17644        266 GYNLSVVCCYGGGSKWDQSK--ALELGAEIVVGTPGRIIDMVK-MGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       266 ~~~~~~~~~~gg~~~~~~~~--~l~~~~dIiV~TP~~L~~~l~-~~~~~l~~i~~lVvDEad~ll  327 (330)
                        ++.+..+-++........  ..-...+++|||...+...-. .....-..+++|||||||++-
T Consensus       223 --~l~~~i~~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk  285 (956)
T PRK04914        223 --NLRFSLFDEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLV  285 (956)
T ss_pred             --CCCeEEEcCcchhhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhc
Confidence              344433322221110000  001136899999887764111 011112468999999999984

>KOG0951|consensus

Probab=98.68  E-value=5.6e-08  Score=101.30  Aligned_cols=123  Identities=24%  Similarity=0.341  Sum_probs=94.9

Q ss_pred             CCCCHHHHHhhhhhcCCC-cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH-Hhcc
Q psy17644        188 TSPTPIQAQAVPAALSGR-DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK-RFGK  265 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~-d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~-~l~~  265 (330)
                      ....|+|.++++.+.+.+ ++++++|+|||||++.-+++++         +.+..++++++|..+.+..++..+. +|..
T Consensus      1142 ~~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~---------~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~ 1212 (1674)
T KOG0951|consen 1142 QDFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR---------PDTIGRAVYIAPLEEIADEQYRDWEKKFSK 1212 (1674)
T ss_pred             cccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC---------CccceEEEEecchHHHHHHHHHHHHHhhcc
Confidence            345899999999998665 5777799999999998887775         1356899999999999988888765 5666


Q ss_pred             CCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        266 GYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       266 ~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ..|..++.+.|..+..  .+.+. ..+|||+||.++-.+ +    ..+.+++.|.||+|.+.
T Consensus      1213 ~~G~~~~~l~ge~s~~--lkl~~-~~~vii~tpe~~d~l-q----~iQ~v~l~i~d~lh~ig 1266 (1674)
T KOG0951|consen 1213 LLGLRIVKLTGETSLD--LKLLQ-KGQVIISTPEQWDLL-Q----SIQQVDLFIVDELHLIG 1266 (1674)
T ss_pred             ccCceEEecCCccccc--hHHhh-hcceEEechhHHHHH-h----hhhhcceEeeehhhhhc
Confidence            6677766666554432  23333 359999999999766 1    67889999999999886

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.66  E-value=1.6e-07  Score=96.24  Aligned_cols=128  Identities=19%  Similarity=0.183  Sum_probs=100.7

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      ..|+++|.-..-++..|  -|+...||-|||++..+|+..+.+.        |..|-||+...-||..=..++..+...+
T Consensus        77 ~r~ydVQliGglvLh~G--~IAEMkTGEGKTLvAtLpayLnAL~--------GkgVhVVTvNdYLA~RDae~mg~vy~fL  146 (925)
T PRK12903         77 KRPYDVQIIGGIILDLG--SVAEMKTGEGKTITSIAPVYLNALT--------GKGVIVSTVNEYLAERDAEEMGKVFNFL  146 (925)
T ss_pred             CCcCchHHHHHHHHhcC--CeeeecCCCCccHHHHHHHHHHHhc--------CCceEEEecchhhhhhhHHHHHHHHHHh
Confidence            46788887766666565  4788999999999999999876654        6678888999999999999999999999


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcCC------CCCCCccEEEeecccccC
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMGA------TKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~~------~~l~~i~~lVvDEad~ll  327 (330)
                      |+.+.++..+.........+  .|||+.+|..-| +++|+.+-      .-.+.+.|.||||+|.||
T Consensus       147 GLsvG~i~~~~~~~~rr~aY--~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSIL  211 (925)
T PRK12903        147 GLSVGINKANMDPNLKREAY--ACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSIL  211 (925)
T ss_pred             CCceeeeCCCCChHHHHHhc--cCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchhee
Confidence            99999988877766544444  489999998775 33444321      124678899999999987

>COG4889 Predicted helicase [General function prediction only]

Probab=98.65  E-value=6.1e-08  Score=97.98  Aligned_cols=147  Identities=20%  Similarity=0.206  Sum_probs=97.5

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCC-----CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCC
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG-----RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGP  241 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g-----~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~  241 (330)
                      -.|+.+.. .++..++.-+.-.+|+|+|++++...+.|     |.-++. ..|+|||++.|-.+ ..+         ...
T Consensus       140 IDW~~f~p-~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIM-AcGTGKTfTsLkis-Eal---------a~~  207 (1518)
T COG4889         140 IDWDIFDP-TELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIM-ACGTGKTFTSLKIS-EAL---------AAA  207 (1518)
T ss_pred             CChhhcCc-cccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEE-ecCCCccchHHHHH-HHH---------hhh
Confidence            34666554 45566666667789999999999998854     334443 47999997765322 222         236


Q ss_pred             eEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCc--------------------hHH-----HHHHHhCCCeEEEE
Q psy17644        242 MGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGS--------------------KWD-----QSKALELGAEIVVG  296 (330)
Q Consensus       242 ~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~--------------------~~~-----~~~~l~~~~dIiV~  296 (330)
                      ++|+|+|+..|..|..+++..-. .+.++...+.+...                    ...     ..+....+--||++
T Consensus       208 ~iL~LvPSIsLLsQTlrew~~~~-~l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFs  286 (1518)
T COG4889         208 RILFLVPSISLLSQTLREWTAQK-ELDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFS  286 (1518)
T ss_pred             heEeecchHHHHHHHHHHHhhcc-CccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEE
Confidence            78999999999999988876532 22333333322110                    000     01112235679999


Q ss_pred             ChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        297 TPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       297 TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      |...+..+-......+..++++|.|||||-
T Consensus       287 TYQSl~~i~eAQe~G~~~fDliicDEAHRT  316 (1518)
T COG4889         287 TYQSLPRIKEAQEAGLDEFDLIICDEAHRT  316 (1518)
T ss_pred             cccchHHHHHHHHcCCCCccEEEecchhcc
Confidence            999998887766667889999999999984

>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=98.59  E-value=2e-08  Score=96.92  Aligned_cols=89  Identities=17%  Similarity=0.234  Sum_probs=62.4

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCC-------------C-------------------ceEEEEECCCchHHHHHH
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGY-------------N-------------------LSVVCCYGGGSKWDQSKA  286 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~-------------~-------------------~~~~~~~gg~~~~~~~~~  286 (330)
                      ..|+||||+|+|..|.++++.+.+++...             +                   .....+++|+....+.-.
T Consensus        36 tRPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~FrlG  115 (442)
T PF06862_consen   36 TRPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDCFRLG  115 (442)
T ss_pred             CCceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccceEEEe
Confidence            35999999999999999999998876531             1                   011112233332222111


Q ss_pred             Hh------------CCCeEEEEChHHHHHHHHc------CCCCCCCccEEEeecccccC
Q psy17644        287 LE------------LGAEIVVGTPGRIIDMVKM------GATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       287 l~------------~~~dIiV~TP~~L~~~l~~------~~~~l~~i~~lVvDEad~ll  327 (330)
                      ++            .++|||||||.+|...+..      ....|++|+++|||.||.|+
T Consensus       116 ik~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~  174 (442)
T PF06862_consen  116 IKFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLL  174 (442)
T ss_pred             EEEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHH
Confidence            11            1689999999999999974      23459999999999999886

; GO: 0005634 nucleus

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=98.58  E-value=3.4e-07  Score=80.97  Aligned_cols=72  Identities=19%  Similarity=0.311  Sum_probs=50.7

Q ss_pred             CCHHHHHhhhhhcCCCc-EEEEcCCCChhHHHHHHHHHHHHHhcC-CCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        190 PTPIQAQAVPAALSGRD-IIGVAKTGSGKTGAFIWPMLVHIMDQK-ELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       190 pt~iQ~~~i~~~~~g~d-~i~~a~TGsGKT~a~llp~l~~i~~~~-~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      +.+-|..++..+++... .++.||.|+|||. .+..++.++.... ......+.++||++||...+..+...+.+
T Consensus         2 ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~-~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    2 LNESQREAIQSALSSNGITLIQGPPGTGKTT-TLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             --HHHHHHHHHHCTSSE-EEEE-STTSSHHH-HHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHcCCCCEEEECCCCCChHH-HHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            56889999999999998 8889999999993 3334444442110 01123578999999999999999999888

>KOG0387|consensus

Probab=98.49  E-value=3.8e-07  Score=91.58  Aligned_cols=136  Identities=21%  Similarity=0.142  Sum_probs=89.7

Q ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHhhhhhc----CCCcEEEEcCCCChhHH--HHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        172 FGFDEVLMKALRKCEYTSPTPIQAQAVPAAL----SGRDIIGVAKTGSGKTG--AFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       172 ~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~--a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      +.++..|..        .+.++|+..+..+.    ++.-.|+.-.+|-|||.  +..|.+|.|--+       -...+||
T Consensus       196 ~~vPg~I~~--------~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S~k-------~~~paLI  260 (923)
T KOG0387|consen  196 FKVPGFIWS--------KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSGK-------LTKPALI  260 (923)
T ss_pred             ccccHHHHH--------HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhccc-------ccCceEE
Confidence            455655543        35689999988875    56678888899999992  233444444211       1256899


Q ss_pred             EcccHHHHHHHHHHHHHhccCCCceEEEEECCCch---------HHHHHHH----hCCCeEEEEChHHHHHHHHcCCCCC
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSK---------WDQSKAL----ELGAEIVVGTPGRIIDMVKMGATKL  312 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~---------~~~~~~l----~~~~dIiV~TP~~L~~~l~~~~~~l  312 (330)
                      |||. .++.||..++..|..  .+++..++|..+.         ......+    .....|+|+|...+.-.  ...+.-
T Consensus       261 VCP~-Tii~qW~~E~~~w~p--~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~--~d~l~~  335 (923)
T KOG0387|consen  261 VCPA-TIIHQWMKEFQTWWP--PFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQ--GDDLLG  335 (923)
T ss_pred             EccH-HHHHHHHHHHHHhCc--ceEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhccc--Cccccc
Confidence            9998 577999999999965  4677777765542         1111111    12467999998777532  112223


Q ss_pred             CCccEEEeecccccC
Q psy17644        313 NRVTFLVLDEADRMF  327 (330)
Q Consensus       313 ~~i~~lVvDEad~ll  327 (330)
                      ..+.|+|+||.|+|=
T Consensus       336 ~~W~y~ILDEGH~Ir  350 (923)
T KOG0387|consen  336 ILWDYVILDEGHRIR  350 (923)
T ss_pred             ccccEEEecCccccc
Confidence            467899999999973

>KOG0391|consensus

Probab=98.48  E-value=6.5e-07  Score=92.85  Aligned_cols=130  Identities=22%  Similarity=0.231  Sum_probs=91.9

Q ss_pred             CCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        190 PTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       190 pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      ++.+|+..+.++.    +.-|.|+.-..|-|||+ -.|.+|.|+.+..    ++..--||||||-.+ ..|.-++++||.
T Consensus       616 LReYQkiGLdWLatLYeknlNGILADEmGLGKTI-QtISllAhLACee----gnWGPHLIVVpTsvi-LnWEMElKRwcP  689 (1958)
T KOG0391|consen  616 LREYQKIGLDWLATLYEKNLNGILADEMGLGKTI-QTISLLAHLACEE----GNWGPHLIVVPTSVI-LNWEMELKRWCP  689 (1958)
T ss_pred             HHHHHHhhHHHHHHHHHhcccceehhhhcccchh-HHHHHHHHHHhcc----cCCCCceEEeechhh-hhhhHHHhhhCC
Confidence            4468888887764    34467888899999994 4566777877653    355556999999655 678899999987


Q ss_pred             CCCceEEEEECCCchHHH-H--HHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcC
Q psy17644        266 GYNLSVVCCYGGGSKWDQ-S--KALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       266 ~~~~~~~~~~gg~~~~~~-~--~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~  329 (330)
                        ++++...||....... +  ....+..||.|+++..+..-+.  .+.-.++.||||||||++-.|
T Consensus       690 --glKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~--AFkrkrWqyLvLDEaqnIKnf  752 (1958)
T KOG0391|consen  690 --GLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLT--AFKRKRWQYLVLDEAQNIKNF  752 (1958)
T ss_pred             --cceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHH--HHHhhccceeehhhhhhhcch
Confidence              5777888885432211 1  1112347999999988776554  233468899999999998654

>KOG1132|consensus

Probab=98.35  E-value=2.8e-06  Score=86.51  Aligned_cols=138  Identities=21%  Similarity=0.261  Sum_probs=88.0

Q ss_pred             CCCCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHH---HHHHHHHHhcCCC------C-------C----------
Q psy17644        188 TSPTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFI---WPMLVHIMDQKEL------E-------P----------  237 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~l---lp~l~~i~~~~~~------~-------~----------  237 (330)
                      ..|+|.|...+..++    ...+.++..|||+|||++.|   |+..++.......      .       .          
T Consensus        20 ~qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~s~e   99 (945)
T KOG1132|consen   20 FQPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEKSEE   99 (945)
T ss_pred             CCcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCchhh
Confidence            357888877665544    67889999999999997655   4444444311100      0       0          


Q ss_pred             --------CCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEEC---------------------------------
Q psy17644        238 --------GDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYG---------------------------------  276 (330)
Q Consensus       238 --------~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~g---------------------------------  276 (330)
                              ...|++.|-.-|..-..|+.+++++.+-.  .+.+++-+                                 
T Consensus       100 ~~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~Y~--vkmtVLgSReq~Cinpev~k~~~~~~~~~~C~k~~~~~~C~  177 (945)
T KOG1132|consen  100 AGEPIACYTGIPKIYYASRTHSQLTQVVRELRRTGYR--VKMTVLGSREQLCINPEVKKLEGNALQNHVCKKLVKSRSCH  177 (945)
T ss_pred             hcCccccccCCceEEEecchHHHHHHHHHHHhhcCCC--CceEEeecchhhccCHHHhhhhcchhhhhHHHhhccccccc
Confidence                    01378788888888889999999876421  11111100                                 


Q ss_pred             -------------------------------CCchHHHHHHHhCCCeEEEEChHHHHHHHHcCC--CCCCCccEEEeecc
Q psy17644        277 -------------------------------GGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA--TKLNRVTFLVLDEA  323 (330)
Q Consensus       277 -------------------------------g~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~--~~l~~i~~lVvDEa  323 (330)
                                                     +.+.....+.+...++||+|-...|++-.-++.  .+|.+ .+||||||
T Consensus       178 f~~~~~~~sl~~~l~~~i~DIEDLVk~Gk~~~~CPYfaSR~l~edAdIIF~PYnYLiDp~iR~~~~v~Lkn-sIVIfDEA  256 (945)
T KOG1132|consen  178 FYKIVEEKSLQPRLHDEIFDIEDLVKIGKKSRGCPYFASRELKEDADIIFCPYNYLIDPKIRRSHKVDLKN-SIVIFDEA  256 (945)
T ss_pred             ccccccccccccccCCCcccHHHHHHhCccCcCCcchhhhhhcccCcEEEechhhhcCHhhhccccccccc-cEEEEecc
Confidence                                           111122234444578999999999999765554  44543 78999999


Q ss_pred             cccCc
Q psy17644        324 DRMFD  328 (330)
Q Consensus       324 d~lld  328 (330)
                      |.|.+
T Consensus       257 HNiEd  261 (945)
T KOG1132|consen  257 HNIED  261 (945)
T ss_pred             ccHHH
Confidence            99865

>KOG0389|consensus

Probab=98.32  E-value=1.2e-06  Score=87.93  Aligned_cols=131  Identities=18%  Similarity=0.225  Sum_probs=86.2

Q ss_pred             CCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        190 PTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       190 pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      +-++|.-.+.++.    .+-+.|+.-..|-||| +-+++.|..+....    .+|| -|||||.-.| ..|.+++.+||.
T Consensus       400 LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKT-iQvIaFlayLkq~g----~~gp-HLVVvPsSTl-eNWlrEf~kwCP  472 (941)
T KOG0389|consen  400 LKDYQLVGVNWLLLLYKKKLNGILADEMGLGKT-IQVIAFLAYLKQIG----NPGP-HLVVVPSSTL-ENWLREFAKWCP  472 (941)
T ss_pred             ccchhhhhHHHHHHHHHccccceehhhccCcch-hHHHHHHHHHHHcC----CCCC-cEEEecchhH-HHHHHHHHHhCC
Confidence            6688888887764    5557788899999999 34444444444332    1344 5999999766 778889999987


Q ss_pred             CCCceEEEEECCCchHHHHHH-HhC---CCeEEEEChHHHHHHH-HcCCCCCCCccEEEeecccccCcC
Q psy17644        266 GYNLSVVCCYGGGSKWDQSKA-LEL---GAEIVVGTPGRIIDMV-KMGATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       266 ~~~~~~~~~~gg~~~~~~~~~-l~~---~~dIiV~TP~~L~~~l-~~~~~~l~~i~~lVvDEad~lld~  329 (330)
                      .  +++-..||....+...+. +..   ..+|||+|+.....-- .+..+.-.++.++|+||+|.|-++
T Consensus       473 s--l~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~  539 (941)
T KOG0389|consen  473 S--LKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNR  539 (941)
T ss_pred             c--eEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhcc
Confidence            4  566666776544333222 222   5899999976543211 111222467899999999998655

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.32  E-value=1.2e-06  Score=91.12  Aligned_cols=134  Identities=20%  Similarity=0.170  Sum_probs=86.1

Q ss_pred             CCHHHHHhhhhhcC---CC-cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        190 PTPIQAQAVPAALS---GR-DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       190 pt~iQ~~~i~~~~~---g~-d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      +.+.|..++..+.+   .. .+++.||||.|||.+.+++++..+...    ....++++++.|+|.++.++++.++.+..
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~----~~~~~r~i~vlP~~t~ie~~~~r~~~~~~  271 (733)
T COG1203         196 GYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEK----IKLKSRVIYVLPFRTIIEDMYRRAKEIFG  271 (733)
T ss_pred             hhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhcc----ccccceEEEEccHHHHHHHHHHHHHhhhc
Confidence            47888888887763   23 677889999999999999988776552    12579999999999999999999998765


Q ss_pred             CCCceEEEEECCCchHHHHHHH---------------hCCCeEEEEChHHHHHHHHcCCC-C-C--CCccEEEeeccccc
Q psy17644        266 GYNLSVVCCYGGGSKWDQSKAL---------------ELGAEIVVGTPGRIIDMVKMGAT-K-L--NRVTFLVLDEADRM  326 (330)
Q Consensus       266 ~~~~~~~~~~gg~~~~~~~~~l---------------~~~~dIiV~TP~~L~~~l~~~~~-~-l--~~i~~lVvDEad~l  326 (330)
                      ..+.......|.... ......               .....++++||..+......... . +  =...++||||+|.+
T Consensus       272 ~~~~~~~~~h~~~~~-~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~  350 (733)
T COG1203         272 LFSVIGKSLHSSSKE-PLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLY  350 (733)
T ss_pred             ccccccccccccccc-hhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhh
Confidence            443332212222211 111000               01245566666665553222111 1 1  12368999999987


Q ss_pred             Cc
Q psy17644        327 FD  328 (330)
Q Consensus       327 ld  328 (330)
                      -+
T Consensus       351 ~~  352 (733)
T COG1203         351 AD  352 (733)
T ss_pred             cc
Confidence            54

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=98.28  E-value=1.2e-06  Score=91.20  Aligned_cols=124  Identities=18%  Similarity=0.154  Sum_probs=92.8

Q ss_pred             HHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEE
Q psy17644        194 QAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVC  273 (330)
Q Consensus       194 Q~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~  273 (330)
                      -.|++-.+.-++--|+...||-|||++..||+....+.        |..|-||+..--||..=.+++..+...+|+++.|
T Consensus       141 dVQLiGgivLh~G~IAEM~TGEGKTLvatlp~yLnAL~--------G~gVHvVTvNDYLA~RDaewm~p~y~flGLtVg~  212 (1025)
T PRK12900        141 DVQLIGGIVLHSGKISEMATGEGKTLVSTLPTFLNALT--------GRGVHVVTVNDYLAQRDKEWMNPVFEFHGLSVGV  212 (1025)
T ss_pred             chHHhhhHHhhcCCccccCCCCCcchHhHHHHHHHHHc--------CCCcEEEeechHhhhhhHHHHHHHHHHhCCeeee
Confidence            33344444444556889999999999999999888775        5556778888899999999999999999999999


Q ss_pred             EECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcC------CCCCCCccEEEeecccccC
Q psy17644        274 CYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMG------ATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       274 ~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~------~~~l~~i~~lVvDEad~ll  327 (330)
                      +..+.........  -.|||..||..-| +++|+.+      ..-.+.+.|.||||+|.+|
T Consensus       213 i~~~~~~~~Rr~a--Y~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvL  271 (1025)
T PRK12900        213 ILNTMRPEERREQ--YLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVL  271 (1025)
T ss_pred             eCCCCCHHHHHHh--CCCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhh
Confidence            8776665554333  3589999998765 3333322      1124678899999999987

>KOG1123|consensus

Probab=98.28  E-value=7.5e-07  Score=85.51  Aligned_cols=123  Identities=20%  Similarity=0.159  Sum_probs=86.8

Q ss_pred             CCCCHHHHHhhhhhc-CC--CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        188 TSPTPIQAQAVPAAL-SG--RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~-~g--~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      ..++|+|..++..++ +|  |..|++.|.|+|||++-+.++..-           ...+||||.+--.+.||...++.|+
T Consensus       301 t~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~ti-----------kK~clvLcts~VSVeQWkqQfk~ws  369 (776)
T KOG1123|consen  301 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACTI-----------KKSCLVLCTSAVSVEQWKQQFKQWS  369 (776)
T ss_pred             cccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeeee-----------cccEEEEecCccCHHHHHHHHHhhc
Confidence            468899999999998 44  689999999999997765544321           3568999999999999999999997


Q ss_pred             cCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcC--------CCCCCCccEEEeeccccc
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG--------ATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~--------~~~l~~i~~lVvDEad~l  326 (330)
                      .-..-.++.......     .....++.|+|+|...+..--++.        .+.-..+.++|+||+|-+
T Consensus       370 ti~d~~i~rFTsd~K-----e~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvv  434 (776)
T KOG1123|consen  370 TIQDDQICRFTSDAK-----ERFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVV  434 (776)
T ss_pred             ccCccceEEeecccc-----ccCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccc
Confidence            654444433333221     113457899999987653211110        112356889999999964

>KOG4439|consensus

Probab=98.27  E-value=1.3e-06  Score=86.90  Aligned_cols=136  Identities=25%  Similarity=0.216  Sum_probs=84.3

Q ss_pred             CCHHHHHhhhhhc-----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCC--CCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        190 PTPIQAQAVPAAL-----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE--PGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       190 pt~iQ~~~i~~~~-----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~--~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      +-|+|..++.++.     .+.-.|+....|-|||++.+--++..-...+...  .....++|||||- .|+.||..++.+
T Consensus       326 LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~Pa-Sli~qW~~Ev~~  404 (901)
T KOG4439|consen  326 LMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPA-SLIHQWEAEVAR  404 (901)
T ss_pred             cchhhhhhhhhhcccccCCCCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCcH-HHHHHHHHHHHH
Confidence            5689999998887     3456777788999999765444443322221111  1112258999997 577899999877


Q ss_pred             hccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHH----HHHcC--CCCCC--CccEEEeecccccC
Q psy17644        263 FGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIID----MVKMG--ATKLN--RVTFLVLDEADRMF  327 (330)
Q Consensus       263 l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~----~l~~~--~~~l~--~i~~lVvDEad~ll  327 (330)
                      -...--+++...+|.+...-..+.++. +||||+|+.-+..    -+...  ...|.  .+..||+||||.+=
T Consensus       405 rl~~n~LsV~~~HG~n~r~i~~~~L~~-YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~Ir  476 (901)
T KOG4439|consen  405 RLEQNALSVYLYHGPNKREISAKELRK-YDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIR  476 (901)
T ss_pred             HHhhcceEEEEecCCccccCCHHHHhh-cceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhhc
Confidence            655545565555554433333444544 8999999865544    11111  11122  34689999999874

>KOG0952|consensus

Probab=98.24  E-value=5.3e-07  Score=92.92  Aligned_cols=132  Identities=23%  Similarity=0.224  Sum_probs=102.5

Q ss_pred             CCCCHHHHHhhhhhcC-CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC
Q psy17644        188 TSPTPIQAQAVPAALS-GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG  266 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~-g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~  266 (330)
                      ....|+|.+.+-.+.. ..+.++.+|||+|||++|-+.+...+..      ..+.+|++++|-..|+....+.+.+....
T Consensus       926 ~~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~------~p~~kvvyIap~kalvker~~Dw~~r~~~  999 (1230)
T KOG0952|consen  926 KYFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSY------YPGSKVVYIAPDKALVKERSDDWSKRDEL  999 (1230)
T ss_pred             cccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhcc------CCCccEEEEcCCchhhcccccchhhhccc
Confidence            3556788888877663 3577888999999999999887755443      24689999999999998888887765554


Q ss_pred             CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC--CCCCccEEEeecccccCc
Q psy17644        267 YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT--KLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       267 ~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~--~l~~i~~lVvDEad~lld  328 (330)
                      .|++++-+.|.....  ...+. .++|+|+||.++..+.+.+..  .+.++..+|+||.|++-+
T Consensus      1000 ~g~k~ie~tgd~~pd--~~~v~-~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~ 1060 (1230)
T KOG0952|consen 1000 PGIKVIELTGDVTPD--VKAVR-EADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGE 1060 (1230)
T ss_pred             CCceeEeccCccCCC--hhhee-cCceEEcccccccCccccccchhhhccccceeecccccccC
Confidence            588888888866654  23333 379999999999998886544  488999999999999864

>KOG0390|consensus

Probab=98.20  E-value=1.7e-05  Score=81.14  Aligned_cols=135  Identities=19%  Similarity=0.178  Sum_probs=90.7

Q ss_pred             CCCHHHHHhhhhhc---CCC-------cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        189 SPTPIQAQAVPAAL---SGR-------DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~---~g~-------d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      .+.|+|++.+.-+.   .|.       -+|+.-..|+|||+. +++++..++++-+.....-.++|||+|. .|+..|.+
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq-~IsflwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkk  315 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQ-CISFIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKK  315 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHH-HHHHHHHHHHhCcCccccccccEEEccH-HHHHHHHH
Confidence            46799999997654   222       344445679999954 3455555665533212223678999998 68899999


Q ss_pred             HHHHhccCCCceEEEEECCCch-HHHHH------HHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        259 EAKRFGKGYNLSVVCCYGGGSK-WDQSK------ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       259 ~~~~l~~~~~~~~~~~~gg~~~-~~~~~------~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ++.+|.....+....++|+... +....      ......-|+|.+.+.+.+..+.  +.+..+.+||+||.|++=
T Consensus       316 EF~KWl~~~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~--il~~~~glLVcDEGHrlk  389 (776)
T KOG0390|consen  316 EFGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK--ILLIRPGLLVCDEGHRLK  389 (776)
T ss_pred             HHHHhccccccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH--HhcCCCCeEEECCCCCcc
Confidence            9999987656777777777764 11111      1112346788888888766553  445689999999999863

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.20  E-value=4.8e-06  Score=85.10  Aligned_cols=98  Identities=14%  Similarity=0.150  Sum_probs=72.2

Q ss_pred             cCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHH---HHH
Q psy17644        211 AKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS---KAL  287 (330)
Q Consensus       211 a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~---~~l  287 (330)
                      +-+|||||.+|+-.+ ..++.       .|..+|||+|...|..|+...++....  +..+..++++.+..+..   ..+
T Consensus       167 ~~~GSGKTevyl~~i-~~~l~-------~Gk~vLvLvPEi~lt~q~~~rl~~~f~--~~~v~~lhS~l~~~~R~~~w~~~  236 (665)
T PRK14873        167 ALPGEDWARRLAAAA-AATLR-------AGRGALVVVPDQRDVDRLEAALRALLG--AGDVAVLSAGLGPADRYRRWLAV  236 (665)
T ss_pred             cCCCCcHHHHHHHHH-HHHHH-------cCCeEEEEecchhhHHHHHHHHHHHcC--CCcEEEECCCCCHHHHHHHHHHH
Confidence            336999999887544 44444       377899999999999999999987653  24677788877654432   233


Q ss_pred             hC-CCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        288 EL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       288 ~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      .. ...|||+|...++       ..+.++.+|||||=|-
T Consensus       237 ~~G~~~IViGtRSAvF-------aP~~~LgLIIvdEEhd  268 (665)
T PRK14873        237 LRGQARVVVGTRSAVF-------APVEDLGLVAIWDDGD  268 (665)
T ss_pred             hCCCCcEEEEcceeEE-------eccCCCCEEEEEcCCc
Confidence            33 4799999965544       4578999999999874

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

Probab=98.15  E-value=1.2e-05  Score=85.53  Aligned_cols=113  Identities=24%  Similarity=0.244  Sum_probs=78.7

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ  283 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~  283 (330)
                      ++..+++--||||||++-+..+- .++..     ...|+++||+-.+.|-.|+.+.+..++.......    .-.+..+.
T Consensus       273 ~~~G~IWHtqGSGKTlTm~~~A~-~l~~~-----~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~----~~~s~~~L  342 (962)
T COG0610         273 GKGGYIWHTQGSGKTLTMFKLAR-LLLEL-----PKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP----KAESTSEL  342 (962)
T ss_pred             CCceEEEeecCCchHHHHHHHHH-HHHhc-----cCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc----cccCHHHH
Confidence            35689999999999976543322 22222     3689999999999999999999999875432211    33445555


Q ss_pred             HHHHhCC-CeEEEEChHHHHHHHHcCC--CCCCCccEEEeeccccc
Q psy17644        284 SKALELG-AEIVVGTPGRIIDMVKMGA--TKLNRVTFLVLDEADRM  326 (330)
Q Consensus       284 ~~~l~~~-~dIiV~TP~~L~~~l~~~~--~~l~~i~~lVvDEad~l  326 (330)
                      ...+..+ ..|||||-.+|...+....  ..-.+=-+||+|||||-
T Consensus       343 k~~l~~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRS  388 (962)
T COG0610         343 KELLEDGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRS  388 (962)
T ss_pred             HHHHhcCCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhc
Confidence            5556544 4899999999998886541  11223347899999983

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.11  E-value=4.7e-06  Score=86.90  Aligned_cols=128  Identities=18%  Similarity=0.193  Sum_probs=94.1

Q ss_pred             CCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCc
Q psy17644        190 PTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNL  269 (330)
Q Consensus       190 pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~  269 (330)
                      +.|+-.|++-.+.-.+--|+...||-|||++..+|+....+.        |..|-||+..--||..=.+++..+...+|+
T Consensus       168 m~~yDVQliGgivLh~G~IAEM~TGEGKTLvAtlp~yLnAL~--------GkgVHvVTVNDYLA~RDaewmgply~fLGL  239 (1112)
T PRK12901        168 MVHYDVQLIGGVVLHQGKIAEMATGEGKTLVATLPVYLNALT--------GNGVHVVTVNDYLAKRDSEWMGPLYEFHGL  239 (1112)
T ss_pred             CcccchHHhhhhhhcCCceeeecCCCCchhHHHHHHHHHHHc--------CCCcEEEEechhhhhccHHHHHHHHHHhCC
Confidence            444444456555555667899999999999999999888775        556778888889999999999999999999


Q ss_pred             eEEEEEC-CCchHHHHHHHhCCCeEEEEChHHH-HHHHHcC------CCCCCCccEEEeecccccC
Q psy17644        270 SVVCCYG-GGSKWDQSKALELGAEIVVGTPGRI-IDMVKMG------ATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       270 ~~~~~~g-g~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~------~~~l~~i~~lVvDEad~ll  327 (330)
                      .+.|+.. +........  .-.|||..+|..-| +++|+.+      ..-.+.+.|.||||+|.+|
T Consensus       240 svg~i~~~~~~~~~rr~--aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSIL  303 (1112)
T PRK12901        240 SVDCIDKHQPNSEARRK--AYNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVL  303 (1112)
T ss_pred             ceeecCCCCCCHHHHHH--hCCCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhh
Confidence            9988765 334433322  33589999997765 3333322      1124568999999999987

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=98.09  E-value=4.9e-06  Score=72.63  Aligned_cols=63  Identities=24%  Similarity=0.282  Sum_probs=42.9

Q ss_pred             CCCHHHHHhhhhhcCCC--cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q psy17644        189 SPTPIQAQAVPAALSGR--DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE  259 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~--d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~  259 (330)
                      ++++-|..++..++...  -++++++.|+|||.+  +-.+...+..      .+.++++++||...+..+.+.
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~--l~~~~~~~~~------~g~~v~~~apT~~Aa~~L~~~   65 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTL--LKALAEALEA------AGKRVIGLAPTNKAAKELREK   65 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHH--HHHHHHHHHH------TT--EEEEESSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHH--HHHHHHHHHh------CCCeEEEECCcHHHHHHHHHh
Confidence            36789999999997433  366669999999943  3333333332      468999999999988876665

>KOG0392|consensus

Probab=98.09  E-value=3.3e-05  Score=81.14  Aligned_cols=133  Identities=20%  Similarity=0.115  Sum_probs=86.5

Q ss_pred             CCHHHHHhhhhhc---C-CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCC-CCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        190 PTPIQAQAVPAAL---S-GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEP-GDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       190 pt~iQ~~~i~~~~---~-g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~-~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      ++.+|++.+.++.   . +=+.|+|--+|-|||+-.+-.+..-..+++.... .+..-.|||||. .|+-.|..++.+|+
T Consensus       976 LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf~ 1054 (1549)
T KOG0392|consen  976 LRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKFF 1054 (1549)
T ss_pred             HHHHHHhccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHhc
Confidence            3457888887753   2 2378999999999997644333333333322211 122337999997 68999999999998


Q ss_pred             cCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ..  +++...+|+-..+...+.--++++|||+++..+..-+..  ..-..+.|.|+||.|-|=
T Consensus      1055 pf--L~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~--l~~~~wNYcVLDEGHVik 1113 (1549)
T KOG0392|consen 1055 PF--LKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDY--LIKIDWNYCVLDEGHVIK 1113 (1549)
T ss_pred             ch--hhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHH--HHhcccceEEecCcceec
Confidence            76  555555665544333333334579999999988743211  011356799999999763

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

Probab=98.09  E-value=2.2e-05  Score=81.56  Aligned_cols=119  Identities=21%  Similarity=0.208  Sum_probs=77.7

Q ss_pred             HHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH-hccCCCceE
Q psy17644        193 IQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR-FGKGYNLSV  271 (330)
Q Consensus       193 iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~-l~~~~~~~~  271 (330)
                      ...+++.++.+.+-++++|+||||||...=.-++....       ..+.++.+.=|.|--|..+...+.. ++...|-.|
T Consensus        54 ~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~-------~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~V  126 (845)
T COG1643          54 VRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGL-------GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETV  126 (845)
T ss_pred             HHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhc-------ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCcee
Confidence            44555566667778899999999999442222222221       2356777777988777777766543 444444444


Q ss_pred             EEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        272 VCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       272 ~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      ....-..+.      ......|-+.|-|.|...+.+.. .|+.+.+|||||||.
T Consensus       127 GY~iRfe~~------~s~~Trik~mTdGiLlrei~~D~-~Ls~ys~vIiDEaHE  173 (845)
T COG1643         127 GYSIRFESK------VSPRTRIKVMTDGILLREIQNDP-LLSGYSVVIIDEAHE  173 (845)
T ss_pred             eEEEEeecc------CCCCceeEEeccHHHHHHHhhCc-ccccCCEEEEcchhh
Confidence            333322221      22346899999999999987543 389999999999994

>KOG1803|consensus

Probab=98.03  E-value=1e-05  Score=79.62  Aligned_cols=66  Identities=20%  Similarity=0.331  Sum_probs=51.3

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEE-cCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGV-AKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK  261 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~-a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~  261 (330)
                      ..+.+-|++|+...++.+++.++ ||+|+|||.+... ++.++++       .+.++||.+||+..+..|.+.+.
T Consensus       184 ~~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvE-iI~qlvk-------~~k~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  184 KNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVE-IISQLVK-------QKKRVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             ccccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHH-HHHHHHH-------cCCeEEEEcCchHHHHHHHHHhc
Confidence            35678899999999988775555 9999999965544 3444444       36799999999999999988644

>KOG0384|consensus

Probab=97.99  E-value=1.8e-05  Score=83.13  Aligned_cols=127  Identities=18%  Similarity=0.239  Sum_probs=86.0

Q ss_pred             CCCCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        188 TSPTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..++.+|...+..++    ++.++|+.-..|-|||+- .+..|..++....   ..||. |||+|... +.-|..++..+
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvq-ti~fl~~l~~~~~---~~gpf-lvvvplst-~~~W~~ef~~w  442 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQ-TITFLSYLFHSLQ---IHGPF-LVVVPLST-ITAWEREFETW  442 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchH-HHHHHHHHHHhhh---ccCCe-EEEeehhh-hHHHHHHHHHH
Confidence            578889999888775    788999999999999932 1223333333221   14564 88888744 46678888888


Q ss_pred             ccCCCceEEEEECCCchHHHHHHHhC---------CCeEEEEChHHHHHHHHcCCCCCC--CccEEEeecccccC
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQSKALEL---------GAEIVVGTPGRIIDMVKMGATKLN--RVTFLVLDEADRMF  327 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~~~~l~~---------~~dIiV~TP~~L~~~l~~~~~~l~--~i~~lVvDEad~ll  327 (330)
                      +   ..++++.+|....++.++.+..         ..++||+|...++.-    ...|+  ...+++|||||+|-
T Consensus       443 ~---~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkD----k~~L~~i~w~~~~vDeahrLk  510 (1373)
T KOG0384|consen  443 T---DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKD----KAELSKIPWRYLLVDEAHRLK  510 (1373)
T ss_pred             h---hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhcc----HhhhccCCcceeeecHHhhcC
Confidence            6   5677777877665555544321         368999998776532    12233  45799999999984

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=97.99  E-value=7e-05  Score=78.59  Aligned_cols=117  Identities=16%  Similarity=0.142  Sum_probs=68.7

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH------hc---cCCCceEEEEE
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR------FG---KGYNLSVVCCY  275 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~------l~---~~~~~~~~~~~  275 (330)
                      .++.+..+||+|||.+|+-.++... +.     ....+.||+||+.+.-..+.+.+..      |.   ....+....+-
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~-~~-----~~~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~  133 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELH-QK-----YGLFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVIN  133 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHH-HH-----cCCcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEe
Confidence            4788889999999998887665443 22     1346899999999888777766541      11   11223333333


Q ss_pred             CCC-------chHHHHHHHhC-------CCeEEEEChHHHHHHHH-cCC----------CC---CCCc-cEEEeeccccc
Q psy17644        276 GGG-------SKWDQSKALEL-------GAEIVVGTPGRIIDMVK-MGA----------TK---LNRV-TFLVLDEADRM  326 (330)
Q Consensus       276 gg~-------~~~~~~~~l~~-------~~dIiV~TP~~L~~~l~-~~~----------~~---l~~i-~~lVvDEad~l  326 (330)
                      ++.       ........+..       ..+|+|.|-+.|..-.. +..          ..   +... -+||+||+|+|
T Consensus       134 S~k~~k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~~  213 (986)
T PRK15483        134 AGDKKKSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHRF  213 (986)
T ss_pred             cCcccccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCCC
Confidence            332       11112222221       46899999988865211 110          11   1111 37899999998


Q ss_pred             C
Q psy17644        327 F  327 (330)
Q Consensus       327 l  327 (330)
                      -
T Consensus       214 ~  214 (986)
T PRK15483        214 P  214 (986)
T ss_pred             C
Confidence            4

>TIGR00376 DNA helicase, putative

Probab=97.98  E-value=8.5e-05  Score=76.05  Aligned_cols=68  Identities=21%  Similarity=0.238  Sum_probs=53.1

Q ss_pred             CCCCHHHHHhhhhhcCC-CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        188 TSPTPIQAQAVPAALSG-RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g-~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..+++.|..++..++.. ..+++.||+|+|||.+. ..++.++..       .+.++|+++||...+.++.+.+...
T Consensus       156 ~~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~-~~ii~~~~~-------~g~~VLv~a~sn~Avd~l~e~l~~~  224 (637)
T TIGR00376       156 PNLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTL-VELIRQLVK-------RGLRVLVTAPSNIAVDNLLERLALC  224 (637)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHH-HHHHHHHHH-------cCCCEEEEcCcHHHHHHHHHHHHhC
Confidence            45789999999998876 55677799999999433 344445444       3679999999999999999888763

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.

>KOG0920|consensus

Probab=97.93  E-value=7.5e-05  Score=77.81  Aligned_cols=124  Identities=16%  Similarity=0.162  Sum_probs=86.4

Q ss_pred             CCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH-hccCCC
Q psy17644        190 PTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR-FGKGYN  268 (330)
Q Consensus       190 pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~-l~~~~~  268 (330)
                      .+..+.+.+.++.+.+-++++|.||+|||.-.---+|.+.....     ...++++--|.|-.|.-+++.+.. .+...|
T Consensus       174 a~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~-----~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g  248 (924)
T KOG0920|consen  174 AYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESG-----AACNIICTQPRRISAISVAERVAKERGESLG  248 (924)
T ss_pred             cHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcC-----CCCeEEecCCchHHHHHHHHHHHHHhccccC
Confidence            35677888888888899999999999999553333455544432     345567777999888888887543 333344


Q ss_pred             ceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        269 LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       269 ~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      -.+..-.+.....      .....+++||-|.|++.+.. ...+..+..+|+||+|.
T Consensus       249 ~~VGYqvrl~~~~------s~~t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHE  298 (924)
T KOG0920|consen  249 EEVGYQVRLESKR------SRETRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHE  298 (924)
T ss_pred             CeeeEEEeeeccc------CCceeEEEecHHHHHHHhcc-CcccccCceeeeeeEEE
Confidence            4443333322221      12368999999999999876 55688999999999994

>KOG1802|consensus

Probab=97.92  E-value=3.5e-05  Score=76.54  Aligned_cols=83  Identities=20%  Similarity=0.167  Sum_probs=64.8

Q ss_pred             HHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q psy17644        181 ALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEA  260 (330)
Q Consensus       181 ~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~  260 (330)
                      .+...++.++..-|..|+.++++..=.|+++|+|+|||++..- ++.|+..+      .+..+|+++|+.-.+.|+...+
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~-IVyhl~~~------~~~~VLvcApSNiAVDqLaeKI  474 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSAT-IVYHLARQ------HAGPVLVCAPSNIAVDQLAEKI  474 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHH-HHHHHHHh------cCCceEEEcccchhHHHHHHHH
Confidence            4566788889999999999999988889999999999966543 34455443      4567899999999999998888


Q ss_pred             HHhccCCCceEEEE
Q psy17644        261 KRFGKGYNLSVVCC  274 (330)
Q Consensus       261 ~~l~~~~~~~~~~~  274 (330)
                      .+-    +++++-+
T Consensus       475 h~t----gLKVvRl  484 (935)
T KOG1802|consen  475 HKT----GLKVVRL  484 (935)
T ss_pred             Hhc----CceEeee
Confidence            765    4555443

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

Probab=97.92  E-value=3.1e-05  Score=69.80  Aligned_cols=86  Identities=23%  Similarity=0.327  Sum_probs=68.1

Q ss_pred             CCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCC-chHHHHHHHhC-CCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        238 GDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGG-SKWDQSKALEL-GAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       238 ~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~-~~~~~~~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      ...|.+|||+.+---|..+++.++.|.. .+..+.-+|.-. ...++...++. ..+|.||||+||..++..+.+.++++
T Consensus       124 ~gsP~~lvvs~SalRa~dl~R~l~~~~~-k~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~l  202 (252)
T PF14617_consen  124 KGSPHVLVVSSSALRAADLIRALRSFKG-KDCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSNL  202 (252)
T ss_pred             CCCCEEEEEcchHHHHHHHHHHHHhhcc-CCchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcccC
Confidence            4579999999998888888888888731 123444455443 56677777775 68999999999999999999999999


Q ss_pred             cEEEeeccc
Q psy17644        316 TFLVLDEAD  324 (330)
Q Consensus       316 ~~lVvDEad  324 (330)
                      .+||||--|
T Consensus       203 ~~ivlD~s~  211 (252)
T PF14617_consen  203 KRIVLDWSY  211 (252)
T ss_pred             eEEEEcCCc
Confidence            999999754

>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=97.89  E-value=0.00013  Score=64.55  Aligned_cols=151  Identities=19%  Similarity=0.296  Sum_probs=94.2

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcC---CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEE
Q psy17644        168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALS---GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGL  244 (330)
Q Consensus       168 ~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~---g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vL  244 (330)
                      +|.-...+..|+=-+.. + --.++.|.++...+++   |++.+.+.-+|.||| ..++|++..++...      ..-|.
T Consensus         4 ~w~p~~~P~wLl~E~e~-~-iliR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKT-sVI~Pmla~~LAdg------~~Lvr   74 (229)
T PF12340_consen    4 NWDPMEYPDWLLFEIES-N-ILIRPVQVEIAREMISPPSGKNSVMQLNMGEGKT-SVIVPMLALALADG------SRLVR   74 (229)
T ss_pred             CCCchhChHHHHHHHHc-C-ceeeHHHHHHHHHHhCCCCCCCeEeeecccCCcc-chHHHHHHHHHcCC------CcEEE
Confidence            45555556655444322 2 2467999999988874   689999999999999 56788888887642      24556


Q ss_pred             EEcccHHHHHHHHHHHHHh-ccCCCceEEEE-ECCC---chH------HHHHHHhCCCeEEEEChHHHHHHHHc------
Q psy17644        245 ILAPTRELSQQIYNEAKRF-GKGYNLSVVCC-YGGG---SKW------DQSKALELGAEIVVGTPGRIIDMVKM------  307 (330)
Q Consensus       245 il~Ptr~La~Qi~~~~~~l-~~~~~~~~~~~-~gg~---~~~------~~~~~l~~~~dIiV~TP~~L~~~l~~------  307 (330)
                      +++|. .|..|.++.++.- +.-.+-++..+ |...   +..      ...........|+++||+.++.+.-.      
T Consensus        75 viVpk-~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~L~~le~l~  153 (229)
T PF12340_consen   75 VIVPK-ALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSFKLKGLERLQ  153 (229)
T ss_pred             EEcCH-HHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHHHHHHHHHH
Confidence            66665 6889999887754 33333333222 2211   111      11112333457999999998764311      


Q ss_pred             -CCC-----------CCCCccEEEeecccccCc
Q psy17644        308 -GAT-----------KLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       308 -~~~-----------~l~~i~~lVvDEad~lld  328 (330)
                       ...           -+.....=|+||+|.+|.
T Consensus       154 ~~~~~~~~~l~~~q~~l~~~~rdilDEsDe~L~  186 (229)
T PF12340_consen  154 DGKPEEARELLKIQKWLDEHSRDILDESDEILS  186 (229)
T ss_pred             hcCHHHHHHHHHHHHHHHhcCCeEeECchhccC
Confidence             111           034455679999998874

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=97.83  E-value=4.7e-05  Score=72.54  Aligned_cols=94  Identities=17%  Similarity=0.207  Sum_probs=58.6

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA  286 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~  286 (330)
                      +++.|..|||||+..+- ++..+..     ...+.+++++++...|...+...+..-...                    
T Consensus         4 ~~I~G~aGTGKTvla~~-l~~~l~~-----~~~~~~~~~l~~n~~l~~~l~~~l~~~~~~--------------------   57 (352)
T PF09848_consen    4 ILITGGAGTGKTVLALN-LAKELQN-----SEEGKKVLYLCGNHPLRNKLREQLAKKYNP--------------------   57 (352)
T ss_pred             EEEEecCCcCHHHHHHH-HHHHhhc-----cccCCceEEEEecchHHHHHHHHHhhhccc--------------------
Confidence            56779999999965432 3333311     124778899999999998888877654200                    


Q ss_pred             HhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        287 LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       287 l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                        ......+..|..+...+..........++|||||||+|.+
T Consensus        58 --~~~~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqrl~~   97 (352)
T PF09848_consen   58 --KLKKSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQRLRT   97 (352)
T ss_pred             --chhhhhhhhhHHHHhhcccccccCCcCCEEEEehhHhhhh
Confidence              0012233444444433322233467889999999999976

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>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=97.75  E-value=5e-05  Score=66.53  Aligned_cols=59  Identities=22%  Similarity=0.137  Sum_probs=40.6

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL  252 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~L  252 (330)
                      ...|.-|..++.++++..-+++.|+.|+|||+..+..++..+...      .--+++|+-|+.+.
T Consensus         3 ~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g------~~~kiii~Rp~v~~   61 (205)
T PF02562_consen    3 KPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEG------EYDKIIITRPPVEA   61 (205)
T ss_dssp             ---SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTT------S-SEEEEEE-S--T
T ss_pred             cCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhC------CCcEEEEEecCCCC
Confidence            345789999999999777788889999999999888888887652      34577887777653

; GO: 0005524 ATP binding; PDB: 3B85_A.

>KOG0388|consensus

Probab=97.71  E-value=7.5e-05  Score=74.71  Aligned_cols=123  Identities=20%  Similarity=0.290  Sum_probs=85.7

Q ss_pred             HHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        192 PIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       192 ~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      .+|...+..+.    +|-+.|+.-..|-|||+ -.+.+|.|+..+...   -|| -|||+|...| ..|.+++.+|+.. 
T Consensus       570 EYQlkGLnWLvnlYdqGiNGILADeMGLGKTV-QsisvlAhLaE~~nI---wGP-FLVVtpaStL-~NWaqEisrFlP~-  642 (1185)
T KOG0388|consen  570 EYQLKGLNWLVNLYDQGINGILADEMGLGKTV-QSISVLAHLAETHNI---WGP-FLVVTPASTL-HNWAQEISRFLPS-  642 (1185)
T ss_pred             HHhhccHHHHHHHHHccccceehhhhccchhH-HHHHHHHHHHHhccC---CCc-eEEeehHHHH-hHHHHHHHHhCcc-
Confidence            56766666654    78888999999999995 456678888776432   245 4888998666 7788889998764 


Q ss_pred             CceEEEEECCCchHHHHHH---------HhCCCeEEEEChHHHHH---HHHcCCCCCCCccEEEeecccccC
Q psy17644        268 NLSVVCCYGGGSKWDQSKA---------LELGAEIVVGTPGRIID---MVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~---------l~~~~dIiV~TP~~L~~---~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                       +++.-.+|+...+.-.+.         -..+.||+|+|...+..   +++     --.+.|.|+|||..+-
T Consensus       643 -~k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDeky~q-----kvKWQYMILDEAQAIK  708 (1185)
T KOG0388|consen  643 -FKVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDEKYLQ-----KVKWQYMILDEAQAIK  708 (1185)
T ss_pred             -ceeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeechHHHHH-----hhhhhheehhHHHHhh
Confidence             677777777765443332         12268999999876542   222     1246899999998763

>KOG0386|consensus

Probab=97.66  E-value=6.8e-05  Score=77.47  Aligned_cols=128  Identities=19%  Similarity=0.233  Sum_probs=80.0

Q ss_pred             CCCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        189 SPTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .+.++|...+.++.    +.-+.|+.-.+|-|||.. .+.++.+++..+.   ..||. |||||+-.|. -|..++-+|+
T Consensus       394 ~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQ-tIsLitYLmE~K~---~~GP~-LvivPlstL~-NW~~Ef~kWa  467 (1157)
T KOG0386|consen  394 ELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQ-TISLITYLMEHKQ---MQGPF-LIIVPLSTLV-NWSSEFPKWA  467 (1157)
T ss_pred             CCchhhhhhhHHHhhccCCCcccccchhcccchHHH-HHHHHHHHHHHcc---cCCCe-EEeccccccC-Cchhhccccc
Confidence            56678888777664    334667778899999954 3455566665433   25776 8899998884 4667777775


Q ss_pred             cCCCceEEEEECCCchHH--HH-HHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        265 KGYNLSVVCCYGGGSKWD--QS-KALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~--~~-~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ..   -....|.|.....  .. .......+|+++|.+.++.  .+..+.--++.|+||||.|+|-
T Consensus       468 PS---v~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik--dk~lLsKI~W~yMIIDEGHRmK  528 (1157)
T KOG0386|consen  468 PS---VQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK--DKALLSKISWKYMIIDEGHRMK  528 (1157)
T ss_pred             cc---eeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC--CHHHHhccCCcceeeccccccc
Confidence            42   2233444443211  01 1112347999999887765  1111112356799999999985

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=97.62  E-value=0.0002  Score=73.78  Aligned_cols=127  Identities=19%  Similarity=0.205  Sum_probs=98.4

Q ss_pred             CHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCce
Q psy17644        191 TPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLS  270 (330)
Q Consensus       191 t~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~  270 (330)
                      +|+-.|.+-.+.....-++-..||-|||++..+|+....+.        |..|.+|+-.--||..-..++.++...+|+.
T Consensus        80 ~~~dVQliG~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~--------gkgVhvVTvNdYLA~RDae~m~~l~~~LGls  151 (822)
T COG0653          80 RHFDVQLLGGIVLHLGDIAEMRTGEGKTLVATLPAYLNALA--------GKGVHVVTVNDYLARRDAEWMGPLYEFLGLS  151 (822)
T ss_pred             ChhhHHHhhhhhhcCCceeeeecCCchHHHHHHHHHHHhcC--------CCCcEEeeehHHhhhhCHHHHHHHHHHcCCc
Confidence            34445566667767778899999999999999998766554        5678888999999999999999999999999


Q ss_pred             EEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcC------CCCCCCccEEEeecccccC
Q psy17644        271 VVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMG------ATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       271 ~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~------~~~l~~i~~lVvDEad~ll  327 (330)
                      +.+...+.........+.  |||..+|-..| ++.++-+      ......+.|.|+||+|.||
T Consensus       152 vG~~~~~m~~~ek~~aY~--~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSIL  213 (822)
T COG0653         152 VGVILAGMSPEEKRAAYA--CDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSIL  213 (822)
T ss_pred             eeeccCCCChHHHHHHHh--cCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhhee
Confidence            999999888776665554  79999997765 2222211      1124468899999999886

>PF13245 AAA_19: Part of AAA domain

Probab=97.61  E-value=0.00028  Score=51.81  Aligned_cols=53  Identities=23%  Similarity=0.429  Sum_probs=36.9

Q ss_pred             CCc-EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q psy17644        204 GRD-IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEA  260 (330)
Q Consensus       204 g~d-~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~  260 (330)
                      +.. +++.++.|||||...+ .++.+++..+.   ..+.++||++||+..+..+.+.+
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~-~~i~~l~~~~~---~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLA-ARIAELLAARA---DPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHH-HHHHHHHHHhc---CCCCeEEEECCCHHHHHHHHHHH
Confidence            444 4458999999995433 34444443211   12678999999999999988887

>KOG0926|consensus

Probab=97.59  E-value=0.00024  Score=72.13  Aligned_cols=116  Identities=21%  Similarity=0.237  Sum_probs=70.5

Q ss_pred             HhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcC--CCCCCCCCeEEEEcccHHHHHHHHHHHH-HhccCCC--ce
Q psy17644        196 QAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQK--ELEPGDGPMGLILAPTRELSQQIYNEAK-RFGKGYN--LS  270 (330)
Q Consensus       196 ~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~--~~~~~~~~~vLil~Ptr~La~Qi~~~~~-~l~~~~~--~~  270 (330)
                      +++.+|...-=+|+||.||||||.  .+|-  +++...  .....++..+=|--|.|-.|.-+..... .++. ++  +.
T Consensus       263 ~IMEaIn~n~vvIIcGeTGsGKTT--QvPQ--FLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa~EL~~-~~~eVs  337 (1172)
T KOG0926|consen  263 RIMEAINENPVVIICGETGSGKTT--QVPQ--FLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVAFELGV-LGSEVS  337 (1172)
T ss_pred             HHHHHhhcCCeEEEecCCCCCccc--cchH--HHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHHHHhcc-Ccccee
Confidence            344445555567888999999993  3442  222211  1111123355566788887776665533 3333 33  33


Q ss_pred             EEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        271 VVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       271 ~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      ....|.|.-        .....|.+.|-|.|+.-+.+. +.|....++||||||.
T Consensus       338 YqIRfd~ti--------~e~T~IkFMTDGVLLrEi~~D-flL~kYSvIIlDEAHE  383 (1172)
T KOG0926|consen  338 YQIRFDGTI--------GEDTSIKFMTDGVLLREIEND-FLLTKYSVIILDEAHE  383 (1172)
T ss_pred             EEEEecccc--------CCCceeEEecchHHHHHHHHh-HhhhhceeEEechhhh
Confidence            344454433        234689999999999877643 3477889999999994

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=97.52  E-value=0.00021  Score=69.74  Aligned_cols=68  Identities=29%  Similarity=0.331  Sum_probs=49.9

Q ss_pred             CCCHHHHHhhhhhcCC-----CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        189 SPTPIQAQAVPAALSG-----RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g-----~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .|+.-|-+||..+..|     +.-.+.|.||||||++..    +-+-+       -+..+||++|.+.||.|++.+++.|
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~A----nVI~~-------~~rPtLV~AhNKTLAaQLy~Efk~f   80 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMA----NVIAK-------VQRPTLVLAHNKTLAAQLYSEFKEF   80 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHH----HHHHH-------hCCCeEEEecchhHHHHHHHHHHHh
Confidence            4667777777776533     567788999999995432    22222       1344799999999999999999999


Q ss_pred             ccCC
Q psy17644        264 GKGY  267 (330)
Q Consensus       264 ~~~~  267 (330)
                      ...-
T Consensus        81 FP~N   84 (663)
T COG0556          81 FPEN   84 (663)
T ss_pred             CcCc
Confidence            7643

>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=97.51  E-value=0.00032  Score=64.87  Aligned_cols=70  Identities=17%  Similarity=0.153  Sum_probs=51.1

Q ss_pred             CCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        190 PTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       190 pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      +|+-|.+++..  ....+++.|..|||||.+.+.-++ +++....   ....++|+|++|+..|..+...+...+.
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~-~ll~~~~---~~~~~Il~lTft~~aa~e~~~ri~~~l~   70 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIA-YLLYEGG---VPPERILVLTFTNAAAQEMRERIRELLE   70 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHH-HHHHTSS---STGGGEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHH-Hhhcccc---CChHHheecccCHHHHHHHHHHHHHhcC
Confidence            46889999988  678899999999999965544343 4444322   2456799999999999999999888644

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 ....

>KOG1805|consensus

Probab=97.50  E-value=0.0005  Score=71.18  Aligned_cols=136  Identities=20%  Similarity=0.171  Sum_probs=84.6

Q ss_pred             CCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcE-EEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q psy17644        171 HFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDI-IGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT  249 (330)
Q Consensus       171 ~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~-i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt  249 (330)
                      ...+.+.+...    ....+..-|++|+-.++..+|. ++.|-+|+|||.+-+. ++..+..       .|.+||+.+=|
T Consensus       655 ~~~~~p~~~~~----~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~-LIkiL~~-------~gkkVLLtsyT  722 (1100)
T KOG1805|consen  655 SKVLIPKIKKI----ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISL-LIKILVA-------LGKKVLLTSYT  722 (1100)
T ss_pred             ccccCchhhHH----HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHH-HHHHHHH-------cCCeEEEEehh
Confidence            34455554442    2345678899999999988875 4458899999944332 2222222       47789999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEECC-CchHH-----------------HHHHHhCCCeEEEEChHHHHHHHHcCCCC
Q psy17644        250 RELSQQIYNEAKRFGKGYNLSVVCCYGG-GSKWD-----------------QSKALELGAEIVVGTPGRIIDMVKMGATK  311 (330)
Q Consensus       250 r~La~Qi~~~~~~l~~~~~~~~~~~~gg-~~~~~-----------------~~~~l~~~~dIiV~TP~~L~~~l~~~~~~  311 (330)
                      ...+..|.-.++.+.    +.+. ..|. .....                 ..+..-....||.||-.++.+.+.    .
T Consensus       723 hsAVDNILiKL~~~~----i~~l-RLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~plf----~  793 (1100)
T KOG1805|consen  723 HSAVDNILIKLKGFG----IYIL-RLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHPLF----V  793 (1100)
T ss_pred             hHHHHHHHHHHhccC----ccee-ecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCchhh----h
Confidence            888777776666652    2221 1121 11111                 112223357899999877776553    2


Q ss_pred             CCCccEEEeecccccC
Q psy17644        312 LNRVTFLVLDEADRMF  327 (330)
Q Consensus       312 l~~i~~lVvDEad~ll  327 (330)
                      .+.++|.|||||-+|+
T Consensus       794 ~R~FD~cIiDEASQI~  809 (1100)
T KOG1805|consen  794 NRQFDYCIIDEASQIL  809 (1100)
T ss_pred             ccccCEEEEccccccc
Confidence            4568999999998875

>KOG1000|consensus

Probab=97.50  E-value=0.00075  Score=65.29  Aligned_cols=125  Identities=17%  Similarity=0.188  Sum_probs=82.4

Q ss_pred             CCCCHHHHHhhhhhc-CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC
Q psy17644        188 TSPTPIQAQAVPAAL-SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG  266 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~-~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~  266 (330)
                      ..+-|+|+..+...+ .|-.+++.-.+|-|||+-.+..+  ..+..      .+| .|||||. .+-..|.+.+.+|...
T Consensus       197 s~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAlaIA--~yyra------Ewp-lliVcPA-svrftWa~al~r~lps  266 (689)
T KOG1000|consen  197 SRLLPFQREGVIFALERGGRILLADEMGLGKTIQALAIA--RYYRA------EWP-LLIVCPA-SVRFTWAKALNRFLPS  266 (689)
T ss_pred             HhhCchhhhhHHHHHhcCCeEEEecccccchHHHHHHHH--HHHhh------cCc-EEEEecH-HHhHHHHHHHHHhccc
Confidence            446799999887766 66778888999999997665333  22221      344 4888997 4557788888888765


Q ss_pred             CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        267 YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       267 ~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      ..- +.++.++...-   ..+.....|.|.+...|..+-..  ..-....+||+||.|.|-+
T Consensus       267 ~~p-i~vv~~~~D~~---~~~~t~~~v~ivSye~ls~l~~~--l~~~~~~vvI~DEsH~Lk~  322 (689)
T KOG1000|consen  267 IHP-IFVVDKSSDPL---PDVCTSNTVAIVSYEQLSLLHDI--LKKEKYRVVIFDESHMLKD  322 (689)
T ss_pred             ccc-eEEEecccCCc---cccccCCeEEEEEHHHHHHHHHH--HhcccceEEEEechhhhhc
Confidence            332 44555554431   12233357889998887654331  2223578999999998743

>PRK10536 hypothetical protein; Provisional

Probab=97.50  E-value=0.00087  Score=60.61  Aligned_cols=61  Identities=18%  Similarity=0.123  Sum_probs=43.2

Q ss_pred             CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q psy17644        185 CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE  251 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~  251 (330)
                      .++..-+..|...+.++.++.-+++.|++|+|||+..+..++..++..      .-.+++|.-|+..
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~------~~~kIiI~RP~v~  115 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHK------DVDRIIVTRPVLQ  115 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcC------CeeEEEEeCCCCC
Confidence            345566889999999998888788889999999977766666555442      2244555556543

>KOG0922|consensus

Probab=97.43  E-value=0.0007  Score=67.63  Aligned_cols=118  Identities=18%  Similarity=0.184  Sum_probs=71.8

Q ss_pred             HHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH-HhccCCCceEE
Q psy17644        194 QAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK-RFGKGYNLSVV  272 (330)
Q Consensus       194 Q~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~-~l~~~~~~~~~  272 (330)
                      -.+++-.+-+.+-+|+.|.||||||.  .+|-  .+.... .  ....++-+.=|.|-.|..++.... ..+..+|-.+.
T Consensus        56 r~~il~~ve~nqvlIviGeTGsGKST--QipQ--yL~eaG-~--~~~g~I~~TQPRRVAavslA~RVAeE~~~~lG~~VG  128 (674)
T KOG0922|consen   56 RDQILYAVEDNQVLIVIGETGSGKST--QIPQ--YLAEAG-F--ASSGKIACTQPRRVAAVSLAKRVAEEMGCQLGEEVG  128 (674)
T ss_pred             HHHHHHHHHHCCEEEEEcCCCCCccc--cHhH--HHHhcc-c--ccCCcEEeecCchHHHHHHHHHHHHHhCCCcCceee
Confidence            34555566677889999999999993  2332  122210 0  122346677788888877776643 34444444443


Q ss_pred             EEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        273 CCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       273 ~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      ...--.+.      -.....|.+.|-|.|+.-+.. ...|+...++||||||.
T Consensus       129 Y~IRFed~------ts~~TrikymTDG~LLRE~l~-Dp~LskYsvIIlDEAHE  174 (674)
T KOG0922|consen  129 YTIRFEDS------TSKDTRIKYMTDGMLLREILK-DPLLSKYSVIILDEAHE  174 (674)
T ss_pred             eEEEeccc------CCCceeEEEecchHHHHHHhc-CCccccccEEEEechhh
Confidence            33211111      111358999999999875542 23478999999999994

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.39  E-value=0.0013  Score=66.81  Aligned_cols=70  Identities=20%  Similarity=0.181  Sum_probs=49.7

Q ss_pred             CHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        191 TPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       191 t~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..+|+.++..++..+-+++.|+.|+|||.+. ..++..+......  ...+++++.+||.-.|..+.+.+...
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~v-~~ll~~l~~~~~~--~~~~~I~l~APTGkAA~rL~e~~~~~  216 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTTV-ARLLLALVKQSPK--QGKLRIALAAPTGKAAARLAESLRKA  216 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHHH-HHHHHHHHHhccc--cCCCcEEEECCcHHHHHHHHHHHHhh
Confidence            3799999999999999999999999999432 2222223222110  11368999999999988888776654

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=97.39  E-value=0.0012  Score=68.75  Aligned_cols=66  Identities=20%  Similarity=0.203  Sum_probs=47.1

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      ...+++.|+.++..+..++-+++.++.|+|||.+  +-.+..++...    +....+++++||...|.++.+
T Consensus       321 ~~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~--l~~i~~~~~~~----~~~~~v~l~ApTg~AA~~L~e  386 (720)
T TIGR01448       321 RKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTI--TRAIIELAEEL----GGLLPVGLAAPTGRAAKRLGE  386 (720)
T ss_pred             CCCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHH--HHHHHHHHHHc----CCCceEEEEeCchHHHHHHHH
Confidence            3578999999999999888899999999999943  22333333321    011568889999888775443

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=97.34  E-value=0.00098  Score=67.84  Aligned_cols=70  Identities=20%  Similarity=0.198  Sum_probs=50.6

Q ss_pred             CHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        191 TPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       191 t~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      ..+|+.|+-..+..+-+++.|++|+|||.+. .-++..+.....   ....++++++||...|.++.+.+....
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v-~~ll~~l~~~~~---~~~~~i~l~APTgkAA~rL~e~~~~~~  223 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTV-AKLLAALIQLAD---GERCRIRLAAPTGKAAARLTESLGKAL  223 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHH-HHHHHHHHHhcC---CCCcEEEEECCcHHHHHHHHHHHHhhh
Confidence            5899999999999999999999999999432 122222322110   123578899999999999888776543

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

Probab=97.34  E-value=0.00053  Score=70.42  Aligned_cols=108  Identities=16%  Similarity=0.175  Sum_probs=66.2

Q ss_pred             CCCcEEEE-cCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        203 SGRDIIGV-AKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       203 ~g~d~i~~-a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      .++.+.++ +|+|||||.+. +..|...++.      ...++|+|+..|.|+.++...++...-. ++....-.++....
T Consensus        47 ~~~~V~vVRSpMGTGKTtaL-i~wLk~~l~~------~~~~VLvVShRrSL~~sL~~rf~~~~l~-gFv~Y~d~~~~~i~  118 (824)
T PF02399_consen   47 QKRGVLVVRSPMGTGKTTAL-IRWLKDALKN------PDKSVLVVSHRRSLTKSLAERFKKAGLS-GFVNYLDSDDYIID  118 (824)
T ss_pred             CCCCeEEEECCCCCCcHHHH-HHHHHHhccC------CCCeEEEEEhHHHHHHHHHHHHhhcCCC-cceeeecccccccc
Confidence            45555554 99999999554 4455554432      4678999999999999999988765211 22211111111110


Q ss_pred             HHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        282 DQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       282 ~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                            ....+-+++....|..+.   ...+.+.++|||||+-..+
T Consensus       119 ------~~~~~rLivqIdSL~R~~---~~~l~~yDvVIIDEv~svL  155 (824)
T PF02399_consen  119 ------GRPYDRLIVQIDSLHRLD---GSLLDRYDVVIIDEVMSVL  155 (824)
T ss_pred             ------ccccCeEEEEehhhhhcc---cccccccCEEEEehHHHHH
Confidence                  012355666666665443   2346678999999987654

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

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.32  E-value=0.0016  Score=67.94  Aligned_cols=62  Identities=15%  Similarity=0.090  Sum_probs=46.2

Q ss_pred             CCCCHHHHHhhhhhcCC-CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAALSG-RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIY  257 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g-~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~  257 (330)
                      ..+++-|+.++..++.+ +-+++.++.|+|||  +++-.+..++..      .+.++++++||.-.|..+.
T Consensus       351 ~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKT--tll~~i~~~~~~------~g~~V~~~ApTg~Aa~~L~  413 (744)
T TIGR02768       351 YRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKS--TMLKAAREAWEA------AGYRVIGAALSGKAAEGLQ  413 (744)
T ss_pred             CCCCHHHHHHHHHHhcCCCEEEEEecCCCCHH--HHHHHHHHHHHh------CCCeEEEEeCcHHHHHHHH
Confidence            45899999999998875 55677799999999  344445555443      4678999999977766543

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.

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=97.29  E-value=0.002  Score=68.11  Aligned_cols=81  Identities=25%  Similarity=0.134  Sum_probs=49.8

Q ss_pred             CHHHHHhhhhhcC--------CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        191 TPIQAQAVPAALS--------GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       191 t~iQ~~~i~~~~~--------g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      ..+|-.|+..+..        |--++-.|.||+|||++=.=.|..  +..    ...|.+..|-.-.|.|-.|+-..+++
T Consensus       410 F~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNARImya--Lsd----~~~g~RfsiALGLRTLTLQTGda~r~  483 (1110)
T TIGR02562       410 FRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANARAMYA--LRD----DKQGARFAIALGLRSLTLQTGHALKT  483 (1110)
T ss_pred             cchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHHHHHHH--hCC----CCCCceEEEEccccceeccchHHHHH
Confidence            4588888887763        223444499999999775432221  111    13466777778888888888777776


Q ss_pred             hccCCCceEEEEECC
Q psy17644        263 FGKGYNLSVVCCYGG  277 (330)
Q Consensus       263 l~~~~~~~~~~~~gg  277 (330)
                      -..-..-...+++||
T Consensus       484 rL~L~~ddLAVlIGs  498 (1110)
T TIGR02562       484 RLNLSDDDLAVLIGG  498 (1110)
T ss_pred             hcCCCccceEEEECH
Confidence            544323334444443

The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=97.29  E-value=0.0008  Score=71.18  Aligned_cols=134  Identities=23%  Similarity=0.193  Sum_probs=86.8

Q ss_pred             CCCCHHHHHhhhhhc-----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAAL-----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~-----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      ..+.++|...+..+.     .+.+.++....|-|||+..+.-+.. ++....   ...+.+||+||+ +++.+|..++.+
T Consensus       337 ~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~-~~~~~~---~~~~~~liv~p~-s~~~nw~~e~~k  411 (866)
T COG0553         337 AELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLS-LLESIK---VYLGPALIVVPA-SLLSNWKREFEK  411 (866)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHh-hhhccc---CCCCCeEEEecH-HHHHHHHHHHhh
Confidence            446677888887654     3677888899999999554433322 222211   125688999998 677899999998


Q ss_pred             hccCCCceEEEEECCCch----HHHHHHHhC-C----CeEEEEChHHHHHHH-HcCCCCCCCccEEEeecccccC
Q psy17644        263 FGKGYNLSVVCCYGGGSK----WDQSKALEL-G----AEIVVGTPGRIIDMV-KMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       263 l~~~~~~~~~~~~gg~~~----~~~~~~l~~-~----~dIiV~TP~~L~~~l-~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      +...... +...+|....    ......+.. .    .+|+++|.+.|.... ......-..+.++|+||||++-
T Consensus       412 ~~~~~~~-~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~ik  485 (866)
T COG0553         412 FAPDLRL-VLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIK  485 (866)
T ss_pred             hCccccc-eeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHHhhceeeeeehhhHHHHh
Confidence            8765443 4445554431    333333322 2    699999999998742 1122334567899999999864

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=97.26  E-value=0.0028  Score=58.35  Aligned_cols=141  Identities=16%  Similarity=0.148  Sum_probs=85.4

Q ss_pred             CCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhc----------CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCC
Q psy17644        170 GHFGFDEVLMKALRKCEYTSPTPIQAQAVPAAL----------SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGD  239 (330)
Q Consensus       170 ~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~----------~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~  239 (330)
                      -.+.|+..++..    |  .++..|.+++-.+.          ..+-.++--.||.||.....--++.+++..       
T Consensus        24 y~~~lp~~~~~~----g--~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~G-------   90 (303)
T PF13872_consen   24 YRLHLPEEVIDS----G--LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRG-------   90 (303)
T ss_pred             cccCCCHHHHhc----c--cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcC-------
Confidence            345677765432    2  46788888876553          234455557799888644333355555542       


Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcC---CCCC----
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG---ATKL----  312 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~---~~~l----  312 (330)
                      ..++|+|..+..|.....+.++.++.. .+.+..+..-..  .....+  .-.||++|...|..--.++   ...+    
T Consensus        91 r~r~vwvS~s~dL~~Da~RDl~DIG~~-~i~v~~l~~~~~--~~~~~~--~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~  165 (303)
T PF13872_consen   91 RKRAVWVSVSNDLKYDAERDLRDIGAD-NIPVHPLNKFKY--GDIIRL--KEGVLFSTYSTLISESQSGGKYRSRLDQLV  165 (303)
T ss_pred             CCceEEEECChhhhhHHHHHHHHhCCC-cccceechhhcc--CcCCCC--CCCccchhHHHHHhHHhccCCccchHHHHH
Confidence            346899999999999999999988654 333333322000  001112  3469999999888765321   1111    


Q ss_pred             -----CCccEEEeecccccCc
Q psy17644        313 -----NRVTFLVLDEADRMFD  328 (330)
Q Consensus       313 -----~~i~~lVvDEad~lld  328 (330)
                           ..=.+|||||||++-.
T Consensus       166 ~W~g~dfdgvivfDEcH~akn  186 (303)
T PF13872_consen  166 DWCGEDFDGVIVFDECHKAKN  186 (303)
T ss_pred             HHHhcCCCceEEeccchhcCC
Confidence                 1125899999998753

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.25  E-value=0.00042  Score=66.34  Aligned_cols=59  Identities=20%  Similarity=0.307  Sum_probs=46.5

Q ss_pred             CCHHHHHhhhhh------cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH
Q psy17644        190 PTPIQAQAVPAA------LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQI  256 (330)
Q Consensus       190 pt~iQ~~~i~~~------~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi  256 (330)
                      +++-|+.++..+      ..+..+++.|+-|+|||  |++-++.+.+..      .+..+++++||--.|..+
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs--~l~~~i~~~~~~------~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKS--FLIKAIIDYLRS------RGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChh--HHHHHHHHHhcc------ccceEEEecchHHHHHhc
Confidence            567788888888      68889999999999999  666666665543      467899999998777655

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.23  E-value=0.002  Score=68.76  Aligned_cols=61  Identities=20%  Similarity=0.137  Sum_probs=45.7

Q ss_pred             CCCCHHHHHhhhhhcCCCc-EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAALSGRD-IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQI  256 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d-~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi  256 (330)
                      ..+++-|.+++..++.+++ +++.+..|+|||.+  +-++..+...      .|.+++.++||--.|..+
T Consensus       345 ~~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~--l~~~~~~~e~------~G~~V~~~ApTGkAA~~L  406 (988)
T PRK13889        345 LVLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM--LGVAREAWEA------AGYEVRGAALSGIAAENL  406 (988)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH--HHHHHHHHHH------cCCeEEEecCcHHHHHHH
Confidence            4689999999999998776 45669999999954  3344444432      478899999998766554

>KOG1131|consensus

Probab=97.20  E-value=0.0029  Score=61.72  Aligned_cols=73  Identities=15%  Similarity=0.119  Sum_probs=41.2

Q ss_pred             CCCCCHHHHHhhhhh----cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        187 YTSPTPIQAQAVPAA----LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~----~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      |...+|-|-.-.--+    -.+-+.++..|+|+|||.+.+--++...+..+.    ...+.++-.-|..-+.....++++
T Consensus        14 Y~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~----~~~KliYCSRTvpEieK~l~El~~   89 (755)
T KOG1131|consen   14 YDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPD----EHRKLIYCSRTVPEIEKALEELKR   89 (755)
T ss_pred             CcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCc----ccceEEEecCcchHHHHHHHHHHH
Confidence            445566665544332    356678999999999997765555554444321    223444544454444444444444


Q ss_pred             h
Q psy17644        263 F  263 (330)
Q Consensus       263 l  263 (330)
                      +
T Consensus        90 l   90 (755)
T KOG1131|consen   90 L   90 (755)
T ss_pred             H
Confidence            3

>KOG1133|consensus

Probab=97.16  E-value=0.0029  Score=63.57  Aligned_cols=42  Identities=26%  Similarity=0.305  Sum_probs=33.4

Q ss_pred             CCCCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      .+|+.||.+.+..++    .|+=.|+.+|||+|||+..+-.++.++
T Consensus        14 y~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL   59 (821)
T KOG1133|consen   14 YTPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWL   59 (821)
T ss_pred             CCchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHH
Confidence            468899998887765    789888889999999987666665544

>KOG0925|consensus

Probab=96.97  E-value=0.0044  Score=60.04  Aligned_cols=88  Identities=17%  Similarity=0.122  Sum_probs=54.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       166 ~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      +..|...+++++..+.+++..--.-+..+...+..+.+.+-+++++.||||||.-.=--++...+..       ...|..
T Consensus        24 ~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~-------~~~v~C   96 (699)
T KOG0925|consen   24 INPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSH-------LTGVAC   96 (699)
T ss_pred             cCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhh-------ccceee
Confidence            5668888888888888776544334455555666677888899999999999932100011111111       123344


Q ss_pred             EcccHHHHHHHHHHH
Q psy17644        246 LAPTRELSQQIYNEA  260 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~  260 (330)
                      --|.|..|.++....
T Consensus        97 TQprrvaamsva~RV  111 (699)
T KOG0925|consen   97 TQPRRVAAMSVAQRV  111 (699)
T ss_pred             cCchHHHHHHHHHHH
Confidence            457777777766553

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.97  E-value=0.0061  Score=62.67  Aligned_cols=67  Identities=30%  Similarity=0.386  Sum_probs=50.3

Q ss_pred             CCCHHHHHhhhhhcC----C-CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        189 SPTPIQAQAVPAALS----G-RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~----g-~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .|+..|..+|..+.+    | +..++.|-||||||+...  .   ++.+      .+..+|||+|+..+|.|++..++.|
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a--~---~~~~------~~~p~Lvi~~n~~~A~ql~~el~~f   77 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMA--N---VIAQ------VNRPTLVIAHNKTLAAQLYNEFKEF   77 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHH--H---HHHH------hCCCEEEEECCHHHHHHHHHHHHHh
Confidence            688899999888753    3 366788999999995432  2   2221      1345799999999999999999999


Q ss_pred             ccC
Q psy17644        264 GKG  266 (330)
Q Consensus       264 ~~~  266 (330)
                      ...
T Consensus        78 ~p~   80 (655)
T TIGR00631        78 FPE   80 (655)
T ss_pred             CCC
Confidence            753

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

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=96.94  E-value=0.00052  Score=55.09  Aligned_cols=18  Identities=39%  Similarity=0.396  Sum_probs=11.3

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      +++-+++.|++|+|||.+
T Consensus         3 ~~~~~~i~G~~G~GKT~~   20 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTL   20 (131)
T ss_dssp             ----EEEEE-TTSSHHHH
T ss_pred             CCcccEEEcCCCCCHHHH
Confidence            345678889999999944

>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=96.80  E-value=0.0086  Score=47.96  Aligned_cols=17  Identities=24%  Similarity=0.454  Sum_probs=14.8

Q ss_pred             CCCcEEEEcCCCChhHH
Q psy17644        203 SGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~  219 (330)
                      .++.+++.|++|+|||.
T Consensus        18 ~~~~v~i~G~~G~GKT~   34 (151)
T cd00009          18 PPKNLLLYGPPGTGKTT   34 (151)
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            36789999999999994

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.

>PHA02533 17 large terminase protein; Provisional

Probab=96.72  E-value=0.0054  Score=61.53  Aligned_cols=122  Identities=16%  Similarity=0.013  Sum_probs=76.5

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCC
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN  268 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~  268 (330)
                      .|.|+|...+..+..+|-.++..+-..|||.+.+.-++...+..      .+..+++++|++..|..+++.++.+....+
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~------~~~~v~i~A~~~~QA~~vF~~ik~~ie~~P  132 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFN------KDKNVGILAHKASMAAEVLDRTKQAIELLP  132 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhC------CCCEEEEEeCCHHHHHHHHHHHHHHHHhCH
Confidence            57899999998876667677777888999976665455444432      356999999999999999998887654332


Q ss_pred             c--eEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        269 L--SVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       269 ~--~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      .  +......  +  .....+.+|+.|.+.|-.       .+...=.+..++|+||+|.+-
T Consensus       133 ~l~~~~i~~~--~--~~~I~l~NGS~I~~lss~-------~~t~rG~~~~~liiDE~a~~~  182 (534)
T PHA02533        133 DFLQPGIVEW--N--KGSIELENGSKIGAYASS-------PDAVRGNSFAMIYIDECAFIP  182 (534)
T ss_pred             HHhhcceeec--C--ccEEEeCCCCEEEEEeCC-------CCccCCCCCceEEEeccccCC
Confidence            1  1000000  0  011223456676554421       111122356789999999753

>KOG0923|consensus

Probab=96.70  E-value=0.0058  Score=61.23  Aligned_cols=120  Identities=18%  Similarity=0.191  Sum_probs=70.3

Q ss_pred             CHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH-HhccCCCc
Q psy17644        191 TPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK-RFGKGYNL  269 (330)
Q Consensus       191 t~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~-~l~~~~~~  269 (330)
                      .++-.+++.++..++=+|+.|.||||||  ..+|-..+  ... . .+.|.++-+--|.|-.|..+...+. .++..+|.
T Consensus       267 y~ykdell~av~e~QVLiI~GeTGSGKT--TQiPQyL~--EaG-y-tk~gk~IgcTQPRRVAAmSVAaRVA~EMgvkLG~  340 (902)
T KOG0923|consen  267 YPYKDELLKAVKEHQVLIIVGETGSGKT--TQIPQYLY--EAG-Y-TKGGKKIGCTQPRRVAAMSVAARVAEEMGVKLGH  340 (902)
T ss_pred             hhhHHHHHHHHHhCcEEEEEcCCCCCcc--ccccHHHH--hcc-c-ccCCceEeecCcchHHHHHHHHHHHHHhCccccc
Confidence            3444555666667778888899999999  34553322  110 0 0123446666788988888776643 33333332


Q ss_pred             eEEE--EECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        270 SVVC--CYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       270 ~~~~--~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      .+..  -|.....        ...-|=+.|-|.|+.=+.. -..|.+..++||||||.
T Consensus       341 eVGYsIRFEdcTS--------ekTvlKYMTDGmLlREfL~-epdLasYSViiiDEAHE  389 (902)
T KOG0923|consen  341 EVGYSIRFEDCTS--------EKTVLKYMTDGMLLREFLS-EPDLASYSVIIVDEAHE  389 (902)
T ss_pred             ccceEEEeccccC--------cceeeeeecchhHHHHHhc-cccccceeEEEeehhhh
Confidence            2211  1111111        1134557898888774432 34588999999999994

>PRK04296 thymidine kinase; Provisional

Probab=96.65  E-value=0.0067  Score=52.58  Aligned_cols=36  Identities=17%  Similarity=0.171  Sum_probs=23.7

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP  248 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P  248 (330)
                      .=.++.+++|+|||.. ++-++.++..       .+.+++|+-|
T Consensus         3 ~i~litG~~GsGKTT~-~l~~~~~~~~-------~g~~v~i~k~   38 (190)
T PRK04296          3 KLEFIYGAMNSGKSTE-LLQRAYNYEE-------RGMKVLVFKP   38 (190)
T ss_pred             EEEEEECCCCCHHHHH-HHHHHHHHHH-------cCCeEEEEec
Confidence            3467789999999944 3344444433       3667888866

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=96.63  E-value=0.0055  Score=63.03  Aligned_cols=48  Identities=19%  Similarity=0.203  Sum_probs=32.0

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      -++=+.+.||+|||.+|+--|...-.+      ..-.+-||||||.+.-.-++.
T Consensus        75 lNiDI~METGTGKTy~YlrtmfeLhk~------YG~~KFIivVPs~AIkeGv~~  122 (985)
T COG3587          75 LNIDILMETGTGKTYTYLRTMFELHKK------YGLFKFIIVVPSLAIKEGVFL  122 (985)
T ss_pred             ceeeEEEecCCCceeeHHHHHHHHHHH------hCceeEEEEeccHHHHhhhHH
Confidence            356667999999999997544432111      234678999999876544333

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.58  E-value=0.0039  Score=49.45  Aligned_cols=17  Identities=47%  Similarity=0.561  Sum_probs=14.3

Q ss_pred             CCcEEEEcCCCChhHHH
Q psy17644        204 GRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a  220 (330)
                      ++.+++.+++|+|||..
T Consensus         2 ~~~~~l~G~~G~GKTtl   18 (148)
T smart00382        2 GEVILIVGPPGSGKTTL   18 (148)
T ss_pred             CCEEEEECCCCCcHHHH
Confidence            56789999999999943

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.

>KOG0924|consensus

Probab=96.57  E-value=0.01  Score=59.76  Aligned_cols=116  Identities=18%  Similarity=0.210  Sum_probs=64.4

Q ss_pred             HHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH-hccCCCceEE
Q psy17644        194 QAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR-FGKGYNLSVV  272 (330)
Q Consensus       194 Q~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~-l~~~~~~~~~  272 (330)
                      +.+++..+...+-+++++.||||||.-  +|  ++++...   -..+..+-+--|.|..|..+...+.. +...+|..+.
T Consensus       361 R~~ll~~ir~n~vvvivgETGSGKTTQ--l~--QyL~edG---Y~~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VG  433 (1042)
T KOG0924|consen  361 RDQLLSVIRENQVVVIVGETGSGKTTQ--LA--QYLYEDG---YADNGMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVG  433 (1042)
T ss_pred             HHHHHHHHhhCcEEEEEecCCCCchhh--hH--HHHHhcc---cccCCeeeecCchHHHHHHHHHHHHHHhCCccccccc
Confidence            344444444566677889999999943  22  2222211   01233444555889888888776543 4333333322


Q ss_pred             EE--ECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        273 CC--YGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       273 ~~--~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      ..  |...+.        ...-|=..|-|.|+.-.-. ...|.+..+||+||||.
T Consensus       434 YsIRFEdvT~--------~~T~IkymTDGiLLrEsL~-d~~L~kYSviImDEAHE  479 (1042)
T KOG0924|consen  434 YSIRFEDVTS--------EDTKIKYMTDGILLRESLK-DRDLDKYSVIIMDEAHE  479 (1042)
T ss_pred             eEEEeeecCC--------CceeEEEeccchHHHHHhh-hhhhhheeEEEechhhh
Confidence            21  111111        1245667888887663211 23467888999999994

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.52  E-value=0.0089  Score=57.21  Aligned_cols=91  Identities=21%  Similarity=0.137  Sum_probs=47.9

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCC-CeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG-PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~-~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      .|+.+++++|||+|||.+...-+...+..       .+ .++.+++ +...-.--++.++.|++..++.+..+..+....
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~-------~G~~~V~lit-~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~  207 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMR-------FGASKVALLT-TDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQ  207 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHh-------cCCCeEEEEe-cccccccHHHHHHHHHHHcCCceEecCCcccHH
Confidence            46788899999999996554333332222       12 2444333 322211123344555555566666555554444


Q ss_pred             HHHHHHhCCCeEEEEChHHH
Q psy17644        282 DQSKALELGAEIVVGTPGRI  301 (330)
Q Consensus       282 ~~~~~l~~~~dIiV~TP~~L  301 (330)
                      .....+....-|+|=|+++.
T Consensus       208 ~~l~~l~~~DlVLIDTaG~~  227 (374)
T PRK14722        208 LALAELRNKHMVLIDTIGMS  227 (374)
T ss_pred             HHHHHhcCCCEEEEcCCCCC
Confidence            44444444444666677654

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=96.49  E-value=0.036  Score=59.87  Aligned_cols=75  Identities=16%  Similarity=0.074  Sum_probs=49.8

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHhhhhhcC-CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q psy17644        174 FDEVLMKALRKCEYTSPTPIQAQAVPAALS-GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL  252 (330)
Q Consensus       174 l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~-g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~L  252 (330)
                      +++..+...... ...+++-|..++..+.. ++=+++.|..|+|||.  ++-.+..+...      .|.+++.++||---
T Consensus       367 v~~~~l~a~~~~-~~~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt--~l~~~~~~~e~------~G~~V~g~ApTgkA  437 (1102)
T PRK13826        367 VREAVLAATFAR-HARLSDEQKTAIEHVAGPARIAAVVGRAGAGKTT--MMKAAREAWEA------AGYRVVGGALAGKA  437 (1102)
T ss_pred             CCHHHHHHHHhc-CCCCCHHHHHHHHHHhccCCeEEEEeCCCCCHHH--HHHHHHHHHHH------cCCeEEEEcCcHHH
Confidence            344444433332 24689999999998864 4556677999999993  33344444432      47889999999777


Q ss_pred             HHHHH
Q psy17644        253 SQQIY  257 (330)
Q Consensus       253 a~Qi~  257 (330)
                      |..+.
T Consensus       438 A~~L~  442 (1102)
T PRK13826        438 AEGLE  442 (1102)
T ss_pred             HHHHH
Confidence            76543

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.47  E-value=0.013  Score=53.94  Aligned_cols=53  Identities=23%  Similarity=0.328  Sum_probs=36.9

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCc-EEEEcCCCChhHHHHHHHHHHHHHhc
Q psy17644        160 ADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRD-IIGVAKTGSGKTGAFIWPMLVHIMDQ  232 (330)
Q Consensus       160 ~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d-~i~~a~TGsGKT~a~llp~l~~i~~~  232 (330)
                      ..+|..+.+|+++++++.+.+.+ .                  ..+- +++.+||||||| +.+..++.++-++
T Consensus        99 R~Ip~~i~~~e~LglP~i~~~~~-~------------------~~~GLILVTGpTGSGKS-TTlAamId~iN~~  152 (353)
T COG2805          99 RLIPSKIPTLEELGLPPIVRELA-E------------------SPRGLILVTGPTGSGKS-TTLAAMIDYINKH  152 (353)
T ss_pred             eccCccCCCHHHcCCCHHHHHHH-h------------------CCCceEEEeCCCCCcHH-HHHHHHHHHHhcc
Confidence            35688888999999888776632 1                  1222 566699999998 4455677777654

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.46  E-value=0.02  Score=59.28  Aligned_cols=70  Identities=17%  Similarity=0.104  Sum_probs=51.9

Q ss_pred             CCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        190 PTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       190 pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      +++-|++++..  ...++++.|..|||||.+ ++.-+.+++....   ....++|+|+.|+..|.++...+.++..
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--VTGPCLVLAGAGSGKTRV-ITNKIAYLIQNCG---YKARNIAAVTFTNKAAREMKERVAKTLG   71 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHH-HHHHHHHHHHhcC---CCHHHeEEEeccHHHHHHHHHHHHHHhC
Confidence            67899998865  346899999999999954 4444555554311   1346789999999999999999887653

Designed to identify rep members of the uvrD/rep subfamily.

>PRK11054 helD DNA helicase IV; Provisional

Probab=96.41  E-value=0.017  Score=59.74  Aligned_cols=75  Identities=21%  Similarity=0.232  Sum_probs=53.2

Q ss_pred             CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        185 CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .....+++-|+.++-..  ..++++.|..|||||.+. +.-+.+++....   ..+.++|+|+.||..|..+.+.+....
T Consensus       192 ~e~~~L~~~Q~~av~~~--~~~~lV~agaGSGKT~vl-~~r~ayLl~~~~---~~~~~IL~ltft~~AA~em~eRL~~~l  265 (684)
T PRK11054        192 VESSPLNPSQARAVVNG--EDSLLVLAGAGSGKTSVL-VARAGWLLARGQ---AQPEQILLLAFGRQAAEEMDERIRERL  265 (684)
T ss_pred             ccCCCCCHHHHHHHhCC--CCCeEEEEeCCCCHHHHH-HHHHHHHHHhCC---CCHHHeEEEeccHHHHHHHHHHHHHhc
Confidence            33457899999988543  356888999999999543 334444443221   134689999999999999999887654


Q ss_pred             c
Q psy17644        265 K  265 (330)
Q Consensus       265 ~  265 (330)
                      .
T Consensus       266 g  266 (684)
T PRK11054        266 G  266 (684)
T ss_pred             C
Confidence            3

>KOG0953|consensus

Probab=96.37  E-value=0.0022  Score=62.91  Aligned_cols=96  Identities=23%  Similarity=0.253  Sum_probs=61.8

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA  286 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~  286 (330)
                      ++.+|||.||||.    .+|+++..        ....++--|.|-||..+++.+...    |+.+-++.|..-...... 
T Consensus       194 i~H~GPTNSGKTy----~ALqrl~~--------aksGvycGPLrLLA~EV~~r~na~----gipCdL~TGeE~~~~~~~-  256 (700)
T KOG0953|consen  194 IMHVGPTNSGKTY----RALQRLKS--------AKSGVYCGPLRLLAHEVYDRLNAL----GIPCDLLTGEERRFVLDN-  256 (700)
T ss_pred             EEEeCCCCCchhH----HHHHHHhh--------hccceecchHHHHHHHHHHHhhhc----CCCccccccceeeecCCC-
Confidence            5556999999995    46677654        345699999999999999999887    444444444222111100 


Q ss_pred             HhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        287 LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       287 l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                       .+.+..+-||-+...        --...++.||||+++|-|
T Consensus       257 -~~~a~hvScTVEM~s--------v~~~yeVAViDEIQmm~D  289 (700)
T KOG0953|consen  257 -GNPAQHVSCTVEMVS--------VNTPYEVAVIDEIQMMRD  289 (700)
T ss_pred             -CCcccceEEEEEEee--------cCCceEEEEehhHHhhcC
Confidence             112455666643221        124578999999998865

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=96.34  E-value=0.025  Score=58.34  Aligned_cols=68  Identities=29%  Similarity=0.346  Sum_probs=51.4

Q ss_pred             CCCCHHHHHhhhhhcC----C-CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAALS----G-RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~----g-~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      ..|++.|..++..+.+    | +..++.+.+|||||+... .++..          .+..+|||+|+...|.|++..++.
T Consensus        11 ~~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia-~l~~~----------~~r~vLIVt~~~~~A~~l~~dL~~   79 (652)
T PRK05298         11 YKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA-NVIAR----------LQRPTLVLAHNKTLAAQLYSEFKE   79 (652)
T ss_pred             CCCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH-HHHHH----------hCCCEEEEECCHHHHHHHHHHHHH
Confidence            3699999999988753    3 256788999999996532 12221          134689999999999999999999


Q ss_pred             hccC
Q psy17644        263 FGKG  266 (330)
Q Consensus       263 l~~~  266 (330)
                      |...
T Consensus        80 ~~~~   83 (652)
T PRK05298         80 FFPE   83 (652)
T ss_pred             hcCC
Confidence            8643

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=96.30  E-value=0.014  Score=53.19  Aligned_cols=120  Identities=17%  Similarity=0.124  Sum_probs=57.5

Q ss_pred             hhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCC
Q psy17644        199 PAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGG  278 (330)
Q Consensus       199 ~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~  278 (330)
                      --+..|.-+++.|++|+|||. +++.++.++..+      .+.+|+++.- -.-..++...+........+......-+.
T Consensus        25 gG~~~g~~~~i~g~~G~GKT~-l~~~~~~~~~~~------~g~~vl~iS~-E~~~~~~~~r~~~~~~~~~~~~~~~~~~~   96 (271)
T cd01122          25 KGLRKGELIILTAGTGVGKTT-FLREYALDLITQ------HGVRVGTISL-EEPVVRTARRLLGQYAGKRLHLPDTVFIY   96 (271)
T ss_pred             EEEcCCcEEEEEcCCCCCHHH-HHHHHHHHHHHh------cCceEEEEEc-ccCHHHHHHHHHHHHhCCCcccCCccccc
Confidence            344567788889999999994 444444444332      2567777753 22344444444332111121111000011


Q ss_pred             chHHHH---HHHhCCCeEEE-E-----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        279 SKWDQS---KALELGAEIVV-G-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       279 ~~~~~~---~~l~~~~dIiV-~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ......   ..+.....+++ -     |+..+...+..-.. -..+++||||-.+.|.
T Consensus        97 ~~~~~~~~~~~~~~~~~l~i~d~~~~~~~~~i~~~i~~~~~-~~~~~~vvID~l~~l~  153 (271)
T cd01122          97 TLEEFDAAFDEFEGTGRLFMYDSFGEYSMDSVLEKVRYMAV-SHGIQHIIIDNLSIMV  153 (271)
T ss_pred             cHHHHHHHHHHhcCCCcEEEEcCCCccCHHHHHHHHHHHHh-cCCceEEEECCHHHHh
Confidence            111111   12221122222 1     45555555542211 1367899999987765

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>KOG1001|consensus

Probab=96.25  E-value=0.019  Score=59.07  Aligned_cols=114  Identities=25%  Similarity=0.204  Sum_probs=68.7

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCC-CCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKE-LEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ  283 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~-~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~  283 (330)
                      +-.|+.--.|-|||...+.-++.+-..... .........|||||+ .+..||..++.+......+.+.+.+|   ....
T Consensus       153 ~ggIladd~glgkt~~ti~l~l~~~~~~~~~~~~~~~kttLivcp~-s~~~qW~~elek~~~~~~l~v~v~~g---r~kd  228 (674)
T KOG1001|consen  153 RGGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPT-SLLTQWKTELEKVTEEDKLSIYVYHG---RTKD  228 (674)
T ss_pred             ccceEeeccccchHHHHHHHHHhcccCCcchhhccccCceeEecch-HHHHHHHHHHhccCCccceEEEEecc---cccc
Confidence            345666778999997655444433221110 001234567999998 56688888886666555555555555   2222


Q ss_pred             HHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        284 SKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       284 ~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ...+ ...+|||+||+.|..    .....-..-.+|+||||.+-
T Consensus       229 ~~el-~~~dVVltTy~il~~----~~l~~i~w~Riildea~~ik  267 (674)
T KOG1001|consen  229 KSEL-NSYDVVLTTYDILKN----SPLVKIKWLRIVLDEAHTIK  267 (674)
T ss_pred             cchh-cCCceEEeeHHHhhc----ccccceeEEEEEeccccccC
Confidence            2223 346899999988874    11111345678999999875

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.18  E-value=0.031  Score=55.23  Aligned_cols=90  Identities=16%  Similarity=0.077  Sum_probs=48.1

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEE-EEccc-HHHHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGL-ILAPT-RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vL-il~Pt-r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      |+-+.++|+||+|||.+...-+-.+....      .+.++. |-+-+ |.-+   .+.++.|+...++.+..+..+....
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~------G~~kV~LI~~Dt~RigA---~EQLr~~AeilGVpv~~~~~~~Dl~  326 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRH------GASKVALLTTDSYRIGG---HEQLRIYGKILGVPVHAVKDAADLR  326 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhc------CCCeEEEEeCCccchhH---HHHHHHHHHHhCCCeeccCCchhHH
Confidence            45577889999999965443332222221      112333 33333 3222   3445555555566555544444444


Q ss_pred             HHHHHHhCCCeEEEEChHHHH
Q psy17644        282 DQSKALELGAEIVVGTPGRII  302 (330)
Q Consensus       282 ~~~~~l~~~~dIiV~TP~~L~  302 (330)
                      .....+...-.|+|-|+++..
T Consensus       327 ~aL~~L~d~d~VLIDTaGr~~  347 (484)
T PRK06995        327 LALSELRNKHIVLIDTIGMSQ  347 (484)
T ss_pred             HHHHhccCCCeEEeCCCCcCh
Confidence            444455555578888998543

>KOG4150|consensus

Probab=96.16  E-value=0.003  Score=62.25  Aligned_cols=139  Identities=12%  Similarity=-0.059  Sum_probs=98.7

Q ss_pred             HHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH
Q psy17644        182 LRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK  261 (330)
Q Consensus       182 l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~  261 (330)
                      +.++.......+|..++..+-.|+++++.-.|.+||.++|.+.++...+.-      .....+++.||.++++...+.+.
T Consensus       279 ~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~------~~s~~~~~~~~~~~~~~~~~~~~  352 (1034)
T KOG4150|consen  279 LNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLC------HATNSLLPSEMVEHLRNGSKGQV  352 (1034)
T ss_pred             HhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcC------cccceecchhHHHHhhccCCceE
Confidence            445566777899999999999999999999999999999999888776553      23456888999998876433322


Q ss_pred             Hhcc---CCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC----CCCCccEEEeeccccc
Q psy17644        262 RFGK---GYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT----KLNRVTFLVLDEADRM  326 (330)
Q Consensus       262 ~l~~---~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~----~l~~i~~lVvDEad~l  326 (330)
                      -...   ....-++-.+.|.+........+.+..+|.+.|...+..+--+..    .+-...++++|++|.-
T Consensus       353 V~~~~I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y  424 (1034)
T KOG4150|consen  353 VHVEVIKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALY  424 (1034)
T ss_pred             EEEEehhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeee
Confidence            1111   111234455667776666777778899999999998875532222    2445677888998854

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=96.14  E-value=0.017  Score=59.84  Aligned_cols=71  Identities=20%  Similarity=0.124  Sum_probs=52.0

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      .+++-|++++...  ...+++.|..|||||.+ ++.-+.+++.+..   -...++|+|+-|+..|..+...+.++..
T Consensus         2 ~Ln~~Q~~av~~~--~g~~lV~AgpGSGKT~v-L~~Ria~Li~~~~---v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919          2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRV-ITNKIAHLIRGCG---YQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCCHHHH-HHHHHHHHHHhcC---CCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            3788999998753  46788999999999955 3444455554311   1245799999999999999998887643

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=96.09  E-value=0.008  Score=59.67  Aligned_cols=125  Identities=16%  Similarity=0.107  Sum_probs=72.8

Q ss_pred             HHHHHhhhhhcC---------CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        192 PIQAQAVPAALS---------GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       192 ~iQ~~~i~~~~~---------g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      |+|+-++-.++.         .+.+++.-+-+.|||.....-++.+++-..    ..++.++++++++..|..+++.++.
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~g----~~~~~i~~~A~~~~QA~~~f~~~~~   76 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLDG----EPGAEIYCAANTRDQAKIVFDEAKK   76 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcCC----ccCceEEEEeCCHHHHHHHHHHHHH
Confidence            567777666651         246888888999999554444454544321    2478999999999999999999998


Q ss_pred             hccCCCceEEEEECCCchHHHHHHHhC-CCeEEEEChHHHHHHHHcC--CCCCCCccEEEeecccccCc
Q psy17644        263 FGKGYNLSVVCCYGGGSKWDQSKALEL-GAEIVVGTPGRIIDMVKMG--ATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       263 l~~~~~~~~~~~~gg~~~~~~~~~l~~-~~dIiV~TP~~L~~~l~~~--~~~l~~i~~lVvDEad~lld  328 (330)
                      +........... .       .+..+. ...|.....+.++..+.+.  ...=.+..++|+||+|.+-+
T Consensus        77 ~i~~~~~l~~~~-~-------~~~~~~~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~i~DE~h~~~~  137 (477)
T PF03354_consen   77 MIEASPELRKRK-K-------PKIIKSNKKEIEFPKTGSFFKALSSDADSLDGLNPSLAIFDELHAHKD  137 (477)
T ss_pred             HHHhChhhccch-h-------hhhhhhhceEEEEcCCCcEEEEEecCCCCccCCCCceEEEeCCCCCCC
Confidence            876532211100 0       000000 1133332223333222221  12223578999999998753

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.99  E-value=0.049  Score=52.43  Aligned_cols=87  Identities=16%  Similarity=0.142  Sum_probs=43.4

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc--cHH-HHHHHHHHHHHhccCCCceEEEEECCCch
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP--TRE-LSQQIYNEAKRFGKGYNLSVVCCYGGGSK  280 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P--tr~-La~Qi~~~~~~l~~~~~~~~~~~~gg~~~  280 (330)
                      .+.++++|+||+|||.....-+ ..+..       .+.++.++..  .|. .+.|    ++.++...++.+..+......
T Consensus       241 ~~vI~LVGptGvGKTTTiaKLA-~~L~~-------~GkkVglI~aDt~RiaAvEQ----Lk~yae~lgipv~v~~d~~~L  308 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAKMA-WQFHG-------KKKTVGFITTDHSRIGTVQQ----LQDYVKTIGFEVIAVRDEAAM  308 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHHHH-HHHHH-------cCCcEEEEecCCcchHHHHH----HHHHhhhcCCcEEecCCHHHH
Confidence            3567888999999994433222 23322       3455555443  342 2333    334444445555444322222


Q ss_pred             HHHHHHHhC--CCe-EEEEChHHHH
Q psy17644        281 WDQSKALEL--GAE-IVVGTPGRII  302 (330)
Q Consensus       281 ~~~~~~l~~--~~d-IiV~TP~~L~  302 (330)
                      ......++.  ++| |||=|||+..
T Consensus       309 ~~aL~~lk~~~~~DvVLIDTaGRs~  333 (436)
T PRK11889        309 TRALTYFKEEARVDYILIDTAGKNY  333 (436)
T ss_pred             HHHHHHHHhccCCCEEEEeCccccC
Confidence            222333332  344 6677888753

>TIGR01075 uvrD DNA helicase II

Probab=95.99  E-value=0.027  Score=58.83  Aligned_cols=72  Identities=15%  Similarity=0.160  Sum_probs=54.3

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      ..+++-|++++...  ...+++.|..|||||.+ +..-+.+++.+..   -...++|+|+-|+..|..+.+.+.++..
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~-L~~Ria~Li~~~~---v~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075         3 DGLNDKQREAVAAP--PGNLLVLAGAGSGKTRV-LTHRIAWLLSVEN---ASPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             cccCHHHHHHHcCC--CCCEEEEecCCCCHHHH-HHHHHHHHHHcCC---CCHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            35889999998653  45799999999999954 4444555555321   1345889999999999999999888754

Designed to identify uvrD members of the uvrD/rep subfamily.

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=95.93  E-value=0.026  Score=55.15  Aligned_cols=32  Identities=22%  Similarity=0.179  Sum_probs=25.2

Q ss_pred             CCHHHHHhhhhhcCCCcEEEEcCCCChhHHHH
Q psy17644        190 PTPIQAQAVPAALSGRDIIGVAKTGSGKTGAF  221 (330)
Q Consensus       190 pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~  221 (330)
                      +-.....++..+..++++++.+++|+|||...
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA  211 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVA  211 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHH
Confidence            34455666777778999999999999999544

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.81  E-value=0.029  Score=52.76  Aligned_cols=45  Identities=29%  Similarity=0.332  Sum_probs=29.8

Q ss_pred             HHHCCCCCCCHHHHHhhhhhc-CCCcEEEEcCCCChhHHHHHHHHHHHH
Q psy17644        182 LRKCEYTSPTPIQAQAVPAAL-SGRDIIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       182 l~~~~~~~pt~iQ~~~i~~~~-~g~d~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      +...|.  +++.|...+..+. .+++++++|+|||||| +++-.++..+
T Consensus       123 lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKT-Tll~aL~~~i  168 (323)
T PRK13833        123 YVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKT-TLANAVIAEI  168 (323)
T ss_pred             HHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHHH
Confidence            344444  5577776665554 6678999999999999 3334444444

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=95.80  E-value=0.091  Score=51.24  Aligned_cols=86  Identities=19%  Similarity=0.160  Sum_probs=45.0

Q ss_pred             cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc--cHHHHHHHHHHHHHhccCCCceEEEEECCCchH--
Q psy17644        206 DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP--TRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW--  281 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P--tr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~--  281 (330)
                      -+++++++|+|||.+..--+  +.+..      .|.+|++++-  .|.-|..   +++.++...++.+...+.+....  
T Consensus       102 vi~lvG~~GvGKTTtaaKLA--~~l~~------~G~kV~lV~~D~~R~aA~e---QLk~~a~~~~vp~~~~~~~~dp~~i  170 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLA--YYYQR------KGFKPCLVCADTFRAGAFD---QLKQNATKARIPFYGSYTESDPVKI  170 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHH--HHHHH------CCCCEEEEcCcccchhHHH---HHHHHhhccCCeEEeecCCCCHHHH
Confidence            46677999999984433211  22222      2456666553  3544443   34445555566665555444321  


Q ss_pred             --HHHHHHh-CCCe-EEEEChHHHH
Q psy17644        282 --DQSKALE-LGAE-IVVGTPGRII  302 (330)
Q Consensus       282 --~~~~~l~-~~~d-IiV~TP~~L~  302 (330)
                        .....++ .++| |||=||+++.
T Consensus       171 ~~~~l~~~~~~~~DvViIDTaGr~~  195 (429)
T TIGR01425       171 ASEGVEKFKKENFDIIIVDTSGRHK  195 (429)
T ss_pred             HHHHHHHHHhCCCCEEEEECCCCCc
Confidence              1122222 3556 5677998873

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.

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=95.75  E-value=0.047  Score=60.38  Aligned_cols=121  Identities=18%  Similarity=0.166  Sum_probs=74.9

Q ss_pred             CCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC-CC
Q psy17644        190 PTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG-YN  268 (330)
Q Consensus       190 pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~-~~  268 (330)
                      .|+-|.++|.  ..++++++.|.-|||||.+.+--++..+...     ..-.++|+|+=|+..|..+...+++-... ..
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~-----~~~~~il~~tFt~~aa~e~~~ri~~~l~~~~~   74 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRG-----VDIDRLLVVTFTNAAAREMKERIEEALQKALQ   74 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcC-----CCHhhEEEEeccHHHHHHHHHHHHHHHHHHHh
Confidence            5889999997  3688999999999999977666666665532     12246899999999999988887764322 11


Q ss_pred             ceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHH-HHcCCC--CCCCccEEEeecccc
Q psy17644        269 LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDM-VKMGAT--KLNRVTFLVLDEADR  325 (330)
Q Consensus       269 ~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~-l~~~~~--~l~~i~~lVvDEad~  325 (330)
                      -..       ......+.+..-...-|+|-..++.- +++...  ++. -.+=|.||...
T Consensus        75 ~~p-------~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~~~l~ld-P~F~i~de~e~  126 (1232)
T TIGR02785        75 QEP-------NSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDLD-PSFRILTDTEQ  126 (1232)
T ss_pred             cCc-------hhHHHHHHHhhccCCeEeeHHHHHHHHHHHhhhhcCCC-CCceeCCHHHH
Confidence            000       11111222222235578998887764 443222  121 13345777653

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.

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=95.68  E-value=0.031  Score=58.38  Aligned_cols=72  Identities=18%  Similarity=0.178  Sum_probs=53.3

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      ..+++-|++++...  ...+++.|..|||||.+ +..-+.+++....   -...++|+|+-|+..|..+.+.+.++..
T Consensus         8 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~v-l~~Ria~Li~~~~---v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          8 DSLNDKQREAVAAP--LGNMLVLAGAGSGKTRV-LVHRIAWLMQVEN---ASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             HhcCHHHHHHHhCC--CCCEEEEecCCCCHHHH-HHHHHHHHHHcCC---CChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            35889999998754  35799999999999954 3344445554321   1345789999999999999999888754

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.68  E-value=0.13  Score=47.18  Aligned_cols=88  Identities=20%  Similarity=0.237  Sum_probs=44.6

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA--PTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~--Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      .+-+++++++|+|||.+..--+ .++..       .+.+++++.  +.|.-+.+   .++.++...++.+.....+.+..
T Consensus        72 ~~vi~l~G~~G~GKTTt~akLA-~~l~~-------~g~~V~li~~D~~r~~a~~---ql~~~~~~~~i~~~~~~~~~dp~  140 (272)
T TIGR00064        72 PNVILFVGVNGVGKTTTIAKLA-NKLKK-------QGKSVLLAAGDTFRAAAIE---QLEEWAKRLGVDVIKQKEGADPA  140 (272)
T ss_pred             CeEEEEECCCCCcHHHHHHHHH-HHHHh-------cCCEEEEEeCCCCCHHHHH---HHHHHHHhCCeEEEeCCCCCCHH
Confidence            3456777999999995433222 22222       355666665  33444332   33344444454443322222221


Q ss_pred             HH-----HHHHhCCCe-EEEEChHHHH
Q psy17644        282 DQ-----SKALELGAE-IVVGTPGRII  302 (330)
Q Consensus       282 ~~-----~~~l~~~~d-IiV~TP~~L~  302 (330)
                      ..     ......+++ |||=||+++.
T Consensus       141 ~~~~~~l~~~~~~~~D~ViIDT~G~~~  167 (272)
T TIGR00064       141 AVAFDAIQKAKARNIDVVLIDTAGRLQ  167 (272)
T ss_pred             HHHHHHHHHHHHCCCCEEEEeCCCCCc
Confidence            11     112235567 7788998874

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.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=95.61  E-value=0.033  Score=52.31  Aligned_cols=48  Identities=27%  Similarity=0.363  Sum_probs=32.4

Q ss_pred             HHHHHHCCCCCCCHHHHHhhhhh-cCCCcEEEEcCCCChhHHHHHHHHHHHH
Q psy17644        179 MKALRKCEYTSPTPIQAQAVPAA-LSGRDIIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       179 ~~~l~~~~~~~pt~iQ~~~i~~~-~~g~d~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      +..+...|+  +++.|...+..+ ..+++++++|+|||||| +++-.++..+
T Consensus       124 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~aL~~~~  172 (319)
T PRK13894        124 LDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKT-TLVNAIINEM  172 (319)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHhh
Confidence            344445554  457777777654 47789999999999999 4444455444

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=95.59  E-value=0.053  Score=44.52  Aligned_cols=38  Identities=26%  Similarity=0.357  Sum_probs=22.2

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL  252 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~L  252 (330)
                      +++.|++|+|||.... -++..+..       .+..++++.....+
T Consensus         2 ~~i~G~~G~GKT~l~~-~i~~~~~~-------~~~~v~~~~~e~~~   39 (165)
T cd01120           2 ILVFGPTGSGKTTLAL-QLALNIAT-------KGGKVVYVDIEEEI   39 (165)
T ss_pred             eeEeCCCCCCHHHHHH-HHHHHHHh-------cCCEEEEEECCcch
Confidence            5788999999994333 22333222       35566666654333

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=95.58  E-value=0.078  Score=55.48  Aligned_cols=72  Identities=19%  Similarity=0.254  Sum_probs=52.9

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      ..++|-|.+++...  ...+++.|..|||||.+.+ .-+.+++.....   ..-++|+|+-|+..|..+.+.+.+++.
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~l~-~ria~Li~~~~i---~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073         3 AHLNPEQREAVKTT--EGPLLIMAGAGSGKTRVLT-HRIAHLIAEKNV---APWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             cccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHH-HHHHHHHHcCCC---CHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            35789999998753  4679999999999995433 334455543211   235789999999999999999887754

Designed to identify pcrA members of the uvrD/rep subfamily.

>KOG0298|consensus

Probab=95.51  E-value=0.022  Score=60.97  Aligned_cols=100  Identities=18%  Similarity=0.178  Sum_probs=63.6

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCC----------CCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEE
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKE----------LEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVV  272 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~----------~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~  272 (330)
                      .|++++..-..|.|||.+-+.-.+.+..+...          ........+|||+|. ++..||+.++.+-+... +++.
T Consensus       373 ~g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~-aIl~QW~~EI~kH~~~~-lKv~  450 (1394)
T KOG0298|consen  373 HGKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPN-AILMQWFEEIHKHISSL-LKVL  450 (1394)
T ss_pred             CCcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcH-HHHHHHHHHHHHhcccc-ceEE
Confidence            45677888889999997766555554322111          011234677999998 56699999999877653 5666


Q ss_pred             EEECCCchHH-HHHHHhCCCeEEEEChHHHHHHH
Q psy17644        273 CCYGGGSKWD-QSKALELGAEIVVGTPGRIIDMV  305 (330)
Q Consensus       273 ~~~gg~~~~~-~~~~l~~~~dIiV~TP~~L~~~l  305 (330)
                      ..+|-..... +...+ -.+|||++|+..|..=+
T Consensus       451 ~Y~Girk~~~~~~~el-~~yDIVlTtYdiLr~El  483 (1394)
T KOG0298|consen  451 LYFGIRKTFWLSPFEL-LQYDIVLTTYDILRNEL  483 (1394)
T ss_pred             EEechhhhcccCchhh-hccCEEEeehHHHHhHh
Confidence            5555221110 11122 24899999999997744

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.51  E-value=0.096  Score=60.33  Aligned_cols=63  Identities=24%  Similarity=0.283  Sum_probs=47.0

Q ss_pred             CCCHHHHHhhhhhcCC--CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q psy17644        189 SPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE  259 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g--~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~  259 (330)
                      .+++-|+.++..++..  +=.++.++.|+|||  +++-.+..+...      .|.++++++||...+.++.+.
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKT--t~l~~l~~~~~~------~G~~V~~lAPTgrAA~~L~e~  493 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGST--EIAQLLLHLASE------QGYEIQIITAGSLSAQELRQK  493 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHH--HHHHHHHHHHHh------cCCeEEEEeCCHHHHHHHHHH
Confidence            5789999999998865  45667799999999  334444455443      478899999998877666554

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.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.50  E-value=0.024  Score=50.61  Aligned_cols=48  Identities=29%  Similarity=0.364  Sum_probs=31.0

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc---cHHHHHHH
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP---TRELSQQI  256 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P---tr~La~Qi  256 (330)
                      ..|.=+++.|++|+||| +|++-++.+...+      .+..+++++.   ..+++.++
T Consensus        11 ~~G~l~lI~G~~G~GKT-~~~~~~~~~~~~~------~g~~vly~s~E~~~~~~~~r~   61 (242)
T cd00984          11 QPGDLIIIAARPSMGKT-AFALNIAENIAKK------QGKPVLFFSLEMSKEQLLQRL   61 (242)
T ss_pred             CCCeEEEEEeCCCCCHH-HHHHHHHHHHHHh------CCCceEEEeCCCCHHHHHHHH
Confidence            45667888899999999 5555555555442      2567788773   34444443

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.

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=95.48  E-value=0.036  Score=52.28  Aligned_cols=64  Identities=19%  Similarity=0.123  Sum_probs=46.5

Q ss_pred             CCCCCCCHHHHHhhhhhcCCC--cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q psy17644        185 CEYTSPTPIQAQAVPAALSGR--DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELS  253 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g~--d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La  253 (330)
                      .|+..-...|..|+.+++.-.  =|.+.++.|||||+..+.+.|..++.++.     -.++||--||..+.
T Consensus       224 wGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~-----y~KiiVtRp~vpvG  289 (436)
T COG1875         224 WGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKR-----YRKIIVTRPTVPVG  289 (436)
T ss_pred             hccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhh-----hceEEEecCCcCcc
Confidence            466666678999999888543  24555999999999999999988887643     34666666765543

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.34  E-value=0.045  Score=50.54  Aligned_cols=19  Identities=42%  Similarity=0.473  Sum_probs=14.7

Q ss_pred             CCCcEEEEcCCCChhHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAF  221 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~  221 (330)
                      .++-+++++|||+|||.+.
T Consensus       193 ~~~vi~~vGptGvGKTTt~  211 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTL  211 (282)
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3456888899999999443

>KOG1015|consensus

Probab=95.31  E-value=0.069  Score=55.86  Aligned_cols=116  Identities=20%  Similarity=0.153  Sum_probs=63.2

Q ss_pred             CCcEEEEcCCCChhHHH---HHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC----CceEEEEEC
Q psy17644        204 GRDIIGVAKTGSGKTGA---FIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY----NLSVVCCYG  276 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a---~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~----~~~~~~~~g  276 (330)
                      |-.+|+.--.|-|||+-   |+--+|.+.   +    ..-.+||||||.. .+..|+.+|.+|....    .+.+..+-.
T Consensus       696 GsGcILAHcMGLGKTlQVvtflhTvL~c~---k----lg~ktaLvV~PlN-t~~NW~~EFekWm~~~e~~~~leV~eL~~  767 (1567)
T KOG1015|consen  696 GSGCILAHCMGLGKTLQVVTFLHTVLLCD---K----LGFKTALVVCPLN-TALNWMNEFEKWMEGLEDDEKLEVSELAT  767 (1567)
T ss_pred             CcchHHHHhhcccceehhhHHHHHHHHhh---c----cCCceEEEEcchH-HHHHHHHHHHHhcccccccccceeehhhh
Confidence            33455555579999943   333333332   1    2356899999985 4588999999997742    233333322


Q ss_pred             CCchHHHHHHHh---CCCeEEEEChHHHHHHHHcCCCC-------------CCCccEEEeecccccC
Q psy17644        277 GGSKWDQSKALE---LGAEIVVGTPGRIIDMVKMGATK-------------LNRVTFLVLDEADRMF  327 (330)
Q Consensus       277 g~~~~~~~~~l~---~~~dIiV~TP~~L~~~l~~~~~~-------------l~~i~~lVvDEad~ll  327 (330)
                      -.........|.   ....|.|.-+..+..+-..+...             -..-++||.||+|.|-
T Consensus       768 vkr~e~R~~~L~~W~~~ggVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLK  834 (1567)
T KOG1015|consen  768 VKRPEERSYMLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILK  834 (1567)
T ss_pred             ccChHHHHHHHHHHHhcCCEEEEehHHHHHHhcccchhhhHHHHHHHHhccCCCCCeEEecchhhhc
Confidence            222222222222   22255555555554443211111             1235899999999874

>PRK08727 hypothetical protein; Validated

Probab=95.27  E-value=0.07  Score=47.74  Aligned_cols=50  Identities=18%  Similarity=0.197  Sum_probs=28.3

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .-+++.|++|+|||..  +.++.+-..+      .+.+++++ |..++...+...+..+
T Consensus        42 ~~l~l~G~~G~GKThL--~~a~~~~~~~------~~~~~~y~-~~~~~~~~~~~~~~~l   91 (233)
T PRK08727         42 DWLYLSGPAGTGKTHL--ALALCAAAEQ------AGRSSAYL-PLQAAAGRLRDALEAL   91 (233)
T ss_pred             CeEEEECCCCCCHHHH--HHHHHHHHHH------cCCcEEEE-eHHHhhhhHHHHHHHH
Confidence            3488899999999933  2232222222      35667765 4445555444444444

>PRK07952 DNA replication protein DnaC; Validated

Probab=95.26  E-value=0.19  Score=45.38  Aligned_cols=42  Identities=19%  Similarity=0.253  Sum_probs=25.3

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQ  255 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Q  255 (330)
                      ..+++.+++|+|||.... .+.+++..       .+..++++ +..+|...
T Consensus       100 ~~~~l~G~~GtGKThLa~-aia~~l~~-------~g~~v~~i-t~~~l~~~  141 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAA-AICNELLL-------RGKSVLII-TVADIMSA  141 (244)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHh-------cCCeEEEE-EHHHHHHH
Confidence            478899999999994332 34444443       24556555 44444433

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.24  E-value=0.094  Score=54.58  Aligned_cols=88  Identities=18%  Similarity=0.134  Sum_probs=43.2

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCC-CeEEEEcc-c-HHHHHHHHHHHHHhccCCCceEEEEECCCch
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG-PMGLILAP-T-RELSQQIYNEAKRFGKGYNLSVVCCYGGGSK  280 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~-~~vLil~P-t-r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~  280 (330)
                      |+=+.+++|||+|||.+...-+......       .+ .++.++.- | |.-+   .+.++.++...++.+..+......
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~-------~G~kkV~lit~Dt~RigA---~eQL~~~a~~~gvpv~~~~~~~~l  254 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAR-------EGADQLALLTTDSFRIGA---LEQLRIYGRILGVPVHAVKDAADL  254 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHH-------cCCCeEEEecCcccchHH---HHHHHHHHHhCCCCccccCCHHHH
Confidence            4456788999999996554333322222       23 24444443 2 2222   334455555555555443332222


Q ss_pred             HHHHHHHhCCCeEEEEChHHH
Q psy17644        281 WDQSKALELGAEIVVGTPGRI  301 (330)
Q Consensus       281 ~~~~~~l~~~~dIiV~TP~~L  301 (330)
                      ......++..--|||=|+++.
T Consensus       255 ~~al~~~~~~D~VLIDTAGRs  275 (767)
T PRK14723        255 RFALAALGDKHLVLIDTVGMS  275 (767)
T ss_pred             HHHHHHhcCCCEEEEeCCCCC
Confidence            222333333334677788854

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.24  E-value=0.069  Score=51.50  Aligned_cols=91  Identities=16%  Similarity=0.103  Sum_probs=44.5

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc-c-cHHHHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA-P-TRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~-P-tr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      ++-++++|+||+|||.+..--+........    ..+.+|.+++ - .|.-+..+   ++.++...++.+..........
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~----~~g~~V~lit~Dt~R~aa~eQ---L~~~a~~lgvpv~~~~~~~~l~  246 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSD----DKSLNIKIITIDNYRIGAKKQ---IQTYGDIMGIPVKAIESFKDLK  246 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhc----cCCCeEEEEeccCccHHHHHH---HHHHhhcCCcceEeeCcHHHHH
Confidence            456888899999999554322222221110    1234444443 3 34444332   5566665666554433322222


Q ss_pred             HHHHHHhCCCe-EEEEChHHHH
Q psy17644        282 DQSKALELGAE-IVVGTPGRII  302 (330)
Q Consensus       282 ~~~~~l~~~~d-IiV~TP~~L~  302 (330)
                      .....+. +++ |||=|++++.
T Consensus       247 ~~L~~~~-~~DlVLIDTaGr~~  267 (388)
T PRK12723        247 EEITQSK-DFDLVLVDTIGKSP  267 (388)
T ss_pred             HHHHHhC-CCCEEEEcCCCCCc
Confidence            2223333 345 5566877654

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=95.20  E-value=0.046  Score=51.25  Aligned_cols=33  Identities=30%  Similarity=0.299  Sum_probs=28.8

Q ss_pred             CCCCCCHHHHHhhhhhcCCC-cEEEEcCCCChhH
Q psy17644        186 EYTSPTPIQAQAVPAALSGR-DIIGVAKTGSGKT  218 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~~g~-d~i~~a~TGsGKT  218 (330)
                      .|...++-|...+-.+..++ ++++++.||||||
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKT  187 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKT  187 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHH
Confidence            45678899999988888776 9999999999999

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=95.11  E-value=0.13  Score=50.66  Aligned_cols=51  Identities=10%  Similarity=0.095  Sum_probs=30.5

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK  261 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~  261 (330)
                      +..+++.|++|+|||  .++.++.+.+...    ..+.+++++.. .++...+...+.
T Consensus       141 ~npl~i~G~~G~GKT--HLl~Ai~~~l~~~----~~~~~v~yv~~-~~f~~~~~~~l~  191 (450)
T PRK14087        141 YNPLFIYGESGMGKT--HLLKAAKNYIESN----FSDLKVSYMSG-DEFARKAVDILQ  191 (450)
T ss_pred             cCceEEECCCCCcHH--HHHHHHHHHHHHh----CCCCeEEEEEH-HHHHHHHHHHHH
Confidence            356889999999999  4444444433321    13456666544 566666655543

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=95.11  E-value=0.065  Score=51.43  Aligned_cols=89  Identities=21%  Similarity=0.194  Sum_probs=53.6

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHH-HhcCCCCCCCCCeEEEEccc-HHHHHHHHHHHHHhccCCCceEEEEECCCc
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHI-MDQKELEPGDGPMGLILAPT-RELSQQIYNEAKRFGKGYNLSVVCCYGGGS  279 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i-~~~~~~~~~~~~~vLil~Pt-r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~  279 (330)
                      .+++-+.++||||.|||.+..=-+.... ...      +...+||-+-| |-=|   ++.++.+++-+++.+..++....
T Consensus       201 ~~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~------~~kVaiITtDtYRIGA---~EQLk~Ya~im~vp~~vv~~~~e  271 (407)
T COG1419         201 EQKRVIALVGPTGVGKTTTLAKLAARYVMLKK------KKKVAIITTDTYRIGA---VEQLKTYADIMGVPLEVVYSPKE  271 (407)
T ss_pred             ccCcEEEEECCCCCcHHHHHHHHHHHHHhhcc------CcceEEEEeccchhhH---HHHHHHHHHHhCCceEEecCHHH
Confidence            4588899999999999954332222222 221      23345665555 4333   34456666666778887877766


Q ss_pred             hHHHHHHHhCCCeEEEEChH
Q psy17644        280 KWDQSKALELGAEIVVGTPG  299 (330)
Q Consensus       280 ~~~~~~~l~~~~dIiV~TP~  299 (330)
                      .......+...-.|+|=|-|
T Consensus       272 l~~ai~~l~~~d~ILVDTaG  291 (407)
T COG1419         272 LAEAIEALRDCDVILVDTAG  291 (407)
T ss_pred             HHHHHHHhhcCCEEEEeCCC
Confidence            66666666664445566654

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.01  E-value=0.077  Score=49.40  Aligned_cols=47  Identities=28%  Similarity=0.362  Sum_probs=29.0

Q ss_pred             HHHHHCCCCCCCHHHHHhhhh-hcCCCcEEEEcCCCChhHHHHHHHHHHHH
Q psy17644        180 KALRKCEYTSPTPIQAQAVPA-ALSGRDIIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       180 ~~l~~~~~~~pt~iQ~~~i~~-~~~g~d~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      ..+.+.|.  +++.|...+.. +..+++++++|+|||||| +++-.++..+
T Consensus       109 ~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~al~~~i  156 (299)
T TIGR02782       109 DDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKT-TLANALLAEI  156 (299)
T ss_pred             HHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHHh
Confidence            34444443  44555555544 446679999999999999 3333444444

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.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.91  E-value=0.12  Score=50.52  Aligned_cols=88  Identities=19%  Similarity=0.172  Sum_probs=42.2

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc--cHHHHHHHHHHHHHhccCCCceEEEEECCCch
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP--TRELSQQIYNEAKRFGKGYNLSVVCCYGGGSK  280 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P--tr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~  280 (330)
                      .|+-+++++|||+|||.+.+--+.......      .+.+|.+|.-  .|.-+   ...++.++...++.+..+......
T Consensus       220 ~~~~i~~vGptGvGKTTt~~kLA~~~~~~~------~g~~V~li~~D~~r~~a---~eqL~~~a~~~~vp~~~~~~~~~l  290 (424)
T PRK05703        220 QGGVVALVGPTGVGKTTTLAKLAARYALLY------GKKKVALITLDTYRIGA---VEQLKTYAKIMGIPVEVVYDPKEL  290 (424)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhc------CCCeEEEEECCccHHHH---HHHHHHHHHHhCCceEccCCHHhH
Confidence            366788889999999954332222221111      2345554442  23322   233444444445554444433322


Q ss_pred             HHHHHHHhCCCe-EEEEChHH
Q psy17644        281 WDQSKALELGAE-IVVGTPGR  300 (330)
Q Consensus       281 ~~~~~~l~~~~d-IiV~TP~~  300 (330)
                      ......+. +++ |||=||++
T Consensus       291 ~~~l~~~~-~~DlVlIDt~G~  310 (424)
T PRK05703        291 AKALEQLR-DCDVILIDTAGR  310 (424)
T ss_pred             HHHHHHhC-CCCEEEEeCCCC
Confidence            22233333 345 66667754

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=94.90  E-value=0.17  Score=53.39  Aligned_cols=16  Identities=31%  Similarity=0.638  Sum_probs=12.5

Q ss_pred             CCccEEEeecccccCc
Q psy17644        313 NRVTFLVLDEADRMFD  328 (330)
Q Consensus       313 ~~i~~lVvDEad~lld  328 (330)
                      ..+.+|||||+|.|..
T Consensus       868 r~v~IIILDEID~L~k  883 (1164)
T PTZ00112        868 RNVSILIIDEIDYLIT  883 (1164)
T ss_pred             ccceEEEeehHhhhCc
Confidence            4567899999998863

>PRK05973 replicative DNA helicase; Provisional

Probab=94.89  E-value=0.12  Score=46.36  Aligned_cols=67  Identities=21%  Similarity=0.334  Sum_probs=43.3

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      ..+||... +..-+..|.-+++.|++|+||| +|++.++....+       +|.+++|++- -+-..|+...+..++
T Consensus        49 ~~~~p~~~-l~GGl~~Gsl~LIaG~PG~GKT-~lalqfa~~~a~-------~Ge~vlyfSl-Ees~~~i~~R~~s~g  115 (237)
T PRK05973         49 AATTPAEE-LFSQLKPGDLVLLGARPGHGKT-LLGLELAVEAMK-------SGRTGVFFTL-EYTEQDVRDRLRALG  115 (237)
T ss_pred             cCCCCHHH-hcCCCCCCCEEEEEeCCCCCHH-HHHHHHHHHHHh-------cCCeEEEEEE-eCCHHHHHHHHHHcC
Confidence            45677443 5555667778888899999999 455555544443       3566777743 344567777777663

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.86  E-value=0.17  Score=50.56  Aligned_cols=20  Identities=40%  Similarity=0.415  Sum_probs=16.0

Q ss_pred             cCCCcEEEEcCCCChhHHHH
Q psy17644        202 LSGRDIIGVAKTGSGKTGAF  221 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~  221 (330)
                      ..|+-++++|+||+|||...
T Consensus       348 ~~G~vIaLVGPtGvGKTTta  367 (559)
T PRK12727        348 ERGGVIALVGPTGAGKTTTI  367 (559)
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            35678888899999999554

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=94.83  E-value=0.073  Score=49.24  Aligned_cols=53  Identities=13%  Similarity=0.220  Sum_probs=35.4

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCC----CCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE----PGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~----~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      .+++++|+|+.|||.     ++.++.......    ...-|.++|-+|...-....+..+-.
T Consensus        62 p~lLivG~snnGKT~-----Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~  118 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTM-----IIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILE  118 (302)
T ss_pred             CceEEecCCCCcHHH-----HHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHH
Confidence            579999999999995     334444332211    11237888888988877777777443

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.83  E-value=0.15  Score=48.88  Aligned_cols=88  Identities=14%  Similarity=0.179  Sum_probs=42.8

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc--cHHHHHHHHHHHHHhccCCCceEEEEECCCch
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP--TRELSQQIYNEAKRFGKGYNLSVVCCYGGGSK  280 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P--tr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~  280 (330)
                      .++-+++++|+|+|||....--+. ++..       .+.++.+++-  .|.-|   ...++.++...++.+.........
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~-~l~~-------~g~~V~lItaDtyR~gA---veQLk~yae~lgvpv~~~~dp~dL  273 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGW-QLLK-------QNRTVGFITTDTFRSGA---VEQFQGYADKLDVELIVATSPAEL  273 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH-HHHH-------cCCeEEEEeCCccCccH---HHHHHHHhhcCCCCEEecCCHHHH
Confidence            466788889999999954332222 2222       2344544442  34322   223444544445544432221111


Q ss_pred             HHHHHHHh--CCCe-EEEEChHHH
Q psy17644        281 WDQSKALE--LGAE-IVVGTPGRI  301 (330)
Q Consensus       281 ~~~~~~l~--~~~d-IiV~TP~~L  301 (330)
                      ......++  .+++ |||=|||+.
T Consensus       274 ~~al~~l~~~~~~D~VLIDTAGr~  297 (407)
T PRK12726        274 EEAVQYMTYVNCVDHILIDTVGRN  297 (407)
T ss_pred             HHHHHHHHhcCCCCEEEEECCCCC
Confidence            22222232  2344 677899884

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=94.81  E-value=0.12  Score=46.88  Aligned_cols=110  Identities=17%  Similarity=0.161  Sum_probs=58.4

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc---HHHHHHHHHHHHHhccCCCceEEEEECCC-c
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT---RELSQQIYNEAKRFGKGYNLSVVCCYGGG-S  279 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt---r~La~Qi~~~~~~l~~~~~~~~~~~~gg~-~  279 (330)
                      |.=+++.|+||.||| +|++.+..++...      .+..|+|++.-   .+++..+.......    .  ...+..|. .
T Consensus        19 g~L~vi~a~pg~GKT-~~~l~ia~~~a~~------~~~~vly~SlEm~~~~l~~R~la~~s~v----~--~~~i~~g~l~   85 (259)
T PF03796_consen   19 GELTVIAARPGVGKT-AFALQIALNAALN------GGYPVLYFSLEMSEEELAARLLARLSGV----P--YNKIRSGDLS   85 (259)
T ss_dssp             T-EEEEEESTTSSHH-HHHHHHHHHHHHT------TSSEEEEEESSS-HHHHHHHHHHHHHTS----T--HHHHHCCGCH
T ss_pred             CcEEEEEecccCCch-HHHHHHHHHHHHh------cCCeEEEEcCCCCHHHHHHHHHHHhhcc----h--hhhhhccccC
Confidence            344566699999999 5666666666553      24678888752   44444444333222    1  11111122 1


Q ss_pred             hHHH------HHHHhCCCeEEE-E----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        280 KWDQ------SKALELGAEIVV-G----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       280 ~~~~------~~~l~~~~dIiV-~----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ..+.      ...+.. ..+.| .    |+..+...+..-......+.+||||-.+.|-
T Consensus        86 ~~e~~~~~~~~~~l~~-~~l~i~~~~~~~~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~  143 (259)
T PF03796_consen   86 DEEFERLQAAAEKLSD-LPLYIEDTPSLTIDDIESKIRRLKREGKKVDVVFIDYLQLLK  143 (259)
T ss_dssp             HHHHHHHHHHHHHHHT-SEEEEEESSS-BHHHHHHHHHHHHHHSTTEEEEEEEEGGGSB
T ss_pred             HHHHHHHHHHHHHHhh-CcEEEECCCCCCHHHHHHHHHHHHhhccCCCEEEechHHHhc
Confidence            1111      122333 34443 3    4455665554322223688999999999874

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 ....

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=94.81  E-value=0.052  Score=52.48  Aligned_cols=108  Identities=12%  Similarity=0.130  Sum_probs=61.8

Q ss_pred             cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH-HHHHHHHHHHHhccCCCceEEEEECCCchHHHH
Q psy17644        206 DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE-LSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS  284 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~-La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~  284 (330)
                      -.++.+..|||||.+.++-++..++...     .+.++|++.+|.. |..-++..+.......++....-......  .+
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~-----~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g~~~~~~~~~~~~--~i   75 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINK-----KQQNILAARKVQNSIRDSVFKDIENLLSIEGINYEFKKSKSSM--EI   75 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcC-----CCcEEEEEehhhhHHHHHHHHHHHHHHHHcCChhheeecCCcc--EE
Confidence            3577799999999888888887777641     3578899999876 66666666766554444432111111100  00


Q ss_pred             HHHhC-CCeEEEECh-HHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        285 KALEL-GAEIVVGTP-GRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       285 ~~l~~-~~dIiV~TP-~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                       .+.. +..|++..- .....+     .....+.++.+|||..+
T Consensus        76 -~~~~~g~~i~f~g~~d~~~~i-----k~~~~~~~~~idEa~~~  113 (396)
T TIGR01547        76 -KILNTGKKFIFKGLNDKPNKL-----KSGAGIAIIWFEEASQL  113 (396)
T ss_pred             -EecCCCeEEEeecccCChhHh-----hCcceeeeehhhhhhhc
Confidence             1112 445555432 111111     11234688999998765

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.

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=94.80  E-value=0.017  Score=49.17  Aligned_cols=50  Identities=18%  Similarity=0.195  Sum_probs=33.0

Q ss_pred             chHHHHHHHhCCCeEEEEChHHHHHHHHcCCC--CCCCccEEEeecccccCc
Q psy17644        279 SKWDQSKALELGAEIVVGTPGRIIDMVKMGAT--KLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       279 ~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~--~l~~i~~lVvDEad~lld  328 (330)
                      ......+.....++|||++..-|++-..+...  ....-.+|||||||.|.+
T Consensus       108 CPY~~~r~~~~~adivi~~y~yl~~~~~~~~~~~~~~~~~ivI~DEAHNL~~  159 (174)
T PF06733_consen  108 CPYYLARELAKNADIVICNYNYLFDPSIRKSLFGIDLKDNIVIFDEAHNLED  159 (174)
T ss_dssp             -HHHHHHHCGGG-SEEEEETHHHHSHHHHHHHCT--CCCEEEEETTGGGCGG
T ss_pred             ChhHHHHHhcccCCEEEeCHHHHhhHHHHhhhccccccCcEEEEecccchHH
Confidence            44455666667799999999988775432221  123447999999999875

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.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.80  E-value=0.07  Score=51.93  Aligned_cols=92  Identities=16%  Similarity=0.082  Sum_probs=46.1

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc-HHHHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT-RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt-r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      .|+-+.++|+||+|||.....-+-..++...     .....+|.+.+ |.-+   ++.+..++..+++.+..+.......
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~-----~~~v~~i~~d~~riga---lEQL~~~a~ilGvp~~~v~~~~dl~  261 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAARAVIRHG-----ADKVALLTTDSYRIGG---HEQLRIYGKLLGVSVRSIKDIADLQ  261 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcC-----CCeEEEEecCCcchhH---HHHHHHHHHHcCCceecCCCHHHHH
Confidence            4556777899999999554432222322211     12234555555 3222   2334445554555555444433333


Q ss_pred             HHHHHHhCCCeEEEEChHHHH
Q psy17644        282 DQSKALELGAEIVVGTPGRII  302 (330)
Q Consensus       282 ~~~~~l~~~~dIiV~TP~~L~  302 (330)
                      .....+...-.|+|-|+|+..
T Consensus       262 ~al~~l~~~d~VLIDTaGrsq  282 (420)
T PRK14721        262 LMLHELRGKHMVLIDTVGMSQ  282 (420)
T ss_pred             HHHHHhcCCCEEEecCCCCCc
Confidence            333334433456677776543

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=94.70  E-value=0.23  Score=50.84  Aligned_cols=73  Identities=11%  Similarity=0.120  Sum_probs=50.4

Q ss_pred             CCCCCHHHHHhhhhhc---CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        187 YTSPTPIQAQAVPAAL---SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~---~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..-|+|.-.+-|..++   ..+-.++.+|-|-|||.+..+.++ ++...      .+.+++|.+|...-+.+++..++++
T Consensus       167 p~~~~~~~~~~id~~~~~fkq~~tV~taPRqrGKS~iVgi~l~-~La~f------~Gi~IlvTAH~~~ts~evF~rv~~~  239 (752)
T PHA03333        167 PEAPSPRTLREIDRIFDEYGKCYTAATVPRRCGKTTIMAIILA-AMISF------LEIDIVVQAQRKTMCLTLYNRVETV  239 (752)
T ss_pred             cCCCChhhHHHHHHHHHHHhhcceEEEeccCCCcHHHHHHHHH-HHHHh------cCCeEEEECCChhhHHHHHHHHHHH
Confidence            3445555444455444   557788889999999965443333 33221      3578999999999999999998887


Q ss_pred             ccC
Q psy17644        264 GKG  266 (330)
Q Consensus       264 ~~~  266 (330)
                      ...
T Consensus       240 le~  242 (752)
T PHA03333        240 VHA  242 (752)
T ss_pred             HHH
Confidence            763

>PRK11823 DNA repair protein RadA; Provisional

Probab=94.63  E-value=0.24  Score=48.81  Aligned_cols=53  Identities=23%  Similarity=0.329  Sum_probs=34.9

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|.-+++.+++|+|||. +++-++..+.+       .+.++||+. +.+...|+...+.+++
T Consensus        79 ~Gs~~lI~G~pG~GKTt-L~lq~a~~~a~-------~g~~vlYvs-~Ees~~qi~~ra~rlg  131 (446)
T PRK11823         79 PGSVVLIGGDPGIGKST-LLLQVAARLAA-------AGGKVLYVS-GEESASQIKLRAERLG  131 (446)
T ss_pred             CCEEEEEECCCCCCHHH-HHHHHHHHHHh-------cCCeEEEEE-ccccHHHHHHHHHHcC
Confidence            45667788999999994 44444444332       356788876 4456677777776664

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=94.44  E-value=0.34  Score=42.92  Aligned_cols=52  Identities=21%  Similarity=0.239  Sum_probs=31.0

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .|.-+++.+++|+|||.. ++.++.+.+.       ++..++++.- .+...++...++.+
T Consensus        19 ~G~~~~i~G~~G~GKT~l-~~~~~~~~~~-------~g~~~~~is~-e~~~~~i~~~~~~~   70 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIF-CLHFAYKGLR-------DGDPVIYVTT-EESRESIIRQAAQF   70 (229)
T ss_pred             CCeEEEEECCCCCChHHH-HHHHHHHHHh-------cCCeEEEEEc-cCCHHHHHHHHHHh
Confidence            567888899999999943 3333333333       2446666653 34445555555544

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.

>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=94.39  E-value=0.099  Score=44.48  Aligned_cols=49  Identities=24%  Similarity=0.400  Sum_probs=32.3

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      +++.|++|+|||. +++.++....+       ++.+++|++ +.+...++...+..++
T Consensus         2 ~li~G~~G~GKT~-l~~~~~~~~~~-------~g~~v~~~s-~e~~~~~~~~~~~~~g   50 (187)
T cd01124           2 TLLSGGPGTGKTT-FALQFLYAGLA-------RGEPGLYVT-LEESPEELIENAESLG   50 (187)
T ss_pred             EEEEcCCCCCHHH-HHHHHHHHHHH-------CCCcEEEEE-CCCCHHHHHHHHHHcC
Confidence            5788999999994 33333333333       466778775 4466777777776663

A related protein is found in archaea.

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=94.38  E-value=0.4  Score=43.36  Aligned_cols=32  Identities=22%  Similarity=0.203  Sum_probs=21.4

Q ss_pred             CCCHHHHHhhhhhc----CCC-cEEEEcCCCChhHHH
Q psy17644        189 SPTPIQAQAVPAAL----SGR-DIIGVAKTGSGKTGA  220 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~----~g~-d~i~~a~TGsGKT~a  220 (330)
                      .+++.+.+++..+.    .+. -++++|++|+|||..
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl   59 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTL   59 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHH
Confidence            35566666665543    333 577889999999943

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.

>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=94.36  E-value=0.011  Score=50.59  Aligned_cols=102  Identities=20%  Similarity=0.162  Sum_probs=40.2

Q ss_pred             EEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH
Q psy17644        208 IGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL  287 (330)
Q Consensus       208 i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l  287 (330)
                      ++.|.-|-||+.+.-+.+.. ++.      ....+++|.+|+.+-+..+++.+.+-.+..+.+......+.   ......
T Consensus         1 VltA~RGRGKSa~lGl~~a~-l~~------~~~~~I~vtAP~~~~~~~lf~~~~~~l~~~~~~~~~~~~~~---~~~~~~   70 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAA-LIQ------KGKIRILVTAPSPENVQTLFEFAEKGLKALGYKEEKKKRIG---QIIKLR   70 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCC-SSS-----------EEEE-SS--S-HHHHHCC---------------------------
T ss_pred             CccCCCCCCHHHHHHHHHHH-HHH------hcCceEEEecCCHHHHHHHHHHHHhhccccccccccccccc---cccccc
Confidence            46789999999654443221 111      12357999999999999888877665544443330000000   000111


Q ss_pred             hCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        288 ELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       288 ~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      ..+..|-+..|..+...-       ...++||||||=.+
T Consensus        71 ~~~~~i~f~~Pd~l~~~~-------~~~DlliVDEAAaI  102 (177)
T PF05127_consen   71 FNKQRIEFVAPDELLAEK-------PQADLLIVDEAAAI  102 (177)
T ss_dssp             --CCC--B--HHHHCCT-----------SCEEECTGGGS
T ss_pred             cccceEEEECCHHHHhCc-------CCCCEEEEechhcC
Confidence            123567777776665322       24589999999543

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.

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=94.35  E-value=0.14  Score=51.30  Aligned_cols=92  Identities=18%  Similarity=0.159  Sum_probs=55.5

Q ss_pred             CCCCHH-HHHHHHHCCCCCCC----HHHHHhhhhhcC--CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEE
Q psy17644        172 FGFDEV-LMKALRKCEYTSPT----PIQAQAVPAALS--GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGL  244 (330)
Q Consensus       172 ~~l~~~-l~~~l~~~~~~~pt----~iQ~~~i~~~~~--g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vL  244 (330)
                      .++... |+.+|.+.--.++.    .||++-=.+|.+  ++-++++|..|||||.+.+ |=+.+++..-.... .+..+|
T Consensus       187 ~~~~dEvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~ek~~ilVVQGaAGSGKTtiAL-HRvAyLlY~~R~~l-~~k~vl  264 (747)
T COG3973         187 TGGRDEVLQRVLEKNSSAKMRDIVETIQKEQNEIIRFEKNKILVVQGAAGSGKTTIAL-HRVAYLLYGYRGPL-QAKPVL  264 (747)
T ss_pred             CchHHHHHHHHHHhccchhHHHHHHHhhHhHHHHHhccCCCeEEEecCCCCCchhHHH-HHHHHHHhcccccc-ccCceE
Confidence            344444 44555554333332    244444444443  4557788999999996544 44444443322222 233399


Q ss_pred             EEcccHHHHHHHHHHHHHhcc
Q psy17644        245 ILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       245 il~Ptr~La~Qi~~~~~~l~~  265 (330)
                      ||.|.|-++.-+.+.+=.++.
T Consensus       265 vl~PN~vFleYis~VLPeLGe  285 (747)
T COG3973         265 VLGPNRVFLEYISRVLPELGE  285 (747)
T ss_pred             EEcCcHHHHHHHHHhchhhcc
Confidence            999999999998888888765

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=94.33  E-value=0.86  Score=48.95  Aligned_cols=80  Identities=9%  Similarity=0.182  Sum_probs=60.6

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.+++|++|+++-+..+++.++++..  +.++..++|+.........   +.. ..+|+|||-     ++. ..+++.+
T Consensus       659 ~g~qv~if~n~i~~~e~l~~~L~~~~p--~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~-----iie-~GIDIp~  730 (926)
T TIGR00580       659 RGGQVFYVHNRIESIEKLATQLRELVP--EARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTT-----IIE-TGIDIPN  730 (926)
T ss_pred             cCCeEEEEECCcHHHHHHHHHHHHhCC--CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECC-----hhh-ccccccc
Confidence            467899999999999999999888643  5688889998876554333   233 489999994     343 3567889


Q ss_pred             ccEEEeeccccc
Q psy17644        315 VTFLVLDEADRM  326 (330)
Q Consensus       315 i~~lVvDEad~l  326 (330)
                      +.+||+..+++.
T Consensus       731 v~~VIi~~a~~~  742 (926)
T TIGR00580       731 ANTIIIERADKF  742 (926)
T ss_pred             CCEEEEecCCCC
Confidence            999999988763

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.

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=94.30  E-value=0.037  Score=55.99  Aligned_cols=122  Identities=19%  Similarity=0.197  Sum_probs=73.8

Q ss_pred             CCCHHHHHhhhhhcC--CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH-HHHhcc
Q psy17644        189 SPTPIQAQAVPAALS--GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE-AKRFGK  265 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~--g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~-~~~l~~  265 (330)
                      ..+|+|...+..+..  -+.++++.++-+|||. .++-++-+.+.+      ....+|++.||..+|...... +..+.+
T Consensus        16 ~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~-~~~n~~g~~i~~------~P~~~l~v~Pt~~~a~~~~~~rl~Pmi~   88 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTE-LLLNWIGYSIDQ------DPGPMLYVQPTDDAAKDFSKERLDPMIR   88 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhH-HHHhhceEEEEe------CCCCEEEEEEcHHHHHHHHHHHHHHHHH
Confidence            567999998888774  3688889999999997 334444444443      235579999999999998854 665544


Q ss_pred             CCCceEEEEEC----CCchHHHHHHHhCCCeEEEE---ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        266 GYNLSVVCCYG----GGSKWDQSKALELGAEIVVG---TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       266 ~~~~~~~~~~g----g~~~~~~~~~l~~~~dIiV~---TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ....-...+..    ........+.+. +..|.++   ||..|.         -..+++|++||.|.+-
T Consensus        89 ~sp~l~~~~~~~~~~~~~~t~~~k~f~-gg~l~~~ga~S~~~l~---------s~~~r~~~~DEvD~~p  147 (557)
T PF05876_consen   89 ASPVLRRKLSPSKSRDSGNTILYKRFP-GGFLYLVGANSPSNLR---------SRPARYLLLDEVDRYP  147 (557)
T ss_pred             hCHHHHHHhCchhhcccCCchhheecC-CCEEEEEeCCCCcccc---------cCCcCEEEEechhhcc
Confidence            33221111111    011111122233 3344443   232222         4578999999999874

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 [].

>PRK08506 replicative DNA helicase; Provisional

Probab=94.26  E-value=0.26  Score=48.94  Aligned_cols=113  Identities=13%  Similarity=0.094  Sum_probs=57.4

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEE-ECCCchH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCC-YGGGSKW  281 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~-~gg~~~~  281 (330)
                      .|.=+++.|+||.||| +|++-+..++..       .+..|+|++. -.-..|+...+.....  ++....+ .|..+..
T Consensus       191 ~G~LivIaarpg~GKT-~fal~ia~~~~~-------~g~~V~~fSl-EMs~~ql~~Rlla~~s--~v~~~~i~~~~l~~~  259 (472)
T PRK08506        191 KGDLIIIAARPSMGKT-TLCLNMALKALN-------QDKGVAFFSL-EMPAEQLMLRMLSAKT--SIPLQNLRTGDLDDD  259 (472)
T ss_pred             CCceEEEEcCCCCChH-HHHHHHHHHHHh-------cCCcEEEEeC-cCCHHHHHHHHHHHhc--CCCHHHHhcCCCCHH
Confidence            3444566699999999 566666666543       2455666643 3445555555433211  2211111 2222222


Q ss_pred             HH------HHHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        282 DQ------SKALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       282 ~~------~~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      .+      ...+.. ..+.|.     |+..+...+++-......+.+||||=.+.|-
T Consensus       260 e~~~~~~a~~~l~~-~~l~I~d~~~~ti~~I~~~~r~l~~~~~~~~lvvIDyLql~~  315 (472)
T PRK08506        260 EWERLSDACDELSK-KKLFVYDSGYVNIHQVRAQLRKLKSQHPEIGLAVIDYLQLMS  315 (472)
T ss_pred             HHHHHHHHHHHHHc-CCeEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEcChhhcc
Confidence            21      122333 345553     4555555444321112358999999988764

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=94.20  E-value=0.27  Score=48.02  Aligned_cols=115  Identities=16%  Similarity=0.143  Sum_probs=55.4

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCC-ch
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGG-SK  280 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~-~~  280 (330)
                      ..|.=+++.|++|+||| +|++.+..++...      .+..|+|++ .-.-..|+...+....  .++....+..|. ..
T Consensus       192 ~~g~liviag~pg~GKT-~~al~ia~~~a~~------~g~~v~~fS-lEm~~~~l~~Rl~~~~--~~v~~~~~~~~~l~~  261 (421)
T TIGR03600       192 VKGDLIVIGARPSMGKT-TLALNIAENVALR------EGKPVLFFS-LEMSAEQLGERLLASK--SGINTGNIRTGRFND  261 (421)
T ss_pred             CCCceEEEEeCCCCCHH-HHHHHHHHHHHHh------CCCcEEEEE-CCCCHHHHHHHHHHHH--cCCCHHHHhcCCCCH
Confidence            34555666799999999 5555555444321      245567765 2233444444432221  122211111222 21


Q ss_pred             HHH------HHHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        281 WDQ------SKALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       281 ~~~------~~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ...      ...+.. ..+.|.     |+..+...+++-......+++||||-.+.|-
T Consensus       262 ~~~~~~~~~~~~l~~-~~l~i~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDyLql~~  318 (421)
T TIGR03600       262 SDFNRLLNAVDRLSE-KDLYIDDTGGLTVAQIRSIARRIKRKKGGLDLIVVDYIQLMA  318 (421)
T ss_pred             HHHHHHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEecccccC
Confidence            111      122222 345553     3444444333211112258899999988774

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=94.09  E-value=0.16  Score=46.09  Aligned_cols=17  Identities=29%  Similarity=0.302  Sum_probs=14.3

Q ss_pred             CCcEEEEcCCCChhHHH
Q psy17644        204 GRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a  220 (330)
                      ..++++.||+|+|||..
T Consensus        42 ~~~vll~GppGtGKTtl   58 (261)
T TIGR02881        42 VLHMIFKGNPGTGKTTV   58 (261)
T ss_pred             cceEEEEcCCCCCHHHH
Confidence            45789999999999944

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=94.07  E-value=0.16  Score=48.80  Aligned_cols=17  Identities=24%  Similarity=0.366  Sum_probs=14.3

Q ss_pred             CCcEEEEcCCCChhHHH
Q psy17644        204 GRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a  220 (330)
                      +.++++.|++|+|||.+
T Consensus        55 ~~~~lI~G~~GtGKT~l   71 (394)
T PRK00411         55 PLNVLIYGPPGTGKTTT   71 (394)
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            36799999999999943

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=94.04  E-value=0.069  Score=52.76  Aligned_cols=50  Identities=28%  Similarity=0.426  Sum_probs=39.2

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .+++++|+||||||..|++|.|..   .       ..-+||.=|-.+|+..+...+++.+
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~---~-------~~s~iV~D~KgEl~~~t~~~r~~~G   94 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLN---Y-------PGSMIVTDPKGELYEKTAGYRKKRG   94 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHh---c-------cCCEEEEECCCcHHHHHHHHHHHCC
Confidence            579999999999999999998743   1       2267888888999887777666653

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

>PRK05748 replicative DNA helicase; Provisional

Probab=93.99  E-value=0.32  Score=47.89  Aligned_cols=112  Identities=17%  Similarity=0.128  Sum_probs=56.4

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH-HhccCCCceEEEEECCC-ch
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK-RFGKGYNLSVVCCYGGG-SK  280 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~-~l~~~~~~~~~~~~gg~-~~  280 (330)
                      .|.=+++.|+||+||| +|.+.++.++...      .+..|+|++ .-.-..|+...+. .++   ++....+..|. ..
T Consensus       202 ~G~livIaarpg~GKT-~~al~ia~~~a~~------~g~~v~~fS-lEms~~~l~~R~l~~~~---~v~~~~i~~~~l~~  270 (448)
T PRK05748        202 PNDLIIVAARPSVGKT-AFALNIAQNVATK------TDKNVAIFS-LEMGAESLVMRMLCAEG---NIDAQRLRTGQLTD  270 (448)
T ss_pred             CCceEEEEeCCCCCch-HHHHHHHHHHHHh------CCCeEEEEe-CCCCHHHHHHHHHHHhc---CCCHHHhhcCCCCH
Confidence            4455666799999999 5666666665432      244566654 3344455555543 222   11111111222 22


Q ss_pred             HHH------HHHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        281 WDQ------SKALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       281 ~~~------~~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      ..+      ...+.. ..+.|.     |+..+...+++-......+++||||=.+.|
T Consensus       271 ~e~~~~~~a~~~l~~-~~~~i~d~~~~ti~~i~~~~r~~~~~~~~~~~vvIDyL~li  326 (448)
T PRK05748        271 DDWPKLTIAMGSLSD-APIYIDDTPGIKVTEIRARCRRLAQEHGGLGLILIDYLQLI  326 (448)
T ss_pred             HHHHHHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccchhc
Confidence            221      122333 345553     445555444321111126889999998877

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=93.97  E-value=0.18  Score=48.32  Aligned_cols=26  Identities=23%  Similarity=0.217  Sum_probs=18.8

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      .-++++++|||||| +++-.++.++..
T Consensus       150 GlilI~G~TGSGKT-T~l~al~~~i~~  175 (372)
T TIGR02525       150 GLGLICGETGSGKS-TLAASIYQHCGE  175 (372)
T ss_pred             CEEEEECCCCCCHH-HHHHHHHHHHHh
Confidence            45788999999999 344556666653

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).

>PRK08181 transposase; Validated

Probab=93.96  E-value=0.16  Score=46.62  Aligned_cols=48  Identities=19%  Similarity=0.307  Sum_probs=29.7

Q ss_pred             hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIY  257 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~  257 (330)
                      +-.+++++++|++|+|||.... .+.+++..       .|-+|++ ++..+|+.++.
T Consensus       103 ~~~~~nlll~Gp~GtGKTHLa~-Aia~~a~~-------~g~~v~f-~~~~~L~~~l~  150 (269)
T PRK08181        103 LAKGANLLLFGPPGGGKSHLAA-AIGLALIE-------NGWRVLF-TRTTDLVQKLQ  150 (269)
T ss_pred             HhcCceEEEEecCCCcHHHHHH-HHHHHHHH-------cCCceee-eeHHHHHHHHH
Confidence            3478899999999999993322 12233333       2445544 45667777653

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=93.93  E-value=0.053  Score=52.24  Aligned_cols=48  Identities=23%  Similarity=0.252  Sum_probs=36.9

Q ss_pred             cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        206 DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      +++++|+||||||.++++|.+..          ....+||+=|--++...+....++.
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~----------~~~s~vv~D~Kge~~~~t~~~r~~~   48 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLT----------WPGSVVVLDPKGENFELTSEHRRAL   48 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhc----------CCCCEEEEccchhHHHHHHHHHHHc
Confidence            47899999999999999987653          1346788888888887776666554

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.

>PRK07004 replicative DNA helicase; Provisional

Probab=93.90  E-value=0.19  Score=49.65  Aligned_cols=114  Identities=16%  Similarity=0.106  Sum_probs=54.9

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEE-ECCCchH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCC-YGGGSKW  281 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~-~gg~~~~  281 (330)
                      .|.=+++.|++|+||| +|++-+..++...      .+..|+|++. -.-..|+...+-....  ++....+ .|..+..
T Consensus       212 ~g~liviaarpg~GKT-~~al~ia~~~a~~------~~~~v~~fSl-EM~~~ql~~R~la~~~--~v~~~~i~~g~l~~~  281 (460)
T PRK07004        212 GGELIIVAGRPSMGKT-AFSMNIGEYVAVE------YGLPVAVFSM-EMPGTQLAMRMLGSVG--RLDQHRMRTGRLTDE  281 (460)
T ss_pred             CCceEEEEeCCCCCcc-HHHHHHHHHHHHH------cCCeEEEEeC-CCCHHHHHHHHHHhhc--CCCHHHHhcCCCCHH
Confidence            3455666799999999 4555555554321      2445666542 2333444444321111  1111111 2222322


Q ss_pred             HH------HHHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        282 DQ------SKALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       282 ~~------~~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ++      ...+.. ..+.|.     |+..+....++-......+.+||||-.+.|-
T Consensus       282 e~~~~~~a~~~l~~-~~l~I~d~~~~~~~~i~~~~r~l~~~~~~~~lviIDYLql~~  337 (460)
T PRK07004        282 DWPKLTHAVQKMSE-AQLFIDETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMS  337 (460)
T ss_pred             HHHHHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEChhhhcc
Confidence            22      122333 456663     4445544333211112357899999988774

>PRK08006 replicative DNA helicase; Provisional

Probab=93.88  E-value=0.66  Score=46.05  Aligned_cols=114  Identities=16%  Similarity=0.073  Sum_probs=55.0

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEE-ECCCchHH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCC-YGGGSKWD  282 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~-~gg~~~~~  282 (330)
                      |.=+++.|.+|.||| +|.+-+..++...      .+..|+|++.- --..|+...+.....  ++....+ .|..+..+
T Consensus       224 G~LiiIaarPgmGKT-afalnia~~~a~~------~g~~V~~fSlE-M~~~ql~~Rlla~~~--~v~~~~i~~~~l~~~e  293 (471)
T PRK08006        224 SDLIIVAARPSMGKT-TFAMNLCENAAML------QDKPVLIFSLE-MPGEQIMMRMLASLS--RVDQTRIRTGQLDDED  293 (471)
T ss_pred             CcEEEEEeCCCCCHH-HHHHHHHHHHHHh------cCCeEEEEecc-CCHHHHHHHHHHHhc--CCCHHHhhcCCCCHHH
Confidence            344555699999999 5666555554421      24456666432 334444444332211  1221111 23333332


Q ss_pred             HH------HHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        283 QS------KALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       283 ~~------~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      +.      ..+.....+.|-     |+..+...+++-......+.+||||=.+.|-
T Consensus       294 ~~~~~~a~~~~~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~  349 (471)
T PRK08006        294 WARISGTMGILLEKRNMYIDDSSGLTPTEVRSRARRIFREHGGLSLIMIDYLQLMR  349 (471)
T ss_pred             HHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHHcc
Confidence            21      122123445553     4555544443211112358999999988763

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=93.85  E-value=0.23  Score=42.49  Aligned_cols=67  Identities=16%  Similarity=0.192  Sum_probs=37.7

Q ss_pred             hhhhhc-CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCC---CCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        197 AVPAAL-SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE---PGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       197 ~i~~~~-~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~---~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      +++-++ .|.=+++.|++|+||| .+++.++.++....+.-   ...+.+||++..-.. ..++...+..+..
T Consensus        24 li~g~~~~g~l~~i~g~~g~GKT-~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~   94 (193)
T PF13481_consen   24 LIDGLLPRGELTLIAGPPGSGKT-TLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALLQ   94 (193)
T ss_dssp             EETTEE-TTSEEEEEECSTSSHH-HHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHT
T ss_pred             eECCcccCCeEEEEEeCCCCCHH-HHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHhc
Confidence            344444 5666888899999999 45566666666432221   113567777765433 5677777776654

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=93.82  E-value=0.34  Score=46.41  Aligned_cols=24  Identities=38%  Similarity=0.465  Sum_probs=17.0

Q ss_pred             hhhhhcCC--CcEEEEcCCCChhHHH
Q psy17644        197 AVPAALSG--RDIIGVAKTGSGKTGA  220 (330)
Q Consensus       197 ~i~~~~~g--~d~i~~a~TGsGKT~a  220 (330)
                      ..|++.++  .++++-|+||+|||++
T Consensus        33 l~~~~~~~~p~n~~iyG~~GTGKT~~   58 (366)
T COG1474          33 LAPALRGERPSNIIIYGPTGTGKTAT   58 (366)
T ss_pred             HHHHhcCCCCccEEEECCCCCCHhHH
Confidence            44555443  3688889999999954

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=93.81  E-value=0.15  Score=45.71  Aligned_cols=53  Identities=21%  Similarity=0.256  Sum_probs=36.2

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|.-+++.|++|+|||.. ++.++...++       ++-++++++ +.+-..++.+.+..++
T Consensus        20 ~gs~~lI~G~pGsGKT~l-a~~~l~~~~~-------~ge~~lyvs-~ee~~~~i~~~~~~~g   72 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIF-SQQFLWNGLQ-------MGEPGIYVA-LEEHPVQVRRNMAQFG   72 (237)
T ss_pred             CCeEEEEEcCCCCCHHHH-HHHHHHHHHH-------cCCcEEEEE-eeCCHHHHHHHHHHhC
Confidence            467888999999999943 3333333223       366778877 5567778888777664

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.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=93.74  E-value=0.17  Score=47.80  Aligned_cols=29  Identities=38%  Similarity=0.453  Sum_probs=21.0

Q ss_pred             hhcCCCcEEEEcCCCChhHHHHHHHHHHHH
Q psy17644        200 AALSGRDIIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       200 ~~~~g~d~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      ++..+++++++|+|||||| +++-.++.++
T Consensus       156 ~v~~~~nili~G~tgSGKT-Tll~aL~~~i  184 (332)
T PRK13900        156 AVISKKNIIISGGTSTGKT-TFTNAALREI  184 (332)
T ss_pred             HHHcCCcEEEECCCCCCHH-HHHHHHHhhC
Confidence            3447889999999999999 3444444444

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=93.67  E-value=0.13  Score=46.82  Aligned_cols=50  Identities=14%  Similarity=0.240  Sum_probs=34.5

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK  261 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~  261 (330)
                      ++.++++.|++|+|||.  ++.++.+-+.+      .|.. ++++++.+|+.++...+.
T Consensus       104 ~~~nl~l~G~~G~GKTh--La~Ai~~~l~~------~g~s-v~f~~~~el~~~Lk~~~~  153 (254)
T COG1484         104 RGENLVLLGPPGVGKTH--LAIAIGNELLK------AGIS-VLFITAPDLLSKLKAAFD  153 (254)
T ss_pred             cCCcEEEECCCCCcHHH--HHHHHHHHHHH------cCCe-EEEEEHHHHHHHHHHHHh
Confidence            78899999999999994  33344333332      2444 555688899888877554

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=93.66  E-value=0.088  Score=49.99  Aligned_cols=29  Identities=21%  Similarity=0.290  Sum_probs=20.4

Q ss_pred             hhhcCCCcEEEEcCCCChhHHHHHHHHHHH
Q psy17644        199 PAALSGRDIIGVAKTGSGKTGAFIWPMLVH  228 (330)
Q Consensus       199 ~~~~~g~d~i~~a~TGsGKT~a~llp~l~~  228 (330)
                      -++..+++++++|+|||||| +++-.++.+
T Consensus       157 ~~v~~~~nilI~G~tGSGKT-Tll~aLl~~  185 (344)
T PRK13851        157 ACVVGRLTMLLCGPTGSGKT-TMSKTLISA  185 (344)
T ss_pred             HHHHcCCeEEEECCCCccHH-HHHHHHHcc
Confidence            34457889999999999999 333333433

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.66  E-value=0.38  Score=46.81  Aligned_cols=19  Identities=37%  Similarity=0.436  Sum_probs=14.0

Q ss_pred             CCcEEEEcCCCChhHHHHH
Q psy17644        204 GRDIIGVAKTGSGKTGAFI  222 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~l  222 (330)
                      ++-+++++++|+|||....
T Consensus       223 ~~vi~lvGptGvGKTTtaa  241 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIA  241 (432)
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3446778999999995433

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=93.64  E-value=0.28  Score=48.84  Aligned_cols=74  Identities=24%  Similarity=0.205  Sum_probs=54.0

Q ss_pred             CCCCHHHHHhhhhhcC----------CCcEEEEcCCCChhHH-HHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAALS----------GRDIIGVAKTGSGKTG-AFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQI  256 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~----------g~d~i~~a~TGsGKT~-a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi  256 (330)
                      ...-|+|+-++-.++.          -+..++..+-+-|||. +..+.+...++..     ..+-...|++|+.+-+.+.
T Consensus        60 ~~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~-----~~~~~~~i~A~s~~qa~~~  134 (546)
T COG4626          60 ESLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNW-----RSGAGIYILAPSVEQAANS  134 (546)
T ss_pred             cccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhh-----hcCCcEEEEeccHHHHHHh
Confidence            3467999999988871          1357777888999983 3334444444443     2578899999999999999


Q ss_pred             HHHHHHhccC
Q psy17644        257 YNEAKRFGKG  266 (330)
Q Consensus       257 ~~~~~~l~~~  266 (330)
                      +..++.....
T Consensus       135 F~~ar~mv~~  144 (546)
T COG4626         135 FNPARDMVKR  144 (546)
T ss_pred             hHHHHHHHHh
Confidence            9998877654

>PRK13764 ATPase; Provisional

Probab=93.62  E-value=0.17  Score=51.51  Aligned_cols=27  Identities=19%  Similarity=0.289  Sum_probs=19.8

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      .+++++++++||||||. ++-.++.++.
T Consensus       256 ~~~~ILIsG~TGSGKTT-ll~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKST-FAQALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHHH-HHHHHHHHHh
Confidence            46789999999999993 4444555553

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=93.62  E-value=0.63  Score=40.49  Aligned_cols=39  Identities=21%  Similarity=0.177  Sum_probs=25.6

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT  249 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt  249 (330)
                      .|+=+.+.+++|+|||.. ++.++.+...       ++.+++++.-.
T Consensus        11 ~g~i~~i~G~~GsGKT~l-~~~~~~~~~~-------~g~~v~yi~~e   49 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNI-CMILAVNAAR-------QGKKVVYIDTE   49 (209)
T ss_pred             CCeEEEEECCCCCCHHHH-HHHHHHHHHh-------CCCeEEEEECC
Confidence            456678889999999943 3444444433       35677777664

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=93.53  E-value=0.37  Score=47.23  Aligned_cols=88  Identities=20%  Similarity=0.188  Sum_probs=42.0

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc-c-HHHHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP-T-RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P-t-r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      ..-+++++++|+|||.+..--+ .++..       .+.++++++. + |..+   +..++.++...++.+..........
T Consensus        95 p~vI~lvG~~GsGKTTtaakLA-~~L~~-------~g~kV~lV~~D~~R~aa---~eQL~~la~~~gvp~~~~~~~~d~~  163 (437)
T PRK00771         95 PQTIMLVGLQGSGKTTTAAKLA-RYFKK-------KGLKVGLVAADTYRPAA---YDQLKQLAEKIGVPFYGDPDNKDAV  163 (437)
T ss_pred             CeEEEEECCCCCcHHHHHHHHH-HHHHH-------cCCeEEEecCCCCCHHH---HHHHHHHHHHcCCcEEecCCccCHH
Confidence            3457788999999995433222 23322       2345554443 3 3332   3334444444455543322222221


Q ss_pred             H----HHHHHhCCCeEEEEChHHHH
Q psy17644        282 D----QSKALELGAEIVVGTPGRII  302 (330)
Q Consensus       282 ~----~~~~l~~~~dIiV~TP~~L~  302 (330)
                      .    ........--|||=||+++.
T Consensus       164 ~i~~~al~~~~~~DvVIIDTAGr~~  188 (437)
T PRK00771        164 EIAKEGLEKFKKADVIIVDTAGRHA  188 (437)
T ss_pred             HHHHHHHHHhhcCCEEEEECCCccc
Confidence            1    11222222235667888765

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=93.53  E-value=0.17  Score=43.39  Aligned_cols=49  Identities=18%  Similarity=0.275  Sum_probs=28.7

Q ss_pred             hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      +-+++++++.|++|+|||.... .+.+.+..       .+..|++ +++.+|+..+..
T Consensus        44 ~~~~~~l~l~G~~G~GKThLa~-ai~~~~~~-------~g~~v~f-~~~~~L~~~l~~   92 (178)
T PF01695_consen   44 IENGENLILYGPPGTGKTHLAV-AIANEAIR-------KGYSVLF-ITASDLLDELKQ   92 (178)
T ss_dssp             -SC--EEEEEESTTSSHHHHHH-HHHHHHHH-------TT--EEE-EEHHHHHHHHHC
T ss_pred             cccCeEEEEEhhHhHHHHHHHH-HHHHHhcc-------CCcceeE-eecCceeccccc
Confidence            3478899999999999995433 23344444       2455555 466677766543

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.

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=93.53  E-value=0.25  Score=45.86  Aligned_cols=28  Identities=18%  Similarity=0.184  Sum_probs=18.9

Q ss_pred             CCc-EEEEcCCCChhHHHHHHHHHHHHHhc
Q psy17644        204 GRD-IIGVAKTGSGKTGAFIWPMLVHIMDQ  232 (330)
Q Consensus       204 g~d-~i~~a~TGsGKT~a~llp~l~~i~~~  232 (330)
                      ... +++.||.|+|||.+. +.+...++..
T Consensus        23 ~~halL~~Gp~G~Gktt~a-~~lA~~l~~~   51 (325)
T COG0470          23 LPHALLFYGPPGVGKTTAA-LALAKELLCE   51 (325)
T ss_pred             CCceeeeeCCCCCCHHHHH-HHHHHHHhCC
Confidence            445 899999999999543 3344555544

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=93.51  E-value=0.62  Score=47.43  Aligned_cols=74  Identities=15%  Similarity=0.267  Sum_probs=54.2

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+..|.++++.+.+.    ++.+..++|+....+....   +++ ..+|||||     +++. ..+++..
T Consensus       256 ~~~k~LVF~nt~~~ae~l~~~L~~~----g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaT-----dv~a-rGIDip~  325 (572)
T PRK04537        256 EGARTMVFVNTKAFVERVARTLERH----GYRVGVLSGDVPQKKRESLLNRFQKGQLEILVAT-----DVAA-RGLHIDG  325 (572)
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHHc----CCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEe-----hhhh-cCCCccC
Confidence            4678999999999999999988765    5788888988776554333   333 47999999     3343 3556778


Q ss_pred             ccEEEeec
Q psy17644        315 VTFLVLDE  322 (330)
Q Consensus       315 i~~lVvDE  322 (330)
                      |.+||.-.
T Consensus       326 V~~VInyd  333 (572)
T PRK04537        326 VKYVYNYD  333 (572)
T ss_pred             CCEEEEcC
Confidence            88877543

>PRK06904 replicative DNA helicase; Validated

Probab=93.47  E-value=0.71  Score=45.82  Aligned_cols=114  Identities=14%  Similarity=0.066  Sum_probs=56.3

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEE-EC-CCchH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCC-YG-GGSKW  281 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~-~g-g~~~~  281 (330)
                      |.=+++.|.+|.|||. |.+-+..++...      .+..|+|++. ---..|+...+......  +....+ .| ..+..
T Consensus       221 G~LiiIaarPg~GKTa-falnia~~~a~~------~g~~Vl~fSl-EMs~~ql~~Rlla~~s~--v~~~~i~~g~~l~~~  290 (472)
T PRK06904        221 SDLIIVAARPSMGKTT-FAMNLCENAAMA------SEKPVLVFSL-EMPAEQIMMRMLASLSR--VDQTKIRTGQNLDQQ  290 (472)
T ss_pred             CcEEEEEeCCCCChHH-HHHHHHHHHHHh------cCCeEEEEec-cCCHHHHHHHHHHhhCC--CCHHHhccCCCCCHH
Confidence            3344555999999994 555555555432      2445666643 24455555554332221  221111 22 12222


Q ss_pred             HH------HHHHhCCCeEEE-----EChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        282 DQ------SKALELGAEIVV-----GTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       282 ~~------~~~l~~~~dIiV-----~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      .+      ...+.....+.|     .|+..+...+++-......+.+||||-.+.|-
T Consensus       291 e~~~~~~a~~~l~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~  347 (472)
T PRK06904        291 DWAKISSTVGMFKQKPNLYIDDSSGLTPTELRSRARRVYRENGGLSLIMVDYLQLMR  347 (472)
T ss_pred             HHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEecHHhcC
Confidence            22      122333344655     35555554443211112358899999888764

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=93.44  E-value=0.29  Score=46.51  Aligned_cols=24  Identities=25%  Similarity=0.368  Sum_probs=17.1

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      ..+++.|++|+|||.+ +-.++.++
T Consensus        41 ~~i~I~G~~GtGKT~l-~~~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAV-TKYVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHH-HHHHHHHH
Confidence            5799999999999943 33344444

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.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=93.44  E-value=0.62  Score=44.75  Aligned_cols=53  Identities=25%  Similarity=0.334  Sum_probs=33.2

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|.=+++.+++|+|||. +++-++..+..       .+.+++|+.-. +...|+...+.+++
T Consensus        81 ~GslvLI~G~pG~GKSt-Lllq~a~~~a~-------~g~~VlYvs~E-Es~~qi~~Ra~rlg  133 (372)
T cd01121          81 PGSVILIGGDPGIGKST-LLLQVAARLAK-------RGGKVLYVSGE-ESPEQIKLRADRLG  133 (372)
T ss_pred             CCeEEEEEeCCCCCHHH-HHHHHHHHHHh-------cCCeEEEEECC-cCHHHHHHHHHHcC
Confidence            45667778999999994 33434444333       24578887654 44567766666653

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.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=93.43  E-value=0.24  Score=47.33  Aligned_cols=27  Identities=19%  Similarity=0.287  Sum_probs=18.3

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      .+.-++++++||||||. .+-.++.++.
T Consensus       133 ~~glilI~GpTGSGKTT-tL~aLl~~i~  159 (358)
T TIGR02524       133 QEGIVFITGATGSGKST-LLAAIIRELA  159 (358)
T ss_pred             cCCEEEEECCCCCCHHH-HHHHHHHHHh
Confidence            45678889999999993 2333444443

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=93.43  E-value=0.53  Score=44.58  Aligned_cols=85  Identities=25%  Similarity=0.297  Sum_probs=41.5

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc--HH-HHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT--RE-LSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt--r~-La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      +=+++++++|+|||.+..-  +.+.+..      .+.+++++...  |. ...|+......    .++.+.....|....
T Consensus       141 ~vi~~~G~~GvGKTTtiak--LA~~l~~------~g~~V~li~~Dt~R~~a~eqL~~~a~~----lgv~v~~~~~g~dp~  208 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAK--LAYYLKK------NGFSVVIAAGDTFRAGAIEQLEEHAER----LGVKVIKHKYGADPA  208 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHH--HHHHHHH------cCCeEEEecCCcCcHHHHHHHHHHHHH----cCCceecccCCCCHH
Confidence            4466779999999943322  2223332      24566555532  33 33454444443    355544333333221


Q ss_pred             H----HH-HHHhCCCe-EEEEChHHH
Q psy17644        282 D----QS-KALELGAE-IVVGTPGRI  301 (330)
Q Consensus       282 ~----~~-~~l~~~~d-IiV~TP~~L  301 (330)
                      .    .. .....+.+ |||=|++++
T Consensus       209 ~v~~~ai~~~~~~~~DvVLIDTaGr~  234 (336)
T PRK14974        209 AVAYDAIEHAKARGIDVVLIDTAGRM  234 (336)
T ss_pred             HHHHHHHHHHHhCCCCEEEEECCCcc
Confidence            1    11 11223455 566788877

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=93.42  E-value=0.25  Score=43.45  Aligned_cols=18  Identities=28%  Similarity=0.307  Sum_probs=15.1

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      .++.+++.|++|+|||..
T Consensus        37 ~~~~lll~G~~G~GKT~l   54 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHL   54 (226)
T ss_pred             CCCeEEEECCCCCCHHHH
Confidence            457899999999999943

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.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=93.37  E-value=0.25  Score=43.68  Aligned_cols=16  Identities=25%  Similarity=0.347  Sum_probs=14.1

Q ss_pred             CCCcEEEEcCCCChhH
Q psy17644        203 SGRDIIGVAKTGSGKT  218 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT  218 (330)
                      .++.++++|++|+|||
T Consensus        41 ~~~~~~l~G~~G~GKT   56 (227)
T PRK08903         41 ADRFFYLWGEAGSGRS   56 (227)
T ss_pred             CCCeEEEECCCCCCHH
Confidence            4567999999999999

>PRK10689 transcription-repair coupling factor; Provisional

Probab=93.35  E-value=0.4  Score=52.59  Aligned_cols=79  Identities=11%  Similarity=0.148  Sum_probs=60.0

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---Hh-CCCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LE-LGAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~-~~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      +.+++|++|+++.+..+++.+.++..  +.++.+++|+.+.......   ++ ...+|+|||     +++. ..+++.++
T Consensus       809 ~gqv~vf~n~i~~ie~la~~L~~~~p--~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaT-----dIie-rGIDIP~v  880 (1147)
T PRK10689        809 GGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCT-----TIIE-TGIDIPTA  880 (1147)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhCC--CCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEEC-----chhh-cccccccC
Confidence            56899999999999999998888754  4577888998876654333   22 358999999     3443 35678899


Q ss_pred             cEEEeeccccc
Q psy17644        316 TFLVLDEADRM  326 (330)
Q Consensus       316 ~~lVvDEad~l  326 (330)
                      .+||+..||+.
T Consensus       881 ~~VIi~~ad~f  891 (1147)
T PRK10689        881 NTIIIERADHF  891 (1147)
T ss_pred             CEEEEecCCCC
Confidence            99999988863

>PRK06921 hypothetical protein; Provisional

Probab=93.35  E-value=0.47  Score=43.38  Aligned_cols=48  Identities=21%  Similarity=0.171  Sum_probs=28.3

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      .+..+++.|++|+|||... ..+.+.+..+      .+..|+++. ..++..++..
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~~------~g~~v~y~~-~~~l~~~l~~  163 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMRK------KGVPVLYFP-FVEGFGDLKD  163 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhhh------cCceEEEEE-HHHHHHHHHH
Confidence            4678999999999999322 2233333331      155666654 4566555543

>TIGR00665 DnaB replicative DNA helicase

Probab=93.34  E-value=0.4  Score=46.97  Aligned_cols=113  Identities=17%  Similarity=0.086  Sum_probs=56.4

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECC-CchH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGG-GSKW  281 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg-~~~~  281 (330)
                      .|.=+++.|++|+||| +|++-++.++...      .+..|++++. -.-..|+...+......  +....+..| ....
T Consensus       194 ~G~l~vi~g~pg~GKT-~~~l~~a~~~a~~------~g~~vl~~Sl-Em~~~~i~~R~~~~~~~--v~~~~~~~g~l~~~  263 (434)
T TIGR00665       194 PSDLIILAARPSMGKT-AFALNIAENAAIK------EGKPVAFFSL-EMSAEQLAMRMLSSESR--VDSQKLRTGKLSDE  263 (434)
T ss_pred             CCeEEEEEeCCCCChH-HHHHHHHHHHHHh------CCCeEEEEeC-cCCHHHHHHHHHHHhcC--CCHHHhccCCCCHH
Confidence            4455667799999999 5666666555431      2455666653 33445555544433222  221111222 2222


Q ss_pred             HH------HHHHhCCCeEEE-E----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        282 DQ------SKALELGAEIVV-G----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       282 ~~------~~~l~~~~dIiV-~----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      +.      ...+.. ..+.| .    |+..+...+++-... ..+++||||=.+.|-
T Consensus       264 ~~~~~~~a~~~l~~-~~l~i~d~~~~~~~~i~~~i~~~~~~-~~~~~vvID~l~~i~  318 (434)
T TIGR00665       264 DWEKLTSAAGKLSE-APLYIDDTPGLTITELRAKARRLKRE-HGLGLIVIDYLQLMS  318 (434)
T ss_pred             HHHHHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHh-cCCCEEEEcchHhcC
Confidence            11      122333 34544 2    445555444322111 247899999887763

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=93.34  E-value=0.26  Score=46.53  Aligned_cols=46  Identities=20%  Similarity=0.295  Sum_probs=29.0

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHH-HHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPML-VHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l-~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      .++++++.|+||+|||.  ++.++ +.++.       .+..|+++ +...|..++..
T Consensus       182 ~~~~Lll~G~~GtGKTh--La~aIa~~l~~-------~g~~V~y~-t~~~l~~~l~~  228 (329)
T PRK06835        182 NNENLLFYGNTGTGKTF--LSNCIAKELLD-------RGKSVIYR-TADELIEILRE  228 (329)
T ss_pred             cCCcEEEECCCCCcHHH--HHHHHHHHHHH-------CCCeEEEE-EHHHHHHHHHH
Confidence            45889999999999994  33333 33433       24556554 55666665533

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=93.28  E-value=0.15  Score=45.04  Aligned_cols=53  Identities=25%  Similarity=0.389  Sum_probs=33.1

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCC-CCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGD-GPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~-~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|.-+++.+++|+|||. |++.++..-+.       + +-++++++ +.+-..++.+.++.++
T Consensus        18 ~gs~~li~G~~GsGKT~-l~~q~l~~~~~-------~~ge~vlyvs-~ee~~~~l~~~~~s~g   71 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTT-LALQFLYNGLK-------NFGEKVLYVS-FEEPPEELIENMKSFG   71 (226)
T ss_dssp             TTSEEEEEESTTSSHHH-HHHHHHHHHHH-------HHT--EEEEE-SSS-HHHHHHHHHTTT
T ss_pred             CCcEEEEEeCCCCCcHH-HHHHHHHHhhh-------hcCCcEEEEE-ecCCHHHHHHHHHHcC
Confidence            56788999999999994 33333332222       2 45677776 4556677777777764

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 ....

>KOG0989|consensus

Probab=93.28  E-value=0.08  Score=48.88  Aligned_cols=19  Identities=21%  Similarity=0.240  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCChhHHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIW  223 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~ll  223 (330)
                      -+.++.||.|+|||.+.++
T Consensus        58 p~~LFyGPpGTGKTStala   76 (346)
T KOG0989|consen   58 PHYLFYGPPGTGKTSTALA   76 (346)
T ss_pred             ceEEeeCCCCCcHhHHHHH
Confidence            4678899999999965543

>PRK08116 hypothetical protein; Validated

Probab=93.28  E-value=1.3  Score=40.49  Aligned_cols=45  Identities=16%  Similarity=0.179  Sum_probs=27.7

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      ..+++.|++|+|||.... ++.+++..+       +..++ .++..+++..+..
T Consensus       115 ~gl~l~G~~GtGKThLa~-aia~~l~~~-------~~~v~-~~~~~~ll~~i~~  159 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAA-CIANELIEK-------GVPVI-FVNFPQLLNRIKS  159 (268)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHHc-------CCeEE-EEEHHHHHHHHHH
Confidence            459999999999994332 345555542       33444 4456666666643

>PRK05595 replicative DNA helicase; Provisional

Probab=93.18  E-value=0.5  Score=46.49  Aligned_cols=113  Identities=15%  Similarity=0.104  Sum_probs=53.3

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ  283 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~  283 (330)
                      |.=+++.|+||+||| +|++.+..++...      .+.+|+|+.. ..-..|+...+............ ..|......+
T Consensus       201 g~liviaarpg~GKT-~~al~ia~~~a~~------~g~~vl~fSl-Ems~~~l~~R~~a~~~~v~~~~~-~~~~l~~~e~  271 (444)
T PRK05595        201 GDMILIAARPSMGKT-TFALNIAEYAALR------EGKSVAIFSL-EMSKEQLAYKLLCSEANVDMLRL-RTGNLEDKDW  271 (444)
T ss_pred             CcEEEEEecCCCChH-HHHHHHHHHHHHH------cCCcEEEEec-CCCHHHHHHHHHHHhcCCCHHHH-hcCCCCHHHH
Confidence            334455699999999 5666665554321      3566777654 23344444443332211111111 1122222221


Q ss_pred             H------HHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        284 S------KALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       284 ~------~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      .      ..+.. ..+.|-     |+..+...+++... -..+++||||-.+.|-
T Consensus       272 ~~~~~~~~~l~~-~~l~i~d~~~~t~~~i~~~~r~~~~-~~~~~~vvIDylql~~  324 (444)
T PRK05595        272 ENIARASGPLAA-AKIFIDDTAGVSVMEMRSKCRRLKI-EHGIDMILIDYLQLMS  324 (444)
T ss_pred             HHHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEeHHHhcc
Confidence            1      11222 344443     33444443332111 1358899999988774

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=93.17  E-value=0.42  Score=46.36  Aligned_cols=47  Identities=11%  Similarity=0.167  Sum_probs=26.1

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIY  257 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~  257 (330)
                      +..+++.|++|+|||... ..+.+.+...     ..+.+++++. ...+..++.
T Consensus       136 ~n~l~l~G~~G~GKThL~-~ai~~~l~~~-----~~~~~v~yi~-~~~~~~~~~  182 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLL-HAIGNEILEN-----NPNAKVVYVS-SEKFTNDFV  182 (405)
T ss_pred             CCeEEEECCCCCcHHHHH-HHHHHHHHHh-----CCCCcEEEEE-HHHHHHHHH
Confidence            346789999999999432 2333444332     1245666664 344444433

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).

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=93.16  E-value=0.33  Score=45.47  Aligned_cols=15  Identities=40%  Similarity=0.561  Sum_probs=13.1

Q ss_pred             cEEEEcCCCChhHHH
Q psy17644        206 DIIGVAKTGSGKTGA  220 (330)
Q Consensus       206 d~i~~a~TGsGKT~a  220 (330)
                      .+++.||+|+|||..
T Consensus        38 ~lll~Gp~GtGKT~l   52 (337)
T PRK12402         38 HLLVQGPPGSGKTAA   52 (337)
T ss_pred             eEEEECCCCCCHHHH
Confidence            689999999999943

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=93.12  E-value=1  Score=42.27  Aligned_cols=88  Identities=24%  Similarity=0.302  Sum_probs=43.2

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc-cc-HHHHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA-PT-RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~-Pt-r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      ++-+++++++|+|||....  .|...+..      .+.+|+++. .+ |..+.+..   ..++...++.++....+....
T Consensus       114 ~~vi~lvGpnGsGKTTt~~--kLA~~l~~------~g~~V~Li~~D~~r~~a~eql---~~~a~~~~i~~~~~~~~~dpa  182 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIG--KLAHKYKA------QGKKVLLAAGDTFRAAAIEQL---QVWGERVGVPVIAQKEGADPA  182 (318)
T ss_pred             CeEEEEECCCCCcHHHHHH--HHHHHHHh------cCCeEEEEecCccchhhHHHH---HHHHHHcCceEEEeCCCCCHH
Confidence            4557778999999994432  22222222      345666654 33 44332222   222223345544443333321


Q ss_pred             HH-----HHHHhCCCe-EEEEChHHHH
Q psy17644        282 DQ-----SKALELGAE-IVVGTPGRII  302 (330)
Q Consensus       282 ~~-----~~~l~~~~d-IiV~TP~~L~  302 (330)
                      ..     ......++| |||=||+++.
T Consensus       183 ~~v~~~l~~~~~~~~D~ViIDTaGr~~  209 (318)
T PRK10416        183 SVAFDAIQAAKARGIDVLIIDTAGRLH  209 (318)
T ss_pred             HHHHHHHHHHHhCCCCEEEEeCCCCCc
Confidence            11     122345566 5667998864

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=93.07  E-value=0.13  Score=52.35  Aligned_cols=49  Identities=20%  Similarity=0.146  Sum_probs=40.3

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ++++++||||||||..|++|.|...          +.-+||+=|--|+...+....+++
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~----------~~S~VV~DpKGEl~~~Ta~~R~~~  207 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW----------EDSVVVHDIKLENYELTSGWREKQ  207 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC----------CCCEEEEeCcHHHHHHHHHHHHHC
Confidence            5789999999999999999988652          345788889999988877777665

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=93.04  E-value=0.45  Score=44.57  Aligned_cols=86  Identities=24%  Similarity=0.313  Sum_probs=50.0

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc--cHHHHHHHHHHHHHhccCCCceEEEE-ECCCch---
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP--TRELSQQIYNEAKRFGKGYNLSVVCC-YGGGSK---  280 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P--tr~La~Qi~~~~~~l~~~~~~~~~~~-~gg~~~---  280 (330)
                      +++++-+|+|||.+-  .=|.+.+++      +|.+||+.+-  .|+-|..+   ++-|++..|+.++.- +|+.+.   
T Consensus       142 il~vGVNG~GKTTTI--aKLA~~l~~------~g~~VllaA~DTFRAaAiEQ---L~~w~er~gv~vI~~~~G~DpAaVa  210 (340)
T COG0552         142 ILFVGVNGVGKTTTI--AKLAKYLKQ------QGKSVLLAAGDTFRAAAIEQ---LEVWGERLGVPVISGKEGADPAAVA  210 (340)
T ss_pred             EEEEecCCCchHhHH--HHHHHHHHH------CCCeEEEEecchHHHHHHHH---HHHHHHHhCCeEEccCCCCCcHHHH
Confidence            566699999999442  234444443      4677776664  36666543   344444456666652 343332   


Q ss_pred             -HHHHHHHhCCCeEEEE-ChHHHHH
Q psy17644        281 -WDQSKALELGAEIVVG-TPGRIID  303 (330)
Q Consensus       281 -~~~~~~l~~~~dIiV~-TP~~L~~  303 (330)
                       .--.....++.|||++ |.|||+.
T Consensus       211 fDAi~~Akar~~DvvliDTAGRLhn  235 (340)
T COG0552         211 FDAIQAAKARGIDVVLIDTAGRLHN  235 (340)
T ss_pred             HHHHHHHHHcCCCEEEEeCcccccC
Confidence             1123444567887665 9999865

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=92.99  E-value=0.51  Score=46.51  Aligned_cols=49  Identities=12%  Similarity=0.188  Sum_probs=27.5

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEA  260 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~  260 (330)
                      ..+++.|++|+|||... -.+.+.+..+.     .+.+++++ +...+..++...+
T Consensus       149 ~~l~l~G~~G~GKThL~-~ai~~~~~~~~-----~~~~v~yi-~~~~~~~~~~~~~  197 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLL-HAIGNYILEKN-----PNAKVVYV-TSEKFTNDFVNAL  197 (450)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHhC-----CCCeEEEE-EHHHHHHHHHHHH
Confidence            56889999999999332 22333333321     24556665 4455555544433

>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=92.99  E-value=0.78  Score=42.95  Aligned_cols=101  Identities=17%  Similarity=0.143  Sum_probs=46.3

Q ss_pred             EEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH----HHHHHHhccCCCceEEEE--ECCCchH
Q psy17644        208 IGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQI----YNEAKRFGKGYNLSVVCC--YGGGSKW  281 (330)
Q Consensus       208 i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi----~~~~~~l~~~~~~~~~~~--~gg~~~~  281 (330)
                      ++.++.|+|||.+.++-++.+++..+.     +..++++ +|...+...    ...+..+... .......  ...... 
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~-----~~~vi~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-   72 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPP-----GRRVIIA-STYRQARDIFGRFWKGIIELLPS-WFEIKFNEWNDRKII-   72 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS-------EEEEE-ESSHHHHHHHHHHHHHHHHTS-T-TTS--EEEE-SSEEE-
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCC-----CcEEEEe-cCHHHHHHHHHHhHHHHHHHHHH-hcCcccccCCCCcEE-
Confidence            467889999998888777777765421     2444555 665554443    3334444443 1222111  111000 


Q ss_pred             HHHHHHhCCCeEEEEChHHH--HHHHHcCCCCCCCccEEEeeccccc
Q psy17644        282 DQSKALELGAEIVVGTPGRI--IDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       282 ~~~~~l~~~~dIiV~TP~~L--~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                           +.+++.|.+.+-..-  ..-+.     =..+.++|+||+-.+
T Consensus        73 -----~~nG~~i~~~~~~~~~~~~~~~-----G~~~~~i~iDE~~~~  109 (384)
T PF03237_consen   73 -----LPNGSRIQFRGADSPDSGDNIR-----GFEYDLIIIDEAAKV  109 (384)
T ss_dssp             -----ETTS-EEEEES-----SHHHHH-----TS--SEEEEESGGGS
T ss_pred             -----ecCceEEEEecccccccccccc-----ccccceeeeeecccC
Confidence                 145666666552211  11111     146789999998665

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.

>PRK08840 replicative DNA helicase; Provisional

Probab=92.92  E-value=0.95  Score=44.84  Aligned_cols=115  Identities=16%  Similarity=0.090  Sum_probs=54.2

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEE-ECCCchH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCC-YGGGSKW  281 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~-~gg~~~~  281 (330)
                      .|.=+++.|++|.||| +|.+-+..++..+      .+..|+|+..- --..|+...+.....  ++....+ .|..+..
T Consensus       216 ~g~LiviaarPg~GKT-afalnia~~~a~~------~~~~v~~fSlE-Ms~~ql~~Rlla~~s--~v~~~~i~~~~l~~~  285 (464)
T PRK08840        216 GSDLIIVAARPSMGKT-TFAMNLCENAAMD------QDKPVLIFSLE-MPAEQLMMRMLASLS--RVDQTKIRTGQLDDE  285 (464)
T ss_pred             CCceEEEEeCCCCchH-HHHHHHHHHHHHh------CCCeEEEEecc-CCHHHHHHHHHHhhC--CCCHHHHhcCCCCHH
Confidence            4444555699999999 4545444444321      24456666532 334555544332211  1211111 2222322


Q ss_pred             HHH------HHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        282 DQS------KALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       282 ~~~------~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      .+.      ..+.....+.|.     |+..+...+++-......+.+||||-.+.|-
T Consensus       286 e~~~~~~a~~~l~~~~~l~I~d~~~~ti~~i~~~~r~~~~~~~~~~lvvIDYLql~~  342 (464)
T PRK08840        286 DWARISSTMGILMEKKNMYIDDSSGLTPTEVRSRARRIAREHGGLSMIMVDYLQLMR  342 (464)
T ss_pred             HHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHhcC
Confidence            221      223222345553     3444444332211112258899999988773

>PRK08760 replicative DNA helicase; Provisional

Probab=92.75  E-value=0.5  Score=46.94  Aligned_cols=113  Identities=16%  Similarity=0.060  Sum_probs=56.3

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ  283 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~  283 (330)
                      |.=+++.|++|.||| +|++-+..++...      .+..|+|++. -.-..|+...+........... ...|..+..++
T Consensus       229 G~LivIaarPg~GKT-afal~iA~~~a~~------~g~~V~~fSl-EMs~~ql~~Rl~a~~s~i~~~~-i~~g~l~~~e~  299 (476)
T PRK08760        229 TDLIILAARPAMGKT-TFALNIAEYAAIK------SKKGVAVFSM-EMSASQLAMRLISSNGRINAQR-LRTGALEDEDW  299 (476)
T ss_pred             CceEEEEeCCCCChh-HHHHHHHHHHHHh------cCCceEEEec-cCCHHHHHHHHHHhhCCCcHHH-HhcCCCCHHHH
Confidence            344555699999999 5666665555432      2445666643 2334555555544322222111 11222222221


Q ss_pred             ------HHHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        284 ------SKALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       284 ------~~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                            ...+.. ..+.|.     |+..+...+++-.. -..+++||||=.+.|-
T Consensus       300 ~~~~~a~~~l~~-~~l~I~d~~~~t~~~I~~~~r~l~~-~~~~~lVvIDyLql~~  352 (476)
T PRK08760        300 ARVTGAIKMLKE-TKIFIDDTPGVSPEVLRSKCRRLKR-EHDLGLIVIDYLQLMS  352 (476)
T ss_pred             HHHHHHHHHHhc-CCEEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEecHHhcC
Confidence                  122333 345554     45555544432111 1357899999888763

>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=92.68  E-value=0.14  Score=48.07  Aligned_cols=41  Identities=32%  Similarity=0.317  Sum_probs=28.0

Q ss_pred             CCCCHHHHHhh-hhhcCCCcEEEEcCCCChhHHHHHHHHHHHH
Q psy17644        188 TSPTPIQAQAV-PAALSGRDIIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       188 ~~pt~iQ~~~i-~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      ..+++.|..-+ -++-.+++++++++|||||| .++.+++..+
T Consensus       126 gt~~~~~~ayL~~~ie~~~siii~G~t~sGKT-t~lnall~~I  167 (312)
T COG0630         126 GTISPEQAAYLWLAIEARKSIIICGGTASGKT-TLLNALLDFI  167 (312)
T ss_pred             CCCCHHHHHHHHHHHHcCCcEEEECCCCCCHH-HHHHHHHHhC
Confidence            44566665544 44558899999999999999 3444444443

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=92.66  E-value=0.41  Score=49.62  Aligned_cols=83  Identities=16%  Similarity=0.092  Sum_probs=53.1

Q ss_pred             HHHCCCCCCCHHHHHhhhhhcCCC--cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q psy17644        182 LRKCEYTSPTPIQAQAVPAALSGR--DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE  259 (330)
Q Consensus       182 l~~~~~~~pt~iQ~~~i~~~~~g~--d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~  259 (330)
                      +.....+.++.-|.+.+..++..+  -+++.|.-|-|||.+.-+.+. .+....     ....++|.+||.+-+..++..
T Consensus       207 l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~-~~~~~~-----~~~~iiVTAP~~~nv~~Lf~f  280 (758)
T COG1444         207 LYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALA-AAARLA-----GSVRIIVTAPTPANVQTLFEF  280 (758)
T ss_pred             HhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHH-HHHHhc-----CCceEEEeCCCHHHHHHHHHH
Confidence            334444555555555666666443  466669999999977665542 222211     145889999999999888888


Q ss_pred             HHHhccCCCce
Q psy17644        260 AKRFGKGYNLS  270 (330)
Q Consensus       260 ~~~l~~~~~~~  270 (330)
                      +.+-....|.+
T Consensus       281 a~~~l~~lg~~  291 (758)
T COG1444         281 AGKGLEFLGYK  291 (758)
T ss_pred             HHHhHHHhCCc
Confidence            76655544443

>PRK12377 putative replication protein; Provisional

Probab=92.64  E-value=0.42  Score=43.28  Aligned_cols=46  Identities=13%  Similarity=0.215  Sum_probs=27.8

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      ...+++.|++|+|||.... .+.+++..       .+..| +.++..+|..++..
T Consensus       101 ~~~l~l~G~~GtGKThLa~-AIa~~l~~-------~g~~v-~~i~~~~l~~~l~~  146 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAA-AIGNRLLA-------KGRSV-IVVTVPDVMSRLHE  146 (248)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHH-------cCCCe-EEEEHHHHHHHHHH
Confidence            3678999999999993222 23334433       24444 44466677776654

>PF12846 AAA_10: AAA-like domain

Probab=92.61  E-value=0.38  Score=43.83  Aligned_cols=42  Identities=31%  Similarity=0.492  Sum_probs=30.7

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQ  254 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~  254 (330)
                      ++++++|+||+|||.+.. .++..++.       .++.++|+=|..+...
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~~~~~-------~g~~~~i~D~~g~~~~   43 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLEQLIR-------RGPRVVIFDPKGDYSP   43 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHH-------cCCCEEEEcCCchHHH
Confidence            578999999999995544 55555555       3678888878766654

>KOG0344|consensus

Probab=92.60  E-value=2.2  Score=42.70  Aligned_cols=95  Identities=18%  Similarity=0.269  Sum_probs=67.5

Q ss_pred             CChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHH---HHHhCC
Q psy17644        214 GSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS---KALELG  290 (330)
Q Consensus       214 GsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~---~~l~~~  290 (330)
                      +.|++..-++++.+.+..      +-.|.+||.+-+.+-|.|++.++..   .-++.+.+++|..+..+.-   ..++.|
T Consensus       367 F~gse~~K~lA~rq~v~~------g~~PP~lIfVQs~eRak~L~~~L~~---~~~i~v~vIh~e~~~~qrde~~~~FR~g  437 (593)
T KOG0344|consen  367 FCGSEKGKLLALRQLVAS------GFKPPVLIFVQSKERAKQLFEELEI---YDNINVDVIHGERSQKQRDETMERFRIG  437 (593)
T ss_pred             eeecchhHHHHHHHHHhc------cCCCCeEEEEecHHHHHHHHHHhhh---ccCcceeeEecccchhHHHHHHHHHhcc
Confidence            566665555555444433      2468899999999999999999873   3467888899987655443   333333


Q ss_pred             -CeEEEEChHHHHHHHHcCCCCCCCccEEEeecc
Q psy17644        291 -AEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEA  323 (330)
Q Consensus       291 -~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEa  323 (330)
                       ..|+|||     +++.++ ++|..+.+||-+..
T Consensus       438 ~IwvLicT-----dll~RG-iDf~gvn~VInyD~  465 (593)
T KOG0344|consen  438 KIWVLICT-----DLLARG-IDFKGVNLVINYDF  465 (593)
T ss_pred             CeeEEEeh-----hhhhcc-ccccCcceEEecCC
Confidence             6899999     566654 78899999998753

>TIGR00959 ffh signal recognition particle protein

Probab=92.50  E-value=0.69  Score=45.28  Aligned_cols=86  Identities=26%  Similarity=0.271  Sum_probs=43.0

Q ss_pred             cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc-cc-HHHHHHHHHHHHHhccCCCceEEEEECCCchHHH
Q psy17644        206 DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA-PT-RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ  283 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~-Pt-r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~  283 (330)
                      -+++++++|+|||.+..--+ .++..+      .+.+++++. -+ |..+.   ..++.++...++.+.....+......
T Consensus       101 vi~~vG~~GsGKTTtaakLA-~~l~~~------~g~kV~lV~~D~~R~~a~---~QL~~~a~~~gvp~~~~~~~~~P~~i  170 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLA-YYLKKK------QGKKVLLVACDLYRPAAI---EQLKVLGQQVGVPVFALGKGQSPVEI  170 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHH-HHHHHh------CCCeEEEEeccccchHHH---HHHHHHHHhcCCceEecCCCCCHHHH
Confidence            46777999999995433222 222211      244555444 33 43332   23444444455555544433333221


Q ss_pred             ----HHH-HhCCCe-EEEEChHHH
Q psy17644        284 ----SKA-LELGAE-IVVGTPGRI  301 (330)
Q Consensus       284 ----~~~-l~~~~d-IiV~TP~~L  301 (330)
                          ... ...+++ |||=||+++
T Consensus       171 ~~~al~~~~~~~~DvVIIDTaGr~  194 (428)
T TIGR00959       171 ARRALEYAKENGFDVVIVDTAGRL  194 (428)
T ss_pred             HHHHHHHHHhcCCCEEEEeCCCcc
Confidence                112 234565 778899975

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.

>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=92.49  E-value=0.28  Score=42.76  Aligned_cols=60  Identities=17%  Similarity=0.109  Sum_probs=29.5

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc--cHHHHHHHHHHHHHhccCCCceEEEEECC
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP--TRELSQQIYNEAKRFGKGYNLSVVCCYGG  277 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P--tr~La~Qi~~~~~~l~~~~~~~~~~~~gg  277 (330)
                      ++++||||+|||.+..=-+.....+        +.++.+++-  .|.-|.   ++++.+++..++.+......
T Consensus         4 i~lvGptGvGKTTt~aKLAa~~~~~--------~~~v~lis~D~~R~ga~---eQL~~~a~~l~vp~~~~~~~   65 (196)
T PF00448_consen    4 IALVGPTGVGKTTTIAKLAARLKLK--------GKKVALISADTYRIGAV---EQLKTYAEILGVPFYVARTE   65 (196)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHT--------T--EEEEEESTSSTHHH---HHHHHHHHHHTEEEEESSTT
T ss_pred             EEEECCCCCchHhHHHHHHHHHhhc--------cccceeecCCCCCccHH---HHHHHHHHHhccccchhhcc
Confidence            5778999999995533222222211        334444442  344443   33444444446665544433

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 ....

>KOG0331|consensus

Probab=92.48  E-value=0.76  Score=45.73  Aligned_cols=72  Identities=15%  Similarity=0.195  Sum_probs=55.6

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhC----CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALEL----GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~----~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|-|+--|.++...+++.    +..+.+++|..+..+....|+.    .+.|+|||-      +-.+.+++..
T Consensus       340 ~~~KvIIFc~tkr~~~~l~~~l~~~----~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATd------VAaRGLDi~d  409 (519)
T KOG0331|consen  340 SEGKVIIFCETKRTCDELARNLRRK----GWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATD------VAARGLDVPD  409 (519)
T ss_pred             CCCcEEEEecchhhHHHHHHHHHhc----CcceeeecccccHHHHHHHHHhcccCCcceEEEcc------cccccCCCcc
Confidence            5679999999999999999888875    3678899998887766555542    489999993      2234667888


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      |++||-
T Consensus       410 V~lVIn  415 (519)
T KOG0331|consen  410 VDLVIN  415 (519)
T ss_pred             ccEEEe
Confidence            888874

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=92.47  E-value=0.22  Score=48.09  Aligned_cols=33  Identities=36%  Similarity=0.468  Sum_probs=23.6

Q ss_pred             hhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhc
Q psy17644        199 PAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQ  232 (330)
Q Consensus       199 ~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~  232 (330)
                      |.-...+++++.|.||||||. ++.+++..++.+
T Consensus        10 ~~~~e~~~~li~G~~GsGKT~-~i~~ll~~~~~~   42 (386)
T PF10412_consen   10 PKDSENRHILIIGATGSGKTQ-AIRHLLDQIRAR   42 (386)
T ss_dssp             -GGGGGG-EEEEE-TTSSHHH-HHHHHHHHHHHT
T ss_pred             ccchhhCcEEEECCCCCCHHH-HHHHHHHHHHHc
Confidence            444567899999999999995 556778777764

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>PRK09165 replicative DNA helicase; Provisional

Probab=92.42  E-value=0.98  Score=45.15  Aligned_cols=119  Identities=15%  Similarity=0.064  Sum_probs=57.5

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCC--------CCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEE
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE--------PGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCY  275 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~--------~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~  275 (330)
                      |.=+++.|+||+||| +|.+.+..++..+..+.        ...+..|+|++ .-.-..|+...+........... ...
T Consensus       217 g~livIaarpg~GKT-~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fS-lEMs~~ql~~R~la~~s~v~~~~-i~~  293 (497)
T PRK09165        217 SDLIILAGRPSMGKT-ALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFS-LEMSAEQLATRILSEQSEISSSK-IRR  293 (497)
T ss_pred             CceEEEEeCCCCChH-HHHHHHHHHHHHhhcccccccccccccCCCeEEEEe-CcCCHHHHHHHHHHHhcCCCHHH-Hhc
Confidence            344566699999999 45555555544321100        01256677764 33445566655443322222211 112


Q ss_pred             CCCchHHH------HHHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        276 GGGSKWDQ------SKALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       276 gg~~~~~~------~~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      |..+..++      ...+.. ..+.|.     |+..+...+++-.. -..+++||||=.+.|-
T Consensus       294 ~~l~~~e~~~l~~a~~~l~~-~~l~I~d~~~~ti~~i~~~ir~l~~-~~~~~lvvIDyLqli~  354 (497)
T PRK09165        294 GKISEEDFEKLVDASQELQK-LPLYIDDTPALSISQLRARARRLKR-QHGLDLLVVDYLQLIR  354 (497)
T ss_pred             CCCCHHHHHHHHHHHHHHhc-CCeEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhcc
Confidence            22222221      122222 345553     44555554443211 1358899999988764

>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=92.40  E-value=0.33  Score=43.15  Aligned_cols=14  Identities=29%  Similarity=0.361  Sum_probs=12.6

Q ss_pred             cEEEEcCCCChhHH
Q psy17644        206 DIIGVAKTGSGKTG  219 (330)
Q Consensus       206 d~i~~a~TGsGKT~  219 (330)
                      ++|+.||+|.|||.
T Consensus        52 h~lf~GPPG~GKTT   65 (233)
T PF05496_consen   52 HMLFYGPPGLGKTT   65 (233)
T ss_dssp             EEEEESSTTSSHHH
T ss_pred             eEEEECCCccchhH
Confidence            68999999999993

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.

>PRK05636 replicative DNA helicase; Provisional

Probab=92.37  E-value=0.46  Score=47.55  Aligned_cols=108  Identities=14%  Similarity=0.170  Sum_probs=50.6

Q ss_pred             CcE-EEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc---ccHHHHHHHHHHHHHhccCCCceEEEEECCC-c
Q psy17644        205 RDI-IGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA---PTRELSQQIYNEAKRFGKGYNLSVVCCYGGG-S  279 (330)
Q Consensus       205 ~d~-i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~---Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~-~  279 (330)
                      .++ ++.|+||+|||. |.+-++.++..+      .+..|+|++   +..+++.++.....      ++....+..|. +
T Consensus       265 G~Liiiaarpg~GKT~-~al~~a~~~a~~------~g~~v~~fSlEMs~~ql~~R~ls~~s------~v~~~~i~~g~l~  331 (505)
T PRK05636        265 GQMIIVAARPGVGKST-LALDFMRSASIK------HNKASVIFSLEMSKSEIVMRLLSAEA------EVRLSDMRGGKMD  331 (505)
T ss_pred             CceEEEEeCCCCCHHH-HHHHHHHHHHHh------CCCeEEEEEeeCCHHHHHHHHHHHhc------CCCHHHHhcCCCC
Confidence            444 556999999994 444444444321      244566663   33444444332211      12111122222 2


Q ss_pred             hHHH------HHHHhCCCeEEEE-C----hHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        280 KWDQ------SKALELGAEIVVG-T----PGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       280 ~~~~------~~~l~~~~dIiV~-T----P~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ...+      ...+.. ..+.|. +    ...+...+++-.. -..+++||||-.+.|-
T Consensus       332 ~~e~~~~~~a~~~l~~-~~l~I~d~~~~ti~~I~~~~r~~~~-~~~~~lvvIDYLql~~  388 (505)
T PRK05636        332 EDAWEKLVQRLGKIAQ-APIFIDDSANLTMMEIRSKARRLKQ-KHDLKLIVVDYLQLMS  388 (505)
T ss_pred             HHHHHHHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhcC
Confidence            2222      122222 445553 3    3334333332111 1358899999998774

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=92.34  E-value=2.4  Score=39.91  Aligned_cols=119  Identities=19%  Similarity=0.246  Sum_probs=63.9

Q ss_pred             CCCCCHHHHHhhhhhc----CCC---cEEEEcCCCChhHHHHHHHHHHHHHhcCCC-----------CCCCCCeEEEE--
Q psy17644        187 YTSPTPIQAQAVPAAL----SGR---DIIGVAKTGSGKTGAFIWPMLVHIMDQKEL-----------EPGDGPMGLIL--  246 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~----~g~---d~i~~a~TGsGKT~a~llp~l~~i~~~~~~-----------~~~~~~~vLil--  246 (330)
                      +..++|+|..++..+.    +||   -+++.|+.|.||+. +...+...++.....           ..++.|-..+|  
T Consensus         2 ~~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~-lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~   80 (319)
T PRK08769          2 TSAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRA-VALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSF   80 (319)
T ss_pred             CccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHH-HHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEec
Confidence            3467889988887765    444   58899999999983 333345566654311           12345777777  


Q ss_pred             cccH-------H-HHHHHHHHHHHhcc---CCCceEEEEECCCchHH--H---HHHHhC---CCeEEEEC--hHHHHHHH
Q psy17644        247 APTR-------E-LSQQIYNEAKRFGK---GYNLSVVCCYGGGSKWD--Q---SKALEL---GAEIVVGT--PGRIIDMV  305 (330)
Q Consensus       247 ~Ptr-------~-La~Qi~~~~~~l~~---~~~~~~~~~~gg~~~~~--~---~~~l~~---~~dIiV~T--P~~L~~~l  305 (330)
                      .|..       . .+.||.+....+..   ..+.+++++........  .   .+.+..   ++-+|+.|  |.+|+.-+
T Consensus        81 ~p~~~~~k~~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTI  160 (319)
T PRK08769         81 IPNRTGDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATI  160 (319)
T ss_pred             CCCcccccccccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHH
Confidence            6642       1 24444433333221   22456666655443222  1   222222   34444444  67776555


Q ss_pred             H
Q psy17644        306 K  306 (330)
Q Consensus       306 ~  306 (330)
                      .
T Consensus       161 r  161 (319)
T PRK08769        161 R  161 (319)
T ss_pred             H
Confidence            4

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=92.33  E-value=0.94  Score=44.25  Aligned_cols=72  Identities=14%  Similarity=0.222  Sum_probs=52.0

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      ...++||.|+|++.|..++..+...    ++.+..+.|+.+..++...   ++. ..+|||||     +.+. ..+++..
T Consensus       244 ~~~~~lVF~~s~~~~~~l~~~L~~~----~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaT-----d~~~-~GiDip~  313 (434)
T PRK11192        244 EVTRSIVFVRTRERVHELAGWLRKA----GINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVAT-----DVAA-RGIDIDD  313 (434)
T ss_pred             CCCeEEEEeCChHHHHHHHHHHHhC----CCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEc-----cccc-cCccCCC
Confidence            3578999999999999999988764    6788888888876555433   333 47899999     2332 3455777


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      +.+||.
T Consensus       314 v~~VI~  319 (434)
T PRK11192        314 VSHVIN  319 (434)
T ss_pred             CCEEEE
Confidence            777763

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=92.29  E-value=0.38  Score=42.95  Aligned_cols=54  Identities=13%  Similarity=0.136  Sum_probs=34.3

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      -.|.-+++.+++|+|||.. ++.++....+       ++.++++++ +.+-..++...+..++
T Consensus        22 ~~g~~~~i~G~~G~GKTtl-~~~~~~~~~~-------~g~~~~yi~-~e~~~~~~~~~~~~~g   75 (230)
T PRK08533         22 PAGSLILIEGDESTGKSIL-SQRLAYGFLQ-------NGYSVSYVS-TQLTTTEFIKQMMSLG   75 (230)
T ss_pred             CCCcEEEEECCCCCCHHHH-HHHHHHHHHh-------CCCcEEEEe-CCCCHHHHHHHHHHhC
Confidence            3577788889999999943 3334444433       356778887 4444456666665553

>PRK06526 transposase; Provisional

Probab=92.22  E-value=0.42  Score=43.43  Aligned_cols=49  Identities=14%  Similarity=0.175  Sum_probs=28.9

Q ss_pred             hhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH
Q psy17644        199 PAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQI  256 (330)
Q Consensus       199 ~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi  256 (330)
                      ..+-.+++++++||+|+|||..... +...+..       .|.+|+++ ....++.++
T Consensus        93 ~fi~~~~nlll~Gp~GtGKThLa~a-l~~~a~~-------~g~~v~f~-t~~~l~~~l  141 (254)
T PRK06526         93 DFVTGKENVVFLGPPGTGKTHLAIG-LGIRACQ-------AGHRVLFA-TAAQWVARL  141 (254)
T ss_pred             chhhcCceEEEEeCCCCchHHHHHH-HHHHHHH-------CCCchhhh-hHHHHHHHH
Confidence            3344778999999999999944332 2223332       24455554 334455555

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.18  E-value=0.37  Score=48.37  Aligned_cols=112  Identities=15%  Similarity=0.054  Sum_probs=55.7

Q ss_pred             EEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH-hccCCCceEEEEECCCchH-HHH--
Q psy17644        209 GVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR-FGKGYNLSVVCCYGGGSKW-DQS--  284 (330)
Q Consensus       209 ~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~-l~~~~~~~~~~~~gg~~~~-~~~--  284 (330)
                      +...||||||++..--+| +.+++      .-..-|+.|............+.. ++..+=..-...++|.... ...  
T Consensus         2 f~matgsgkt~~ma~lil-~~y~k------gyr~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn~   74 (812)
T COG3421           2 FEMATGSGKTLVMAGLIL-ECYKK------GYRNFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVNN   74 (812)
T ss_pred             cccccCCChhhHHHHHHH-HHHHh------chhhEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeecc
Confidence            456899999976544333 44443      123457777665555444333221 0000000001111111100 000  


Q ss_pred             -HHHhCCCeEEEEChHHHHHHHHcCC---C---CCCCccE-EEeecccccC
Q psy17644        285 -KALELGAEIVVGTPGRIIDMVKMGA---T---KLNRVTF-LVLDEADRMF  327 (330)
Q Consensus       285 -~~l~~~~dIiV~TP~~L~~~l~~~~---~---~l~~i~~-lVvDEad~ll  327 (330)
                       .....+..|.++|-.+|...+.+..   +   ++.+..+ ++-||||+|-
T Consensus        75 fsehnd~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln  125 (812)
T COG3421          75 FSEHNDAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLN  125 (812)
T ss_pred             cCccCCceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhh
Confidence             1123357899999999988775432   2   2444444 4679999974

>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=92.05  E-value=0.61  Score=41.29  Aligned_cols=48  Identities=17%  Similarity=0.227  Sum_probs=27.0

Q ss_pred             CcEEEEcCCCChhHHHHHHHHH-HHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPML-VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEA  260 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l-~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~  260 (330)
                      .-+++.|++|+|||.  |+.++ +.+.+..     .+.+|+++... +.+..+...+
T Consensus        35 ~~l~l~G~~G~GKTH--LL~Ai~~~~~~~~-----~~~~v~y~~~~-~f~~~~~~~~   83 (219)
T PF00308_consen   35 NPLFLYGPSGLGKTH--LLQAIANEAQKQH-----PGKRVVYLSAE-EFIREFADAL   83 (219)
T ss_dssp             SEEEEEESTTSSHHH--HHHHHHHHHHHHC-----TTS-EEEEEHH-HHHHHHHHHH
T ss_pred             CceEEECCCCCCHHH--HHHHHHHHHHhcc-----ccccceeecHH-HHHHHHHHHH
Confidence            357888999999995  33333 3443321     35677776443 4444444433

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.

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=91.99  E-value=0.51  Score=46.40  Aligned_cols=80  Identities=15%  Similarity=0.072  Sum_probs=53.7

Q ss_pred             HHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q psy17644        178 LMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIY  257 (330)
Q Consensus       178 l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~  257 (330)
                      ++..+.+ ++..+...|+.+.-..-.|+- .+.+-.|||||...++-+ .++..++     ..-+++|.+=|+.|+.++.
T Consensus       152 ~l~~ies-kIanfD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Ka-a~lh~kn-----Pd~~I~~Tfftk~L~s~~r  223 (660)
T COG3972         152 LLDTIES-KIANFDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKA-AELHSKN-----PDSRIAFTFFTKILASTMR  223 (660)
T ss_pred             HHHHHHH-HHhcccchhheeeeecCCchh-hhhcccCCCchhHHHHHH-HHHhcCC-----CCceEEEEeehHHHHHHHH
Confidence            4444433 344556678777666666666 567778999996544333 3333322     3568899999999999999


Q ss_pred             HHHHHhcc
Q psy17644        258 NEAKRFGK  265 (330)
Q Consensus       258 ~~~~~l~~  265 (330)
                      ..+.+|+.
T Consensus       224 ~lv~~F~f  231 (660)
T COG3972         224 TLVPEFFF  231 (660)
T ss_pred             HHHHHHHH
Confidence            98888764

>PRK10867 signal recognition particle protein; Provisional

Probab=91.94  E-value=0.76  Score=45.02  Aligned_cols=86  Identities=24%  Similarity=0.256  Sum_probs=42.6

Q ss_pred             cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHH
Q psy17644        206 DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA--PTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ  283 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~--Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~  283 (330)
                      -+++++++|+|||.+..--+ .++..+      .+.++++++  +.|..+.   +.++.++...++.+.....+.+....
T Consensus       102 vI~~vG~~GsGKTTtaakLA-~~l~~~------~G~kV~lV~~D~~R~aa~---eQL~~~a~~~gv~v~~~~~~~dp~~i  171 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLA-KYLKKK------KKKKVLLVAADVYRPAAI---EQLKTLGEQIGVPVFPSGDGQDPVDI  171 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHH-HHHHHh------cCCcEEEEEccccchHHH---HHHHHHHhhcCCeEEecCCCCCHHHH
Confidence            46677999999995433222 233221      145555554  2344433   23344444456655443222232221


Q ss_pred             H----H-HHhCCCe-EEEEChHHH
Q psy17644        284 S----K-ALELGAE-IVVGTPGRI  301 (330)
Q Consensus       284 ~----~-~l~~~~d-IiV~TP~~L  301 (330)
                      .    . ....+++ |||=||+++
T Consensus       172 ~~~a~~~a~~~~~DvVIIDTaGrl  195 (433)
T PRK10867        172 AKAALEEAKENGYDVVIVDTAGRL  195 (433)
T ss_pred             HHHHHHHHHhcCCCEEEEeCCCCc
Confidence            1    1 1223455 677799976

>PRK04328 hypothetical protein; Provisional

Probab=91.92  E-value=0.39  Score=43.39  Aligned_cols=53  Identities=23%  Similarity=0.327  Sum_probs=34.8

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|.-+++.+++|+|||. +++.++...++       ++-+++|++ +.+-..++.+.+..++
T Consensus        22 ~gs~ili~G~pGsGKT~-l~~~fl~~~~~-------~ge~~lyis-~ee~~~~i~~~~~~~g   74 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSI-FSQQFLWNGLQ-------MGEPGVYVA-LEEHPVQVRRNMRQFG   74 (249)
T ss_pred             CCcEEEEEcCCCCCHHH-HHHHHHHHHHh-------cCCcEEEEE-eeCCHHHHHHHHHHcC
Confidence            46778889999999994 33333433333       355667765 6566677777777764

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=91.91  E-value=0.53  Score=42.79  Aligned_cols=37  Identities=16%  Similarity=0.076  Sum_probs=25.3

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA  247 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~  247 (330)
                      .|.-+++.+++|+|||. |++.++.+...       ++-+++|++
T Consensus        35 ~gs~~lI~G~pGtGKT~-l~~qf~~~~a~-------~Ge~vlyis   71 (259)
T TIGR03878        35 AYSVINITGVSDTGKSL-MVEQFAVTQAS-------RGNPVLFVT   71 (259)
T ss_pred             CCcEEEEEcCCCCCHHH-HHHHHHHHHHh-------CCCcEEEEE
Confidence            56778889999999994 45444444333       356777776

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>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=91.86  E-value=0.24  Score=45.14  Aligned_cols=29  Identities=31%  Similarity=0.353  Sum_probs=20.5

Q ss_pred             hcCCCcEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      +..+..++++|+||||||. ++-.++..+-
T Consensus       124 v~~~~~ili~G~tGSGKTT-~l~all~~i~  152 (270)
T PF00437_consen  124 VRGRGNILISGPTGSGKTT-LLNALLEEIP  152 (270)
T ss_dssp             HHTTEEEEEEESTTSSHHH-HHHHHHHHCH
T ss_pred             cccceEEEEECCCccccch-HHHHHhhhcc
Confidence            3467899999999999993 3344454443

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 ....

>PRK06321 replicative DNA helicase; Provisional

Probab=91.73  E-value=1.2  Score=44.13  Aligned_cols=111  Identities=14%  Similarity=0.088  Sum_probs=55.7

Q ss_pred             CcE-EEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEE-EECCCchHH
Q psy17644        205 RDI-IGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVC-CYGGGSKWD  282 (330)
Q Consensus       205 ~d~-i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~-~~gg~~~~~  282 (330)
                      .++ ++.|++|.||| +|++.+..++...      .+..|+|++ .-.-..|+...+.....  ++...- ..|..+...
T Consensus       226 G~LiiiaarPgmGKT-afal~ia~~~a~~------~g~~v~~fS-LEMs~~ql~~Rlla~~s--~v~~~~i~~~~l~~~e  295 (472)
T PRK06321        226 SNLMILAARPAMGKT-ALALNIAENFCFQ------NRLPVGIFS-LEMTVDQLIHRIICSRS--EVESKKISVGDLSGRD  295 (472)
T ss_pred             CcEEEEEeCCCCChH-HHHHHHHHHHHHh------cCCeEEEEe-ccCCHHHHHHHHHHhhc--CCCHHHhhcCCCCHHH
Confidence            454 55699999999 5666666665432      244556554 22334455544432211  222111 123333322


Q ss_pred             HH------HHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        283 QS------KALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       283 ~~------~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      +.      ..+.. ..+.|-     |...+...+++-.. -..+++||||-.+.|-
T Consensus       296 ~~~~~~a~~~l~~-~~~~idd~~~~ti~~i~~~~r~~~~-~~~~~lvvIDyLql~~  349 (472)
T PRK06321        296 FQRIVSVVNEMQE-HTLLIDDQPGLKITDLRARARRMKE-SYDIQFLIIDYLQLLS  349 (472)
T ss_pred             HHHHHHHHHHHHc-CCEEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHHcC
Confidence            21      23333 346664     44455544433211 1358899999988774

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=91.64  E-value=1.2  Score=43.39  Aligned_cols=71  Identities=17%  Similarity=0.164  Sum_probs=51.7

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---hC-CCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---EL-GAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~~-~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      ..++||.|+|+..|..++..+...    +..+..++|+....++...+   +. ..+|||||-     .+. ..+++..+
T Consensus       255 ~~~~lVF~~t~~~~~~l~~~L~~~----g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTd-----v~~-rGiDip~v  324 (423)
T PRK04837        255 PDRAIIFANTKHRCEEIWGHLAAD----GHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATD-----VAA-RGLHIPAV  324 (423)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhC----CCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEec-----hhh-cCCCcccc
Confidence            568999999999999988888764    67888888887765543333   33 479999993     333 35567777


Q ss_pred             cEEEe
Q psy17644        316 TFLVL  320 (330)
Q Consensus       316 ~~lVv  320 (330)
                      .+||.
T Consensus       325 ~~VI~  329 (423)
T PRK04837        325 THVFN  329 (423)
T ss_pred             CEEEE
Confidence            77764

>PTZ00110 helicase; Provisional

Probab=91.64  E-value=1.4  Score=44.57  Aligned_cols=72  Identities=15%  Similarity=0.265  Sum_probs=51.5

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHH---HHhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK---ALEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~---~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+.-|..+...++..    ++.+.+++|+....+...   .++. ...|||||-     .+. ..+++..
T Consensus       376 ~~~k~LIF~~t~~~a~~l~~~L~~~----g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTd-----v~~-rGIDi~~  445 (545)
T PTZ00110        376 DGDKILIFVETKKGADFLTKELRLD----GWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATD-----VAS-RGLDVKD  445 (545)
T ss_pred             cCCeEEEEecChHHHHHHHHHHHHc----CCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcc-----hhh-cCCCccc
Confidence            4679999999999999998888753    567788888887655433   3333 468999993     222 3456677


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      |.+||.
T Consensus       446 v~~VI~  451 (545)
T PTZ00110        446 VKYVIN  451 (545)
T ss_pred             CCEEEE
Confidence            777764

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=91.63  E-value=0.51  Score=40.52  Aligned_cols=31  Identities=35%  Similarity=0.405  Sum_probs=23.9

Q ss_pred             CCHHHHHhhhhhc-CCCcEEEEcCCCChhHHH
Q psy17644        190 PTPIQAQAVPAAL-SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       190 pt~iQ~~~i~~~~-~g~d~i~~a~TGsGKT~a  220 (330)
                      .++-|...+...+ .|..++++++||||||..
T Consensus        10 ~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTl   41 (186)
T cd01130          10 FSPLQAAYLWLAVEARKNILISGGTGSGKTTL   41 (186)
T ss_pred             CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            4566777776655 678899999999999943

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.

>KOG3089|consensus

Probab=91.55  E-value=0.035  Score=48.44  Aligned_cols=33  Identities=39%  Similarity=0.704  Sum_probs=30.0

Q ss_pred             CCeEEEEChHHHHHHHHcCCCCCCCccEEEeec
Q psy17644        290 GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDE  322 (330)
Q Consensus       290 ~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDE  322 (330)
                      ..++-||||+|+..+++...+.++.+.++|+|=
T Consensus       196 ~v~~gIgTp~Ri~~lv~~~~f~~~~lk~iIlD~  228 (271)
T KOG3089|consen  196 VVHLGIGTPGRIKELVKQGGFNLSPLKFIILDW  228 (271)
T ss_pred             ceeEeecCcHHHHHHHHhcCCCCCcceeEEeec
Confidence            468889999999999999889999999999984

>PHA02535 P terminase ATPase subunit; Provisional

Probab=91.52  E-value=0.73  Score=46.52  Aligned_cols=86  Identities=15%  Similarity=0.071  Sum_probs=60.6

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q psy17644        174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELS  253 (330)
Q Consensus       174 l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La  253 (330)
                      ++......|...-...+.++|+..+..-...+.-++.-.-=.|||..|..-++...+..       |-..++|.|++..|
T Consensus       123 ~s~~~~~~l~~~~~~~l~~YQ~~W~~~~~~~r~r~ilKSRQiG~T~~fA~EA~~dal~~-------G~nqiflSas~~QA  195 (581)
T PHA02535        123 ISDEQTEKLIEAFLDSLFDYQKHWYRAGLHHRTRNILKSRQIGATYYFAREALEDALLT-------GRNQIFLSASKAQA  195 (581)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHhCccccceeeEeeecccchHHHHHHHHHHHHHhc-------CCceEEECCCHHHH
Confidence            44444455544444567799999886533345555555556789999888888777653       45679999999999


Q ss_pred             HHHHHHHHHhccC
Q psy17644        254 QQIYNEAKRFGKG  266 (330)
Q Consensus       254 ~Qi~~~~~~l~~~  266 (330)
                      ......+..+++.
T Consensus       196 ~~f~~yi~~~a~~  208 (581)
T PHA02535        196 HVFKQYIIAFARE  208 (581)
T ss_pred             HHHHHHHHHHHHh
Confidence            9988888888654

>KOG0333|consensus

Probab=91.46  E-value=1.1  Score=44.41  Aligned_cols=71  Identities=17%  Similarity=0.207  Sum_probs=52.2

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      ..|.+||.+.|..-|.-+...+.+.    +.+++.++||....+....   ++. ..+|+|||--      --..++..+
T Consensus       516 ~~ppiIIFvN~kk~~d~lAk~LeK~----g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDv------AgRGIDIpn  585 (673)
T KOG0333|consen  516 FDPPIIIFVNTKKGADALAKILEKA----GYKVTTLHGGKSQEQRENALADFREGTGDILVATDV------AGRGIDIPN  585 (673)
T ss_pred             CCCCEEEEEechhhHHHHHHHHhhc----cceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecc------cccCCCCCc
Confidence            4688999999999998888888876    5789999999987665444   334 5799999932      122445666


Q ss_pred             ccEEE
Q psy17644        315 VTFLV  319 (330)
Q Consensus       315 i~~lV  319 (330)
                      |.+||
T Consensus       586 VSlVi  590 (673)
T KOG0333|consen  586 VSLVI  590 (673)
T ss_pred             cceee
Confidence            66654

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=91.43  E-value=0.25  Score=48.08  Aligned_cols=33  Identities=27%  Similarity=0.388  Sum_probs=22.8

Q ss_pred             hhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        198 VPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       198 i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      +|.-...+++++.|+||||||.+ +..++..++.
T Consensus        36 ~~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~~~   68 (410)
T cd01127          36 FPKDAEEAHTMIIGTTGTGKTTQ-IRELLASIRA   68 (410)
T ss_pred             CCcchhhccEEEEcCCCCCHHHH-HHHHHHHHHh
Confidence            34444568999999999999964 4445555544

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=91.40  E-value=0.2  Score=51.80  Aligned_cols=49  Identities=22%  Similarity=0.161  Sum_probs=35.6

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ++++++|+||||||..|++|-|...          ...+||+=|--++...+....++.
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~----------~gS~VV~DpKGE~~~~Ta~~R~~~  188 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTF----------KGSVIALDVKGELFELTSRARKAS  188 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcC----------CCCEEEEeCCchHHHHHHHHHHhC
Confidence            4889999999999999999987542          235677777777766555544443

>PRK09183 transposase/IS protein; Provisional

Probab=91.33  E-value=0.55  Score=42.76  Aligned_cols=47  Identities=21%  Similarity=0.145  Sum_probs=28.5

Q ss_pred             hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQI  256 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi  256 (330)
                      +-.|.++++.||+|+|||....  ++.+....      .|..++++ +..+|..++
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~--al~~~a~~------~G~~v~~~-~~~~l~~~l  145 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAI--ALGYEAVR------AGIKVRFT-TAADLLLQL  145 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHH--HHHHHHHH------cCCeEEEE-eHHHHHHHH
Confidence            4578899999999999994333  22222221      35566655 445565443

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=91.33  E-value=1.5  Score=38.00  Aligned_cols=89  Identities=21%  Similarity=0.172  Sum_probs=51.7

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA  286 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~  286 (330)
                      .++++++.||||...+--+-++..        .+-++++..|-..-         ++    +...+...-|...      
T Consensus         7 ~~i~gpM~SGKT~eLl~r~~~~~~--------~g~~v~vfkp~iD~---------R~----~~~~V~Sr~G~~~------   59 (201)
T COG1435           7 EFIYGPMFSGKTEELLRRARRYKE--------AGMKVLVFKPAIDT---------RY----GVGKVSSRIGLSS------   59 (201)
T ss_pred             EEEEccCcCcchHHHHHHHHHHHH--------cCCeEEEEeccccc---------cc----ccceeeeccCCcc------
Confidence            467899999999644433333222        46788888885322         11    1222222112211      


Q ss_pred             HhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        287 LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       287 l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                          .-++|-++..+...+........ +.+|.||||+-+-
T Consensus        60 ----~A~~i~~~~~i~~~i~~~~~~~~-~~~v~IDEaQF~~   95 (201)
T COG1435          60 ----EAVVIPSDTDIFDEIAALHEKPP-VDCVLIDEAQFFD   95 (201)
T ss_pred             ----cceecCChHHHHHHHHhcccCCC-cCEEEEehhHhCC
Confidence                24667777788887765433332 8899999998653

>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=91.17  E-value=2.5  Score=35.45  Aligned_cols=84  Identities=23%  Similarity=0.271  Sum_probs=39.4

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc-ccH-HHHHHHHHHHHHhccCCCceEEEEECCCchHH--
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA-PTR-ELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWD--  282 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~-Ptr-~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~--  282 (330)
                      +++.+++|+|||.... -+...+..       .+.+++++. .++ .-.   ...+..++...++.+...........  
T Consensus         3 ~~~~G~~G~GKTt~~~-~la~~~~~-------~g~~v~~i~~D~~~~~~---~~~l~~~~~~~~~~~~~~~~~~~~~~~~   71 (173)
T cd03115           3 ILLVGLQGVGKTTTAA-KLALYLKK-------KGKKVLLVAADTYRPAA---IEQLRVLGEQVGVPVFEEGEGKDPVSIA   71 (173)
T ss_pred             EEEECCCCCCHHHHHH-HHHHHHHH-------CCCcEEEEEcCCCChHH---HHHHHHhcccCCeEEEecCCCCCHHHHH
Confidence            4677999999995432 22223322       245555443 432 222   22344444444554443322222211  


Q ss_pred             --HH-HHHhCCCe-EEEEChHHH
Q psy17644        283 --QS-KALELGAE-IVVGTPGRI  301 (330)
Q Consensus       283 --~~-~~l~~~~d-IiV~TP~~L  301 (330)
                        .. .....+.+ |||=||+..
T Consensus        72 ~~~~~~~~~~~~d~viiDt~g~~   94 (173)
T cd03115          72 KRAIEHAREENFDVVIVDTAGRL   94 (173)
T ss_pred             HHHHHHHHhCCCCEEEEECcccc
Confidence              11 12334554 677788875

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.

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=91.15  E-value=1.7  Score=44.73  Aligned_cols=15  Identities=20%  Similarity=0.381  Sum_probs=12.7

Q ss_pred             CCccEEEeecccccC
Q psy17644        313 NRVTFLVLDEADRMF  327 (330)
Q Consensus       313 ~~i~~lVvDEad~ll  327 (330)
                      .+.+++||||||+|-
T Consensus       118 g~~KV~IIDEah~Ls  132 (647)
T PRK07994        118 GRFKVYLIDEVHMLS  132 (647)
T ss_pred             CCCEEEEEechHhCC
Confidence            467899999999885

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=91.09  E-value=1.4  Score=42.49  Aligned_cols=17  Identities=35%  Similarity=0.315  Sum_probs=15.4

Q ss_pred             CCCcEEEEcCCCChhHH
Q psy17644        203 SGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~  219 (330)
                      .|+-.++.|+.|.|||.
T Consensus       168 kGQR~lIvgppGvGKTT  184 (416)
T PRK09376        168 KGQRGLIVAPPKAGKTV  184 (416)
T ss_pred             cCceEEEeCCCCCChhH
Confidence            78899999999999994

>PRK10436 hypothetical protein; Provisional

Probab=91.03  E-value=0.89  Score=44.95  Aligned_cols=38  Identities=32%  Similarity=0.365  Sum_probs=22.5

Q ss_pred             HHHHHhhhhhc--CCCcEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        192 PIQAQAVPAAL--SGRDIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       192 ~iQ~~~i~~~~--~g~d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      +.|...+..++  .+--++++++||||||.+ +..+|.++.
T Consensus       204 ~~~~~~l~~~~~~~~GliLvtGpTGSGKTTt-L~a~l~~~~  243 (462)
T PRK10436        204 PAQLAQFRQALQQPQGLILVTGPTGSGKTVT-LYSALQTLN  243 (462)
T ss_pred             HHHHHHHHHHHHhcCCeEEEECCCCCChHHH-HHHHHHhhC
Confidence            34444444433  233477889999999943 334566653

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=90.99  E-value=0.5  Score=42.83  Aligned_cols=54  Identities=26%  Similarity=0.405  Sum_probs=38.4

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      .|+.+++.+++|+||| .|++.++.....       .|-+++++ -+.+...++.+.+..++-
T Consensus        22 ~g~~~lI~G~pGsGKT-~f~~qfl~~~~~-------~ge~vlyv-s~~e~~~~l~~~~~~~g~   75 (260)
T COG0467          22 RGSVVLITGPPGTGKT-IFALQFLYEGAR-------EGEPVLYV-STEESPEELLENARSFGW   75 (260)
T ss_pred             CCcEEEEEcCCCCcHH-HHHHHHHHHHHh-------cCCcEEEE-EecCCHHHHHHHHHHcCC
Confidence            5788999999999999 566666655544       24445554 566777888888877644

>PTZ00293 thymidine kinase; Provisional

Probab=90.98  E-value=1.1  Score=39.40  Aligned_cols=39  Identities=13%  Similarity=0.106  Sum_probs=25.5

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR  250 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr  250 (330)
                      |+=.++.||++||||. -||-.+.+...       .+.+++++-|..
T Consensus         4 G~i~vi~GpMfSGKTt-eLLr~i~~y~~-------ag~kv~~~kp~~   42 (211)
T PTZ00293          4 GTISVIIGPMFSGKTT-ELMRLVKRFTY-------SEKKCVVIKYSK   42 (211)
T ss_pred             eEEEEEECCCCChHHH-HHHHHHHHHHH-------cCCceEEEEecc
Confidence            4445778999999994 34444443332       356788888853

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.91  E-value=1.1  Score=47.46  Aligned_cols=15  Identities=20%  Similarity=0.381  Sum_probs=12.7

Q ss_pred             CCccEEEeecccccC
Q psy17644        313 NRVTFLVLDEADRMF  327 (330)
Q Consensus       313 ~~i~~lVvDEad~ll  327 (330)
                      .+.+++||||||+|-
T Consensus       118 gk~KViIIDEAh~LT  132 (944)
T PRK14949        118 GRFKVYLIDEVHMLS  132 (944)
T ss_pred             CCcEEEEEechHhcC
Confidence            467899999999984

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=90.86  E-value=1.1  Score=42.82  Aligned_cols=31  Identities=19%  Similarity=0.375  Sum_probs=21.0

Q ss_pred             hcCCC---cEEEEcCCCChhHHHHHHHHHHHHHhc
Q psy17644        201 ALSGR---DIIGVAKTGSGKTGAFIWPMLVHIMDQ  232 (330)
Q Consensus       201 ~~~g~---d~i~~a~TGsGKT~a~llp~l~~i~~~  232 (330)
                      +.+|+   -+++.|+.|.|||. +...+..+++..
T Consensus        39 ~~~grl~ha~L~~G~~G~GKtt-lA~~lA~~Llc~   72 (351)
T PRK09112         39 YREGKLHHALLFEGPEGIGKAT-LAFHLANHILSH   72 (351)
T ss_pred             HHcCCCCeeEeeECCCCCCHHH-HHHHHHHHHcCC
Confidence            34555   58899999999983 333455666663

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=90.83  E-value=1.2  Score=44.70  Aligned_cols=17  Identities=24%  Similarity=0.210  Sum_probs=13.9

Q ss_pred             CcEEEEcCCCChhHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAF  221 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~  221 (330)
                      +.++++|+.|+|||.+.
T Consensus        44 ~a~Lf~Gp~G~GKTT~A   60 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSA   60 (507)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            36899999999999543

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=90.79  E-value=1.9  Score=42.49  Aligned_cols=72  Identities=11%  Similarity=0.191  Sum_probs=51.3

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      ...++||.|+|+.-|..++..+...    ++.+..++|+.+.......   ++. ..+|||||-     .+. ..+++..
T Consensus       244 ~~~~~lVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTd-----v~~-rGiDip~  313 (456)
T PRK10590        244 NWQQVLVFTRTKHGANHLAEQLNKD----GIRSAAIHGNKSQGARTRALADFKSGDIRVLVATD-----IAA-RGLDIEE  313 (456)
T ss_pred             CCCcEEEEcCcHHHHHHHHHHHHHC----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcc-----HHh-cCCCccc
Confidence            3568999999999999998888764    5778888988876554333   333 478999993     333 3456677


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      |.+||.
T Consensus       314 v~~VI~  319 (456)
T PRK10590        314 LPHVVN  319 (456)
T ss_pred             CCEEEE
Confidence            776664

>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=90.77  E-value=0.35  Score=43.52  Aligned_cols=23  Identities=35%  Similarity=0.580  Sum_probs=17.6

Q ss_pred             cEEEEcCCCChhHHHHHHHHHHHH
Q psy17644        206 DIIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      .++++|++||||| .+++-+|.++
T Consensus        15 r~viIG~sGSGKT-~li~~lL~~~   37 (241)
T PF04665_consen   15 RMVIIGKSGSGKT-TLIKSLLYYL   37 (241)
T ss_pred             eEEEECCCCCCHH-HHHHHHHHhh
Confidence            6789999999999 5565566554

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=90.75  E-value=1.5  Score=43.22  Aligned_cols=72  Identities=10%  Similarity=0.163  Sum_probs=51.4

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      ..++||.|+|+.-|..++..+...    +..+..++|+....++...   +++ ..+|+|||-     .+. ..+++..+
T Consensus       242 ~~~~lVF~~t~~~~~~l~~~L~~~----~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTd-----v~~-rGiDi~~v  311 (460)
T PRK11776        242 PESCVVFCNTKKECQEVADALNAQ----GFSALALHGDLEQRDRDQVLVRFANRSCSVLVATD-----VAA-RGLDIKAL  311 (460)
T ss_pred             CCceEEEECCHHHHHHHHHHHHhC----CCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEec-----ccc-cccchhcC
Confidence            457899999999999999988765    5788889998876554333   333 478999992     222 34556677


Q ss_pred             cEEEee
Q psy17644        316 TFLVLD  321 (330)
Q Consensus       316 ~~lVvD  321 (330)
                      .+||.-
T Consensus       312 ~~VI~~  317 (460)
T PRK11776        312 EAVINY  317 (460)
T ss_pred             CeEEEe
Confidence            776653

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=90.74  E-value=0.52  Score=43.07  Aligned_cols=38  Identities=26%  Similarity=0.308  Sum_probs=22.7

Q ss_pred             HHHHHhhhhhc-CC-CcEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        192 PIQAQAVPAAL-SG-RDIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       192 ~iQ~~~i~~~~-~g-~d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      +.|.+.+..++ .. .-++++++||||||. ++-.++.++.
T Consensus        66 ~~~~~~l~~~~~~~~GlilisG~tGSGKTT-~l~all~~i~  105 (264)
T cd01129          66 PENLEIFRKLLEKPHGIILVTGPTGSGKTT-TLYSALSELN  105 (264)
T ss_pred             HHHHHHHHHHHhcCCCEEEEECCCCCcHHH-HHHHHHhhhC
Confidence            44555554433 23 357788999999993 3344555543

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=90.69  E-value=0.35  Score=42.03  Aligned_cols=23  Identities=30%  Similarity=0.406  Sum_probs=15.3

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      +++++|||||||.. +..++.++.
T Consensus         4 ilI~GptGSGKTTl-l~~ll~~~~   26 (198)
T cd01131           4 VLVTGPTGSGKSTT-LAAMIDYIN   26 (198)
T ss_pred             EEEECCCCCCHHHH-HHHHHHHhh
Confidence            57789999999943 333444443

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.

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=90.65  E-value=3.2  Score=44.16  Aligned_cols=73  Identities=12%  Similarity=0.178  Sum_probs=54.0

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhC----CCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALEL----GAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~----~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      +..+||.+|++.-+.+++..+++... .++.+..++|+.+..++...+..    ...|||||.     +.. ..+.+..|
T Consensus       209 ~g~iLVFlpg~~eI~~l~~~L~~~~~-~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATn-----IAE-rgItIp~V  281 (819)
T TIGR01970       209 TGSILVFLPGQAEIRRVQEQLAERLD-SDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATN-----IAE-TSLTIEGI  281 (819)
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhhcC-CCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecc-----hHh-hcccccCc
Confidence            46799999999999999998876322 36788899999998887766653    258999994     333 34556677


Q ss_pred             cEEE
Q psy17644        316 TFLV  319 (330)
Q Consensus       316 ~~lV  319 (330)
                      .+||
T Consensus       282 ~~VI  285 (819)
T TIGR01970       282 RVVI  285 (819)
T ss_pred             eEEE
Confidence            7655

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.

>PF13173 AAA_14: AAA domain

Probab=90.50  E-value=1.2  Score=35.61  Aligned_cols=17  Identities=35%  Similarity=0.372  Sum_probs=14.0

Q ss_pred             CCCcEEEEcCCCChhHH
Q psy17644        203 SGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~  219 (330)
                      +++-+++.|+.|+|||.
T Consensus         1 n~~~~~l~G~R~vGKTt   17 (128)
T PF13173_consen    1 NRKIIILTGPRGVGKTT   17 (128)
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            35667888999999993

>PHA00729 NTP-binding motif containing protein

Probab=90.42  E-value=1.1  Score=39.96  Aligned_cols=14  Identities=43%  Similarity=0.527  Sum_probs=12.6

Q ss_pred             cEEEEcCCCChhHH
Q psy17644        206 DIIGVAKTGSGKTG  219 (330)
Q Consensus       206 d~i~~a~TGsGKT~  219 (330)
                      ++++.|++|+|||.
T Consensus        19 nIlItG~pGvGKT~   32 (226)
T PHA00729         19 SAVIFGKQGSGKTT   32 (226)
T ss_pred             EEEEECCCCCCHHH
Confidence            68999999999993

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=90.41  E-value=1  Score=50.68  Aligned_cols=63  Identities=22%  Similarity=0.222  Sum_probs=45.3

Q ss_pred             CCCHHHHHhhhhhcCC--CcEEEEcCCCChhHHHH--HHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q psy17644        189 SPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAF--IWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIY  257 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g--~d~i~~a~TGsGKT~a~--llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~  257 (330)
                      .+++-|+.++..++..  +-+++.+..|+|||.+.  ++-++..+..      ..+..++.++||-..+..+.
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e------~~g~~V~glAPTgkAa~~L~  901 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPE------SERPRVVGLGPTHRAVGEMR  901 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhh------ccCceEEEEechHHHHHHHH
Confidence            6899999999999855  66777899999999442  2333332222      24678899999987776653

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

Probab=90.40  E-value=2.1  Score=43.01  Aligned_cols=82  Identities=13%  Similarity=0.281  Sum_probs=56.6

Q ss_pred             HHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---h-CCCeEEEECh
Q psy17644        223 WPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---E-LGAEIVVGTP  298 (330)
Q Consensus       223 lp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~-~~~dIiV~TP  298 (330)
                      +.+|.+++...     ...++||.|.|+..|..+...+...    |+++..++|+.......+.+   + ...+|+|||-
T Consensus       261 ~~~L~~ll~~~-----~~~~~IVF~~tk~~~~~l~~~l~~~----g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTD  331 (513)
T COG0513         261 LELLLKLLKDE-----DEGRVIVFVRTKRLVEELAESLRKR----GFKVAALHGDLPQEERDRALEKFKDGELRVLVATD  331 (513)
T ss_pred             HHHHHHHHhcC-----CCCeEEEEeCcHHHHHHHHHHHHHC----CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEec
Confidence            34455555532     2347999999999999988777776    58899999998876654433   2 2589999994


Q ss_pred             HHHHHHHHcCCCCCCCccEEE
Q psy17644        299 GRIIDMVKMGATKLNRVTFLV  319 (330)
Q Consensus       299 ~~L~~~l~~~~~~l~~i~~lV  319 (330)
                           .. .+.+++..+.+||
T Consensus       332 -----va-aRGiDi~~v~~Vi  346 (513)
T COG0513         332 -----VA-ARGLDIPDVSHVI  346 (513)
T ss_pred             -----hh-hccCCccccceeE
Confidence                 22 3355566666665

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=90.35  E-value=1.1  Score=38.03  Aligned_cols=45  Identities=18%  Similarity=0.209  Sum_probs=28.8

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      +++.+++|||||. |...++..          .+.++++++-.+.+-..+...+.+
T Consensus         2 ~li~G~~~sGKS~-~a~~~~~~----------~~~~~~y~at~~~~d~em~~rI~~   46 (169)
T cd00544           2 ILVTGGARSGKSR-FAERLAAE----------LGGPVTYIATAEAFDDEMAERIAR   46 (169)
T ss_pred             EEEECCCCCCHHH-HHHHHHHh----------cCCCeEEEEccCcCCHHHHHHHHH
Confidence            4788999999994 33322211          245788888777765555555444

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.23  E-value=0.95  Score=44.85  Aligned_cols=16  Identities=31%  Similarity=0.237  Sum_probs=13.2

Q ss_pred             cEEEEcCCCChhHHHH
Q psy17644        206 DIIGVAKTGSGKTGAF  221 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~  221 (330)
                      -++++||.|+|||.+.
T Consensus        42 a~Lf~GP~GtGKTTlA   57 (484)
T PRK14956         42 AYIFFGPRGVGKTTIA   57 (484)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3699999999999543

>TIGR00767 rho transcription termination factor Rho

Probab=90.19  E-value=0.83  Score=44.20  Aligned_cols=18  Identities=33%  Similarity=0.276  Sum_probs=16.2

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      .|+-+++.+++|+|||..
T Consensus       167 ~Gq~~~IvG~~g~GKTtL  184 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVL  184 (415)
T ss_pred             CCCEEEEECCCCCChhHH
Confidence            789999999999999953

Members of this family differ in the specificity of RNA binding.

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=90.09  E-value=0.79  Score=41.49  Aligned_cols=19  Identities=32%  Similarity=0.230  Sum_probs=16.6

Q ss_pred             hcCCCcEEEEcCCCChhHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~  219 (330)
                      +-.|+-+++.++.|+|||.
T Consensus        13 i~~Gqr~~I~G~~G~GKTT   31 (249)
T cd01128          13 IGKGQRGLIVAPPKAGKTT   31 (249)
T ss_pred             cCCCCEEEEECCCCCCHHH
Confidence            3478999999999999994

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.07  E-value=1.8  Score=41.42  Aligned_cols=15  Identities=27%  Similarity=0.262  Sum_probs=12.4

Q ss_pred             cEEEEcCCCChhHHH
Q psy17644        206 DIIGVAKTGSGKTGA  220 (330)
Q Consensus       206 d~i~~a~TGsGKT~a  220 (330)
                      -+++.||.|+|||..
T Consensus        40 ~~L~~Gp~G~GKTtl   54 (363)
T PRK14961         40 AWLLSGTRGVGKTTI   54 (363)
T ss_pred             EEEEecCCCCCHHHH
Confidence            358999999999944

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=90.01  E-value=0.46  Score=48.89  Aligned_cols=50  Identities=18%  Similarity=0.219  Sum_probs=37.4

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..++++.|+||+|||..+++|.+..          -+.-++|+=|-.|+...+....+++
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIPnLL~----------~~gS~VV~DpKgEl~~~Ta~~R~~~  273 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVPTALK----------WGGPLVVLDPSTEVAPMVSEHRRDA  273 (641)
T ss_pred             CceEEEEeCCCCCccceEehhhhhc----------CCCCEEEEeCcHHHHHHHHHHHHHC
Confidence            3688999999999999999997642          1345677778888877666655554

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=89.98  E-value=1  Score=46.09  Aligned_cols=110  Identities=17%  Similarity=0.186  Sum_probs=66.9

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC--CceEEEEECCCc
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY--NLSVVCCYGGGS  279 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~--~~~~~~~~gg~~  279 (330)
                      +..|-.++..|--.|||.... +++..++..-     .|-++++++|.+..+..++++++.+++..  +..+..+.| ..
T Consensus       252 fkqk~tVflVPRR~GKTwivv-~iI~~ll~s~-----~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG-e~  324 (738)
T PHA03368        252 FRQRATVFLVPRRHGKTWFLV-PLIALALATF-----RGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG-ET  324 (738)
T ss_pred             hhccceEEEecccCCchhhHH-HHHHHHHHhC-----CCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC-cE
Confidence            345678888899999996444 5555555431     37899999999999999999998875532  111111222 11


Q ss_pred             hHHHHHHHhCC--CeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        280 KWDQSKALELG--AEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       280 ~~~~~~~l~~~--~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      .   ...+.++  +.|.++|-      -+.+...=..+.+||||||+.+-
T Consensus       325 I---~i~f~nG~kstI~FaSa------rntNsiRGqtfDLLIVDEAqFIk  365 (738)
T PHA03368        325 I---SFSFPDGSRSTIVFASS------HNTNGIRGQDFNLLFVDEANFIR  365 (738)
T ss_pred             E---EEEecCCCccEEEEEec------cCCCCccCCcccEEEEechhhCC
Confidence            1   0112223  25555531      11222334478999999998763

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=89.84  E-value=0.87  Score=46.87  Aligned_cols=55  Identities=24%  Similarity=0.386  Sum_probs=38.8

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH--HHHHHHHHHHHhcc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE--LSQQIYNEAKRFGK  265 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~--La~Qi~~~~~~l~~  265 (330)
                      ..++++++|+||+|||..+. .++...+.       .+..++|+=|-..  |...+...++..+.
T Consensus       175 ~~~H~lv~G~TGsGKT~l~~-~l~~q~i~-------~g~~viv~DpKgD~~l~~~~~~~~~~~G~  231 (634)
T TIGR03743       175 RVGHTLVLGTTGVGKTRLAE-LLITQDIR-------RGDVVIVIDPKGDADLKRRMRAEAKRAGR  231 (634)
T ss_pred             CCCcEEEECCCCCCHHHHHH-HHHHHHHH-------cCCeEEEEeCCCchHHHHHHHHHHHHhCC
Confidence            45789999999999996653 44444444       2566777778754  77777777777654

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=89.83  E-value=1.3  Score=38.81  Aligned_cols=46  Identities=22%  Similarity=0.126  Sum_probs=25.0

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR  250 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr  250 (330)
                      .|+=+.+.+++|+|||...+ .++........ ..+...+++++..-.
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~-~ia~~~~~~~~-~~g~~~~v~yi~~e~   63 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCL-QLAVEAQLPGE-LGGLEGKVVYIDTEG   63 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHH-HHHHHhhcccc-cCCCcceEEEEecCC
Confidence            35667778999999995433 33333322110 011125677776543

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.

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=89.73  E-value=0.34  Score=49.96  Aligned_cols=48  Identities=21%  Similarity=0.150  Sum_probs=35.1

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      .++++.|+||||||..+++|.|...          +..+||+=|--|+...+....++
T Consensus       145 ~hvLviApTrSGKgvg~VIPnLL~~----------~~S~VV~D~KGEl~~~Ta~~R~~  192 (663)
T PRK13876        145 EHVLCFAPTRSGKGVGLVVPTLLTW----------PGSAIVHDIKGENWQLTAGFRAR  192 (663)
T ss_pred             ceEEEEecCCCCcceeEehhhHHhC----------CCCEEEEeCcchHHHHHHHHHHh
Confidence            5889999999999999999987652          23566666777776655554444

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=89.72  E-value=0.53  Score=48.66  Aligned_cols=54  Identities=15%  Similarity=0.159  Sum_probs=35.4

Q ss_pred             HHHHHHHHHCCCCCCCHHHHHhhhhh--cCCCcEEEEcCCCChhHHHHHHHHHHHHHhc
Q psy17644        176 EVLMKALRKCEYTSPTPIQAQAVPAA--LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQ  232 (330)
Q Consensus       176 ~~l~~~l~~~~~~~pt~iQ~~~i~~~--~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~  232 (330)
                      ..|.+.+++.+-.  +++.-.-+|..  ...++++++|.||||||. .+..+|..+.++
T Consensus       157 ~~l~k~lk~~~~~--s~i~I~gvPip~~~E~~H~li~GttGSGKS~-~i~~LL~~ir~R  212 (732)
T PRK13700        157 KDVARMLKKDGKD--SDIRIGDLPIIRDSEIQNFCLHGTVGAGKSE-VIRRLANYARQR  212 (732)
T ss_pred             HHHHHHHHhcCCC--CCeeEccccCCcchhhcceEEeCCCCCCHHH-HHHHHHHHHHHc
Confidence            4566666665543  34444445543  466899999999999996 345666666654

>KOG2004|consensus

Probab=89.71  E-value=1.9  Score=44.48  Aligned_cols=82  Identities=26%  Similarity=0.330  Sum_probs=52.5

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWD  282 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~  282 (330)
                      +|+=+++.+|+|-|||..                                +..|.+.+.+      --+.+..||.+...
T Consensus       437 qGkIlCf~GPPGVGKTSI--------------------------------~kSIA~ALnR------kFfRfSvGG~tDvA  478 (906)
T KOG2004|consen  437 QGKILCFVGPPGVGKTSI--------------------------------AKSIARALNR------KFFRFSVGGMTDVA  478 (906)
T ss_pred             CCcEEEEeCCCCCCcccH--------------------------------HHHHHHHhCC------ceEEEeccccccHH
Confidence            677788889999999932                                2222222211      12345678877655


Q ss_pred             HHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        283 QSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       283 ~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      .++.-++  --|=+-||++.+.+++-...   --++.|||+|.+.
T Consensus       479 eIkGHRR--TYVGAMPGkiIq~LK~v~t~---NPliLiDEvDKlG  518 (906)
T KOG2004|consen  479 EIKGHRR--TYVGAMPGKIIQCLKKVKTE---NPLILIDEVDKLG  518 (906)
T ss_pred             hhcccce--eeeccCChHHHHHHHhhCCC---CceEEeehhhhhC
Confidence            5444333  24557899999999864442   2368899999886

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=89.69  E-value=1.5  Score=45.83  Aligned_cols=15  Identities=20%  Similarity=0.375  Sum_probs=12.7

Q ss_pred             CCccEEEeecccccC
Q psy17644        313 NRVTFLVLDEADRMF  327 (330)
Q Consensus       313 ~~i~~lVvDEad~ll  327 (330)
                      .+.+++||||+|+|-
T Consensus       118 gr~KVIIIDEah~LT  132 (830)
T PRK07003        118 ARFKVYMIDEVHMLT  132 (830)
T ss_pred             CCceEEEEeChhhCC
Confidence            457899999999885

>KOG1806|consensus

Probab=89.58  E-value=0.7  Score=49.02  Aligned_cols=72  Identities=18%  Similarity=0.269  Sum_probs=55.8

Q ss_pred             CCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        186 EYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .+-..||-|-.+|-..+.-..+.+.+|+|+|||...+- ++..+..+     ..+++++|++.+.....|.++.+.++
T Consensus       735 n~v~ft~~qveai~sg~qpgltmvvgppgtgktd~avq-il~~lyhn-----~p~qrTlivthsnqaln~lfeKi~~~  806 (1320)
T KOG1806|consen  735 NQVKFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAVQ-ILSVLYHN-----SPNQRTLIVTHSNQALNQLFEKIMAL  806 (1320)
T ss_pred             chhccCHHHHHHHHhcCCCCceeeecCCCCCCcchhhh-hhhhhhhc-----CCCcceEEEEecccchhHHHHHHHhc
Confidence            45567899999999999889999999999999954332 22222222     25789999999999999998887765

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=89.54  E-value=6  Score=40.83  Aligned_cols=80  Identities=18%  Similarity=0.286  Sum_probs=54.5

Q ss_pred             CCCeEEEEcccHH--------HHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHH
Q psy17644        239 DGPMGLILAPTRE--------LSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVK  306 (330)
Q Consensus       239 ~~~~vLil~Ptr~--------La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~  306 (330)
                      ++.+++|+||+.+        -+.++++.+....  .+..+..++|+....+....   ++. ..+|||||.     ++.
T Consensus       447 ~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~--~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~-----vie  519 (630)
T TIGR00643       447 KGRQAYVVYPLIEESEKLDLKAAEALYERLKKAF--PKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATT-----VIE  519 (630)
T ss_pred             hCCcEEEEEccccccccchHHHHHHHHHHHHhhC--CCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECc-----eee
Confidence            4678999999763        3455666665543  35678889998876554333   333 479999994     222


Q ss_pred             cCCCCCCCccEEEeeccccc
Q psy17644        307 MGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       307 ~~~~~l~~i~~lVvDEad~l  326 (330)
                       ...++.++.++|+..+++.
T Consensus       520 -~GvDiP~v~~VIi~~~~r~  538 (630)
T TIGR00643       520 -VGVDVPNATVMVIEDAERF  538 (630)
T ss_pred             -cCcccCCCcEEEEeCCCcC
Confidence             3567888999998888763

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=89.53  E-value=0.93  Score=39.97  Aligned_cols=53  Identities=26%  Similarity=0.416  Sum_probs=33.9

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|.-+++.+++|+|||. |++.++...++       ++-++++++- .+...++.+.+..++
T Consensus        15 ~g~~~li~G~~G~GKt~-~~~~~~~~~~~-------~g~~~~y~s~-e~~~~~l~~~~~~~~   67 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTT-FSLQFLYQGLK-------NGEKAMYISL-EEREERILGYAKSKG   67 (224)
T ss_pred             CCeEEEEECCCCCCHHH-HHHHHHHHHHh-------CCCeEEEEEC-CCCHHHHHHHHHHcC
Confidence            35677888999999994 44444444333       3556666644 455677777777664

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.

>cd03114 ArgK-like The function of this protein family is unkown

Probab=89.52  E-value=7.5  Score=32.04  Aligned_cols=14  Identities=29%  Similarity=0.254  Sum_probs=11.2

Q ss_pred             EEEEcCCCChhHHH
Q psy17644        207 IIGVAKTGSGKTGA  220 (330)
Q Consensus       207 ~i~~a~TGsGKT~a  220 (330)
                      +.++++.|+|||..
T Consensus         2 i~~~G~~GsGKTt~   15 (148)
T cd03114           2 IGITGVPGAGKSTL   15 (148)
T ss_pred             EEEECCCCCcHHHH
Confidence            46779999999943

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=89.48  E-value=0.55  Score=46.79  Aligned_cols=38  Identities=24%  Similarity=0.376  Sum_probs=22.9

Q ss_pred             CHHHHHhhhhhcCC-Cc-EEEEcCCCChhHHHHHHHHHHHH
Q psy17644        191 TPIQAQAVPAALSG-RD-IIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       191 t~iQ~~~i~~~~~g-~d-~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      ++-|.+.+..++.. +. ++++|+||||||.. +-.++.++
T Consensus       227 ~~~~~~~l~~~~~~~~GlilitGptGSGKTTt-L~a~L~~l  266 (486)
T TIGR02533       227 SPELLSRFERLIRRPHGIILVTGPTGSGKTTT-LYAALSRL  266 (486)
T ss_pred             CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHH-HHHHHhcc
Confidence            35555555555533 33 56789999999933 33345554

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=89.47  E-value=0.78  Score=45.69  Aligned_cols=54  Identities=22%  Similarity=0.311  Sum_probs=39.0

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      .|.-+++.+++|+|||. +++.++....+       ++-+++|++ +-+-..|+...+..++-
T Consensus       262 ~gs~~li~G~~G~GKt~-l~~~f~~~~~~-------~ge~~~y~s-~eEs~~~i~~~~~~lg~  315 (484)
T TIGR02655       262 KDSIILATGATGTGKTL-LVSKFLENACA-------NKERAILFA-YEESRAQLLRNAYSWGI  315 (484)
T ss_pred             CCcEEEEECCCCCCHHH-HHHHHHHHHHH-------CCCeEEEEE-eeCCHHHHHHHHHHcCC
Confidence            45678888999999994 44444444443       466778876 67888888888888753

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.

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=89.42  E-value=1.2  Score=46.13  Aligned_cols=71  Identities=18%  Similarity=0.183  Sum_probs=51.9

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      .+++-|++++...  .-.+++.|..|||||.+-.- -+.|++.....   ....+|.|+=|+-.|.++...+.++..
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~-Ria~li~~~~v---~p~~Il~vTFTnkAA~em~~Rl~~~~~   72 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTE-RIAYLIAAGGV---DPEQILAITFTNKAAAEMRERLLKLLG   72 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHH-HHHHHHHcCCc---ChHHeeeeechHHHHHHHHHHHHHHhC
Confidence            4788999998777  56788889999999955433 33444443221   233588888899999999999888865

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=89.40  E-value=0.42  Score=44.21  Aligned_cols=15  Identities=27%  Similarity=0.355  Sum_probs=13.3

Q ss_pred             CcEEEEcCCCChhHH
Q psy17644        205 RDIIGVAKTGSGKTG  219 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~  219 (330)
                      +.+++.||+|+|||.
T Consensus        31 ~~~ll~Gp~G~GKT~   45 (305)
T TIGR00635        31 DHLLLYGPPGLGKTT   45 (305)
T ss_pred             CeEEEECCCCCCHHH
Confidence            568999999999993

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=89.39  E-value=1.4  Score=45.15  Aligned_cols=55  Identities=25%  Similarity=0.367  Sum_probs=40.3

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccH--HHHHHHHHHHHHhcc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR--ELSQQIYNEAKRFGK  265 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr--~La~Qi~~~~~~l~~  265 (330)
                      ...+++++|+||+|||..+.+-+.+.+ +       .+..++|+=|-.  ++...++..+++.++
T Consensus       179 ~~gHtlV~GtTGsGKT~l~~~li~q~i-~-------~g~~vi~fDpkgD~el~~~~~~~~~~~GR  235 (643)
T TIGR03754       179 RVGHTLVLGTTRVGKTRLAELLITQDI-R-------RGDVVIVFDPKGDADLLKRMYAEAKRAGR  235 (643)
T ss_pred             ccCceEEECCCCCCHHHHHHHHHHHHH-H-------cCCeEEEEeCCCCHHHHHHHHHHHHHhCC
Confidence            356899999999999976655444433 3       366788888875  577788888887765

Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=89.34  E-value=0.29  Score=50.42  Aligned_cols=46  Identities=24%  Similarity=0.194  Sum_probs=34.8

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEA  260 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~  260 (330)
                      ++++++|+||||||..+++|.|..          .+..+||+=|-.++...+....
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL~----------~~~S~VV~D~KGE~~~~Tag~R  221 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLLS----------WGHSSVITDLKGELWALTAGWR  221 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchhh----------CCCCEEEEeCcHHHHHHHHHHH
Confidence            679999999999999999998754          1345777778888765544443

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=89.34  E-value=1.7  Score=41.69  Aligned_cols=27  Identities=15%  Similarity=0.212  Sum_probs=19.3

Q ss_pred             cEEEEcCCCChhHHHHHHHHHHHHHhcC
Q psy17644        206 DIIGVAKTGSGKTGAFIWPMLVHIMDQK  233 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~llp~l~~i~~~~  233 (330)
                      -+++.||.|+||+. +...+...++.+.
T Consensus        43 A~Lf~Gp~G~GK~~-lA~~~A~~Llc~~   69 (365)
T PRK07471         43 AWLIGGPQGIGKAT-LAYRMARFLLATP   69 (365)
T ss_pred             eEEEECCCCCCHHH-HHHHHHHHHhCCC
Confidence            57899999999983 3344556676653

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=89.30  E-value=0.97  Score=42.90  Aligned_cols=39  Identities=26%  Similarity=0.216  Sum_probs=27.3

Q ss_pred             HHHHHHCCCCCCCHHHHHhhhhhc-CCCcEEEEcCCCChhHH
Q psy17644        179 MKALRKCEYTSPTPIQAQAVPAAL-SGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       179 ~~~l~~~~~~~pt~iQ~~~i~~~~-~g~d~i~~a~TGsGKT~  219 (330)
                      +..+.+.|+  +++.+...+..+. .+++++++++||||||.
T Consensus       154 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTT  193 (340)
T TIGR03819       154 LDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTT  193 (340)
T ss_pred             HHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHH
Confidence            444455554  4466666666555 56799999999999993

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.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.28  E-value=1.3  Score=44.25  Aligned_cols=23  Identities=17%  Similarity=0.132  Sum_probs=15.8

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      ++++||.|+|||.+.. .+..++.
T Consensus        39 ~Lf~GppGtGKTTlA~-~lA~~l~   61 (504)
T PRK14963         39 YLFSGPRGVGKTTTAR-LIAMAVN   61 (504)
T ss_pred             EEEECCCCCCHHHHHH-HHHHHHh
Confidence            5899999999995533 3344444

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=89.25  E-value=4.8  Score=42.80  Aligned_cols=73  Identities=16%  Similarity=0.174  Sum_probs=54.6

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhC----CCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALEL----GAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~----~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      ...+||.+|++.-+.++++.+..... .++.+..++|+.+...+...+..    ...|||||.     +.. ..+.+..|
T Consensus       212 ~g~iLVFlpg~~ei~~l~~~L~~~~~-~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATn-----IAE-rsLtIp~V  284 (812)
T PRK11664        212 SGSLLLFLPGVGEIQRVQEQLASRVA-SDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATN-----IAE-TSLTIEGI  284 (812)
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHhcc-CCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecc-----hHH-hcccccCc
Confidence            46789999999999999999886321 25778889999998777766653    258999995     333 35567778


Q ss_pred             cEEE
Q psy17644        316 TFLV  319 (330)
Q Consensus       316 ~~lV  319 (330)
                      .+||
T Consensus       285 ~~VI  288 (812)
T PRK11664        285 RLVV  288 (812)
T ss_pred             eEEE
Confidence            7666

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=89.23  E-value=0.49  Score=43.07  Aligned_cols=25  Identities=28%  Similarity=0.251  Sum_probs=19.9

Q ss_pred             HhhhhhcCCCcEEEEcCCCChhHHH
Q psy17644        196 QAVPAALSGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       196 ~~i~~~~~g~d~i~~a~TGsGKT~a  220 (330)
                      +++..+..|+++++.|++|+|||..
T Consensus        13 ~~l~~l~~g~~vLL~G~~GtGKT~l   37 (262)
T TIGR02640        13 RALRYLKSGYPVHLRGPAGTGKTTL   37 (262)
T ss_pred             HHHHHHhcCCeEEEEcCCCCCHHHH
Confidence            3444556899999999999999944

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).

>TIGR00416 sms DNA repair protein RadA

Probab=89.22  E-value=2.1  Score=42.29  Aligned_cols=53  Identities=25%  Similarity=0.276  Sum_probs=34.8

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|.=+++.+++|+|||. +++.++..+..       ++.++||+.. .+...|+...+.+++
T Consensus        93 ~GsvilI~G~pGsGKTT-L~lq~a~~~a~-------~g~kvlYvs~-EEs~~qi~~ra~rlg  145 (454)
T TIGR00416        93 PGSLILIGGDPGIGKST-LLLQVACQLAK-------NQMKVLYVSG-EESLQQIKMRAIRLG  145 (454)
T ss_pred             CCeEEEEEcCCCCCHHH-HHHHHHHHHHh-------cCCcEEEEEC-cCCHHHHHHHHHHcC
Confidence            45667788999999994 44444444433       3457888865 355677777666664

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)).

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.16  E-value=1  Score=46.19  Aligned_cols=16  Identities=19%  Similarity=0.341  Sum_probs=13.1

Q ss_pred             CCCccEEEeecccccC
Q psy17644        312 LNRVTFLVLDEADRMF  327 (330)
Q Consensus       312 l~~i~~lVvDEad~ll  327 (330)
                      ..+.+++||||+|+|-
T Consensus       122 ~gr~KViIIDEah~Ls  137 (700)
T PRK12323        122 AGRFKVYMIDEVHMLT  137 (700)
T ss_pred             cCCceEEEEEChHhcC
Confidence            3467899999999985

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=89.14  E-value=0.37  Score=44.89  Aligned_cols=27  Identities=41%  Similarity=0.460  Sum_probs=19.3

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      ++.-|+++++|||||||+...  .|..++
T Consensus        95 L~KSNILLiGPTGsGKTlLAq--TLAk~L  121 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLLAQ--TLAKIL  121 (408)
T ss_pred             eeeccEEEECCCCCcHHHHHH--HHHHHh
Confidence            455689999999999995433  444444

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=89.11  E-value=1  Score=52.22  Aligned_cols=64  Identities=23%  Similarity=0.215  Sum_probs=45.0

Q ss_pred             CCCCHHHHHhhhhhcCC--CcEEEEcCCCChhHHHH--HHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAF--IWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIY  257 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g--~d~i~~a~TGsGKT~a~--llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~  257 (330)
                      ..+++.|+.++..++.+  +-+++.+..|+|||...  ++-.+..++..      .+.+++.++||..-+.++.
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~------~g~~v~glApT~~Aa~~L~ 1085 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES------EQLQVIGLAPTHEAVGELK 1085 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh------cCCeEEEEeChHHHHHHHH
Confidence            46899999999998865  45666799999999443  11222222321      4678999999987776653

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.

>TIGR00763 lon ATP-dependent protease La

Probab=89.06  E-value=1.4  Score=46.65  Aligned_cols=18  Identities=33%  Similarity=0.368  Sum_probs=14.7

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      .|..+++.+|+|+|||..
T Consensus       346 ~~~~lll~GppG~GKT~l  363 (775)
T TIGR00763       346 KGPILCLVGPPGVGKTSL  363 (775)
T ss_pred             CCceEEEECCCCCCHHHH
Confidence            456789999999999943

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.

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=88.98  E-value=0.73  Score=40.73  Aligned_cols=26  Identities=31%  Similarity=0.478  Sum_probs=19.0

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      ++++.+.|.||||||.+ +--++..++
T Consensus        23 ~~H~~I~G~TGsGKS~~-~~~ll~~l~   48 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNT-VKVLLEELL   48 (229)
T ss_pred             cceEEEECCCCCCHHHH-HHHHHHHHH
Confidence            48899999999999943 333555555

It contains several conserved aspartates and histidines that could be metal ligands.

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=88.98  E-value=2.8  Score=37.38  Aligned_cols=57  Identities=16%  Similarity=0.142  Sum_probs=28.9

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCC-----CCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELE-----PGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~-----~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      .++.|+.|+|||...+ .+..++..-++.-     ...+.+|||+.-- .-..++.+.+..++.
T Consensus         4 ~ll~g~~G~GKS~lal-~la~~va~G~~~~g~~~~~~~~~~Vlyi~~E-d~~~~i~~Rl~~i~~   65 (239)
T cd01125           4 SALVAPGGTGKSSLLL-VLALAMALGKNLFGGGLKVTEPGRVVYLSAE-DPREEIHRRLEAILQ   65 (239)
T ss_pred             eEEEcCCCCCHHHHHH-HHHHHHhcCccccCCccccCCCceEEEEECC-CCHHHHHHHHHHHHh
Confidence            5788999999994433 3333333222111     1245678888722 222334444444433

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=88.90  E-value=1.4  Score=41.35  Aligned_cols=17  Identities=24%  Similarity=0.210  Sum_probs=14.2

Q ss_pred             CCcEEEEcCCCChhHHH
Q psy17644        204 GRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a  220 (330)
                      .+.+++.||+|+|||..
T Consensus        51 ~~~~ll~GppG~GKT~l   67 (328)
T PRK00080         51 LDHVLLYGPPGLGKTTL   67 (328)
T ss_pred             CCcEEEECCCCccHHHH
Confidence            35789999999999943

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=88.89  E-value=4.4  Score=40.14  Aligned_cols=73  Identities=18%  Similarity=0.232  Sum_probs=52.8

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH----hCCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL----ELGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l----~~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+..+||.|+|+..|..++..++..    ++.+..++|+.+.......+    ....+|||||-.     +. ..+++..
T Consensus       225 ~~~~~IIF~~s~~~~e~la~~L~~~----g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~-----~~-~GID~p~  294 (470)
T TIGR00614       225 KGKSGIIYCPSRKKSEQVTASLQNL----GIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVA-----FG-MGINKPD  294 (470)
T ss_pred             CCCceEEEECcHHHHHHHHHHHHhc----CCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEech-----hh-ccCCccc
Confidence            4567899999999999999988765    67888889988766543322    235799999942     22 3556677


Q ss_pred             ccEEEee
Q psy17644        315 VTFLVLD  321 (330)
Q Consensus       315 i~~lVvD  321 (330)
                      +++||.-
T Consensus       295 V~~VI~~  301 (470)
T TIGR00614       295 VRFVIHY  301 (470)
T ss_pred             ceEEEEe
Confidence            7777753

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

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.87  E-value=2.1  Score=42.97  Aligned_cols=16  Identities=25%  Similarity=0.214  Sum_probs=13.0

Q ss_pred             cEEEEcCCCChhHHHH
Q psy17644        206 DIIGVAKTGSGKTGAF  221 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~  221 (330)
                      -++++|+.|+|||.+.
T Consensus        40 a~Lf~Gp~G~GKTt~A   55 (509)
T PRK14958         40 AYLFTGTRGVGKTTIS   55 (509)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4689999999999543

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=88.84  E-value=1.8  Score=44.77  Aligned_cols=18  Identities=22%  Similarity=0.182  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCChhHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFI  222 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~l  222 (330)
                      +.+|++|+.|+|||.+..
T Consensus        39 Ha~Lf~GP~GvGKTTlAr   56 (709)
T PRK08691         39 HAYLLTGTRGVGKTTIAR   56 (709)
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            357999999999995443

>PRK08939 primosomal protein DnaI; Reviewed

Probab=88.80  E-value=0.89  Score=42.48  Aligned_cols=46  Identities=13%  Similarity=0.273  Sum_probs=26.7

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIY  257 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~  257 (330)
                      .++.+++.|++|+|||  |++.++.+-+..      .|..++++ ....++.++.
T Consensus       155 ~~~gl~L~G~~G~GKT--hLa~Aia~~l~~------~g~~v~~~-~~~~l~~~lk  200 (306)
T PRK08939        155 KVKGLYLYGDFGVGKS--YLLAAIANELAK------KGVSSTLL-HFPEFIRELK  200 (306)
T ss_pred             CCCeEEEECCCCCCHH--HHHHHHHHHHHH------cCCCEEEE-EHHHHHHHHH
Confidence            3578999999999999  444444443332      24455444 2224544443

>PRK13767 ATP-dependent helicase; Provisional

Probab=88.79  E-value=4  Score=43.85  Aligned_cols=75  Identities=13%  Similarity=0.115  Sum_probs=50.8

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccC--CCceEEEEECCCchHHHH---HHHhC-CCeEEEEChHHHHHHHHcCCCCCC
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKG--YNLSVVCCYGGGSKWDQS---KALEL-GAEIVVGTPGRIIDMVKMGATKLN  313 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~--~~~~~~~~~gg~~~~~~~---~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~  313 (330)
                      +.++||.|+||..|..++..+++....  .+..+.+.+|+.+.....   ..+++ ...|||||..     +. ..+++.
T Consensus       284 ~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~-----Le-~GIDip  357 (876)
T PRK13767        284 HRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTS-----LE-LGIDIG  357 (876)
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECCh-----HH-hcCCCC
Confidence            467999999999999999998875432  245677788888765543   23343 3688999852     22 244566


Q ss_pred             CccEEEe
Q psy17644        314 RVTFLVL  320 (330)
Q Consensus       314 ~i~~lVv  320 (330)
                      .+++||.
T Consensus       358 ~Vd~VI~  364 (876)
T PRK13767        358 YIDLVVL  364 (876)
T ss_pred             CCcEEEE
Confidence            6666664

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.74  E-value=0.64  Score=47.77  Aligned_cols=16  Identities=25%  Similarity=0.225  Sum_probs=13.2

Q ss_pred             cEEEEcCCCChhHHHH
Q psy17644        206 DIIGVAKTGSGKTGAF  221 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~  221 (330)
                      -+|++|+.|+|||.+.
T Consensus        39 AyLF~GPpGvGKTTlA   54 (702)
T PRK14960         39 AYLFTGTRGVGKTTIA   54 (702)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5689999999999544

>KOG0991|consensus

Probab=88.72  E-value=0.42  Score=42.73  Aligned_cols=18  Identities=28%  Similarity=0.497  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCChhHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFI  222 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~l  222 (330)
                      -++++.+|+|.|||.+.+
T Consensus        49 P~liisGpPG~GKTTsi~   66 (333)
T KOG0991|consen   49 PNLIISGPPGTGKTTSIL   66 (333)
T ss_pred             CceEeeCCCCCchhhHHH
Confidence            479999999999996543

>KOG0744|consensus

Probab=88.72  E-value=2.5  Score=39.65  Aligned_cols=69  Identities=14%  Similarity=0.098  Sum_probs=38.2

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCC-eEEEEcccHH-----------HHHHHHHHHHHhccCCCce
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGP-MGLILAPTRE-----------LSQQIYNEAKRFGKGYNLS  270 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~-~vLil~Ptr~-----------La~Qi~~~~~~l~~~~~~~  270 (330)
                      ..|=+++.||+|+||| ..|-++.+++.-+   .....+ ..||=.....           |+.++++.+..+....+.-
T Consensus       176 ~NRliLlhGPPGTGKT-SLCKaLaQkLSIR---~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~l  251 (423)
T KOG0744|consen  176 WNRLILLHGPPGTGKT-SLCKALAQKLSIR---TNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNL  251 (423)
T ss_pred             eeeEEEEeCCCCCChh-HHHHHHHHhheee---ecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcE
Confidence            4456778899999999 3444445554321   111122 2344444444           5566666666666665555


Q ss_pred             EEEEE
Q psy17644        271 VVCCY  275 (330)
Q Consensus       271 ~~~~~  275 (330)
                      ++++.
T Consensus       252 VfvLI  256 (423)
T KOG0744|consen  252 VFVLI  256 (423)
T ss_pred             EEEEe
Confidence            55443

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.53  E-value=1.7  Score=44.36  Aligned_cols=17  Identities=24%  Similarity=0.266  Sum_probs=13.4

Q ss_pred             CcEEEEcCCCChhHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAF  221 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~  221 (330)
                      +.+|++|+.|+|||.+.
T Consensus        39 ~a~Lf~Gp~G~GKTtlA   55 (585)
T PRK14950         39 HAYLFTGPRGVGKTSTA   55 (585)
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            34689999999999443

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=88.52  E-value=0.98  Score=46.40  Aligned_cols=82  Identities=28%  Similarity=0.326  Sum_probs=52.9

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWD  282 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~  282 (330)
                      .|.=+++++|+|.|||                                .|+..|.+.+.+-      -+.+..||.....
T Consensus       349 kGpILcLVGPPGVGKT--------------------------------SLgkSIA~al~Rk------fvR~sLGGvrDEA  390 (782)
T COG0466         349 KGPILCLVGPPGVGKT--------------------------------SLGKSIAKALGRK------FVRISLGGVRDEA  390 (782)
T ss_pred             CCcEEEEECCCCCCch--------------------------------hHHHHHHHHhCCC------EEEEecCccccHH
Confidence            4445666699999999                                2444444443321      2345678777665


Q ss_pred             HHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        283 QSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       283 ~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      .++.-++  --|=+-||+++.-+.+....   -=++++||+|.|.
T Consensus       391 EIRGHRR--TYIGamPGrIiQ~mkka~~~---NPv~LLDEIDKm~  430 (782)
T COG0466         391 EIRGHRR--TYIGAMPGKIIQGMKKAGVK---NPVFLLDEIDKMG  430 (782)
T ss_pred             Hhccccc--cccccCChHHHHHHHHhCCc---CCeEEeechhhcc
Confidence            5555444  23456799999988764432   2378999999986

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=88.52  E-value=0.95  Score=49.90  Aligned_cols=57  Identities=19%  Similarity=0.265  Sum_probs=43.2

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      .+.++++.|..|||||.+-..=++..++...   +..-..+|||+-|+.-+..+...+..
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~---~~~v~~ILvvTFT~aAa~Emk~RI~~   71 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGG---PLDVDEILVVTFTKAAAAEMKERIRD   71 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcC---CCChhHeeeeeccHHHHHHHHHHHHH
Confidence            5779999999999999776666666665531   12456889999999988888777654

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=88.50  E-value=8.4  Score=36.31  Aligned_cols=87  Identities=20%  Similarity=0.194  Sum_probs=48.1

Q ss_pred             CHHHHHhhhhhc----CCC---cEEEEcCCCChhHHHHHHHHHHHHHhcCCCC--------------CCCCCeEEEEccc
Q psy17644        191 TPIQAQAVPAAL----SGR---DIIGVAKTGSGKTGAFIWPMLVHIMDQKELE--------------PGDGPMGLILAPT  249 (330)
Q Consensus       191 t~iQ~~~i~~~~----~g~---d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~--------------~~~~~~vLil~Pt  249 (330)
                      +|+|...+..+.    +||   -.++.|+.|.||+. +...+...++......              .++.|-+.++.|.
T Consensus         4 yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~-lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~   82 (325)
T PRK06871          4 YPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQ-LIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPI   82 (325)
T ss_pred             CcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHH-HHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccc
Confidence            466666666554    443   57789999999983 3333445666532111              2345778888883


Q ss_pred             --H-HHHHHHHHHHHHh---ccCCCceEEEEECCC
Q psy17644        250 --R-ELSQQIYNEAKRF---GKGYNLSVVCCYGGG  278 (330)
Q Consensus       250 --r-~La~Qi~~~~~~l---~~~~~~~~~~~~gg~  278 (330)
                        + --+.|+.+....+   ....+.+++.+....
T Consensus        83 ~~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~  117 (325)
T PRK06871         83 DNKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAE  117 (325)
T ss_pred             cCCCCCHHHHHHHHHHHhhccccCCceEEEEechh
Confidence              1 2344444333332   223355666665544

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=88.45  E-value=1.8  Score=49.49  Aligned_cols=66  Identities=20%  Similarity=0.195  Sum_probs=44.9

Q ss_pred             CCCCHHHHHhhhhhcCC--CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIY  257 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g--~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~  257 (330)
                      ..+++.|+.++..++.+  +-+++.+..|+|||..  +-.+..++...  ....+.+++.++||---|.++.
T Consensus       966 ~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~--l~~v~~~~~~l--~~~~~~~V~glAPTgrAAk~L~ 1033 (1747)
T PRK13709        966 EGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQ--FRAVMSAVNTL--PESERPRVVGLGPTHRAVGEMR 1033 (1747)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHH--HHHHHHHHHHh--hcccCceEEEECCcHHHHHHHH
Confidence            46899999999999975  4577779999999943  32332222210  0124578899999987776543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=88.40  E-value=3.1  Score=42.85  Aligned_cols=71  Identities=14%  Similarity=0.215  Sum_probs=51.3

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      ..++||.|+|+.-|.+++..+...    +..+..++|..+..+....   ++. ..+|||||     +++.+ .+++.+|
T Consensus       245 ~~~~IVF~~tk~~a~~l~~~L~~~----g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVAT-----dv~ar-GIDip~V  314 (629)
T PRK11634        245 FDAAIIFVRTKNATLEVAEALERN----GYNSAALNGDMNQALREQTLERLKDGRLDILIAT-----DVAAR-GLDVERI  314 (629)
T ss_pred             CCCEEEEeccHHHHHHHHHHHHhC----CCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEc-----chHhc-CCCcccC
Confidence            467999999999999999888764    5678888888776554333   333 47999999     33333 4567777


Q ss_pred             cEEEe
Q psy17644        316 TFLVL  320 (330)
Q Consensus       316 ~~lVv  320 (330)
                      .+||.
T Consensus       315 ~~VI~  319 (629)
T PRK11634        315 SLVVN  319 (629)
T ss_pred             CEEEE
Confidence            77764

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=88.34  E-value=1.9  Score=41.45  Aligned_cols=18  Identities=28%  Similarity=0.261  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCChhHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFI  222 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~l  222 (330)
                      .++|+.+|.|+|||..+-
T Consensus        49 ~SmIl~GPPG~GKTTlA~   66 (436)
T COG2256          49 HSMILWGPPGTGKTTLAR   66 (436)
T ss_pred             ceeEEECCCCCCHHHHHH
Confidence            378999999999995443

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=88.18  E-value=6.1  Score=37.22  Aligned_cols=58  Identities=17%  Similarity=0.104  Sum_probs=35.6

Q ss_pred             CHHHHHhhhhhc--CCC---cEEEEcCCCChhHHHHHHHHHHHHHhcCCC---------------CCCCCCeEEEEccc
Q psy17644        191 TPIQAQAVPAAL--SGR---DIIGVAKTGSGKTGAFIWPMLVHIMDQKEL---------------EPGDGPMGLILAPT  249 (330)
Q Consensus       191 t~iQ~~~i~~~~--~g~---d~i~~a~TGsGKT~a~llp~l~~i~~~~~~---------------~~~~~~~vLil~Pt  249 (330)
                      +|+|...|..+.  .+|   -+++.|+.|.|||... ..+...++.....               ..++.|-..++.|+
T Consensus         3 yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la-~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~   80 (325)
T PRK08699          3 YPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFA-RFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPL   80 (325)
T ss_pred             CCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHH-HHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecc
Confidence            467777776665  233   5889999999998432 2334445543211               01345888889884

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=88.12  E-value=3.5  Score=40.84  Aligned_cols=71  Identities=8%  Similarity=0.135  Sum_probs=48.0

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      ..++||.|+++.-|..++..+.+.    +..+..++|+....++...   ++. ...|||||-     .+. ..+++..+
T Consensus       335 ~~~~IVF~~s~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~-----~l~-~GIDi~~v  404 (475)
T PRK01297        335 WERVMVFANRKDEVRRIEERLVKD----GINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATD-----VAG-RGIHIDGI  404 (475)
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEcc-----ccc-cCCcccCC
Confidence            468999999999999998888654    5677778888776555333   333 468899983     222 23445556


Q ss_pred             cEEEe
Q psy17644        316 TFLVL  320 (330)
Q Consensus       316 ~~lVv  320 (330)
                      +++|.
T Consensus       405 ~~VI~  409 (475)
T PRK01297        405 SHVIN  409 (475)
T ss_pred             CEEEE
Confidence            65554

>PRK05642 DNA replication initiation factor; Validated

Probab=88.08  E-value=1.5  Score=39.16  Aligned_cols=43  Identities=21%  Similarity=0.159  Sum_probs=25.8

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQI  256 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi  256 (330)
                      ..++++|++|+|||..  +.++.+.+..      .+.+++++. ..++....
T Consensus        46 ~~l~l~G~~G~GKTHL--l~a~~~~~~~------~~~~v~y~~-~~~~~~~~   88 (234)
T PRK05642         46 SLIYLWGKDGVGRSHL--LQAACLRFEQ------RGEPAVYLP-LAELLDRG   88 (234)
T ss_pred             CeEEEECCCCCCHHHH--HHHHHHHHHh------CCCcEEEee-HHHHHhhh
Confidence            5688999999999933  3333332221      245666654 45665543

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=88.03  E-value=0.88  Score=43.19  Aligned_cols=26  Identities=31%  Similarity=0.293  Sum_probs=17.7

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      .+..++++|+||||||. ++-.++.++
T Consensus       121 ~~g~ili~G~tGSGKTT-~l~al~~~i  146 (343)
T TIGR01420       121 PRGLILVTGPTGSGKST-TLASMIDYI  146 (343)
T ss_pred             cCcEEEEECCCCCCHHH-HHHHHHHhh
Confidence            35678899999999993 333344444

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.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.96  E-value=1.8  Score=44.56  Aligned_cols=17  Identities=24%  Similarity=0.296  Sum_probs=13.7

Q ss_pred             CcEEEEcCCCChhHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAF  221 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~  221 (330)
                      ..+|+.|+.|+|||.+.
T Consensus        39 ~a~Lf~Gp~G~GKttlA   55 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSA   55 (620)
T ss_pred             ceEEEECCCCCChHHHH
Confidence            45789999999999443

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=87.95  E-value=0.59  Score=47.90  Aligned_cols=49  Identities=20%  Similarity=0.280  Sum_probs=35.4

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .++++.|+||||||..+++|.+..   .       +.-+||+=|..|+..-+...-++.
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnLL~---~-------~gS~VV~DpKgE~~~~Ta~~R~~~  260 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTALK---Y-------GGPLVCLDPSTEVAPMVCEHRRQA  260 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhhhc---C-------CCCEEEEEChHHHHHHHHHHHHHc
Confidence            689999999999999999997543   1       234677777777766555544444

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=87.92  E-value=2.4  Score=43.03  Aligned_cols=105  Identities=16%  Similarity=0.167  Sum_probs=67.9

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC-CCceEEEEECCCchH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG-YNLSVVCCYGGGSKW  281 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~-~~~~~~~~~gg~~~~  281 (330)
                      ..|-.++..|---||| .|+.|++..+++.-     .|-++.|+++-|..+.-++.++..-+.. .+.+.+.-.      
T Consensus       201 KQkaTVFLVPRRHGKT-Wf~VpiIsllL~s~-----~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~vi~~------  268 (668)
T PHA03372        201 KQKATVFLVPRRHGKT-WFIIPIISFLLKNI-----IGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHTIEN------  268 (668)
T ss_pred             hccceEEEecccCCce-ehHHHHHHHHHHhh-----cCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccceeee------
Confidence            4567888889999999 68889998888742     5889999999999988888876543321 121111110      


Q ss_pred             HHHHHHhCCCeEEEEChHHH-----HHHHHcCCCCCCCccEEEeeccccc
Q psy17644        282 DQSKALELGAEIVVGTPGRI-----IDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       282 ~~~~~l~~~~dIiV~TP~~L-----~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                             ++--|.+.-|+.=     ....+.+.+.=....+|+|||||-+
T Consensus       269 -------k~~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI  311 (668)
T PHA03372        269 -------KDNVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFI  311 (668)
T ss_pred             -------cCcEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhcc
Confidence                   1224444444321     1112334445567899999999965

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=87.89  E-value=3.3  Score=39.10  Aligned_cols=116  Identities=16%  Similarity=0.144  Sum_probs=62.5

Q ss_pred             CCHHHHHhhhhhcCC----CcEEEEcCCCChhHHHHHHHHHHHHHhcCCC--------------CCCCCCeEEEEcccH-
Q psy17644        190 PTPIQAQAVPAALSG----RDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL--------------EPGDGPMGLILAPTR-  250 (330)
Q Consensus       190 pt~iQ~~~i~~~~~g----~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~--------------~~~~~~~vLil~Ptr-  250 (330)
                      .+|+|...|..++..    +-+++.|+.|.|||. +...+...++.....              ..++.|-+.++.|.. 
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~-~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~   82 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRA-LAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEA   82 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHH-HHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCC
Confidence            468888888887733    258889999999993 333344556553211              123457888888842 


Q ss_pred             ---HHHHHHHHHHHHhcc---CCCceEEEEECCCc--hHHH---HHHHhC---CCeEEEEC--hHHHHHHHH
Q psy17644        251 ---ELSQQIYNEAKRFGK---GYNLSVVCCYGGGS--KWDQ---SKALEL---GAEIVVGT--PGRIIDMVK  306 (330)
Q Consensus       251 ---~La~Qi~~~~~~l~~---~~~~~~~~~~gg~~--~~~~---~~~l~~---~~dIiV~T--P~~L~~~l~  306 (330)
                         --+.|+.+....+..   ..+.+++.+.....  ...+   .+.+..   ++-+|++|  |.+|..-+.
T Consensus        83 ~~~i~id~iR~l~~~~~~~~~~~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~  154 (328)
T PRK05707         83 DKTIKVDQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIK  154 (328)
T ss_pred             CCCCCHHHHHHHHHHHhhccccCCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHH
Confidence               234555544333322   23455665543222  2111   223333   44555555  556655443

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=87.79  E-value=1.1  Score=45.56  Aligned_cols=26  Identities=23%  Similarity=0.045  Sum_probs=17.1

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      +-+|+.||.|+|||.... .+...+.+
T Consensus        39 hA~Lf~GP~GvGKTTlA~-~lAk~L~C   64 (605)
T PRK05896         39 HAYIFSGPRGIGKTSIAK-IFAKAINC   64 (605)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHhcC
Confidence            457899999999994433 23344443

>PF14516 AAA_35: AAA-like domain

Probab=87.64  E-value=1.9  Score=40.67  Aligned_cols=115  Identities=16%  Similarity=0.203  Sum_probs=62.0

Q ss_pred             HHHHHhhhhhcC-CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccH------HHHHHHHHH-HHHh
Q psy17644        192 PIQAQAVPAALS-GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR------ELSQQIYNE-AKRF  263 (330)
Q Consensus       192 ~iQ~~~i~~~~~-g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr------~La~Qi~~~-~~~l  263 (330)
                      |+...++..+.+ |+-+.+.||-.+||| +.+.-+++++.+       .+-++++|-=..      .-..+.... +..+
T Consensus        18 ~~e~~~~~~i~~~G~~~~I~apRq~GKT-Sll~~l~~~l~~-------~~~~~v~id~~~~~~~~~~~~~~f~~~~~~~i   89 (331)
T PF14516_consen   18 PAEQECYQEIVQPGSYIRIKAPRQMGKT-SLLLRLLERLQQ-------QGYRCVYIDLQQLGSAIFSDLEQFLRWFCEEI   89 (331)
T ss_pred             HHHHHHHHHHhcCCCEEEEECcccCCHH-HHHHHHHHHHHH-------CCCEEEEEEeecCCCcccCCHHHHHHHHHHHH
Confidence            588999989887 999999999999999 334444555443       245555443211      112223333 2233


Q ss_pred             ccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC-CCCCccEEEeecccccCc
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT-KLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~-~l~~i~~lVvDEad~lld  328 (330)
                      ++.+++..       .......       -.++.+.++..+++.... ....==+|+|||+|++++
T Consensus        90 ~~~L~l~~-------~l~~~w~-------~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~  141 (331)
T PF14516_consen   90 SRQLKLDE-------KLDEYWD-------EEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFE  141 (331)
T ss_pred             HHHcCCCh-------hHHHHHH-------HhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhcc
Confidence            33333321       1111111       124455565555543211 122334899999999985

>KOG1016|consensus

Probab=87.63  E-value=4.5  Score=42.17  Aligned_cols=92  Identities=23%  Similarity=0.226  Sum_probs=54.2

Q ss_pred             CCCcEEEEcCCCChhHH---HHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC---------Cce
Q psy17644        203 SGRDIIGVAKTGSGKTG---AFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY---------NLS  270 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~---a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~---------~~~  270 (330)
                      +|-.+|+.-..|-|||+   .|+=.+|.|-         ...+||+|+|-..| +.|+.++..|...+         .+.
T Consensus       281 sGFGCILAHSMGLGKTlQVisF~diflRhT---------~AKtVL~ivPiNTl-QNWlsEfnmWiP~y~sD~~vrpR~F~  350 (1387)
T KOG1016|consen  281 SGFGCILAHSMGLGKTLQVISFSDIFLRHT---------KAKTVLVIVPINTL-QNWLSEFNMWIPKYFSDTGVRPRSFE  350 (1387)
T ss_pred             CCcceeeeeccccCceeEEeehhHHHhhcC---------ccceEEEEEehHHH-HHHHHHhhhhcCCCcccCCCccceeE
Confidence            34456777778999994   3554444441         35689999998776 66777777775432         244


Q ss_pred             EEEEECCCchHHHHHH-HhC---CCeEEEEChHHHHHH
Q psy17644        271 VVCCYGGGSKWDQSKA-LEL---GAEIVVGTPGRIIDM  304 (330)
Q Consensus       271 ~~~~~gg~~~~~~~~~-l~~---~~dIiV~TP~~L~~~  304 (330)
                      +.++..|.....++.. +..   ...|++.-.+.+.-+
T Consensus       351 vf~LnD~~KT~~~Rakvi~~Wv~~GGVlLvGYemfRLL  388 (1387)
T KOG1016|consen  351 VFLLNDGVKTFDQRAKVIEQWVQTGGVLLVGYEMFRLL  388 (1387)
T ss_pred             EEEecCchhhHHHHHHHHHHHhccCCEEEehHHHHHHH
Confidence            5555555544443322 221   235666556555443

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=87.63  E-value=1.6  Score=40.59  Aligned_cols=14  Identities=29%  Similarity=0.522  Sum_probs=11.0

Q ss_pred             cEEE-EcCCCChhHH
Q psy17644        206 DIIG-VAKTGSGKTG  219 (330)
Q Consensus       206 d~i~-~a~TGsGKT~  219 (330)
                      ++++ .|++|+|||.
T Consensus        44 ~~lll~G~~G~GKT~   58 (316)
T PHA02544         44 NMLLHSPSPGTGKTT   58 (316)
T ss_pred             eEEEeeCcCCCCHHH
Confidence            4455 7999999994

>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=87.53  E-value=5.4  Score=31.04  Aligned_cols=76  Identities=18%  Similarity=0.290  Sum_probs=50.5

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHH---HHHhCC-CeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS---KALELG-AEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~---~~l~~~-~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.++++..+.++...+++.    +..+..+.|+.......   ..+..+ ..|+|+|...      ....++..
T Consensus        27 ~~~~~lvf~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~------~~G~d~~~   96 (131)
T cd00079          27 KGGKVLIFCPSKKMLDELAELLRKP----GIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVI------ARGIDLPN   96 (131)
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHhc----CCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChh------hcCcChhh
Confidence            3578899999999999999888872    56677888877644332   223333 5788988521      12445666


Q ss_pred             ccEEEeeccc
Q psy17644        315 VTFLVLDEAD  324 (330)
Q Consensus       315 i~~lVvDEad  324 (330)
                      +..+|+....
T Consensus        97 ~~~vi~~~~~  106 (131)
T cd00079          97 VSVVINYDLP  106 (131)
T ss_pred             CCEEEEeCCC
Confidence            7777665543

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=87.53  E-value=6.6  Score=36.72  Aligned_cols=59  Identities=17%  Similarity=0.127  Sum_probs=30.5

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH-HHHHHHHHHHHh
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE-LSQQIYNEAKRF  263 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~-La~Qi~~~~~~l  263 (330)
                      .|.=+.+++++|+|||. +++.++........ ....+.+++||.--.. -..++.+.+..+
T Consensus       101 ~g~vtei~G~~GsGKT~-l~~~~~~~~~~~~~-~gg~~~~~~yi~te~~f~~~rl~~~~~~~  160 (317)
T PRK04301        101 TQSITEFYGEFGSGKTQ-ICHQLAVNVQLPEE-KGGLEGKAVYIDTEGTFRPERIEQMAEAL  160 (317)
T ss_pred             CCcEEEEECCCCCCHhH-HHHHHHHHhccccc-cCCCCceEEEEeCCCCcCHHHHHHHHHHc
Confidence            35667788999999994 44433333222111 1112347777764321 244444444443

>PHA02542 41 41 helicase; Provisional

Probab=87.49  E-value=2.4  Score=42.14  Aligned_cols=34  Identities=15%  Similarity=0.127  Sum_probs=21.6

Q ss_pred             cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc
Q psy17644        206 DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA  247 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~  247 (330)
                      =+++.|++|.||| +|++-+..++..       .|..|+|+.
T Consensus       192 LiiIaarPgmGKT-tfalniA~~~a~-------~g~~Vl~fS  225 (473)
T PHA02542        192 LNVLLAGVNVGKS-LGLCSLAADYLQ-------QGYNVLYIS  225 (473)
T ss_pred             EEEEEcCCCccHH-HHHHHHHHHHHh-------cCCcEEEEe
Confidence            3556699999999 455555555543       245566664

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=87.49  E-value=4.5  Score=41.13  Aligned_cols=18  Identities=28%  Similarity=0.274  Sum_probs=14.1

Q ss_pred             CcEEEEcCCCChhHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFI  222 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~l  222 (330)
                      +-+|++||.|+|||.+.-
T Consensus        39 hayLf~Gp~GtGKTt~Ak   56 (559)
T PRK05563         39 HAYLFSGPRGTGKTSAAK   56 (559)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            457889999999995443

>cd01394 radB RadB

Probab=87.44  E-value=1  Score=39.46  Aligned_cols=36  Identities=19%  Similarity=0.206  Sum_probs=23.6

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      .|+=+++.+++|+||| .+++.++..+..       .+.+++++
T Consensus        18 ~g~i~~i~G~~GsGKT-~l~~~~a~~~~~-------~g~~v~yi   53 (218)
T cd01394          18 RGTVTQVYGPPGTGKT-NIAIQLAVETAG-------QGKKVAYI   53 (218)
T ss_pred             CCeEEEEECCCCCCHH-HHHHHHHHHHHh-------cCCeEEEE
Confidence            3456778899999999 444445544433       35566776

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>KOG1533|consensus

Probab=87.34  E-value=0.56  Score=41.89  Aligned_cols=24  Identities=21%  Similarity=0.310  Sum_probs=18.8

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      .++++|+||||| +|+.-+.+.+..
T Consensus         5 qvVIGPPgSGKs-TYc~g~~~fls~   28 (290)
T KOG1533|consen    5 QVVIGPPGSGKS-TYCNGMSQFLSA   28 (290)
T ss_pred             eEEEcCCCCCcc-chhhhHHHHHHH
Confidence            478899999999 688777666554

>TIGR02012 tigrfam_recA protein RecA

Probab=87.33  E-value=1.5  Score=41.32  Aligned_cols=28  Identities=25%  Similarity=0.228  Sum_probs=20.6

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      .|+=+.+.+++|+||| .++++++....+
T Consensus        54 ~G~iteI~G~~GsGKT-tLaL~~~~~~~~   81 (321)
T TIGR02012        54 RGRIIEIYGPESSGKT-TLALHAIAEAQK   81 (321)
T ss_pred             CCeEEEEECCCCCCHH-HHHHHHHHHHHH
Confidence            4567888899999999 455666665544

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=87.30  E-value=0.86  Score=45.01  Aligned_cols=40  Identities=28%  Similarity=0.383  Sum_probs=26.2

Q ss_pred             CHHHHHhhhhhcCCC-c-EEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        191 TPIQAQAVPAALSGR-D-IIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       191 t~iQ~~~i~~~~~g~-d-~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      ++.|...+-.+++.. - +++.||||||||. .+..+|+.+..
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKTT-TLY~~L~~ln~  284 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKTT-TLYAALSELNT  284 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHH-HHHHHHHHhcC
Confidence            567777777666443 3 4455999999993 44456666544

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=87.22  E-value=12  Score=38.98  Aligned_cols=80  Identities=19%  Similarity=0.311  Sum_probs=53.5

Q ss_pred             CCCeEEEEcccHH--------HHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHH
Q psy17644        239 DGPMGLILAPTRE--------LSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVK  306 (330)
Q Consensus       239 ~~~~vLil~Ptr~--------La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~  306 (330)
                      ++.+++|+||+.+        -+..+++.+.+...  +..+..++|+....+....   ++. ..+|||||.     .+.
T Consensus       470 ~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~--~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~-----vie  542 (681)
T PRK10917        470 KGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFP--ELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATT-----VIE  542 (681)
T ss_pred             cCCcEEEEEcccccccchhHHHHHHHHHHHHHHCC--CCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECc-----cee
Confidence            4678999999643        34555666655432  3678889998776554333   333 369999993     332


Q ss_pred             cCCCCCCCccEEEeeccccc
Q psy17644        307 MGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       307 ~~~~~l~~i~~lVvDEad~l  326 (330)
                       ...++.++.++|+..+++.
T Consensus       543 -~GiDip~v~~VIi~~~~r~  561 (681)
T PRK10917        543 -VGVDVPNATVMVIENAERF  561 (681)
T ss_pred             -eCcccCCCcEEEEeCCCCC
Confidence             3567788899998888763

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=87.20  E-value=3.7  Score=42.55  Aligned_cols=77  Identities=16%  Similarity=0.312  Sum_probs=54.8

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHH---HHHhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS---KALEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      ++.++||+|+|+..|..+.+.+...    ++.+..++|+.......   ..++. ..+|+|||     ..+. ..+.+..
T Consensus       441 ~g~~vLIf~~tk~~ae~L~~~L~~~----gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t-----~~L~-rGfDiP~  510 (655)
T TIGR00631       441 RNERVLVTTLTKKMAEDLTDYLKEL----GIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGI-----NLLR-EGLDLPE  510 (655)
T ss_pred             CCCEEEEEECCHHHHHHHHHHHhhh----ccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEc-----Chhc-CCeeeCC
Confidence            5789999999999999999888775    56777787876654332   23333 47899988     3333 4556788


Q ss_pred             ccEEEeecccc
Q psy17644        315 VTFLVLDEADR  325 (330)
Q Consensus       315 i~~lVvDEad~  325 (330)
                      +.++|+=+++.
T Consensus       511 v~lVvi~Dadi  521 (655)
T TIGR00631       511 VSLVAILDADK  521 (655)
T ss_pred             CcEEEEeCccc
Confidence            88887766654

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

>PRK07773 replicative DNA helicase; Validated

Probab=87.14  E-value=1.6  Score=46.78  Aligned_cols=113  Identities=19%  Similarity=0.076  Sum_probs=55.3

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ  283 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~  283 (330)
                      |.=+++.|++|+||| +|++.++.++..+      .+..++|++ .-.-..|+...+........... ...|..+...+
T Consensus       217 G~livIagrPg~GKT-~fal~ia~~~a~~------~~~~V~~fS-lEms~~ql~~R~~s~~~~i~~~~-i~~g~l~~~~~  287 (886)
T PRK07773        217 GQLIIVAARPSMGKT-TFGLDFARNCAIR------HRLAVAIFS-LEMSKEQLVMRLLSAEAKIKLSD-MRSGRMSDDDW  287 (886)
T ss_pred             CcEEEEEeCCCCCcH-HHHHHHHHHHHHh------cCCeEEEEe-cCCCHHHHHHHHHHHhcCCCHHH-HhcCCCCHHHH
Confidence            334666799999999 5666666665432      234556654 33444555555543322211111 11122222221


Q ss_pred             ------HHHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        284 ------SKALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       284 ------~~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                            ...+. ...|.|.     |+..+...+.+-.. -..+++||||=.+.|-
T Consensus       288 ~~~~~a~~~l~-~~~i~i~d~~~~~i~~i~~~~r~~~~-~~~~~lvvIDyLql~~  340 (886)
T PRK07773        288 TRLARAMGEIS-EAPIFIDDTPNLTVMEIRAKARRLRQ-EANLGLIVVDYLQLMT  340 (886)
T ss_pred             HHHHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchhhcC
Confidence                  11222 2345552     44555443322111 1358899999988764

>PRK06749 replicative DNA helicase; Provisional

Probab=87.07  E-value=3.7  Score=40.27  Aligned_cols=37  Identities=24%  Similarity=0.298  Sum_probs=23.7

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA  247 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~  247 (330)
                      .|.=+++.|++|.||| +|++-+..++..       .+..|+|+.
T Consensus       185 ~G~LiiIaarPgmGKT-afal~ia~~~a~-------~g~~v~~fS  221 (428)
T PRK06749        185 EGDFVVLGARPSMGKT-AFALNVGLHAAK-------SGAAVGLFS  221 (428)
T ss_pred             CCcEEEEEeCCCCCch-HHHHHHHHHHHh-------cCCCEEEEE
Confidence            3344555699999999 566666666653       244556664

>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=87.02  E-value=2.4  Score=39.51  Aligned_cols=39  Identities=18%  Similarity=0.400  Sum_probs=23.3

Q ss_pred             EEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q psy17644        208 IGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL  252 (330)
Q Consensus       208 i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~L  252 (330)
                      ++-||||+||+-     +|..++..+... ...-.|++|+|+...
T Consensus        91 ~VYGPTG~GKSq-----LlRNLis~~lI~-P~PETVfFItP~~~m  129 (369)
T PF02456_consen   91 VVYGPTGSGKSQ-----LLRNLISCQLIQ-PPPETVFFITPQKDM  129 (369)
T ss_pred             EEECCCCCCHHH-----HHHHhhhcCccc-CCCCceEEECCCCCC
Confidence            344999999992     334444332211 123468999998654

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

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=87.01  E-value=3.4  Score=37.91  Aligned_cols=21  Identities=29%  Similarity=0.284  Sum_probs=16.4

Q ss_pred             CCCcEEEEcCCCChhHHHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIW  223 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~ll  223 (330)
                      .+..+++++++|+|||..+..
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~   94 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAK   94 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHH
Confidence            456788889999999965553

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=87.00  E-value=0.93  Score=42.32  Aligned_cols=19  Identities=47%  Similarity=0.501  Sum_probs=16.3

Q ss_pred             hcCCCcEEEEcCCCChhHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~  219 (330)
                      +..++.++++++||||||.
T Consensus       141 v~~~~~ili~G~tGsGKTT  159 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTT  159 (308)
T ss_pred             hhCCCEEEEECCCCCCHHH
Confidence            3478899999999999993

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.

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=86.86  E-value=0.86  Score=46.32  Aligned_cols=37  Identities=27%  Similarity=0.312  Sum_probs=23.2

Q ss_pred             HHHHHhhhhhcC-C-CcEEEEcCCCChhHHHHHHHHHHHH
Q psy17644        192 PIQAQAVPAALS-G-RDIIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       192 ~iQ~~~i~~~~~-g-~d~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      +-|.+.+..++. . --++++|+||||||.+ +..++.++
T Consensus       302 ~~~~~~l~~~~~~~~Glilv~G~tGSGKTTt-l~a~l~~~  340 (564)
T TIGR02538       302 PDQKALFLEAIHKPQGMVLVTGPTGSGKTVS-LYTALNIL  340 (564)
T ss_pred             HHHHHHHHHHHHhcCCeEEEECCCCCCHHHH-HHHHHHhh
Confidence            555555555443 2 3467889999999943 34455555

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.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=86.79  E-value=1  Score=31.55  Aligned_cols=32  Identities=16%  Similarity=0.231  Sum_probs=20.5

Q ss_pred             hhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        197 AVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       197 ~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      .++.-..|...++.+++|||||..  +=++..++
T Consensus        16 ~~~~~~~g~~tli~G~nGsGKSTl--lDAi~~~L   47 (62)
T PF13555_consen   16 TIDFDPRGDVTLITGPNGSGKSTL--LDAIQTVL   47 (62)
T ss_pred             EEeecCCCcEEEEECCCCCCHHHH--HHHHHHHH
Confidence            333333456789999999999943  33444444

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=86.75  E-value=0.42  Score=42.13  Aligned_cols=13  Identities=38%  Similarity=0.506  Sum_probs=11.1

Q ss_pred             EEEEcCCCChhHH
Q psy17644        207 IIGVAKTGSGKTG  219 (330)
Q Consensus       207 ~i~~a~TGsGKT~  219 (330)
                      +++.|..|+|||.
T Consensus         1 ~vv~G~pGsGKSt   13 (234)
T PF01443_consen    1 IVVHGVPGSGKST   13 (234)
T ss_pred             CEEEcCCCCCHHH
Confidence            4678999999994

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

>COG1086 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]

Probab=86.59  E-value=6.2  Score=39.74  Aligned_cols=92  Identities=22%  Similarity=0.273  Sum_probs=62.8

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCC-hhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH-HHHHHHHHHHhccC
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGS-GKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL-SQQIYNEAKRFGKG  266 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGs-GKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~L-a~Qi~~~~~~l~~~  266 (330)
                      .|-+.....+...+.||.+++.+.||| |+.+|      .++++       .+|+.|++.-.-|. ..++..+++.... 
T Consensus       235 ~pV~~d~~~i~~~~~gK~vLVTGagGSiGsel~------~qil~-------~~p~~i~l~~~~E~~~~~i~~el~~~~~-  300 (588)
T COG1086         235 PPVALDTELIGAMLTGKTVLVTGGGGSIGSELC------RQILK-------FNPKEIILFSRDEYKLYLIDMELREKFP-  300 (588)
T ss_pred             CCCCCCHHHHHhHcCCCEEEEeCCCCcHHHHHH------HHHHh-------cCCCEEEEecCchHHHHHHHHHHHhhCC-
Confidence            466667778888899999999999999 88844      45554       36777777766555 4556666776544 


Q ss_pred             CCceEEEEECCCchHHHHHHHhCC--CeEEE
Q psy17644        267 YNLSVVCCYGGGSKWDQSKALELG--AEIVV  295 (330)
Q Consensus       267 ~~~~~~~~~gg~~~~~~~~~l~~~--~dIiV  295 (330)
                       ..+.....|...........-.+  +|+|+
T Consensus       301 -~~~~~~~igdVrD~~~~~~~~~~~kvd~Vf  330 (588)
T COG1086         301 -ELKLRFYIGDVRDRDRVERAMEGHKVDIVF  330 (588)
T ss_pred             -CcceEEEecccccHHHHHHHHhcCCCceEE
Confidence             45666777776666555554444  66665

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.55  E-value=3.2  Score=42.31  Aligned_cols=15  Identities=27%  Similarity=0.337  Sum_probs=12.5

Q ss_pred             EEEEcCCCChhHHHH
Q psy17644        207 IIGVAKTGSGKTGAF  221 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~  221 (330)
                      .|++|+.|+|||.+.
T Consensus        41 yLf~Gp~G~GKtt~A   55 (576)
T PRK14965         41 FLFTGARGVGKTSTA   55 (576)
T ss_pred             EEEECCCCCCHHHHH
Confidence            588999999999544

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.42  E-value=3  Score=42.02  Aligned_cols=16  Identities=25%  Similarity=0.216  Sum_probs=12.9

Q ss_pred             cEEEEcCCCChhHHHH
Q psy17644        206 DIIGVAKTGSGKTGAF  221 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~  221 (330)
                      -+|+.|+.|+|||.+.
T Consensus        40 a~Lf~Gp~G~GKTt~A   55 (527)
T PRK14969         40 AYLFTGTRGVGKTTLA   55 (527)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3689999999999543

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=86.36  E-value=5.7  Score=35.00  Aligned_cols=44  Identities=20%  Similarity=0.119  Sum_probs=24.2

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP  248 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P  248 (330)
                      .|+=+.+.+++|+|||.. ++.++.+...... ..+.+..++++.-
T Consensus        18 ~g~i~~i~G~~GsGKT~l-~~~l~~~~~~~~~-~~g~~~~viyi~~   61 (235)
T cd01123          18 TGSITEIFGEFGSGKTQL-CHQLAVTVQLPIE-LGGLEGKAVYIDT   61 (235)
T ss_pred             CCeEEEEECCCCCCHHHH-HHHHHHHeeCccc-cCCCCccEEEEeC
Confidence            456678889999999943 3333322222110 0112356777764

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>KOG0741|consensus

Probab=86.34  E-value=3  Score=41.67  Aligned_cols=108  Identities=20%  Similarity=0.303  Sum_probs=63.2

Q ss_pred             CCCCCCCCCCCCC---CCHHHHHHHHHCC---CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCC
Q psy17644        161 DPPYPVSSFGHFG---FDEVLMKALRKCE---YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKE  234 (330)
Q Consensus       161 ~~p~p~~~f~~~~---l~~~l~~~l~~~~---~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~  234 (330)
                      .+..|--.|+++|   |+.++...+++.-   ...|.-+.+-.+++   -|-+++-+|+|+|||+..-  -+-.++..|.
T Consensus       210 ~ii~Pdf~Fe~mGIGGLd~EFs~IFRRAFAsRvFpp~vie~lGi~H---VKGiLLyGPPGTGKTLiAR--qIGkMLNAre  284 (744)
T KOG0741|consen  210 SIINPDFNFESMGIGGLDKEFSDIFRRAFASRVFPPEVIEQLGIKH---VKGILLYGPPGTGKTLIAR--QIGKMLNARE  284 (744)
T ss_pred             cccCCCCChhhcccccchHHHHHHHHHHHHhhcCCHHHHHHcCccc---eeeEEEECCCCCChhHHHH--HHHHHhcCCC
Confidence            3456667788885   6777766665532   12222233333333   2568888999999996532  2334455565


Q ss_pred             CCCCCCCeEE--EEccc----HHHHHHHHHHHHHhccCCCceEEE
Q psy17644        235 LEPGDGPMGL--ILAPT----RELSQQIYNEAKRFGKGYNLSVVC  273 (330)
Q Consensus       235 ~~~~~~~~vL--il~Pt----r~La~Qi~~~~~~l~~~~~~~~~~  273 (330)
                      +..-+||.+|  ||--+    |.|-....++.+.++...++.++.
T Consensus       285 PKIVNGPeIL~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIII  329 (744)
T KOG0741|consen  285 PKIVNGPEILNKYVGESEENVRKLFADAEEEQRRLGANSGLHIII  329 (744)
T ss_pred             CcccCcHHHHHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEE
Confidence            5556777654  44444    445455555667777666666554

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=86.10  E-value=1.6  Score=44.39  Aligned_cols=30  Identities=30%  Similarity=0.305  Sum_probs=21.8

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHhc
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQ  232 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~  232 (330)
                      ...+++++.|+||||||. ++-.+|..+..+
T Consensus       174 ~e~~h~li~G~tGsGKs~-~i~~ll~~~~~~  203 (566)
T TIGR02759       174 SETQHILIHGTTGSGKSV-AIRKLLRWIRQR  203 (566)
T ss_pred             ccccceEEEcCCCCCHHH-HHHHHHHHHHhc
Confidence            355799999999999994 444556665543

The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).

>PRK04195 replication factor C large subunit; Provisional

Probab=86.04  E-value=2.2  Score=42.46  Aligned_cols=16  Identities=25%  Similarity=0.412  Sum_probs=14.0

Q ss_pred             CCcEEEEcCCCChhHH
Q psy17644        204 GRDIIGVAKTGSGKTG  219 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~  219 (330)
                      .+.+++.||+|+|||.
T Consensus        39 ~~~lLL~GppG~GKTt   54 (482)
T PRK04195         39 KKALLLYGPPGVGKTS   54 (482)
T ss_pred             CCeEEEECCCCCCHHH
Confidence            4678999999999994

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.00  E-value=2.5  Score=43.10  Aligned_cols=16  Identities=25%  Similarity=0.405  Sum_probs=13.1

Q ss_pred             CCCccEEEeecccccC
Q psy17644        312 LNRVTFLVLDEADRMF  327 (330)
Q Consensus       312 l~~i~~lVvDEad~ll  327 (330)
                      ....+++||||||+|-
T Consensus       116 ~~~~KVvIIDEah~Lt  131 (584)
T PRK14952        116 QSRYRIFIVDEAHMVT  131 (584)
T ss_pred             cCCceEEEEECCCcCC
Confidence            3567899999999884

>TIGR03689 pup_AAA proteasome ATPase

Probab=85.95  E-value=2.1  Score=42.94  Aligned_cols=17  Identities=24%  Similarity=0.303  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCChhHHH
Q psy17644        204 GRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a  220 (330)
                      .+.+++.||+|+|||..
T Consensus       216 p~GILLyGPPGTGKT~L  232 (512)
T TIGR03689       216 PKGVLLYGPPGCGKTLI  232 (512)
T ss_pred             CcceEEECCCCCcHHHH
Confidence            46799999999999953

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>PTZ00424 helicase 45; Provisional

Probab=85.89  E-value=6.3  Score=37.79  Aligned_cols=71  Identities=13%  Similarity=0.255  Sum_probs=50.7

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      ..++||.|+|+.-|..+...+...    +..+..++|+....++...   ++. ..+|||||-     .+. ..+++..+
T Consensus       267 ~~~~ivF~~t~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~-----~l~-~GiDip~v  336 (401)
T PTZ00424        267 ITQAIIYCNTRRKVDYLTKKMHER----DFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTD-----LLA-RGIDVQQV  336 (401)
T ss_pred             CCeEEEEecCcHHHHHHHHHHHHC----CCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcc-----ccc-CCcCcccC
Confidence            467899999999998888877654    6678888998876654332   333 479999993     222 35567777


Q ss_pred             cEEEe
Q psy17644        316 TFLVL  320 (330)
Q Consensus       316 ~~lVv  320 (330)
                      .+||.
T Consensus       337 ~~VI~  341 (401)
T PTZ00424        337 SLVIN  341 (401)
T ss_pred             CEEEE
Confidence            77775

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=85.78  E-value=3.1  Score=42.72  Aligned_cols=72  Identities=18%  Similarity=0.157  Sum_probs=51.9

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---h-CCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---E-LGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~-~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+.-|.+++..++..    ++.+..+++|.+.......+   . ...+|||||..     + ...+++.+
T Consensus       235 ~~~~~IIFc~tr~~~e~la~~L~~~----g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a-----~-~~GIDip~  304 (607)
T PRK11057        235 RGKSGIIYCNSRAKVEDTAARLQSR----GISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVA-----F-GMGINKPN  304 (607)
T ss_pred             CCCCEEEEECcHHHHHHHHHHHHhC----CCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEech-----h-hccCCCCC
Confidence            3567899999999999999988765    67888888988765543332   2 24789999942     2 23556677


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      +++||.
T Consensus       305 V~~VI~  310 (607)
T PRK11057        305 VRFVVH  310 (607)
T ss_pred             cCEEEE
Confidence            777764

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=85.76  E-value=2.2  Score=45.80  Aligned_cols=40  Identities=20%  Similarity=0.412  Sum_probs=28.3

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE  251 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~  251 (330)
                      .+++++|+||||||+... .++..++..      .+++++|+=|-++
T Consensus       476 ~n~~I~G~TGSGKS~l~~-~li~q~~~~------~~~~v~IiD~g~s  515 (893)
T TIGR03744       476 AHLLILGPTGAGKSATLT-NLLMQVMAV------HRPRLFIVEAGNS  515 (893)
T ss_pred             ccEEEECCCCCCHHHHHH-HHHHHHHHh------cCCEEEEEcCCCC
Confidence            478999999999995443 334444332      3689999988876

Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves.

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=85.66  E-value=4.1  Score=37.61  Aligned_cols=15  Identities=33%  Similarity=0.503  Sum_probs=12.8

Q ss_pred             cEEEEcCCCChhHHH
Q psy17644        206 DIIGVAKTGSGKTGA  220 (330)
Q Consensus       206 d~i~~a~TGsGKT~a  220 (330)
                      .+++.|++|+|||.+
T Consensus        40 ~~ll~G~~G~GKt~~   54 (319)
T PRK00440         40 HLLFAGPPGTGKTTA   54 (319)
T ss_pred             eEEEECCCCCCHHHH
Confidence            489999999999943

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=85.62  E-value=0.73  Score=41.98  Aligned_cols=25  Identities=36%  Similarity=0.452  Sum_probs=15.5

Q ss_pred             CCCc-EEEEcCCCChhHHHHHHHHHHH
Q psy17644        203 SGRD-IIGVAKTGSGKTGAFIWPMLVH  228 (330)
Q Consensus       203 ~g~d-~i~~a~TGsGKT~a~llp~l~~  228 (330)
                      ..|. +|++++|||||+.+ +..++.|
T Consensus       125 ~kRGLviiVGaTGSGKSTt-mAaMi~y  150 (375)
T COG5008         125 AKRGLVIIVGATGSGKSTT-MAAMIGY  150 (375)
T ss_pred             ccCceEEEECCCCCCchhh-HHHHhcc
Confidence            3344 55669999999833 3344444

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=85.48  E-value=4.8  Score=34.11  Aligned_cols=15  Identities=27%  Similarity=0.195  Sum_probs=12.4

Q ss_pred             cEEEEcCCCChhHHH
Q psy17644        206 DIIGVAKTGSGKTGA  220 (330)
Q Consensus       206 d~i~~a~TGsGKT~a  220 (330)
                      -+++.+++|||||..
T Consensus         3 ~ili~G~~~sGKS~~   17 (170)
T PRK05800          3 LILVTGGARSGKSRF   17 (170)
T ss_pred             EEEEECCCCccHHHH
Confidence            478889999999943

>KOG0741|consensus

Probab=85.46  E-value=3.6  Score=41.09  Aligned_cols=69  Identities=20%  Similarity=0.176  Sum_probs=41.5

Q ss_pred             CCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhc------------CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCC
Q psy17644        171 HFGFDEVLMKALRKCEYTSPTPIQAQAVPAAL------------SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPG  238 (330)
Q Consensus       171 ~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~------------~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~  238 (330)
                      .||.++.-++.+...|.-.-.+.-.+.+....            .-..+++.+|.|||||....-.++.          .
T Consensus       493 AFG~see~l~~~~~~Gmi~~g~~v~~il~~G~llv~qvk~s~~s~lvSvLl~Gp~~sGKTaLAA~iA~~----------S  562 (744)
T KOG0741|consen  493 AFGISEEDLERFVMNGMINWGPPVTRILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTALAAKIALS----------S  562 (744)
T ss_pred             ccCCCHHHHHHHHhCCceeecccHHHHHhhHHHHHHHhhccccCcceEEEEecCCCCChHHHHHHHHhh----------c
Confidence            36778877777777665444443333332211            1146899999999999543322221          2


Q ss_pred             CCCeEEEEccc
Q psy17644        239 DGPMGLILAPT  249 (330)
Q Consensus       239 ~~~~vLil~Pt  249 (330)
                      .-|.+=|+.|-
T Consensus       563 ~FPFvKiiSpe  573 (744)
T KOG0741|consen  563 DFPFVKIISPE  573 (744)
T ss_pred             CCCeEEEeChH
Confidence            46888788774

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=85.41  E-value=2.7  Score=37.32  Aligned_cols=53  Identities=11%  Similarity=0.124  Sum_probs=32.5

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|.-+++.+++|+|||.. +..++....+       ++-+++++.-- +-..++...+..++
T Consensus        24 ~g~~~~i~G~~GsGKt~l-~~~~~~~~~~-------~g~~~~y~~~e-~~~~~~~~~~~~~g   76 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVL-SQQFVYGALK-------QGKKVYVITTE-NTSKSYLKQMESVK   76 (234)
T ss_pred             CCcEEEEECCCCCChHHH-HHHHHHHHHh-------CCCEEEEEEcC-CCHHHHHHHHHHCC
Confidence            356678889999999943 3333333222       35667776543 44566777666664

>PRK09694 helicase Cas3; Provisional

Probab=85.38  E-value=6  Score=42.37  Aligned_cols=76  Identities=16%  Similarity=0.235  Sum_probs=47.7

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHH-------HHHH-hCC----CeEEEEChHHHHHHHH
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ-------SKAL-ELG----AEIVVGTPGRIIDMVK  306 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~-------~~~l-~~~----~dIiV~TP~~L~~~l~  306 (330)
                      .+.++||+++|+.-|.++++.+++... ....+.++++.......       ...+ +++    ..|||+|     +.++
T Consensus       559 ~g~~vLVf~NTV~~Aq~ly~~L~~~~~-~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaT-----QViE  632 (878)
T PRK09694        559 AGAQVCLICNLVDDAQKLYQRLKELNN-TQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVAT-----QVVE  632 (878)
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhhCC-CCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEEC-----cchh
Confidence            467899999999999999999987532 13467777877654332       1222 222    3699999     3333


Q ss_pred             cCCCCCCCccEEEeec
Q psy17644        307 MGATKLNRVTFLVLDE  322 (330)
Q Consensus       307 ~~~~~l~~i~~lVvDE  322 (330)
                      ++ .++ +++++|-|-
T Consensus       633 ~G-LDI-d~DvlItdl  646 (878)
T PRK09694        633 QS-LDL-DFDWLITQL  646 (878)
T ss_pred             he-eec-CCCeEEECC
Confidence            32 222 355666654

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=85.28  E-value=1.9  Score=42.98  Aligned_cols=54  Identities=30%  Similarity=0.423  Sum_probs=36.2

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHH-HHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVH-IMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~-i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      .|+-+++.+++|+|||. |++.++.+ +..       .+-++|+++- -+-..++.+.+..++-
T Consensus        20 ~g~~~Li~G~pGsGKT~-la~qfl~~g~~~-------~ge~~lyvs~-eE~~~~l~~~~~~~G~   74 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTL-FSIQFLYNGIIH-------FDEPGVFVTF-EESPQDIIKNARSFGW   74 (484)
T ss_pred             CCeEEEEEcCCCCCHHH-HHHHHHHHHHHh-------CCCCEEEEEE-ecCHHHHHHHHHHcCC
Confidence            56889999999999994 44444333 322       2456777764 4677777777777753

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.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=85.19  E-value=1.4  Score=46.24  Aligned_cols=17  Identities=29%  Similarity=0.393  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCChhHHH
Q psy17644        204 GRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a  220 (330)
                      ..++++.|++|+|||..
T Consensus       203 ~~n~lL~G~pG~GKT~l  219 (731)
T TIGR02639       203 KNNPLLVGEPGVGKTAI  219 (731)
T ss_pred             CCceEEECCCCCCHHHH
Confidence            45899999999999954

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

Probab=85.15  E-value=3.9  Score=41.10  Aligned_cols=72  Identities=15%  Similarity=0.232  Sum_probs=51.0

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---hC-CCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---EL-GAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~~-~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      .+++||.++|+.-|..+...+...   .++++..++|+....++...+   +. ...|||||-     .+. ..+++.++
T Consensus       367 ~~~~iVFv~s~~~a~~l~~~L~~~---~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTd-----vl~-rGiDip~v  437 (518)
T PLN00206        367 KPPAVVFVSSRLGADLLANAITVV---TGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATG-----VLG-RGVDLLRV  437 (518)
T ss_pred             CCCEEEEcCCchhHHHHHHHHhhc---cCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEec-----Hhh-ccCCcccC
Confidence            468999999999998888777643   357788889988766554333   33 478999994     232 35567777


Q ss_pred             cEEEe
Q psy17644        316 TFLVL  320 (330)
Q Consensus       316 ~~lVv  320 (330)
                      ++||.
T Consensus       438 ~~VI~  442 (518)
T PLN00206        438 RQVII  442 (518)
T ss_pred             CEEEE
Confidence            77764

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=85.03  E-value=0.53  Score=43.17  Aligned_cols=19  Identities=37%  Similarity=0.620  Sum_probs=16.9

Q ss_pred             hcCCCcEEEEcCCCChhHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~  219 (330)
                      +.+++.++++|++|+|||.
T Consensus        30 ~~~~~pvLl~G~~GtGKT~   48 (272)
T PF12775_consen   30 LSNGRPVLLVGPSGTGKTS   48 (272)
T ss_dssp             HHCTEEEEEESSTTSSHHH
T ss_pred             HHcCCcEEEECCCCCchhH
Confidence            3488999999999999995

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.99  E-value=6.4  Score=38.10  Aligned_cols=16  Identities=38%  Similarity=0.258  Sum_probs=13.2

Q ss_pred             cEEEEcCCCChhHHHH
Q psy17644        206 DIIGVAKTGSGKTGAF  221 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~  221 (330)
                      .+|++||.|+|||.+.
T Consensus        40 a~lf~Gp~G~GKtt~A   55 (397)
T PRK14955         40 GYIFSGLRGVGKTTAA   55 (397)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4789999999999543

>KOG0330|consensus

Probab=84.97  E-value=4.1  Score=39.02  Aligned_cols=70  Identities=17%  Similarity=0.151  Sum_probs=46.9

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh----CCCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE----LGAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~----~~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      |..+||.|.|-.-+..+.-.++.+    ++....+.|..+.......+.    ..++|+|||-      +-.+..+...+
T Consensus       300 g~s~iVF~~t~~tt~~la~~L~~l----g~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TD------VaSRGLDip~V  369 (476)
T KOG0330|consen  300 GNSVIVFCNTCNTTRFLALLLRNL----GFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTD------VASRGLDIPHV  369 (476)
T ss_pred             CCcEEEEEeccchHHHHHHHHHhc----CcceecccchhhHHHHHHHHHHHhccCCcEEEecc------hhcccCCCCCc
Confidence            567889999977776666555554    778888888776655433332    2589999994      22335556677


Q ss_pred             cEEE
Q psy17644        316 TFLV  319 (330)
Q Consensus       316 ~~lV  319 (330)
                      ++||
T Consensus       370 d~VV  373 (476)
T KOG0330|consen  370 DVVV  373 (476)
T ss_pred             eEEE
Confidence            7665

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

Probab=84.87  E-value=7.8  Score=36.69  Aligned_cols=81  Identities=20%  Similarity=0.294  Sum_probs=58.0

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEEC-CCchHHHHHHHhCC-CeEEEEChHHHHHHHHcCCCCCCCcc
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYG-GGSKWDQSKALELG-AEIVVGTPGRIIDMVKMGATKLNRVT  316 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~g-g~~~~~~~~~l~~~-~dIiV~TP~~L~~~l~~~~~~l~~i~  316 (330)
                      ++.-+||.+|+.+.+.|+...+++....  .++.++.+ .....+....++.| .+|+|+|     .+++++. .+.+++
T Consensus       304 ~~~P~liF~p~I~~~eq~a~~lk~~~~~--~~i~~Vhs~d~~R~EkV~~fR~G~~~lLiTT-----TILERGV-Tfp~vd  375 (441)
T COG4098         304 TGRPVLIFFPEIETMEQVAAALKKKLPK--ETIASVHSEDQHRKEKVEAFRDGKITLLITT-----TILERGV-TFPNVD  375 (441)
T ss_pred             cCCcEEEEecchHHHHHHHHHHHhhCCc--cceeeeeccCccHHHHHHHHHcCceEEEEEe-----ehhhccc-ccccce
Confidence            5677899999999999999999654332  23333333 23455666777775 6899999     4666544 467899


Q ss_pred             EEEeecccccC
Q psy17644        317 FLVLDEADRMF  327 (330)
Q Consensus       317 ~lVvDEad~ll  327 (330)
                      ++|++=-|+++
T Consensus       376 V~Vlgaeh~vf  386 (441)
T COG4098         376 VFVLGAEHRVF  386 (441)
T ss_pred             EEEecCCcccc
Confidence            99999888776

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=84.74  E-value=11  Score=35.82  Aligned_cols=58  Identities=16%  Similarity=0.007  Sum_probs=29.5

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH-HHHHHHHHHHHh
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE-LSQQIYNEAKRF  263 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~-La~Qi~~~~~~l  263 (330)
                      |.=+.+++++|+|||...+--+++..+..  ...+.+.+++||.--.. -..++.+.+..+
T Consensus       126 G~ItEI~G~~GsGKTql~lqlav~~qlp~--~~gg~~~~vvyIdTE~tF~peRl~~ia~~~  184 (344)
T PLN03187        126 RCITEAFGEFRSGKTQLAHTLCVTTQLPT--EMGGGNGKVAYIDTEGTFRPDRIVPIAERF  184 (344)
T ss_pred             CeEEEEecCCCCChhHHHHHHHHHHhcch--hhCCCCceEEEEEcCCCCCHHHHHHHHHHc
Confidence            35566889999999943222222222211  11122468888876332 234444444444

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.62  E-value=2.1  Score=43.86  Aligned_cols=15  Identities=20%  Similarity=0.434  Sum_probs=12.9

Q ss_pred             CCccEEEeecccccC
Q psy17644        313 NRVTFLVLDEADRMF  327 (330)
Q Consensus       313 ~~i~~lVvDEad~ll  327 (330)
                      .+.+++||||+|+|.
T Consensus       123 g~~KV~IIDEvh~Ls  137 (618)
T PRK14951        123 GRFKVFMIDEVHMLT  137 (618)
T ss_pred             CCceEEEEEChhhCC
Confidence            467899999999985

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=84.49  E-value=2.7  Score=46.46  Aligned_cols=56  Identities=18%  Similarity=0.090  Sum_probs=41.7

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .+++++.|.-|||||.+..--++..++..     ...-++|+|+-|+.-|..+...+....
T Consensus        10 ~~~~~~~a~agsgkt~~l~~~~~~~~~~~-----~~~~~i~~~t~t~~aa~em~~Ri~~~L   65 (1141)
T TIGR02784        10 KTSAWVSANAGSGKTHVLTQRVIRLLLNG-----VPPSKILCLTYTKAAAAEMQNRVFDRL   65 (1141)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHcC-----CCCCeEEEEecCHHHHHHHHHHHHHHH
Confidence            57899999999999966555555444432     124588999999999999888876554

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.

>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]

Probab=84.44  E-value=5.3  Score=39.11  Aligned_cols=113  Identities=19%  Similarity=0.223  Sum_probs=54.4

Q ss_pred             CCCcEEEE-cCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCc-h
Q psy17644        203 SGRDIIGV-AKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGS-K  280 (330)
Q Consensus       203 ~g~d~i~~-a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~-~  280 (330)
                      ...|+++. |.+|.||| +|++-++..+...     .+.|.+++  .+.--+.|++..+...  ..++....+-.|.. .
T Consensus       194 ~~~dLii~AaRP~mGKT-afalnia~n~a~~-----~~~~v~iF--SLEM~~eql~~R~Ls~--~s~v~~~kirtg~l~~  263 (435)
T COG0305         194 RPGDLIIVAARPGMGKT-ALALNIALNAAAD-----GRKPVAIF--SLEMSEEQLVMRLLSS--ESGIESSKLRTGRLSD  263 (435)
T ss_pred             ccCCEEEEccCCCCChH-HHHHHHHHHHHHh-----cCCCeEEE--EccCCHHHHHHHhhcc--ccccchhccccccccH
Confidence            44566666 88999999 4555555554442     12343333  3333455655554332  22333333333432 2


Q ss_pred             HHH------HHHHhCCCeEEE-EChHHHHHHH----HcCCCCCCCccEEEeecccccC
Q psy17644        281 WDQ------SKALELGAEIVV-GTPGRIIDMV----KMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       281 ~~~------~~~l~~~~dIiV-~TP~~L~~~l----~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ..+      ...+... .|.| -||+-=..-+    ++-.. -..+.++|+|=.+.|.
T Consensus       264 ~d~~~l~~a~~~l~~~-~i~IdD~~~~si~eir~~aRrlk~-~~~l~~i~iDYLqLm~  319 (435)
T COG0305         264 DEWERLIKAASELSEA-PIFIDDTPGLTITEIRSKARRLKL-KHNLGLIVIDYLQLMT  319 (435)
T ss_pred             HHHHHHHHHHHHHhhC-CeeecCCCcCCHHHHHHHHHHHHH-hcCccEEEEEEEEeec
Confidence            222      1223333 3544 3444322222    21111 2238999999887764

>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=84.38  E-value=1.9  Score=37.33  Aligned_cols=27  Identities=22%  Similarity=0.353  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      ..++++.|.||||||.+. ..++..++.
T Consensus        38 ~~h~li~G~tgsGKS~~l-~~ll~~l~~   64 (205)
T PF01580_consen   38 NPHLLIAGATGSGKSTLL-RTLLLSLAL   64 (205)
T ss_dssp             S-SEEEE--TTSSHHHHH-HHHHHHHHT
T ss_pred             CceEEEEcCCCCCccHHH-HHHHHHHHH
Confidence            348999999999999543 334444444

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.

>PRK08084 DNA replication initiation factor; Provisional

Probab=84.35  E-value=2.1  Score=38.25  Aligned_cols=17  Identities=18%  Similarity=0.266  Sum_probs=14.2

Q ss_pred             CCCcEEEEcCCCChhHH
Q psy17644        203 SGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~  219 (330)
                      .++.++++||+|+|||.
T Consensus        44 ~~~~l~l~Gp~G~GKTh   60 (235)
T PRK08084         44 HSGYIYLWSREGAGRSH   60 (235)
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            34678999999999993

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=84.24  E-value=7.6  Score=41.99  Aligned_cols=72  Identities=14%  Similarity=0.194  Sum_probs=52.0

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC---CCeEEEEChHHHHHHHHcCCCCCC
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL---GAEIVVGTPGRIIDMVKMGATKLN  313 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~---~~dIiV~TP~~L~~~l~~~~~~l~  313 (330)
                      +.++||+|.++..+..+.+.++..   .|+++..++||.+..+..+.   ++.   ++.|+|||-      +-....++.
T Consensus       493 ~~KvLVF~~~~~t~~~L~~~L~~~---~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTd------vgseGlNlq  563 (956)
T PRK04914        493 SEKVLVICAKAATALQLEQALRER---EGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSE------IGSEGRNFQ  563 (956)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHhhc---cCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEech------hhccCCCcc
Confidence            679999999999999999888542   36788899999886655333   332   588999993      222355677


Q ss_pred             CccEEEe
Q psy17644        314 RVTFLVL  320 (330)
Q Consensus       314 ~i~~lVv  320 (330)
                      .+.+||.
T Consensus       564 ~a~~VIn  570 (956)
T PRK04914        564 FASHLVL  570 (956)
T ss_pred             cccEEEE
Confidence            7766654

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=84.19  E-value=1.9  Score=37.98  Aligned_cols=37  Identities=22%  Similarity=0.248  Sum_probs=23.1

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA  247 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~  247 (330)
                      .|.-+++.+++|+|||. +++.++.....       .+-+++++.
T Consensus        22 ~g~i~~i~G~~GsGKT~-l~~~la~~~~~-------~~~~v~yi~   58 (225)
T PRK09361         22 RGTITQIYGPPGSGKTN-ICLQLAVEAAK-------NGKKVIYID   58 (225)
T ss_pred             CCeEEEEECCCCCCHHH-HHHHHHHHHHH-------CCCeEEEEE
Confidence            35667888999999994 34444444433       244556654

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=83.92  E-value=12  Score=31.69  Aligned_cols=17  Identities=41%  Similarity=0.581  Sum_probs=14.5

Q ss_pred             CCCcEEEEcCCCChhHH
Q psy17644        203 SGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~  219 (330)
                      ++|-++++||+|+|||.
T Consensus         1 ~~r~ivl~Gpsg~GK~~   17 (183)
T PF00625_consen    1 KRRPIVLVGPSGSGKST   17 (183)
T ss_dssp             SSSEEEEESSTTSSHHH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            36778999999999994

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=83.72  E-value=2.2  Score=42.71  Aligned_cols=54  Identities=26%  Similarity=0.406  Sum_probs=35.4

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|+-+++.+++|+|||. |++.++.+.+.+      .+-++|++ -+-+-..|+.+.+..++
T Consensus        30 ~Gs~~li~G~pGsGKT~-l~~qf~~~~~~~------~ge~~lyi-s~ee~~~~i~~~~~~~g   83 (509)
T PRK09302         30 KGRPTLVSGTAGTGKTL-FALQFLVNGIKR------FDEPGVFV-TFEESPEDIIRNVASFG   83 (509)
T ss_pred             CCcEEEEEeCCCCCHHH-HHHHHHHHHHHh------cCCCEEEE-EccCCHHHHHHHHHHcC
Confidence            46778889999999993 444444443331      15566666 45566677777777764

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=83.59  E-value=2.7  Score=39.55  Aligned_cols=39  Identities=21%  Similarity=0.164  Sum_probs=25.8

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT  249 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt  249 (330)
                      .|+=+.+.+++|+||| .++++++....+       .+.+++||..-
T Consensus        54 ~G~iteI~Gp~GsGKT-tLal~~~~~~~~-------~g~~~vyId~E   92 (325)
T cd00983          54 KGRIIEIYGPESSGKT-TLALHAIAEAQK-------LGGTVAFIDAE   92 (325)
T ss_pred             CCeEEEEECCCCCCHH-HHHHHHHHHHHH-------cCCCEEEECcc
Confidence            3567788899999999 556665555443       24556666543

RecA couples ATP hydrolysis to DNA strand exchange.

>KOG0341|consensus

Probab=83.50  E-value=3.7  Score=39.36  Aligned_cols=56  Identities=21%  Similarity=0.230  Sum_probs=43.2

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEECh
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTP  298 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP  298 (330)
                      ..|.|||.+-.+.-+..|++.+--    .|+..+.++||.........   ++. .-||+|+|-
T Consensus       420 T~PpVLIFaEkK~DVD~IhEYLLl----KGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATD  479 (610)
T KOG0341|consen  420 TSPPVLIFAEKKADVDDIHEYLLL----KGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATD  479 (610)
T ss_pred             CCCceEEEeccccChHHHHHHHHH----ccceeEEeecCcchhHHHHHHHHHhcCCCceEEEec
Confidence            579999999999998888887643    27889999999987665433   333 369999993

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=83.48  E-value=2.5  Score=43.38  Aligned_cols=16  Identities=38%  Similarity=0.258  Sum_probs=13.2

Q ss_pred             cEEEEcCCCChhHHHH
Q psy17644        206 DIIGVAKTGSGKTGAF  221 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~  221 (330)
                      .+|++||.|.|||.+.
T Consensus        40 a~Lf~Gp~GvGKttlA   55 (620)
T PRK14954         40 GYIFSGLRGVGKTTAA   55 (620)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4789999999999543

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=83.32  E-value=6  Score=40.39  Aligned_cols=71  Identities=18%  Similarity=0.242  Sum_probs=50.4

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh----CCCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE----LGAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~----~~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      +.++||.|+||..|.+++..+...    ++.+..++||.+.......+.    ...+|||||-     .+. ..+++.++
T Consensus       224 ~~~~IIf~~sr~~~e~la~~L~~~----g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~-----a~~-~GID~p~v  293 (591)
T TIGR01389       224 GQSGIIYASSRKKVEELAERLESQ----GISALAYHAGLSNKVRAENQEDFLYDDVKVMVATN-----AFG-MGIDKPNV  293 (591)
T ss_pred             CCCEEEEECcHHHHHHHHHHHHhC----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEec-----hhh-ccCcCCCC
Confidence            567899999999999999988764    577888899887655443322    3579999993     222 24456677


Q ss_pred             cEEEe
Q psy17644        316 TFLVL  320 (330)
Q Consensus       316 ~~lVv  320 (330)
                      ++||.
T Consensus       294 ~~VI~  298 (591)
T TIGR01389       294 RFVIH  298 (591)
T ss_pred             CEEEE
Confidence            77664

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.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=83.22  E-value=5.2  Score=37.75  Aligned_cols=27  Identities=22%  Similarity=0.234  Sum_probs=20.1

Q ss_pred             HHHhhhhhcCCCcEEEEcCCCChhHHH
Q psy17644        194 QAQAVPAALSGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       194 Q~~~i~~~~~g~d~i~~a~TGsGKT~a  220 (330)
                      ..++-.+......|++.|++|+||+.+
T Consensus        12 ~~~~~~~a~~~~pVLI~GE~GtGK~~l   38 (329)
T TIGR02974        12 LEQVSRLAPLDRPVLIIGERGTGKELI   38 (329)
T ss_pred             HHHHHHHhCCCCCEEEECCCCChHHHH
Confidence            344444455778899999999999943

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PRK06893 DNA replication initiation factor; Validated

Probab=83.19  E-value=1.7  Score=38.62  Aligned_cols=15  Identities=20%  Similarity=-0.002  Sum_probs=12.5

Q ss_pred             CcEEEEcCCCChhHH
Q psy17644        205 RDIIGVAKTGSGKTG  219 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~  219 (330)
                      ..++++|++|+|||.
T Consensus        40 ~~l~l~G~~G~GKTh   54 (229)
T PRK06893         40 PFFYIWGGKSSGKSH   54 (229)
T ss_pred             CeEEEECCCCCCHHH
Confidence            346889999999993

>KOG0780|consensus

Probab=83.08  E-value=7.3  Score=37.49  Aligned_cols=86  Identities=17%  Similarity=0.149  Sum_probs=45.4

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc-c-HHHHHHHHHHHHHhccCCCceEEEEECCCchHHH-
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP-T-RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ-  283 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P-t-r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~-  283 (330)
                      +++++-.|+|||.+..--+  +.+++      .|-++.++|- | |+-|.   +.++..+...++.++..|.....-.- 
T Consensus       104 imfVGLqG~GKTTtc~KlA--~y~kk------kG~K~~LvcaDTFRagAf---DQLkqnA~k~~iP~ygsyte~dpv~ia  172 (483)
T KOG0780|consen  104 IMFVGLQGSGKTTTCTKLA--YYYKK------KGYKVALVCADTFRAGAF---DQLKQNATKARVPFYGSYTEADPVKIA  172 (483)
T ss_pred             EEEEeccCCCcceeHHHHH--HHHHh------cCCceeEEeecccccchH---HHHHHHhHhhCCeeEecccccchHHHH
Confidence            4455889999995433222  22332      4666666664 3 55553   34444444445555544443332211 


Q ss_pred             ----HHHHhCCCeEEEE-ChHHHHH
Q psy17644        284 ----SKALELGAEIVVG-TPGRIID  303 (330)
Q Consensus       284 ----~~~l~~~~dIiV~-TP~~L~~  303 (330)
                          .+..+.+++|||+ |.+|+..
T Consensus       173 ~egv~~fKke~fdvIIvDTSGRh~q  197 (483)
T KOG0780|consen  173 SEGVDRFKKENFDVIIVDTSGRHKQ  197 (483)
T ss_pred             HHHHHHHHhcCCcEEEEeCCCchhh
Confidence                1223457887654 8888744

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=82.95  E-value=3.8  Score=42.04  Aligned_cols=18  Identities=22%  Similarity=0.121  Sum_probs=14.1

Q ss_pred             CcEEEEcCCCChhHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFI  222 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~l  222 (330)
                      ..+|+.++.|+|||.+..
T Consensus        39 ha~Lf~GPpG~GKTtiAr   56 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIAR   56 (624)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            357889999999995543

>PHA00350 putative assembly protein

Probab=82.93  E-value=2.2  Score=41.33  Aligned_cols=17  Identities=24%  Similarity=0.088  Sum_probs=13.3

Q ss_pred             EEEEcCCCChhHHHHHH
Q psy17644        207 IIGVAKTGSGKTGAFIW  223 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~ll  223 (330)
                      .++.|..|||||+..+.
T Consensus         4 ~l~tG~pGSGKT~~aV~   20 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVV   20 (399)
T ss_pred             EEEecCCCCchhHHHHH
Confidence            36679999999976654

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=82.87  E-value=2.7  Score=42.06  Aligned_cols=53  Identities=26%  Similarity=0.307  Sum_probs=35.0

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|.-+++.+++|+|||. |++.++...+.       ++-+++|++- .+...++...+..++
T Consensus       272 ~g~~~li~G~~G~GKT~-l~~~~~~~~~~-------~g~~~~yis~-e~~~~~i~~~~~~~g  324 (509)
T PRK09302        272 RGSIILVSGATGTGKTL-LASKFAEAACR-------RGERCLLFAF-EESRAQLIRNARSWG  324 (509)
T ss_pred             CCcEEEEEcCCCCCHHH-HHHHHHHHHHh-------CCCcEEEEEe-cCCHHHHHHHHHHcC
Confidence            45677788999999994 44444444433       3567777754 455677777777664

>TIGR02746 TraC-F-type type-IV secretion system protein TraC

Probab=82.68  E-value=3  Score=44.15  Aligned_cols=40  Identities=20%  Similarity=0.238  Sum_probs=26.9

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL  252 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~L  252 (330)
                      .+++++|+||||||..... ++..++.       .+++++|+=|.++-
T Consensus       431 ~n~~I~G~tGsGKS~~~~~-l~~~~~~-------~g~~v~iiD~~~sy  470 (797)
T TIGR02746       431 YNIAVVGGSGAGKSFFMQE-LIVDNLS-------RGGKVWVIDVGRSY  470 (797)
T ss_pred             cceEEEcCCCCCHHHHHHH-HHHHHHh-------CCCEEEEEeCCCCH
Confidence            4799999999999955433 3333333       35777887776543

The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=82.65  E-value=4.3  Score=39.42  Aligned_cols=41  Identities=15%  Similarity=0.102  Sum_probs=26.9

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR  250 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr  250 (330)
                      +.-+++.|++|+|||  .|+.++.+...+.    ..+++++++..-.
T Consensus       113 ~nplfi~G~~GlGKT--HLl~Aign~~~~~----~~~a~v~y~~se~  153 (408)
T COG0593         113 YNPLFIYGGVGLGKT--HLLQAIGNEALAN----GPNARVVYLTSED  153 (408)
T ss_pred             CCcEEEECCCCCCHH--HHHHHHHHHHHhh----CCCceEEeccHHH
Confidence            567888899999999  4555555444332    1345777776644

>PF05729 NACHT: NACHT domain

Probab=82.60  E-value=2.7  Score=34.31  Aligned_cols=25  Identities=16%  Similarity=0.357  Sum_probs=17.0

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhc
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQ  232 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~  232 (330)
                      +++.|+.|+|||. ++-.++..+...
T Consensus         3 l~I~G~~G~GKSt-ll~~~~~~~~~~   27 (166)
T PF05729_consen    3 LWISGEPGSGKST-LLRKLAQQLAEE   27 (166)
T ss_pred             EEEECCCCCChHH-HHHHHHHHHHhc
Confidence            6788999999994 444455555443

>KOG2227|consensus

Probab=82.50  E-value=2.6  Score=41.34  Aligned_cols=52  Identities=15%  Similarity=0.271  Sum_probs=28.9

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc-HHHHHHHHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT-RELSQQIYNEA  260 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt-r~La~Qi~~~~  260 (330)
                      .+..+.+++.+|+|||.+. .-++.++-+.     ...+.+++|-=| ...+..++..+
T Consensus       174 t~gSlYVsG~PGtgkt~~l-~rvl~~~~~~-----~~~~~~v~inc~sl~~~~aiF~kI  226 (529)
T KOG2227|consen  174 TSGSLYVSGQPGTGKTALL-SRVLDSLSKS-----SKSPVTVYINCTSLTEASAIFKKI  226 (529)
T ss_pred             cCcceEeeCCCCcchHHHH-HHHHHhhhhh-----cccceeEEEeeccccchHHHHHHH
Confidence            3468999999999999432 1133333221     234555555444 25555555543

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=82.48  E-value=2.4  Score=34.73  Aligned_cols=24  Identities=25%  Similarity=0.356  Sum_probs=17.5

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      +.++++.+|||| +++-.+++.+..
T Consensus         3 v~VvG~~~sGKT-Tl~~~Li~~l~~   26 (140)
T PF03205_consen    3 VQVVGPKNSGKT-TLIRKLINELKR   26 (140)
T ss_dssp             EEEEESTTSSHH-HHHHHHHHHHHH
T ss_pred             EEEECCCCCCHH-HHHHHHHHHHhH
Confidence            578899999999 455556666654

>PF02302 PTS_IIB: PTS system, Lactose/Cellobiose specific IIB subunit; InterPro: IPR003501 The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes

Probab=82.43  E-value=1.9  Score=31.95  Aligned_cols=57  Identities=16%  Similarity=0.121  Sum_probs=34.8

Q ss_pred             eEEEEcccHHHHHHHH-HHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHH
Q psy17644        242 MGLILAPTRELSQQIY-NEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI  301 (330)
Q Consensus       242 ~vLil~Ptr~La~Qi~-~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L  301 (330)
                      ++|++|++---...+. ..+++.++..++.+....+....   .......+|+|++||.--
T Consensus         1 kIlvvC~~Gi~TS~~~~~~i~~~~~~~gi~~~~~~~~~~~---~~~~~~~~D~il~~~~i~   58 (90)
T PF02302_consen    1 KILVVCGSGIGTSLMVANKIKKALKELGIEVEVSAGSILE---VEEIADDADLILLTPQIA   58 (90)
T ss_dssp             EEEEEESSSSHHHHHHHHHHHHHHHHTTECEEEEEEETTT---HHHHHTT-SEEEEEESSG
T ss_pred             CEEEECCChHHHHHHHHHHHHHHHHhccCceEEEEecccc---cccccCCCcEEEEcCccc
Confidence            5788888755545555 55666666667766655554221   233445689999998544

The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This signature is often found downstream of IPR003352 from INTERPRO.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TVM_A 2WY2_D 1IIB_A 2WWV_D 1H9C_A 1E2B_A 2L2Q_A 2KYR_A 3CZC_A 3NBM_A ....

>PRK09354 recA recombinase A; Provisional

Probab=82.35  E-value=3.2  Score=39.47  Aligned_cols=28  Identities=21%  Similarity=0.197  Sum_probs=19.5

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      .|+=+.+.+++|||||. ++++++....+
T Consensus        59 ~G~IteI~G~~GsGKTt-Lal~~~~~~~~   86 (349)
T PRK09354         59 RGRIVEIYGPESSGKTT-LALHAIAEAQK   86 (349)
T ss_pred             CCeEEEEECCCCCCHHH-HHHHHHHHHHH
Confidence            35677788999999994 55555555443

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 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=82.33  E-value=1  Score=38.69  Aligned_cols=21  Identities=33%  Similarity=0.398  Sum_probs=14.7

Q ss_pred             CCcEEEEcCCCChhHHHHHHH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWP  224 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp  224 (330)
                      ...++++||.|||||..|..-
T Consensus         3 ~~~vlL~Gps~SGKTaLf~~L   23 (181)
T PF09439_consen    3 RPTVLLVGPSGSGKTALFSQL   23 (181)
T ss_dssp             --EEEEE-STTSSHHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHHH
Confidence            456889999999999766543

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 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.

>COG3451 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]

Probab=82.29  E-value=1.8  Score=45.71  Aligned_cols=14  Identities=36%  Similarity=0.539  Sum_probs=12.9

Q ss_pred             CcEEEEcCCCChhH
Q psy17644        205 RDIIGVAKTGSGKT  218 (330)
Q Consensus       205 ~d~i~~a~TGsGKT  218 (330)
                      .+.+++|+||+|||
T Consensus       437 ghT~I~G~tGaGKT  450 (796)
T COG3451         437 GHTLIIGPTGAGKT  450 (796)
T ss_pred             CCeEEECCCCCCHH
Confidence            47999999999999

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=82.18  E-value=17  Score=34.47  Aligned_cols=88  Identities=17%  Similarity=0.166  Sum_probs=50.8

Q ss_pred             CCHHHHHhhhhhc----CCC---cEEEEcCCCChhHHHHHHHHHHHHHhcCCCC--------------CCCCCeEEEEcc
Q psy17644        190 PTPIQAQAVPAAL----SGR---DIIGVAKTGSGKTGAFIWPMLVHIMDQKELE--------------PGDGPMGLILAP  248 (330)
Q Consensus       190 pt~iQ~~~i~~~~----~g~---d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~--------------~~~~~~vLil~P  248 (330)
                      .+|+|...|..+.    +||   -.++.|+.|.||+. +...+...++...+..              .++.|-+.++.|
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~-lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p   81 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDA-LIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTP   81 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHH-HHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEec
Confidence            4567777776654    443   67899999999983 3334455566532211              235688888888


Q ss_pred             cH----HHHHHHHHHHHHhcc---CCCceEEEEECCC
Q psy17644        249 TR----ELSQQIYNEAKRFGK---GYNLSVVCCYGGG  278 (330)
Q Consensus       249 tr----~La~Qi~~~~~~l~~---~~~~~~~~~~gg~  278 (330)
                      ..    --+.|+.+....+..   ..+.+++.+....
T Consensus        82 ~~~~~~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae  118 (334)
T PRK07993         82 EKGKSSLGVDAVREVTEKLYEHARLGGAKVVWLPDAA  118 (334)
T ss_pred             ccccccCCHHHHHHHHHHHhhccccCCceEEEEcchH
Confidence            53    235555554444432   2245666665433

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=82.07  E-value=8  Score=39.04  Aligned_cols=16  Identities=19%  Similarity=0.501  Sum_probs=13.4

Q ss_pred             CCCccEEEeecccccC
Q psy17644        312 LNRVTFLVLDEADRMF  327 (330)
Q Consensus       312 l~~i~~lVvDEad~ll  327 (330)
                      ....+++||||||+|-
T Consensus       115 ~~~~KVvIIDEad~Lt  130 (535)
T PRK08451        115 MARFKIFIIDEVHMLT  130 (535)
T ss_pred             cCCeEEEEEECcccCC
Confidence            4577899999999984

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=81.90  E-value=15  Score=34.54  Aligned_cols=116  Identities=15%  Similarity=0.174  Sum_probs=61.3

Q ss_pred             CCHHHHHhhhhhc----CCC---cEEEEcCCCChhHHHHHHHHHHHHHhcCCC-------------CCCCCCeEEEEccc
Q psy17644        190 PTPIQAQAVPAAL----SGR---DIIGVAKTGSGKTGAFIWPMLVHIMDQKEL-------------EPGDGPMGLILAPT  249 (330)
Q Consensus       190 pt~iQ~~~i~~~~----~g~---d~i~~a~TGsGKT~a~llp~l~~i~~~~~~-------------~~~~~~~vLil~Pt  249 (330)
                      +.|+|...+..+.    ++|   -+++.|+.|.||+. +...+...++.....             ..++.|-..+|.|.
T Consensus         4 ~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~-lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~   82 (319)
T PRK06090          4 DYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVES-LVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPE   82 (319)
T ss_pred             CcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHH-HHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecC
Confidence            4567766666554    444   68899999999983 333344555543211             12345888888885


Q ss_pred             H---H-HHHHHHHHHHHhcc----CCCceEEEEECCCchHHH-----HHHHhC---CCeE-EEEC-hHHHHHHHHc
Q psy17644        250 R---E-LSQQIYNEAKRFGK----GYNLSVVCCYGGGSKWDQ-----SKALEL---GAEI-VVGT-PGRIIDMVKM  307 (330)
Q Consensus       250 r---~-La~Qi~~~~~~l~~----~~~~~~~~~~gg~~~~~~-----~~~l~~---~~dI-iV~T-P~~L~~~l~~  307 (330)
                      .   . -+.||. .+..+..    ..+.+++.+.........     .+.+..   +.-+ ++|+ |.+|+.-+..
T Consensus        83 ~~~~~I~vdqiR-~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~S  157 (319)
T PRK06090         83 KEGKSITVEQIR-QCNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVS  157 (319)
T ss_pred             cCCCcCCHHHHH-HHHHHHhhCcccCCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHh
Confidence            3   2 344443 3333322    234567766654433221     122222   2333 3443 6677765543

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=81.66  E-value=4.5  Score=37.31  Aligned_cols=28  Identities=25%  Similarity=0.497  Sum_probs=18.6

Q ss_pred             EChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        296 GTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       296 ~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      --|+-|..++.    ++..=++|.|||.|+|.
T Consensus        89 eK~gDlaaiLt----~Le~~DVLFIDEIHrl~  116 (332)
T COG2255          89 EKPGDLAAILT----NLEEGDVLFIDEIHRLS  116 (332)
T ss_pred             cChhhHHHHHh----cCCcCCeEEEehhhhcC
Confidence            33555555554    35566789999999874

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=81.55  E-value=6.5  Score=37.14  Aligned_cols=58  Identities=17%  Similarity=0.187  Sum_probs=41.7

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHH-------HHhC-CCeEEEECh
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK-------ALEL-GAEIVVGTP  298 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~-------~l~~-~~dIiV~TP  298 (330)
                      .+.++||+|+|+.-|..++..+++.+.  +..+..++|+........       .++. ...|||||.
T Consensus       221 ~~~~~lVf~~t~~~~~~~~~~L~~~~~--~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~  286 (358)
T TIGR01587       221 KGGKIAIIVNTVDRAQEFYQQLKENAP--EEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQ  286 (358)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHhhcC--CCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECc
Confidence            357899999999999999999887643  346778888876544322       2332 467999984

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.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=81.47  E-value=14  Score=34.62  Aligned_cols=58  Identities=14%  Similarity=-0.028  Sum_probs=31.4

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH-HHHHHHHHHHHh
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE-LSQQIYNEAKRF  263 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~-La~Qi~~~~~~l  263 (330)
                      |.=+.+++++|+|||...+..+++..+..  ...+.+.+|+||.--.. -..++.+.+..+
T Consensus        96 G~iteI~G~~GsGKTql~lqla~~~~~~~--~~gg~~~~vvYIdtE~~f~~eRi~~~a~~~  154 (313)
T TIGR02238        96 MSITEVFGEFRCGKTQLSHTLCVTAQLPR--EMGGGNGKVAYIDTEGTFRPDRIRAIAERF  154 (313)
T ss_pred             CeEEEEECCCCCCcCHHHHHHHHHHhcch--hhcCCCCeEEEEEcCCCCCHHHHHHHHHHc
Confidence            45677889999999943322222222110  11123568888874432 245555555554

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=81.30  E-value=5.6  Score=37.91  Aligned_cols=72  Identities=19%  Similarity=0.319  Sum_probs=48.9

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEE
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFL  318 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~l  318 (330)
                      .+.++||+++|+.-|..++..++...  .+..+..++|........+..  ..+|+|||.     .+.+ .+++..+ ++
T Consensus       271 ~~~k~LIf~nt~~~~~~l~~~L~~~~--~~~~~~~l~g~~~~~~R~~~~--~~~iLVaTd-----v~~r-GiDi~~~-~v  339 (357)
T TIGR03158       271 PGERGAIILDSLDEVNRLSDLLQQQG--LGDDIGRITGFAPKKDRERAM--QFDILLGTS-----TVDV-GVDFKRD-WL  339 (357)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHhhhC--CCceEEeeecCCCHHHHHHhc--cCCEEEEec-----HHhc-ccCCCCc-eE
Confidence            46689999999999999999998752  244566677766665543332  468999994     3443 3444444 56


Q ss_pred             Eee
Q psy17644        319 VLD  321 (330)
Q Consensus       319 VvD  321 (330)
                      |++
T Consensus       340 i~~  342 (357)
T TIGR03158       340 IFS  342 (357)
T ss_pred             EEC
Confidence            665

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.

>PHA00012 I assembly protein

Probab=81.28  E-value=9.2  Score=36.09  Aligned_cols=23  Identities=22%  Similarity=0.222  Sum_probs=17.2

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      -++.|..|||||+..+..++..+
T Consensus         4 ylITGkPGSGKSl~aV~~I~~~L   26 (361)
T PHA00012          4 YVVTGKLGAGKTLVAVSRIQDKL   26 (361)
T ss_pred             EEEecCCCCCchHHHHHHHHHHH
Confidence            36779999999987776555544

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=81.26  E-value=19  Score=34.25  Aligned_cols=58  Identities=16%  Similarity=0.164  Sum_probs=35.4

Q ss_pred             CHHHHHhhhhhcC--C---CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCC---------------CCCCCeEEEEccc
Q psy17644        191 TPIQAQAVPAALS--G---RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELE---------------PGDGPMGLILAPT  249 (330)
Q Consensus       191 t~iQ~~~i~~~~~--g---~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~---------------~~~~~~vLil~Pt  249 (330)
                      +|+|...+..+.+  +   +-+++.|+.|.||+... ..+...++......               .++.|-..++.|.
T Consensus         3 yPW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA-~~~A~~LlC~~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p~   80 (342)
T PRK06964          3 YPWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFA-QHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPE   80 (342)
T ss_pred             CcccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHH-HHHHHHHcCCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecc
Confidence            4677777766553  2   36788999999999433 33445555543110               1345777778775

>TIGR00602 rad24 checkpoint protein rad24

Probab=81.03  E-value=6  Score=40.77  Aligned_cols=46  Identities=13%  Similarity=0.244  Sum_probs=25.4

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHH
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a  220 (330)
                      .+++++-..+..+..++..       +....+ ....++-+++.||+|+|||.+
T Consensus        81 ~~ldel~~~~~ki~~l~~~-------l~~~~~-~~~~~~illL~GP~GsGKTTl  126 (637)
T TIGR00602        81 ETQHELAVHKKKIEEVETW-------LKAQVL-ENAPKRILLITGPSGCGKSTT  126 (637)
T ss_pred             CCHHHhcCcHHHHHHHHHH-------HHhccc-ccCCCcEEEEECCCCCCHHHH
Confidence            3466666666665554321       000000 012334478889999999954

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

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=80.89  E-value=2.7  Score=39.08  Aligned_cols=44  Identities=20%  Similarity=0.188  Sum_probs=24.2

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP  248 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P  248 (330)
                      .|.=+.+++++|+|||. |++.++.......... ..+.+++||.-
T Consensus        94 ~g~i~ei~G~~g~GKT~-l~~~~~~~~~~~~~~g-~~~~~~~yi~t  137 (310)
T TIGR02236        94 TQAITEVFGEFGSGKTQ-ICHQLAVNVQLPEEKG-GLGGKAVYIDT  137 (310)
T ss_pred             CCeEEEEECCCCCCHHH-HHHHHHHHhcCCcccC-CCcceEEEEEC
Confidence            35567788999999993 4444433332111111 11237788763

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=80.79  E-value=1.5  Score=35.67  Aligned_cols=44  Identities=25%  Similarity=0.341  Sum_probs=25.6

Q ss_pred             hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQ  255 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Q  255 (330)
                      +..|.-+++.++.|+||| +|+-.++..+          +...-|-.||-.|++.
T Consensus        19 l~~~~~i~l~G~lGaGKT-tl~~~l~~~l----------g~~~~v~SPTf~lv~~   62 (133)
T TIGR00150        19 LDFGTVVLLKGDLGAGKT-TLVQGLLQGL----------GIQGNVTSPTFTLVNE   62 (133)
T ss_pred             CCCCCEEEEEcCCCCCHH-HHHHHHHHHc----------CCCCcccCCCeeeeee
Confidence            345566777899999999 3444344332          1112366787555443

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=80.52  E-value=20  Score=37.15  Aligned_cols=76  Identities=16%  Similarity=0.330  Sum_probs=52.5

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHH---HHHhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS---KALEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||+|+|+..|..+...+...    ++.+..++|+.......   ..++. ...|+|||     ..+. ..+.+..
T Consensus       445 ~g~~viIf~~t~~~ae~L~~~L~~~----gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t-----~~L~-rGfdlp~  514 (652)
T PRK05298        445 KGERVLVTTLTKRMAEDLTDYLKEL----GIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGI-----NLLR-EGLDIPE  514 (652)
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHhhc----ceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEe-----CHHh-CCccccC
Confidence            5789999999999999988888764    67778887876643332   22322 46888888     3333 3456777


Q ss_pred             ccEEEeeccc
Q psy17644        315 VTFLVLDEAD  324 (330)
Q Consensus       315 i~~lVvDEad  324 (330)
                      ++++|+=+++
T Consensus       515 v~lVii~d~e  524 (652)
T PRK05298        515 VSLVAILDAD  524 (652)
T ss_pred             CcEEEEeCCc
Confidence            8877765554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	330
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		1e-53
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		4e-47
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		4e-35
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		4e-33
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		8e-33
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		6e-29
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		2e-28
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		9e-27
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		4e-26
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		5e-24
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		1e-22
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		2e-22
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		3e-22
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		4e-22
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		1e-21
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-21
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		1e-21
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-21
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		1e-21
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		2e-21
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		3e-21
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		3e-21
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		3e-21
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		4e-21
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		9e-21
3ly5_A	262	Ddx18 Dead-Domain Length = 262		1e-20
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		3e-20
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		3e-20
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		4e-20
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		5e-20
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		6e-20
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		8e-20
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		1e-19
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		2e-19
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		3e-19
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		3e-19
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		5e-19
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		6e-19
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-18
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		8e-18
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		9e-18
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		1e-14
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		8e-14
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-13
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-13
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		1e-13
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-13
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		1e-13
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		1e-13
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		9e-04

>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 =  206 bits (525), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 103/205 (50%), Positives = 131/205 (63%)
Query: 126 EVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKC 185
           + EKNFYQ H D+AR T QE +  R    ITV G + P PV +F    F   +M  + + 
Sbjct: 2   KFEKNFYQEHPDLARRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQ 61
Query: 186 EYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI 245
            +T PT IQAQ  P ALSG D++GVA+TGSGKT +++ P +VHI  Q  LE GDGP+ L+
Sbjct: 62  NFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLV 121
Query: 246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMV 305
           LAPTREL+QQ+   A  + +   L   C YGG  K  Q + LE G EI + TPGR+ID +
Sbjct: 122 LAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFL 181
Query: 306 KMGATKLNRVTFLVLDEADRMFDMG 330
           + G T L R T+LVLDEADRM DMG
Sbjct: 182 ECGKTNLRRTTYLVLDEADRMLDMG 206

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score =  184 bits (468), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 93/189 (49%), Positives = 119/189 (62%)
Query: 142 TPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAA 201
           T QE +  R    ITV G + P PV +F    F   +M  + +  +T PT IQAQ  P A
Sbjct: 4   TAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVA 63
Query: 202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK 261
           LSG D++GVA+TGSGKT +++ P +VHI  Q  LE GDGP+ L+LAPTREL+QQ+   A 
Sbjct: 64  LSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAA 123
Query: 262 RFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLD 321
            + +   L   C YGG  K  Q + LE G EI + TPGR+ID ++ G T L R T+LVLD
Sbjct: 124 EYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLD 183
Query: 322 EADRMFDMG 330
           EADRM DMG
Sbjct: 184 EADRMLDMG 192

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  145 bits (365), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 73/177 (41%), Positives = 107/177 (60%), Gaps = 2/177 (1%)
Query: 155 ITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTG 214
           + V+G+D P P+  F      ++++  + K  Y  PTPIQ  ++P   SGRD++  A+TG
Sbjct: 44  VKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTG 103
Query: 215 SGKTGAFIWPMLVHIM-DQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVC 273
           SGKT AF+ P+L  ++ D  ELE G  P  +I++PTREL+ QI+NEA++F     L +  
Sbjct: 104 SGKTAAFLLPILSKLLEDPHELELGR-PQVVIVSPTRELAIQIFNEARKFAFESYLKIGI 162
Query: 274 CYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            YGG S   Q++ +  G  +V+ TPGR++D V           F+VLDEADRM DMG
Sbjct: 163 VYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMG 219

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  138 bits (347), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 74/194 (38%), Positives = 104/194 (53%), Gaps = 19/194 (9%)
Query: 153 SGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAK 212
           S +  +G + P  + SF      E++M  +    YT PTP+Q  A+P     RD++  A+
Sbjct: 1   SMVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQ 60
Query: 213 TGSGKTGAFIWPMLVHIMDQKELEPGDG----------------PMGLILAPTRELSQQI 256
           TGSGKT AF+ P+L  I       PG+                 P+ L+LAPTREL+ QI
Sbjct: 61  TGSGKTAAFLLPILSQIYSDG---PGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQI 117
Query: 257 YNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVT 316
           Y EA++F     +     YGG     Q + LE G  ++V TPGR++DM++ G   L+   
Sbjct: 118 YEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCK 177
Query: 317 FLVLDEADRMFDMG 330
           +LVLDEADRM DMG
Sbjct: 178 YLVLDEADRMLDMG 191

>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 =  137 bits (345), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 70/185 (37%), Positives = 101/185 (54%), Gaps = 8/185 (4%)
Query: 154 GITVSGADPPYP----VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIG 209
            I VS   P Y     + +F     D  +   +    Y  PTPIQ  A+PA L  RDI+ 
Sbjct: 6   SIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMA 65
Query: 210 VAKTGSGKTGAFIWPMLVHI----MDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK 265
            A+TGSGKT AF+ P++ H+    ++Q+       P  LILAPTREL+ QI +E+++F  
Sbjct: 66  CAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSL 125
Query: 266 GYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR 325
              L     YGG     Q + +++G  ++V TPGR++D ++     L    ++VLDEADR
Sbjct: 126 NTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADR 185
Query: 326 MFDMG 330
           M DMG
Sbjct: 186 MLDMG 190

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score =  124 bits (312), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 71/162 (43%), Positives = 94/162 (58%), Gaps = 4/162 (2%)
Query: 169 FGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVH 228
           F  F     +++AL     T+PTPIQA A+P AL G+D+IG A+TG+GKT AF  P+   
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 229 IMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE 288
           +   +E   G  P  L+L PTREL+ Q+ +E        +L VV  YGG     Q +AL 
Sbjct: 63  LAPSQE--RGRKPRALVLTPTRELALQVASELTAVAP--HLKVVAVYGGTGYGKQKEALL 118
Query: 289 LGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            GA+ VV TPGR +D ++ G   L+RV   VLDEAD M  MG
Sbjct: 119 RGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMG 160

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score =  123 bits (308), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 70/162 (43%), Positives = 94/162 (58%), Gaps = 4/162 (2%)
Query: 169 FGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVH 228
           F  F     +++AL     T+PTPI+A A+P AL G+D+IG A+TG+GKT AF  P+   
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 229 IMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE 288
           +   +E   G  P  L+L PTREL+ Q+ +E        +L VV  YGG     Q +AL 
Sbjct: 63  LAPSQE--RGRKPRALVLTPTRELALQVASELTAVAP--HLKVVAVYGGTGYGKQKEALL 118
Query: 289 LGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            GA+ VV TPGR +D ++ G   L+RV   VLDEAD M  MG
Sbjct: 119 RGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMG 160

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score =  117 bits (293), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 66/163 (40%), Positives = 92/163 (56%), Gaps = 6/163 (3%)
Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLV 227
           +F   G  +VL +A  +  +T PT IQ +A+P AL GRDIIG+A+TGSGKTGAF  P+L 
Sbjct: 44  TFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILN 103
Query: 228 HIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL 287
            +     LE       L+L PTREL+ QI  + +  G    +      GG     QS AL
Sbjct: 104 AL-----LETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL 158
Query: 288 ELGAEIVVGTPGRIIDMVK-MGATKLNRVTFLVLDEADRMFDM 329
                I++ TPGR+ID ++      L  + +LV+DEADR+ +M
Sbjct: 159 AKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNM 201

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score =  115 bits (288), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 61/154 (39%), Positives = 95/154 (61%), Gaps = 4/154 (2%)
Query: 178 LMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQK-ELE 236
           L+K++ +     PTPIQ+QA P  L G D+I VA+TG+GKT +++ P  +H+  Q    E
Sbjct: 31  LLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISRE 90
Query: 237 PGDGPMGLILAPTRELSQQIYNEAKRFG-KGYNLSVVCCYGGGSKWDQSKALELGAEIVV 295
             +GP  L+L PTREL+  +  E  ++  KG  L  +C YGG ++  Q + +  G +I++
Sbjct: 91  QRNGPGMLVLTPTRELALHVEAECSKYSYKG--LKSICIYGGRNRNGQIEDISKGVDIII 148
Query: 296 GTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM 329
            TPGR+ D+    +  L  +T+LV+DEAD+M DM
Sbjct: 149 ATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDM 182

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score =  108 bits (269), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 59/164 (35%), Positives = 92/164 (56%), Gaps = 8/164 (4%)
Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGR-DIIGVAKTGSGKTGAFIWPML 226
           +F      + ++ A+R   +  PT IQ + +P  L+   +I+  A+TGSGKT +F  P L
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIP-L 65
Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA 286
           + ++++      +G   +IL PTREL+ Q+ +E +      NL +   YGG + + Q KA
Sbjct: 66  IELVNE-----NNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKA 120
Query: 287 LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           L+  A IVVGTPGRI+D +  G   L  V + +LDEAD   + G
Sbjct: 121 LK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXG 163

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score =  103 bits (257), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 62/169 (36%), Positives = 95/169 (56%), Gaps = 9/169 (5%)
Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           ++ F  F   +  +K L++ +Y   T IQ Q +  AL G+D++G AKTGSGKT AF+ P+
Sbjct: 24  ITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPV 83
Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
           L   + + +    DG   LI++PTREL+ Q +   ++ GK ++ S     GG     +++
Sbjct: 84  L-EALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAE 142
Query: 286 ALELGAEIVVGTPGRII----DMVKMGATKLNRVTFLVLDEADRMFDMG 330
            +     I+V TPGR++    + V   AT L     LVLDEADR+ DMG
Sbjct: 143 RIN-NINILVCTPGRLLQHMDETVSFHATDLQ---MLVLDEADRILDMG 187

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score =  102 bits (255), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 54/162 (33%), Positives = 88/162 (54%), Gaps = 7/162 (4%)
Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           ++F  F     L+  + +  +  P+PIQ +A+P A++GRDI+  AK G+GKT AF+ P L
Sbjct: 21  NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL 80
Query: 227 VHIMDQKELEPGDGPM-GLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
                 ++++P    +  LI+ PTREL+ Q     +  GK   +S +   GG +  D   
Sbjct: 81  ------EKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDIL 134
Query: 286 ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF 327
            L     I+VGTPGR++D+       L+  +  ++DEAD+M 
Sbjct: 135 RLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKML 176

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score =  102 bits (254), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 55/162 (33%), Positives = 92/162 (56%), Gaps = 6/162 (3%)
Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           + F  +     L+  + +  +  P+PIQ +++P ALSGRDI+  AK G+GK+GA++ P+L
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62
Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSK 285
              +D K+    D    +++ PTREL+ Q+     +  K      V+   GG +  D   
Sbjct: 63  ER-LDLKK----DNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIM 117
Query: 286 ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF 327
            L+    +V+ TPGRI+D++K G  K++ V  +VLDEAD++ 
Sbjct: 118 RLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLL 159

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score =  102 bits (253), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 56/169 (33%), Positives = 90/169 (53%), Gaps = 11/169 (6%)
Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           + F  F F   +++A++   +  PT IQ + +P AL G   +G ++TG+GKT A++ P+ 
Sbjct: 4   TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPI- 62
Query: 227 VHIMDQKELEPGDGPM-GLILAPTRELSQQIYNEAKRFG----KGYNLSVVCCYGGGSKW 281
                 ++++P    +  +I APTREL+ QIY+E  +      K   +   C  GG  K 
Sbjct: 63  -----XEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQ 117
Query: 282 DQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
              + L +   IV+GTPGRI D ++  A  ++    LV+DEAD   D G
Sbjct: 118 KALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLXLDXG 166

>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 =  100 bits (249), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 55/163 (33%), Positives = 86/163 (52%), Gaps = 5/163 (3%)
Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLV 227
           +F   G  E L++ +    +  P+ IQ +A+   + GRD+I  +++G+GKT  F   +L 
Sbjct: 39  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVL- 97
Query: 228 HIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL 287
             +D +  E       LILAPTREL+ QI       G   N+    C GG +  +  + L
Sbjct: 98  QCLDIQVRET----QALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL 153
Query: 288 ELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           + G  +V GTPGR+ DM++  + +   +  LVLDEAD M + G
Sbjct: 154 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG 196

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  100 bits (249), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 55/163 (33%), Positives = 86/163 (52%), Gaps = 5/163 (3%)
Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLV 227
           +F   G  E L++ +    +  P+ IQ +A+   + GRD+I  +++G+GKT  F   +L 
Sbjct: 38  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVL- 96
Query: 228 HIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL 287
             +D +  E       LILAPTREL+ QI       G   N+    C GG +  +  + L
Sbjct: 97  QCLDIQVRET----QALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL 152
Query: 288 ELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           + G  +V GTPGR+ DM++  + +   +  LVLDEAD M + G
Sbjct: 153 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG 195

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  100 bits (249), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 58/169 (34%), Positives = 91/169 (53%), Gaps = 9/169 (5%)
Query: 163 PYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFI 222
           P  +S F  F     L++A+  C +  P+ +Q + +P A+ G D++  AK+G GKT  F+
Sbjct: 3   PGHMSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFV 62
Query: 223 WPMLVHIMDQKELEPGDGPMG-LILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSK 280
              L      ++LEP  G +  L++  TREL+ QI  E +RF K   N+ V   +GG S 
Sbjct: 63  LATL------QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSI 116
Query: 281 WDQSKALELGA-EIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD 328
               + L+     IVVGTPGRI+ + +  +  L  +   +LDEAD+M +
Sbjct: 117 KKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDEADKMLE 165

>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 =  100 bits (249), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 55/163 (33%), Positives = 86/163 (52%), Gaps = 5/163 (3%)
Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLV 227
           +F   G  E L++ +    +  P+ IQ +A+   + GRD+I  +++G+GKT  F   +L 
Sbjct: 39  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVL- 97
Query: 228 HIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL 287
             +D +  E       LILAPTREL+ QI       G   N+    C GG +  +  + L
Sbjct: 98  QCLDIQVRET----QALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL 153
Query: 288 ELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           + G  +V GTPGR+ DM++  + +   +  LVLDEAD M + G
Sbjct: 154 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG 196

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  100 bits (248), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 55/163 (33%), Positives = 86/163 (52%), Gaps = 5/163 (3%)
Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLV 227
           +F   G  E L++ +    +  P+ IQ +A+   + GRD+I  +++G+GKT  F   +L 
Sbjct: 17  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVL- 75
Query: 228 HIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL 287
             +D +  E       LILAPTREL+ QI       G   N+    C GG +  +  + L
Sbjct: 76  QCLDIQVRET----QALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL 131
Query: 288 ELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           + G  +V GTPGR+ DM++  + +   +  LVLDEAD M + G
Sbjct: 132 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG 174

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 99.4 bits (246), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 65/191 (34%), Positives = 106/191 (55%), Gaps = 15/191 (7%)
Query: 149 LRAKSGITVSGADPPYPVSSFGH----FGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG 204
           LR K  I V G D P P+++F      +  +  L++ +    +  PTPIQ QA+P  L G
Sbjct: 7   LRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHG 66
Query: 205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGD-GPMGLILAPTRELSQQIYNEAKRF 263
           R+++  A TGSGKT AF  P+L+ +      +P + G   LI++PTREL+ QI+ E  + 
Sbjct: 67  RELLASAPTGSGKTLAFSIPILMQLK-----QPANKGFRALIISPTRELASQIHRELIKI 121
Query: 264 --GKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG--ATKLNRVTFLV 319
             G G+ + ++      +K    K+ +   +I+V TP R+I ++K       L  V +LV
Sbjct: 122 SEGTGFRIHMIHKAAVAAKKFGPKSSK-KFDILVTTPNRLIYLLKQDPPGIDLASVEWLV 180
Query: 320 LDEADRMFDMG 330
           +DE+D++F+ G
Sbjct: 181 VDESDKLFEDG 191

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 99.4 bits (246), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 54/163 (33%), Positives = 86/163 (52%), Gaps = 5/163 (3%)
Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLV 227
           +F   G  E L++ +    +  P+ IQ +A+   + GRD+I  +++G+GKT  F   +L 
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVL- 60
Query: 228 HIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL 287
             +D +  E       LILAPTREL+ Q+       G   N+    C GG +  +  + L
Sbjct: 61  QCLDIQVRET----QALILAPTRELAVQVQKGLLALGDYMNVQCHACIGGTNVGEDIRKL 116
Query: 288 ELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           + G  +V GTPGR+ DM++  + +   +  LVLDEAD M + G
Sbjct: 117 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG 159

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 99.4 bits (246), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 57/170 (33%), Positives = 90/170 (52%), Gaps = 9/170 (5%)
Query: 162 PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAF 221
           P +  S F  F     L++A+  C +  P+ +Q + +P A+ G D++  AK+G GKT  F
Sbjct: 3   PGHMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVF 62
Query: 222 IWPMLVHIMDQKELEPGDGPMG-LILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGS 279
           +   L      ++LEP  G +  L++  TREL+ QI  E +RF K   N+ V   +GG S
Sbjct: 63  VLATL------QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLS 116
Query: 280 KWDQSKALELGA-EIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD 328
                + L+     IVVGTPGRI+ + +  +  L  +   +LDE D+M +
Sbjct: 117 IKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLE 166

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 99.0 bits (245), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 57/170 (33%), Positives = 90/170 (52%), Gaps = 9/170 (5%)
Query: 162 PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAF 221
           P +  S F  F     L++A+  C +  P+ +Q + +P A+ G D++  AK+G GKT  F
Sbjct: 3   PGHMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVF 62
Query: 222 IWPMLVHIMDQKELEPGDGPMG-LILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGS 279
           +   L      ++LEP  G +  L++  TREL+ QI  E +RF K   N+ V   +GG S
Sbjct: 63  VLATL------QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLS 116
Query: 280 KWDQSKALELGA-EIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD 328
                + L+     IVVGTPGRI+ + +  +  L  +   +LDE D+M +
Sbjct: 117 IKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLE 166

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 98.6 bits (244), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 54/163 (33%), Positives = 86/163 (52%), Gaps = 5/163 (3%)
Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLV 227
           +F   G  E L++ +    +  P+ IQ +A+   + GRD+I  +++G+GKT  F   +L 
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVL- 60
Query: 228 HIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL 287
             +D +  E       LILAPTREL+ Q+       G   N+    C GG +  +  + L
Sbjct: 61  QCLDIQVRET----QALILAPTRELAVQVQKGLLALGDYMNVQSHACIGGTNVGEDIRKL 116
Query: 288 ELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           + G  +V GTPGR+ DM++  + +   +  LVLDEAD M + G
Sbjct: 117 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG 159

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 97.4 bits (241), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 60/178 (33%), Positives = 93/178 (52%), Gaps = 9/178 (5%)
Query: 154 GITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKT 213
           G  V G+      S F  F     L++A+  C +  P+ +Q + +P A+ G D++  AK+
Sbjct: 1   GSDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKS 60
Query: 214 GSGKTGAFIWPMLVHIMDQKELEPGDGPMG-LILAPTRELSQQIYNEAKRFGKGY-NLSV 271
           G GKT  F+   L      ++LEP  G +  L++  TREL+ QI  E +RF K   N+ V
Sbjct: 61  GMGKTAVFVLATL------QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKV 114
Query: 272 VCCYGGGS-KWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD 328
              +GG S K D+    +    IVVGTPGRI+ + +  +  L  +   +LDE D+M +
Sbjct: 115 AVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLE 172

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 96.7 bits (239), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 56/157 (35%), Positives = 90/157 (57%), Gaps = 2/157 (1%)
Query: 175 DEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKE 234
           +E  +KA+++  +T+ T IQ +++   L GRD++  AKTGSGKT AF+ P  V ++ +  
Sbjct: 62  NENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPA-VELIVKLR 120
Query: 235 LEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIV 294
             P +G   LIL+PTREL+ Q +   K     +  +     GG ++  +++ L  G  I+
Sbjct: 121 FMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINII 180
Query: 295 VGTPGRIID-MVKMGATKLNRVTFLVLDEADRMFDMG 330
           V TPGR++D M          +  LV+DEADR+ D+G
Sbjct: 181 VATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVG 217

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 95.9 bits (237), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 54/157 (34%), Positives = 90/157 (57%), Gaps = 12/157 (7%)
Query: 174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQK 233
            +E + +A+R+  + + T +Q++ +P  L G++++  AKTGSGKT A+  P+L       
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPIL------- 53
Query: 234 ELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEI 293
           EL    G   L++ PTREL++Q+ +  +  G+  +  V   YGG     Q   +   A+I
Sbjct: 54  EL----GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADI 108
Query: 294 VVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           VV TPGR++D+   G   L+    +++DEAD MF+MG
Sbjct: 109 VVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMG 145

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 95.9 bits (237), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 59/165 (35%), Positives = 94/165 (56%), Gaps = 9/165 (5%)
Query: 174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAFIWPMLVHIMD 231
            D+ + KA+ + E+   TP+Q + +   LS    D+I  AKTG+GKT AF+ P+  H+++
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 232 QKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK-GYNLSVVCCYG--GGSKWD--QSKA 286
            K  +       +I+APTR+L+ QI  E K+     Y L    C    GG+ +    +K 
Sbjct: 88  TK-FDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKM 146
Query: 287 LELGAEIVVGTPGRIIDMVKMGATKLNR-VTFLVLDEADRMFDMG 330
            +L   IV+ TPGR+ID+++  + K  R V + VLDEADR+ ++G
Sbjct: 147 NKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIG 191

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 95.5 bits (236), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 57/166 (34%), Positives = 83/166 (50%), Gaps = 6/166 (3%)
Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           V SF      E L++ +    +  P+ IQ +A+   + G D+I  A++G+GKT  F    
Sbjct: 39  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFA--- 95
Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
            + I+ Q EL+       L+LAPTREL+QQI       G     S   C GG +   + +
Sbjct: 96  -ISILQQIELDLK-ATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQ 153
Query: 286 ALELGA-EIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L++ A  I+VGTPGR+ DM+         +   VLDEAD M   G
Sbjct: 154 KLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG 199

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 95.1 bits (235), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 57/166 (34%), Positives = 83/166 (50%), Gaps = 6/166 (3%)
Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           V SF      E L++ +    +  P+ IQ +A+   + G D+I  A++G+GKT  F    
Sbjct: 13  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFA--- 69
Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
            + I+ Q EL+       L+LAPTREL+QQI       G     S   C GG +   + +
Sbjct: 70  -ISILQQIELDLK-ATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQ 127
Query: 286 ALELGA-EIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L++ A  I+VGTPGR+ DM+         +   VLDEAD M   G
Sbjct: 128 KLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG 173

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 94.7 bits (234), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 59/165 (35%), Positives = 94/165 (56%), Gaps = 9/165 (5%)
Query: 174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAFIWPMLVHIMD 231
            D+ + KA+ + E+   TP+Q + +   LS    D+I  AKTG+GKT AF+ P+  H+++
Sbjct: 79  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 138
Query: 232 QKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK-GYNLSVVCCYG--GGSKWD--QSKA 286
            K  +       +I+APTR+L+ QI  E K+     Y L    C    GG+ +    +K 
Sbjct: 139 TK-FDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKM 197
Query: 287 LELGAEIVVGTPGRIIDMVKMGATKLNR-VTFLVLDEADRMFDMG 330
            +L   IV+ TPGR+ID+++  + K  R V + VLDEADR+ ++G
Sbjct: 198 NKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIG 242

>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 = 94.4 bits (233), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 59/165 (35%), Positives = 94/165 (56%), Gaps = 9/165 (5%)
Query: 174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAFIWPMLVHIMD 231
            D+ + KA+ + E+   TP+Q + +   LS    D+I  AKTG+GKT AF+ P+  H+++
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 232 QKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK-GYNLSVVCCYG--GGSKWD--QSKA 286
            K  +       +I+APTR+L+ QI  E K+     Y L    C    GG+ +    +K 
Sbjct: 88  TK-FDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKM 146
Query: 287 LELGAEIVVGTPGRIIDMVKMGATKLNR-VTFLVLDEADRMFDMG 330
            +L   IV+ TPGR+ID+++  + K  R V + VLDEADR+ ++G
Sbjct: 147 NKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIG 191

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 94.0 bits (232), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 54/165 (32%), Positives = 84/165 (50%), Gaps = 6/165 (3%)
Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           V  F     DE L++ +    +  P+ IQ +A+   + G D++  A++G+GKTG F    
Sbjct: 21  VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 80
Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
           L     Q+       P  L+LAPTREL+ QI           ++ V  C GG S  + ++
Sbjct: 81  L-----QRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAE 135
Query: 286 ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L   A+IVVGTPGR+ D ++    + +++   +LDEAD M   G
Sbjct: 136 GLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG 179

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 93.2 bits (230), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 52/170 (30%), Positives = 90/170 (52%), Gaps = 13/170 (7%)
Query: 162 PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTG 219
           P Y   SF   G    L+K +   ++  P+ IQ +A+P  L    R++I  +++G+GKT 
Sbjct: 17  PLYSAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTA 76
Query: 220 AFIWPMLVHIMDQKELEPGDG-PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGG 278
           AF   ML  +       P D  P  + LAP+REL++Q     +  GK   ++        
Sbjct: 77  AFSLTMLTRV------NPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDS 130
Query: 279 SKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD 328
             ++++K  ++ A+++VGTPG ++D+++    +L ++   VLDEAD M D
Sbjct: 131 --FEKNK--QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLD 176

>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 = 92.8 bits (229), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 54/165 (32%), Positives = 84/165 (50%), Gaps = 6/165 (3%)
Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           V  F     DE L++ +    +  P+ IQ +A+   + G D++  A++G+GKTG F    
Sbjct: 13  VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 72
Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
           L     Q+       P  L+LAPTREL+ QI           ++ V  C GG S  + ++
Sbjct: 73  L-----QRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAE 127
Query: 286 ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L   A+IVVGTPGR+ D ++    + +++   +LDEAD M   G
Sbjct: 128 GLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG 171

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 92.4 bits (228), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 54/165 (32%), Positives = 84/165 (50%), Gaps = 6/165 (3%)
Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           V  F     DE L++ +    +  P+ IQ +A+   + G D++  A++G+GKTG F    
Sbjct: 20  VYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 79
Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
           L     Q+       P  L+LAPTREL+ QI           ++ V  C GG S  + ++
Sbjct: 80  L-----QRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAE 134
Query: 286 ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L   A+IVVGTPGR+ D ++    + +++   +LDEAD M   G
Sbjct: 135 GLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG 178

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score = 91.7 bits (226), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 56/166 (33%), Positives = 82/166 (49%), Gaps = 6/166 (3%)
Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           V SF      E L++ +    +  P+ IQ +A+   + G D+I  A++G+G T  F    
Sbjct: 14  VDSFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFA--- 70
Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
            + I+ Q EL+       L+LAPTREL+QQI       G     S   C GG +   + +
Sbjct: 71  -ISILQQIELDL-XATQALVLAPTRELAQQIQXVVMALGDYMGASCHACIGGTNVRAEVQ 128
Query: 286 ALELGA-EIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L++ A  I+VGTPGR+ DM+         +   VLDEAD M   G
Sbjct: 129 XLQMEAPHIIVGTPGRVFDMLNRRYLSPXYIXMFVLDEADEMLSRG 174

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score = 91.7 bits (226), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 56/166 (33%), Positives = 84/166 (50%), Gaps = 6/166 (3%)
Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           V +F      E L++ +    +  P+ IQ +A+   + G D+I  A++G+GKT  F    
Sbjct: 29  VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFA--- 85
Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
            + I+ Q E+E  +    L+LAPTREL+QQI       G     +   C GG +  ++ +
Sbjct: 86  -ISILQQLEIEFKE-TQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQ 143
Query: 286 ALELGA-EIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L+  A  IVVGTPGR+ DM+         +   VLDEAD M   G
Sbjct: 144 KLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRG 189

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 89.7 bits (221), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 53/165 (32%), Positives = 82/165 (49%), Gaps = 6/165 (3%)
Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           V  F     DE L++ +    +  P+ IQ +A+   + G D++  A++G+GKTG F    
Sbjct: 20  VYKFDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAA 79
Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
           L     Q+       P  L LAPTREL+ QI           ++ V  C GG S  + ++
Sbjct: 80  L-----QRIDTSVKAPQALXLAPTRELALQIQKVVXALAFHXDIKVHACIGGTSFVEDAE 134
Query: 286 ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L   A+IVVGTPGR+ D ++    + +++   +LDEAD     G
Sbjct: 135 GLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKXFILDEADEXLSSG 178

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 87.8 bits (216), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 50/164 (30%), Positives = 88/164 (53%), Gaps = 13/164 (7%)
Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAFIWPM 225
           SF   G    L+K +   ++  P+ IQ +A+P  L    R++I  +++G+GKT AF   M
Sbjct: 6   SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 226 LVHIMDQKELEPGDG-PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS 284
           L  +       P D  P  + LAP+REL++Q     +  GK   ++          ++++
Sbjct: 66  LTRV------NPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDS--FEKN 117
Query: 285 KALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD 328
           K  ++ A+++VGTPG ++D+++    +L ++   VLDEAD M D
Sbjct: 118 K--QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLD 159

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 87.4 bits (215), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 50/164 (30%), Positives = 88/164 (53%), Gaps = 13/164 (7%)
Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAFIWPM 225
           SF   G    L+K +   ++  P+ IQ +A+P  L    R++I  +++G+GKT AF   M
Sbjct: 6   SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 226 LVHIMDQKELEPGDG-PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS 284
           L  +       P D  P  + LAP+REL++Q     +  GK   ++          ++++
Sbjct: 66  LTRV------NPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDS--FEKN 117
Query: 285 KALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD 328
           K  ++ A+++VGTPG ++D+++    +L ++   VLDEAD M D
Sbjct: 118 K--QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLD 159

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 77.4 bits (189), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 57/189 (30%), Positives = 90/189 (47%), Gaps = 10/189 (5%)
Query: 142 TPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAA 201
           T Q+    R ++G  V  A+P    + F        +++ LR   +  P+P+Q +A+P  
Sbjct: 4   TAQDLSSPRTRTG-DVLLAEP----ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLG 58
Query: 202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAK 261
             G D+I  AK+G+GKT  F    L    D   LE     + LILAPTRE++ QI++   
Sbjct: 59  RCGLDLIVQAKSGTGKTCVFSTIAL----DSLVLENLSTQI-LILAPTREIAVQIHSVIT 113
Query: 262 RFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLD 321
             G          + GG+   Q K       I VG+PGRI  ++++       +   +LD
Sbjct: 114 AIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILD 173
Query: 322 EADRMFDMG 330
           EAD++ + G
Sbjct: 174 EADKLLEEG 182

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 73.9 bits (180), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 51/170 (30%), Positives = 86/170 (50%), Gaps = 12/170 (7%)
Query: 162 PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTG 219
           P Y V SF        L++ +    +  P+ IQ  A+P  L+   +++I  +++G+GKT 
Sbjct: 87  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 146
Query: 220 AFIWPMLVHIMDQKELEPGDG-PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGG 278
           AF+  ML  +      EP +  P  L L+PT EL+ Q     ++ GK Y    +     G
Sbjct: 147 AFVLAMLSQV------EPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG 200
Query: 279 SKWDQSKALELGAEIVVGTPGRIIDMV-KMGATKLNRVTFLVLDEADRMF 327
           +K ++ +  ++  +IV+GTPG ++D   K+      ++   VLDEAD M 
Sbjct: 201 NKLERGQ--KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 248

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 73.9 bits (180), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 51/170 (30%), Positives = 87/170 (51%), Gaps = 12/170 (7%)
Query: 162 PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTG 219
           P Y V SF        L++ +    +  P+ IQ  A+P  L+   +++I  +++G+GKT 
Sbjct: 87  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 146
Query: 220 AFIWPMLVHIMDQKELEPGDG-PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGG 278
           AF+  ML       ++EP +  P  L L+PT EL+ Q     ++ GK Y    +     G
Sbjct: 147 AFVLAML------SQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG 200
Query: 279 SKWDQSKALELGAEIVVGTPGRIIDMV-KMGATKLNRVTFLVLDEADRMF 327
           +K ++ +  ++  +IV+GTPG ++D   K+      ++   VLDEAD M 
Sbjct: 201 NKLERGQ--KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 248

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 73.9 bits (180), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 51/170 (30%), Positives = 87/170 (51%), Gaps = 12/170 (7%)
Query: 162 PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTG 219
           P Y V SF        L++ +    +  P+ IQ  A+P  L+   +++I  +++G+GKT 
Sbjct: 36  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 95
Query: 220 AFIWPMLVHIMDQKELEPGDG-PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGG 278
           AF+  ML       ++EP +  P  L L+PT EL+ Q     ++ GK Y    +     G
Sbjct: 96  AFVLAML------SQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG 149
Query: 279 SKWDQSKALELGAEIVVGTPGRIIDMV-KMGATKLNRVTFLVLDEADRMF 327
           +K ++ +  ++  +IV+GTPG ++D   K+      ++   VLDEAD M 
Sbjct: 150 NKLERGQ--KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 197

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 73.6 bits (179), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 51/170 (30%), Positives = 87/170 (51%), Gaps = 12/170 (7%)
Query: 162 PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTG 219
           P Y V SF        L++ +    +  P+ IQ  A+P  L+   +++I  +++G+GKT 
Sbjct: 57  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 116
Query: 220 AFIWPMLVHIMDQKELEPGDG-PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGG 278
           AF+  ML       ++EP +  P  L L+PT EL+ Q     ++ GK Y    +     G
Sbjct: 117 AFVLAML------SQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG 170
Query: 279 SKWDQSKALELGAEIVVGTPGRIIDMV-KMGATKLNRVTFLVLDEADRMF 327
           +K ++ +  ++  +IV+GTPG ++D   K+      ++   VLDEAD M 
Sbjct: 171 NKLERGQ--KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 218

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 73.6 bits (179), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 51/170 (30%), Positives = 87/170 (51%), Gaps = 12/170 (7%)
Query: 162 PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTG 219
           P Y V SF        L++ +    +  P+ IQ  A+P  L+   +++I  +++G+GKT 
Sbjct: 20  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 79
Query: 220 AFIWPMLVHIMDQKELEPGDG-PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGG 278
           AF+  ML       ++EP +  P  L L+PT EL+ Q     ++ GK Y    +     G
Sbjct: 80  AFVLAML------SQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG 133
Query: 279 SKWDQSKALELGAEIVVGTPGRIIDMV-KMGATKLNRVTFLVLDEADRMF 327
           +K ++ +  ++  +IV+GTPG ++D   K+      ++   VLDEAD M 
Sbjct: 134 NKLERGQ--KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 181

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 73.6 bits (179), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 51/171 (29%), Positives = 86/171 (50%), Gaps = 12/171 (7%)
Query: 161 DPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKT 218
            P Y V SF        L++ +    +  P+ IQ  A+P  L+   +++I  +++G+GKT
Sbjct: 19  SPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKT 78
Query: 219 GAFIWPMLVHIMDQKELEPGDG-PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGG 277
            AF+  ML  +      EP +  P  L L+PT EL+ Q     ++ GK Y    +     
Sbjct: 79  AAFVLAMLSQV------EPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVR 132
Query: 278 GSKWDQSKALELGAEIVVGTPGRIIDMV-KMGATKLNRVTFLVLDEADRMF 327
           G+K ++ +  ++  +IV+GTPG ++D   K+      ++   VLDEAD M 
Sbjct: 133 GNKLERGQ--KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 181

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 41.2 bits (95), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 40/136 (29%), Positives = 63/136 (46%), Gaps = 14/136 (10%)
Query: 193 IQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL 252
           I  + + A     + + V  TG GKT       L+ +M  +      G   L+LAPT+ L
Sbjct: 12  IYQEVIYAKCKETNCLIVLPTGLGKT-------LIAMMIAEYRLTKYGGKVLMLAPTKPL 64
Query: 253 SQQIYNEAKRFGKGYNL---SVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA 309
              +   A+ F + +NL    +V   G  S  ++SKA    A+++V TP  I + +  G 
Sbjct: 65  ---VLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWA-RAKVIVATPQTIENDLLAGR 120
Query: 310 TKLNRVTFLVLDEADR 325
             L  V+ +V DEA R
Sbjct: 121 ISLEDVSLIVFDEAHR 136

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	330
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	1e-119
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-110
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-102
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-100
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	1e-100
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	3e-96
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	4e-64
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	5e-64
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	6e-63
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	1e-61
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	7e-61
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	6e-59
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	8e-59
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	9e-59
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-58
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-58
3bor_A	237	Human initiation factor 4A-II; translation initiat	3e-58
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	5e-58
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	2e-57
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	6e-57
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	3e-56
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	6e-56
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	5e-55
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-54
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	5e-54
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	2e-53
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	5e-52
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	5e-50
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	4e-49
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	6e-48
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	5e-47
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-16
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-13
3b6e_A	216	Interferon-induced helicase C domain-containing P;	1e-12
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	7e-12
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	1e-10
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	8e-10
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	9e-10
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	9e-10
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	2e-09
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	8e-09
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	2e-08
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	7e-08
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	9e-07
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	1e-05
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	6e-05

>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 =  341 bits (877), Expect = e-119
 Identities = 93/192 (48%), Positives = 120/192 (62%)

Query: 139 ARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAV 198
           +  T QE +  R    ITV G + P PV +F    F   +M  + +  +T PT IQAQ  
Sbjct: 1   SMRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 60

Query: 199 PAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN 258
           P ALSG D++GVA+TGSGKT +++ P +VHI  Q  LE GDGP+ L+LAPTREL+QQ+  
Sbjct: 61  PVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQ 120

Query: 259 EAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFL 318
            A  + +   L   C YGG  K  Q + LE G EI + TPGR+ID ++ G T L R T+L
Sbjct: 121 VAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYL 180

Query: 319 VLDEADRMFDMG 330
           VLDEADRM DMG
Sbjct: 181 VLDEADRMLDMG 192

>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 =  326 bits (838), Expect = e-110
 Identities = 73/213 (34%), Positives = 111/213 (52%), Gaps = 8/213 (3%)

Query: 126 EVEKNFYQPHEDIARLTPQEAQELRA--------KSGITVSGADPPYPVSSFGHFGFDEV 177
           E    FY P E         +  + +           + V+G+D P P+  F      ++
Sbjct: 7   EFPGEFYIPPEPSNDAIEIFSSGIASGIHFSKYNNIPVKVTGSDVPQPIQHFTSADLRDI 66

Query: 178 LMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEP 237
           ++  + K  Y  PTPIQ  ++P   SGRD++  A+TGSGKT AF+ P+L  +++      
Sbjct: 67  IIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELE 126

Query: 238 GDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGT 297
              P  +I++PTREL+ QI+NEA++F     L +   YGG S   Q++ +  G  +V+ T
Sbjct: 127 LGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIAT 186

Query: 298 PGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           PGR++D V           F+VLDEADRM DMG
Sbjct: 187 PGRLLDFVDRTFITFEDTRFVVLDEADRMLDMG 219

>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 =  299 bits (769), Expect = e-102
 Identities = 63/178 (35%), Positives = 98/178 (55%), Gaps = 3/178 (1%)

Query: 155 ITVSGADPPYPVSSFGH-FGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKT 213
            +      P P   F   F     L+K++ +     PTPIQ+QA P  L G D+I VA+T
Sbjct: 7   KSGEKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQT 66

Query: 214 GSGKTGAFIWPMLVHIMDQ-KELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVV 272
           G+GKT +++ P  +H+  Q    E  +GP  L+L PTREL+  +  E  ++     L  +
Sbjct: 67  GTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSY-KGLKSI 125

Query: 273 CCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           C YGG ++  Q + +  G +I++ TPGR+ D+    +  L  +T+LV+DEAD+M DM 
Sbjct: 126 CIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDME 183

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  300 bits (771), Expect = e-100
 Identities = 72/189 (38%), Positives = 101/189 (53%), Gaps = 13/189 (6%)

Query: 155 ITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTG 214
           +  +G + P  + SF      E++M  +    YT PTP+Q  A+P     RD++  A+TG
Sbjct: 3   VEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTG 62

Query: 215 SGKTGAFIWPMLVHIMDQKELEP-------------GDGPMGLILAPTRELSQQIYNEAK 261
           SGKT AF+ P+L  I      E                 P+ L+LAPTREL+ QIY EA+
Sbjct: 63  SGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEAR 122

Query: 262 RFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLD 321
           +F     +     YGG     Q + LE G  ++V TPGR++DM++ G   L+   +LVLD
Sbjct: 123 KFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLD 182

Query: 322 EADRMFDMG 330
           EADRM DMG
Sbjct: 183 EADRMLDMG 191

>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 =  293 bits (752), Expect = e-100
 Identities = 68/182 (37%), Positives = 102/182 (56%), Gaps = 6/182 (3%)

Query: 155 ITVSGAD--PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAK 212
           ++V+G D      + +F     D  +   +    Y  PTPIQ  A+PA L  RDI+  A+
Sbjct: 9   VSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQ 68

Query: 213 TGSGKTGAFIWPMLVHIM----DQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN 268
           TGSGKT AF+ P++ H++    +Q+       P  LILAPTREL+ QI +E+++F     
Sbjct: 69  TGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTP 128

Query: 269 LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD 328
           L     YGG     Q + +++G  ++V TPGR++D ++     L    ++VLDEADRM D
Sbjct: 129 LRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLD 188

Query: 329 MG 330
           MG
Sbjct: 189 MG 190

>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 =  284 bits (729), Expect = 3e-96
 Identities = 60/197 (30%), Positives = 99/197 (50%), Gaps = 14/197 (7%)

Query: 144 QEAQELRAKSGITVSGADPPYPVSSFGH----FGFDEVLMKALRKCEYTSPTPIQAQAVP 199
            +   LR K  I V G D P P+++F      +  +  L++ +    +  PTPIQ QA+P
Sbjct: 2   MKINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIP 61

Query: 200 AALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE 259
             L GR+++  A TGSGKT AF  P+L+ +          G   LI++PTREL+ QI+ E
Sbjct: 62  VMLHGRELLASAPTGSGKTLAFSIPILMQLKQP----ANKGFRALIISPTRELASQIHRE 117

Query: 260 AKRFGKGYNLSVVCCYGGGSKWDQ-SKALELGAEIVVGTPGRIIDMVKMGATKLN--RVT 316
             +  +G    +   +       +         +I+V TP R+I ++K     ++   V 
Sbjct: 118 LIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVE 177

Query: 317 FLVLDEADRMFD---MG 330
           +LV+DE+D++F+    G
Sbjct: 178 WLVVDESDKLFEDGKTG 194

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  201 bits (513), Expect = 4e-64
 Identities = 58/168 (34%), Positives = 90/168 (53%), Gaps = 9/168 (5%)

Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           + F  F F   +++A++   +  PT IQ + +P AL G  ++G ++TG+GKT A++ P++
Sbjct: 4   TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIM 63

Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK----GYNLSVVCCYGGGSKWD 282
             I   +          +I APTREL+ QIY+E  +  K       +   C  GG  K  
Sbjct: 64  EKI-KPER----AEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQK 118

Query: 283 QSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
             + L +   IV+GTPGRI D ++  A  ++    LV+DEAD M DMG
Sbjct: 119 ALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMG 166

>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 =  202 bits (515), Expect = 5e-64
 Identities = 67/199 (33%), Positives = 95/199 (47%), Gaps = 6/199 (3%)

Query: 133 QPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTP 192
              +        ++ E                   +F   G  +VL +A  +  +T PT 
Sbjct: 9   SGVDLGTENLYFQSMEEHDSPTEASQPIVEEEETKTFKDLGVTDVLCEACDQLGWTKPTK 68

Query: 193 IQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL 252
           IQ +A+P AL GRDIIG+A+TGSGKTGAF  P+L        LE       L+L PTREL
Sbjct: 69  IQIEAIPLALQGRDIIGLAETGSGKTGAFALPIL-----NALLETPQRLFALVLTPTREL 123

Query: 253 SQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT-K 311
           + QI  + +  G    +      GG     QS AL     I++ TPGR+ID ++      
Sbjct: 124 AFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFN 183

Query: 312 LNRVTFLVLDEADRMFDMG 330
           L  + +LV+DEADR+ +M 
Sbjct: 184 LRALKYLVMDEADRILNMD 202

>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 =  197 bits (504), Expect = 6e-63
 Identities = 71/163 (43%), Positives = 94/163 (57%), Gaps = 4/163 (2%)

Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLV 227
            F  F     +++AL     T+PTPIQA A+P AL G+D+IG A+TG+GKT AF  P+  
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61

Query: 228 HIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL 287
            +   +  E G  P  L+L PTREL+ Q+ +E        +L VV  YGG     Q +AL
Sbjct: 62  RLAPSQ--ERGRKPRALVLTPTRELALQVASELTAVAP--HLKVVAVYGGTGYGKQKEAL 117

Query: 288 ELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
             GA+ VV TPGR +D ++ G   L+RV   VLDEAD M  MG
Sbjct: 118 LRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMG 160

>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 (499), Expect = 1e-61
 Identities = 58/166 (34%), Positives = 93/166 (56%), Gaps = 3/166 (1%)

Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           ++ F  F   +  +K L++ +Y   T IQ Q +  AL G+D++G AKTGSGKT AF+ P+
Sbjct: 24  ITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPV 83

Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
           L   + + +    DG   LI++PTREL+ Q +   ++ GK ++ S     GG     +++
Sbjct: 84  L-EALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAE 142

Query: 286 ALELGAEIVVGTPGRIIDMVKMGAT-KLNRVTFLVLDEADRMFDMG 330
            +     I+V TPGR++  +    +     +  LVLDEADR+ DMG
Sbjct: 143 RIN-NINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMG 187

>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 =  192 bits (490), Expect = 7e-61
 Identities = 55/165 (33%), Positives = 92/165 (55%), Gaps = 6/165 (3%)

Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           + F  +     L+  + +  +  P+PIQ +++P ALSGRDI+  AK G+GK+GA++ P+L
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62

Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG-YNLSVVCCYGGGSKWDQSK 285
             + D K+    D    +++ PTREL+ Q+     +  K      V+   GG +  D   
Sbjct: 63  ERL-DLKK----DNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIM 117

Query: 286 ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L+    +V+ TPGRI+D++K G  K++ V  +VLDEAD++    
Sbjct: 118 RLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD 162

>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 =  188 bits (479), Expect = 6e-59
 Identities = 55/165 (33%), Positives = 84/165 (50%), Gaps = 6/165 (3%)

Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           V  F     DE L++ +    +  P+ IQ +A+   + G D++  A++G+GKTG F    
Sbjct: 13  VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 72

Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
           L  I D         P  L+LAPTREL+ QI           ++ V  C GG S  + ++
Sbjct: 73  LQRI-DTSVKA----PQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAE 127

Query: 286 ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L   A+IVVGTPGR+ D ++    + +++   +LDEAD M   G
Sbjct: 128 GLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG 171

>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 =  193 bits (493), Expect = 8e-59
 Identities = 55/165 (33%), Positives = 86/165 (52%), Gaps = 5/165 (3%)

Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
             +F   G  E L++ +    +  P+ IQ +A+   + GRD+I  +++G+GKT  F   +
Sbjct: 36  TPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISV 95

Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
           L  + D +  E       LILAPTREL+ QI       G   N+    C GG +  +  +
Sbjct: 96  LQCL-DIQVRET----QALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIR 150

Query: 286 ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L+ G  +V GTPGR+ DM++  + +   +  LVLDEAD M + G
Sbjct: 151 KLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG 195

>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 =  189 bits (481), Expect = 9e-59
 Identities = 64/216 (29%), Positives = 111/216 (51%), Gaps = 3/216 (1%)

Query: 116 PIDHSTIVYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFD 175
              HS+ V    E  ++Q   ++ +    E +       + ++GA      +S  +   +
Sbjct: 4   HHHHSSGVDLGTENLYFQSMNNVEKPDNDEDESEVPSLPLGLTGAFEDTSFASLCN-LVN 62

Query: 176 EVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL 235
           E  +KA+++  +T+ T IQ +++   L GRD++  AKTGSGKT AF+ P +  ++ +   
Sbjct: 63  ENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAV-ELIVKLRF 121

Query: 236 EPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVV 295
            P +G   LIL+PTREL+ Q +   K     +  +     GG ++  +++ L  G  I+V
Sbjct: 122 MPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIV 181

Query: 296 GTPGRIID-MVKMGATKLNRVTFLVLDEADRMFDMG 330
            TPGR++D M          +  LV+DEADR+ D+G
Sbjct: 182 ATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVG 217

>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 =  193 bits (492), Expect = 1e-58
 Identities = 54/164 (32%), Positives = 85/164 (51%), Gaps = 5/164 (3%)

Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           ++F  F     L+  + +  +  P+PIQ +A+P A++GRDI+  AK G+GKT AF+ P L
Sbjct: 21  NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL 80

Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA 286
             +   K     +    LI+ PTREL+ Q     +  GK   +S +   GG +  D    
Sbjct: 81  EKV-KPKL----NKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILR 135

Query: 287 LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           L     I+VGTPGR++D+       L+  +  ++DEAD+M    
Sbjct: 136 LNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRD 179

>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 =  191 bits (488), Expect = 1e-58
 Identities = 60/164 (36%), Positives = 91/164 (55%), Gaps = 8/164 (4%)

Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGR-DIIGVAKTGSGKTGAFIWPML 226
           +F      + ++ A+R   +  PT IQ + +P  L+   +I+  A+TGSGKT +F  P++
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66

Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA 286
             +         +G   +IL PTREL+ Q+ +E +      NL +   YGG + + Q KA
Sbjct: 67  ELV------NENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKA 120

Query: 287 LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           L+  A IVVGTPGRI+D +  G   L  V + +LDEAD M +MG
Sbjct: 121 LK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMG 163

>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 =  187 bits (476), Expect = 3e-58
 Identities = 53/166 (31%), Positives = 81/166 (48%), Gaps = 6/166 (3%)

Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           V +F      E L++ +    +  P+ IQ +A+   + G D+I  A++G+GKT  F   +
Sbjct: 29  VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISI 88

Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
           L  + + +  E       L+LAPTREL+QQI       G     +   C GG +  ++ +
Sbjct: 89  LQQL-EIEFKE----TQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQ 143

Query: 286 ALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L+     IVVGTPGR+ DM+         +   VLDEAD M   G
Sbjct: 144 KLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRG 189

>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 =  191 bits (487), Expect = 5e-58
 Identities = 55/171 (32%), Positives = 85/171 (49%), Gaps = 6/171 (3%)

Query: 160 ADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTG 219
            +    V  F     DE L++ +    +  P+ IQ +A+   + G D++  A++G+GKTG
Sbjct: 14  TNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTG 73

Query: 220 AFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGS 279
            F    L  I D         P  L+LAPTREL+ QI           ++ V  C GG S
Sbjct: 74  TFSIAALQRI-DTSV----KAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTS 128

Query: 280 KWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
             + ++ L   A+IVVGTPGR+ D ++    + +++   +LDEAD M   G
Sbjct: 129 FVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG 178

>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 =  184 bits (469), Expect = 2e-57
 Identities = 48/165 (29%), Positives = 77/165 (46%), Gaps = 7/165 (4%)

Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           + F        +++ LR   +  P+P+Q +A+P    G D+I  AK+G+GKT  F    L
Sbjct: 24  ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIAL 83

Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSK 285
             +   + L        LILAPTRE++ QI++     G     L      GG        
Sbjct: 84  DSL-VLENLS----TQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKT 138

Query: 286 ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L+    I VG+PGRI  ++++       +   +LDEAD++ + G
Sbjct: 139 RLK-KCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEG 182

>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 =  188 bits (481), Expect = 6e-57
 Identities = 54/166 (32%), Positives = 79/166 (47%), Gaps = 6/166 (3%)

Query: 166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPM 225
           V SF      E L++ +    +  P+ IQ +A+   + G D+I  A++G+GKT  F   +
Sbjct: 39  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISI 98

Query: 226 LVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK 285
           L  I +            L+LAPTREL+QQI       G     S   C GG +   + +
Sbjct: 99  LQQI-ELDLKA----TQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQ 153

Query: 286 ALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            L++    I+VGTPGR+ DM+         +   VLDEAD M   G
Sbjct: 154 KLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG 199

>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 =  184 bits (470), Expect = 3e-56
 Identities = 52/156 (33%), Positives = 89/156 (57%), Gaps = 12/156 (7%)

Query: 175 DEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKE 234
           +E + +A+R+  + + T +Q++ +P  L G++++  AKTGSGKT A+  P+L     +  
Sbjct: 2   NEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPIL-----EL- 55

Query: 235 LEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIV 294
                G   L++ PTREL++Q+ +  +  G+  +  V   YGG     Q   +   A+IV
Sbjct: 56  -----GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIV 109

Query: 295 VGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           V TPGR++D+   G   L+    +++DEAD MF+MG
Sbjct: 110 VATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMG 145

>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 =  180 bits (459), Expect = 6e-56
 Identities = 57/168 (33%), Positives = 88/168 (52%), Gaps = 10/168 (5%)

Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           S F  F     L++A+  C +  P+ +Q + +P A+ G D++  AK+G GKT  F+   L
Sbjct: 14  SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 73

Query: 227 VHIMDQKELEPGDG-PMGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQS 284
                Q+ LEP  G    L++  TREL+ QI  E +RF K   N+ V   +GG S     
Sbjct: 74  -----QQ-LEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE 127

Query: 285 KALELGAE-IVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD-MG 330
           + L+     IVVGTPGRI+ + +  +  L  +   +LDE D+M + + 
Sbjct: 128 EVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 175

>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 =  187 bits (477), Expect = 5e-55
 Identities = 54/181 (29%), Positives = 87/181 (48%), Gaps = 9/181 (4%)

Query: 158 SGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGS 215
             +      S       D+ + KA+ + E+   TP+Q + +   LS    D+I  AKTG+
Sbjct: 12  DNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGT 71

Query: 216 GKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG----YNLSV 271
           GKT AF+ P+    +   + +       +I+APTR+L+ QI  E K+           + 
Sbjct: 72  GKTFAFLIPIF-QHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYAC 130

Query: 272 VCCYGGGSKWDQSKALE-LGAEIVVGTPGRIIDMVKMGATKL-NRVTFLVLDEADRMFDM 329
           V   GG         +  L   IV+ TPGR+ID+++  + K    V + VLDEADR+ ++
Sbjct: 131 VSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEI 190

Query: 330 G 330
           G
Sbjct: 191 G 191

>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 =  186 bits (473), Expect = 1e-54
 Identities = 57/206 (27%), Positives = 94/206 (45%), Gaps = 9/206 (4%)

Query: 133 QPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTP 192
           +  ED   +   +    +         +      S       D+ + KA+ + E+   TP
Sbjct: 38  RSREDDDEVHFDKTTFSKLIHVPKEDNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTP 97

Query: 193 IQAQAVPAALSG--RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR 250
           +Q + +   LS    D+I  AKTG+GKT AF+ P+    +   + +       +I+APTR
Sbjct: 98  VQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIF-QHLINTKFDSQYMVKAVIVAPTR 156

Query: 251 ELSQQIYNEAKRFGKGY----NLSVVCCYGGGSKWDQSKALE-LGAEIVVGTPGRIIDMV 305
           +L+ QI  E K+           + V   GG         +  L   IV+ TPGR+ID++
Sbjct: 157 DLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVL 216

Query: 306 KMGATKLNR-VTFLVLDEADRMFDMG 330
           +  + K  R V + VLDEADR+ ++G
Sbjct: 217 EKYSNKFFRFVDYKVLDEADRLLEIG 242

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  181 bits (460), Expect = 5e-54
 Identities = 27/159 (16%), Positives = 48/159 (30%), Gaps = 15/159 (9%)

Query: 176 EVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL 235
           E      +K      T  Q       + G+    VA TG GKT   +   L         
Sbjct: 8   EDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR----- 62

Query: 236 EPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALEL----GA 291
               G    ++ PT  L +Q     ++      + +   Y    K ++ K  +       
Sbjct: 63  ---KGKKSALVFPTVTLVKQTLERLQKLAD-EKVKIFGFYSSMKKEEKEKFEKSFEEDDY 118

Query: 292 EIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            I+V +   +            R  F+ +D+ D +    
Sbjct: 119 HILVFSTQFVSK--NREKLSQKRFDFVFVDDVDAVLKAS 155

>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 =  178 bits (455), Expect = 2e-53
 Identities = 57/168 (33%), Positives = 88/168 (52%), Gaps = 10/168 (5%)

Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           S F  F     L++A+  C +  P+ +Q + +P A+ G D++  AK+G GKT  F+   L
Sbjct: 8   SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 67

Query: 227 VHIMDQKELEPGDG-PMGLILAPTRELSQQIYNEAKRFGKG-YNLSVVCCYGGGSKWDQS 284
                Q+ LEP  G    L++  TREL+ QI  E +RF K   N+ V   +GG S     
Sbjct: 68  -----QQ-LEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE 121

Query: 285 KALELGAE-IVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD-MG 330
           + L+     IVVGTPGRI+ + +  +  L  +   +LDE D+M + + 
Sbjct: 122 EVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 169

>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 =  175 bits (446), Expect = 5e-52
 Identities = 48/168 (28%), Positives = 85/168 (50%), Gaps = 11/168 (6%)

Query: 164 YPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAF 221
               SF   G    L+K +   ++  P+ IQ +A+P  L    R++I  +++G+GKT AF
Sbjct: 2   AMAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAF 61

Query: 222 IWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW 281
              ML  + + ++  P      + LAP+REL++Q     +  GK   ++           
Sbjct: 62  SLTMLTRV-NPEDASP----QAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDS--- 113

Query: 282 DQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM 329
              K  ++ A+++VGTPG ++D+++    +L ++   VLDEAD M D 
Sbjct: 114 -FEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQ 160

>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 =  168 bits (427), Expect = 4e-49
 Identities = 50/174 (28%), Positives = 82/174 (47%), Gaps = 13/174 (7%)

Query: 162 PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTG 219
           P Y V SF        L++ +    +  P+ IQ  A+P  L+   +++I  +++G+GKT 
Sbjct: 20  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 79

Query: 220 AFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGG 278
           AF+  ML  + +         P  L L+PT EL+ Q     ++ GK Y  L +     G 
Sbjct: 80  AFVLAMLSQV-EPANKY----PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGN 134

Query: 279 SKWDQSKALELGAEIVVGTPGRIIDMV-KMGATKLNRVTFLVLDEADRMFD-MG 330
                 +  ++  +IV+GTPG ++D   K+      ++   VLDEAD M    G
Sbjct: 135 K---LERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQG 185

>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 =  162 bits (411), Expect = 6e-48
 Identities = 50/174 (28%), Positives = 82/174 (47%), Gaps = 13/174 (7%)

Query: 162 PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTG 219
           P Y V SF        L++ +    +  P+ IQ  A+P  L+   +++I  +++G+GKT 
Sbjct: 87  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 146

Query: 220 AFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGG 278
           AF+  ML  + +         P  L L+PT EL+ Q     ++ GK Y  L +     G 
Sbjct: 147 AFVLAMLSQV-EPANKY----PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGN 201

Query: 279 SKWDQSKALELGAEIVVGTPGRIIDMV-KMGATKLNRVTFLVLDEADRMFD-MG 330
                 +  ++  +IV+GTPG ++D   K+      ++   VLDEAD M    G
Sbjct: 202 K---LERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQG 252

>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 =  164 bits (417), Expect = 5e-47
 Identities = 56/253 (22%), Positives = 98/253 (38%), Gaps = 16/253 (6%)

Query: 86  QDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHSTIVYEEVEKNFYQPHEDIARLTPQE 145
              D             +  +K K       +  +    +  E+                
Sbjct: 8   LAVDEQEAAAESLSNLHLKEEKIKPDTNGAVVKTNANAEKTDEEEKEDRAAQSLLNKLIR 67

Query: 146 AQELRAKSGITVSGADPPYP---VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAAL 202
           +  +   + + V   DP  P   V SF        L++ +    +  P+ IQ  A+P  L
Sbjct: 68  SNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLML 127

Query: 203 SG--RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEA 260
           +   +++I  +++G+GKT AF+  ML  + +         P  L L+PT EL+ Q     
Sbjct: 128 AEPPQNLIAQSQSGTGKTAAFVLAMLSQV-EPANKY----PQCLCLSPTYELALQTGKVI 182

Query: 261 KRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMV-KMGATKLNRVTFL 318
           ++ GK Y  L +     G       +  ++  +IV+GTPG ++D   K+      ++   
Sbjct: 183 EQMGKFYPELKLAYAVRGNK---LERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVF 239

Query: 319 VLDEADRMFD-MG 330
           VLDEAD M    G
Sbjct: 240 VLDEADVMIATQG 252

>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 = 78.7 bits (193), Expect = 2e-16
 Identities = 34/141 (24%), Positives = 51/141 (36%), Gaps = 9/141 (6%)

Query: 190 PTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT 249
           P   Q           + + V  TG GKT   I  M+        L    G + L+LAPT
Sbjct: 10  PRIYQEVIYAKCK-ETNCLIVLPTGLGKT--LIAMMIAEYR----LTKYGGKV-LMLAPT 61

Query: 250 RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA 309
           + L  Q     +R         +    G    ++       A+++V TP  I + +  G 
Sbjct: 62  KPLVLQHAESFRRLF-NLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGR 120

Query: 310 TKLNRVTFLVLDEADRMFDMG 330
             L  V+ +V DEA R     
Sbjct: 121 ISLEDVSLIVFDEAHRAVGNY 141

>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 = 69.9 bits (170), Expect = 2e-13
 Identities = 61/352 (17%), Positives = 107/352 (30%), Gaps = 99/352 (28%)

Query: 23  DTDSDE----------DPLDAFMKGID-KEVKQEAKGVKTKKIEEVKGIRDDIDHEDDEE 71
           D ++ E             DAF+   D K+V+   K + +K  EE+    D I    D  
Sbjct: 8   DFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSK--EEI----DHIIMSKDAV 61

Query: 72  SYYRYM----EENPNAGLQD-NDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHSTIVYEE 126
           S    +           +Q   +  + + Y    +PI   K++   P       T +Y E
Sbjct: 62  SGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPI---KTEQRQPSMM----TRMYIE 114

Query: 127 VEKNFYQ-----PHEDIARLTP----QEA-QELRAKSGITVSGADPPYPVSSFGHFGF-D 175
                Y         +++RL P    ++A  ELR    + +            G  G   
Sbjct: 115 QRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI-----------DGVLGSGK 163

Query: 176 EVLMKALRKCEYTSPTPIQAQAVPAALSGRDI--IGVAKTGSGKTGAFIWPM--LVHIMD 231
             +  AL  C         +  V   +  + I  + +    S      +  +  L++ +D
Sbjct: 164 TWV--ALDVC--------LSYKVQCKMDFK-IFWLNLKNCNS--PETVLEMLQKLLYQID 210

Query: 232 QKELEPGDGPMGLILAPTRELSQQIYNEAKRF--GKGYN-----LSVVCCYGGGSKWDQS 284
                  D       +  +     I  E +R    K Y      L  V         +  
Sbjct: 211 PNWTSRSDHS-----SNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV--------QNAK 257

Query: 285 --KALELGAEIVVGTPGR---IIDMVKMGATKLNRVTF----LVLDEADRMF 327
              A  L  +I++ T  R   + D +    T    +      L  DE   + 
Sbjct: 258 AWNAFNLSCKILLTT--RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL 307

>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 = 65.2 bits (159), Expect = 1e-12
 Identities = 27/140 (19%), Positives = 55/140 (39%), Gaps = 16/140 (11%)

Query: 194 QAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL- 252
           Q +    AL G++II    TGSGKT   +   +      K+ +  +    ++L     L 
Sbjct: 38  QMEVAQPALEGKNIIICLPTGSGKT--RVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLV 95

Query: 253 SQQIYNEAKRFG-KGYNLSVVCCYGGGSKWDQSKALEL--GAEIVVGTPGRIIDMV---- 305
            Q    E + F  K Y +  +     G    +    E+    +I++ T   + + +    
Sbjct: 96  EQLFRKEFQPFLKKWYRVIGLS----GDTQLKISFPEVVKSCDIIISTAQILENSLLNLE 151

Query: 306 --KMGATKLNRVTFLVLDEA 323
             +    +L+  + +++DE 
Sbjct: 152 NGEDAGVQLSDFSLIIIDEC 171

>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 = 65.3 bits (159), Expect = 7e-12
 Identities = 33/152 (21%), Positives = 65/152 (42%), Gaps = 12/152 (7%)

Query: 172 FGFDEVLMKALRKCEYTSPTPIQAQAVPAAL-SGRDIIGVAKTGSGKTGAFIWPMLVHIM 230
              DE +   L++    S  P QA+A+ + +  G++ +    T SGKT      M+  I+
Sbjct: 6   LRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRIL 65

Query: 231 DQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELG 290
                    G   + + P + L+++ + E + + K   L V    G    +D        
Sbjct: 66  T-------QGGKAVYIVPLKALAEEKFQEFQDWEK-IGLRVAMATGD---YDSKDEWLGK 114

Query: 291 AEIVVGTPGRIIDMVKMGATKLNRVTFLVLDE 322
            +I++ T  +   +++ G++ +  V  LV DE
Sbjct: 115 YDIIIATAEKFDSLLRHGSSWIKDVKILVADE 146

>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 = 61.7 bits (150), Expect = 1e-10
 Identities = 31/150 (20%), Positives = 60/150 (40%), Gaps = 12/150 (8%)

Query: 173 GFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQ 232
                 +  L++       P QA+AV    SG++++    T +GKT      M+   +  
Sbjct: 9   SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG 68

Query: 233 KELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAE 292
                      L + P R L+ + Y   K++ K   L +    G    ++         +
Sbjct: 69  G--------KSLYVVPLRALAGEKYESFKKWEK-IGLRIGISTGD---YESRDEHLGDCD 116

Query: 293 IVVGTPGRIIDMVKMGATKLNRVTFLVLDE 322
           I+V T  +   +++  A+ +  V+ LV+DE
Sbjct: 117 IIVTTSEKADSLIRNRASWIKAVSCLVVDE 146

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 58.8 bits (141), Expect = 8e-10
 Identities = 27/134 (20%), Positives = 53/134 (39%), Gaps = 4/134 (2%)

Query: 194 QAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELS 253
           Q +    A  G++ I  A TG GKT  F+  ++     +K      G   +  A    + 
Sbjct: 9   QLELALPAKKGKNTIICAPTGCGKT--FVSLLICEHHLKKFPCGQKG-KVVFFANQIPVY 65

Query: 254 QQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA-TKL 312
           +Q      R+ +    ++    G  S     + +    +I++ TP  +++ +  GA   L
Sbjct: 66  EQQATVFSRYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSL 125

Query: 313 NRVTFLVLDEADRM 326
           +  T ++ DE    
Sbjct: 126 SVFTLMIFDECHNT 139

>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 = 58.8 bits (141), Expect = 9e-10
 Identities = 30/140 (21%), Positives = 57/140 (40%), Gaps = 8/140 (5%)

Query: 190 PTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT 249
               Q +    A++G++ +  A TGSGKT  F+  ++     Q         + + LA  
Sbjct: 8   ARSYQIELAQPAINGKNALICAPTGSGKT--FVSILICEHHFQNMPAGRKAKV-VFLATK 64

Query: 250 REL-SQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS-KALELGAEIVVGTPGRIIDMVKM 307
             +  QQ       F +      V    G +  + S + +   ++I+V TP  +++  + 
Sbjct: 65  VPVYEQQKNVFKHHFER--QGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFED 122

Query: 308 GA-TKLNRVTFLVLDEADRM 326
           G  T L+  T ++ DE    
Sbjct: 123 GTLTSLSIFTLMIFDECHNT 142

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 58.8 bits (141), Expect = 9e-10
 Identities = 26/138 (18%), Positives = 56/138 (40%), Gaps = 4/138 (2%)

Query: 190 PTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT 249
           P   Q +    A+ G++ I  A TG GKT   +     H+    + + G     +  A  
Sbjct: 14  PRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKG---KVVFFANQ 70

Query: 250 RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA 309
             + +Q  +   ++ + +   V    G  ++    + +    +I++ TP  +++ +K G 
Sbjct: 71  IPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGT 130

Query: 310 -TKLNRVTFLVLDEADRM 326
              L+  T ++ DE    
Sbjct: 131 IPSLSIFTLMIFDECHNT 148

>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 = 58.1 bits (139), Expect = 2e-09
 Identities = 47/264 (17%), Positives = 89/264 (33%), Gaps = 12/264 (4%)

Query: 67  EDDEESYYRYMEENPNAGLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHSTIVYEE 126
           + + E   +  E    A       +     D++  P + + +              + E+
Sbjct: 134 DRECEEIQQISENRSKAAGITKLIECLCRSDKEHWPKSLQLALDTTGYYRASELWDIRED 193

Query: 127 VEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCE 186
             K+      D        A E   ++ +T S    P    S       E + K     E
Sbjct: 194 NAKDVDSEMTD--------ASEDCLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYE 245

Query: 187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL 246
                  Q +    A++G++ +  A TGSGKT  F+  ++     Q         + + L
Sbjct: 246 TKKARSYQIELAQPAINGKNALICAPTGSGKT--FVSILICEHHFQNMPAGRKAKV-VFL 302

Query: 247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVK 306
           A    + +Q  N  K   +    SV    G        + +   ++I+V TP  +++  +
Sbjct: 303 ATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFE 362

Query: 307 MGA-TKLNRVTFLVLDEADRMFDM 329
            G  T L+  T ++ DE       
Sbjct: 363 DGTLTSLSIFTLMIFDECHNTTGN 386

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 55.9 bits (135), Expect = 8e-09
 Identities = 33/161 (20%), Positives = 61/161 (37%), Gaps = 15/161 (9%)

Query: 163 PYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAAL-SGRDIIGVAKTGSGKTGAF 221
             P+           +++ ++K       P Q +AV   L  G  ++  + TGSGKT   
Sbjct: 7   WMPIEDLK---LPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIA 63

Query: 222 IWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW 281
              ++  ++        +G   + + P R L+ + Y   K +       V    G     
Sbjct: 64  EMGIISFLLK-------NGGKAIYVTPLRALTNEKYLTFKDWEL-IGFKVAMTSGDY--- 112

Query: 282 DQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDE 322
           D   A     +I++ T  ++  + +     LN V + VLDE
Sbjct: 113 DTDDAWLKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDE 153

>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 = 54.1 bits (130), Expect = 2e-08
 Identities = 38/138 (27%), Positives = 50/138 (36%), Gaps = 30/138 (21%)

Query: 188 TSPTPIQAQAVPAALS-GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL 246
            S    Q +A+   L   R  I V  TGSGKT        V +    EL        LI+
Sbjct: 92  ISLRDYQEKALERWLVDKRGCI-VLPTGSGKT-------HVAMAAINEL----STPTLIV 139

Query: 247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVK 306
            PT  L++Q       FG+      V  + G  K  +         + V T     D   
Sbjct: 140 VPTLALAEQWKERLGIFGE----EYVGEFSGRIKELKP--------LTVST----YDSAY 183

Query: 307 MGATKL-NRVTFLVLDEA 323
           + A KL NR   L+ DE 
Sbjct: 184 VNAEKLGNRFMLLIFDEV 201

>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 = 53.0 bits (126), Expect = 7e-08
 Identities = 39/186 (20%), Positives = 71/186 (38%), Gaps = 10/186 (5%)

Query: 145 EAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG 204
           +A E   ++ +T S    P    S       E + K     E       Q +    A++G
Sbjct: 204 DASEDCLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYETKKARSYQIELAQPAING 263

Query: 205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG 264
           ++ +  A TGSGKT  F+  ++     Q         + + LA    + +Q  N  K   
Sbjct: 264 KNALICAPTGSGKT--FVSILICEHHFQNMPAGRKAKV-VFLATKVPVYEQQKNVFKHH- 319

Query: 265 KGYNLSVVCCYG--GGSKWDQSKALEL-GAEIVVGTPGRIIDMVKMGA-TKLNRVTFLVL 320
             +        G  G +  + S    +  ++I+V TP  +++  + G  T L+  T ++ 
Sbjct: 320 --FERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIF 377

Query: 321 DEADRM 326
           DE    
Sbjct: 378 DECHNT 383

>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} Length = 1108

 Score = 49.5 bits (117), Expect = 9e-07
 Identities = 51/310 (16%), Positives = 93/310 (30%), Gaps = 45/310 (14%)

Query: 29  DPLDAFMKGID-----KEVKQEAKGVKTKKIEEVKGIRDDIDHEDDEESYYRYMEENPNA 83
           DP   FM   D     +E   E       +      + D  DH  D++       E    
Sbjct: 30  DPFTEFMDSTDLFDVFEETPVELPTDSNGEKNADTNVGDTPDHTQDKKH----GLEEEKE 85

Query: 84  GLQDNDSDVDLEYDEDGNPIAPKKSKYIDPLPPIDHSTIVYEEVEKNFYQPHEDIARLTP 143
             ++N+S+               K      +P +  S       E +  +   +   L  
Sbjct: 86  EHEENNSENKKIKSNKSKTEDKNKK---VVVPVLADSFEQEASREVDASKGLTNSETLQV 142

Query: 144 QEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPI-----QAQAV 198
           ++  ++R    +    A PP          +D   +   ++       P      Q  A+
Sbjct: 143 EQDGKVRLSHQVRHQVALPP---------NYDYTPIAEHKRVNEARTYPFTLDPFQDTAI 193

Query: 199 PAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN 258
                G  ++  A T +GKT   +    +    +           +  +P + LS Q Y 
Sbjct: 194 SCIDRGESVLVSAHTSAGKT--VVAEYAIAQSLKN------KQRVIYTSPIKALSNQKYR 245

Query: 259 EAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFL 318
           E         L       G    +        A  +V T   +  M+  G+  +  V ++
Sbjct: 246 ELLAEFGDVGLMT-----GDITINPD------AGCLVMTTEILRSMLYRGSEVMREVAWV 294

Query: 319 VLDEADRMFD 328
           + DE   M D
Sbjct: 295 IFDEVHYMRD 304

>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 Length = 237

 Score = 45.1 bits (107), Expect = 1e-05
 Identities = 34/132 (25%), Positives = 48/132 (36%), Gaps = 30/132 (22%)

Query: 194 QAQAVPAALS-GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL 252
           Q +A+   L   R  I V  TGSGKT   +    ++ +             LI+ PT  L
Sbjct: 98  QEKALERWLVDKRGCI-VLPTGSGKT--HVAMAAINELSTPT---------LIVVPTLAL 145

Query: 253 SQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKL 312
           ++Q       FG+      V  + G  K            + V T     D   + A KL
Sbjct: 146 AEQWKERLGIFGE----EYVGEFSGRIKEL--------KPLTVST----YDSAYVNAEKL 189

Query: 313 -NRVTFLVLDEA 323
            NR   L+ DE 
Sbjct: 190 GNRFMLLIFDEV 201

>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 = 43.8 bits (103), Expect = 6e-05
 Identities = 24/153 (15%), Positives = 45/153 (29%), Gaps = 26/153 (16%)

Query: 175 DEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKE 234
           D V ++++     +      +       S +     A TGSGK+      +      Q  
Sbjct: 203 DFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTK----VPAAYAAQ-- 256

Query: 235 LEPGDGPMGLILAPTRELSQQIYNE-AKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEI 293
                G   L+L P+   +       +K  G   N+               + +  GA +
Sbjct: 257 -----GYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRT-----------GVRTITTGAPV 300

Query: 294 VVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM 326
              T G+ +     G         ++ DE    
Sbjct: 301 TYSTYGKFLA---DGGCSGGAYDIIICDECHST 330

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	330
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	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
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.98
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.98
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.98
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.97
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.97
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.97
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.97
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.96
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.96
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.95
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.95
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.95
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.95
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.95
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.95
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.95
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.95
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.94
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.93
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.93
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.92
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.91
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.91
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.9
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.9
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.9
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.9
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.9
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.9
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.9
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.9
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.89
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.89
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.89
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.89
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.88
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.88
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.88
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.85
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.85
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.84
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.84
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.83
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.83
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.82
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.81
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.8
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.79
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.77
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.77
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.75
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.74
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.73
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.7
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.69
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.68
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.63
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.63
3h1t_A	590	Type I site-specific restriction-modification syst	99.63
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.62
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.59
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.58
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.56
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.54
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.49
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.45
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.35
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.34
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.31
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.3
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.87
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.26
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.24
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.13
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.09
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.03
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.92
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.53
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.37
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.3
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.04
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	96.49
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	96.38
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	96.19
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.12
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	96.08
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	95.72
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	95.71
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	95.65
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	95.55
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	95.46
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	95.17
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	95.04
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	94.86
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	94.79
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	94.76
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	94.69
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	94.44
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	94.44
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	94.37
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	94.11
2r6a_A	454	DNAB helicase, replicative helicase; replication,	94.09
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	93.44
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	93.35
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	93.28
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	93.26
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	93.18
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	93.16
2chg_A	226	Replication factor C small subunit; DNA-binding pr	93.08
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	93.03
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	93.0
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	92.87
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	92.86
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	92.84
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	92.76
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	92.64
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	92.56
2z43_A	324	DNA repair and recombination protein RADA; archaea	92.35
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	92.33
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	92.19
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	92.13
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	92.09
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	91.91
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	91.9
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	91.65
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	91.36
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	90.6
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	90.58
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	90.58
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	90.47
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	90.4
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	90.34
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	90.3
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	90.26
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	89.8
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	89.74
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	89.32
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	89.29
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	89.23
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	89.02
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	88.74
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	88.53
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	88.38
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	88.21
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	88.17
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	88.04
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	88.01
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	87.28
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	87.18
3co5_A	143	Putative two-component system transcriptional RES	87.15
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	87.02
2qgz_A	308	Helicase loader, putative primosome component; str	86.52
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	85.49
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	85.36
4a74_A	231	DNA repair and recombination protein RADA; hydrola	85.23
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	85.21
3io5_A	333	Recombination and repair protein; storage dimer, i	85.06
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	85.03
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	84.86
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	84.81
2eyu_A	261	Twitching motility protein PILT; pilus retraction	84.59
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	84.5
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	84.14
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	84.09
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	83.2
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	83.18
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	83.15
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	82.85
3bos_A	242	Putative DNA replication factor; P-loop containing	82.78
1yks_A	440	Genome polyprotein [contains: flavivirin protease	82.25
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	81.67
1xp8_A	366	RECA protein, recombinase A; recombination, radior	81.37
1u94_A	356	RECA protein, recombinase A; homologous recombinat	81.23
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	81.19
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	80.97
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	80.83
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	80.76
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	80.68
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	80.63
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	80.62
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	80.42
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	80.3

>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=4e-38  Score=282.20  Aligned_cols=190  Identities=49%  Similarity=0.768  Sum_probs=176.1

Q ss_pred             cCHHHHHHHHHHcCcEeeCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHH
Q psy17644        141 LTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       141 ~~~~~~~~~r~~~~i~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a  220 (330)
                      ++.+++..+|...++.+.|...|.|+.+|.+++|++.+++++.+.||..|+|+|.++|+.+++|+|++++++||||||++
T Consensus         3 ~~~~~~~~~~~~~~i~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~   82 (242)
T 3fe2_A            3 RTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLS   82 (242)
T ss_dssp             ---CHHHHHHHHHTEEEESSCCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHH
T ss_pred             CCHHHHHHHHhcCceEEeCCCCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHH
Confidence            45667889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHH
Q psy17644        221 FIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGR  300 (330)
Q Consensus       221 ~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~  300 (330)
                      |++|++.++...+......++++|||+|||+||.|+++.+++++...++++.+++||.....+...+..+++|+|+||++
T Consensus        83 ~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~  162 (242)
T 3fe2_A           83 YLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGR  162 (242)
T ss_dssp             HHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHH
T ss_pred             HHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcCCCCEEEECHHH
Confidence            99999999987654444568999999999999999999999999888999999999999988888888889999999999


Q ss_pred             HHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        301 IIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       301 L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      |.+++.++...++++.+|||||||+|+++|
T Consensus       163 l~~~l~~~~~~~~~~~~lViDEah~l~~~~  192 (242)
T 3fe2_A          163 LIDFLECGKTNLRRTTYLVLDEADRMLDMG  192 (242)
T ss_dssp             HHHHHHHTSCCCTTCCEEEETTHHHHHHTT
T ss_pred             HHHHHHcCCCCcccccEEEEeCHHHHhhhC
Confidence            999999888889999999999999999876

>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=6e-37  Score=297.33  Aligned_cols=178  Identities=38%  Similarity=0.677  Sum_probs=166.8

Q ss_pred             cCcEeeCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhc
Q psy17644        153 SGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQ  232 (330)
Q Consensus       153 ~~i~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~  232 (330)
                      ..+.+.|.++|.|+.+|.+++|++.+++++.++||..|||+|+++||.+++|+|++++|+||||||++|++|++.+++..
T Consensus        42 ~~~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~  121 (434)
T 2db3_A           42 IPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLED  121 (434)
T ss_dssp             SCEEEESSSCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHS
T ss_pred             ceeEecCCCCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhc
Confidence            35778999999999999999999999999999999999999999999999999999999999999999999999999886


Q ss_pred             CCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCC
Q psy17644        233 KELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKL  312 (330)
Q Consensus       233 ~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l  312 (330)
                      .......++++|||+|||+||.|+++.+++++...++++.+++||.....+...+..+++|+|+||++|.+++.++...+
T Consensus       122 ~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l  201 (434)
T 2db3_A          122 PHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITF  201 (434)
T ss_dssp             CCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCC
T ss_pred             ccccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCccc
Confidence            54334568999999999999999999999999888899999999999988888888899999999999999999888889


Q ss_pred             CCccEEEeecccccCcCC
Q psy17644        313 NRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       313 ~~i~~lVvDEad~lld~G  330 (330)
                      +++++|||||||+|++||
T Consensus       202 ~~~~~lVlDEah~~~~~g  219 (434)
T 2db3_A          202 EDTRFVVLDEADRMLDMG  219 (434)
T ss_dssp             TTCCEEEEETHHHHTSTT
T ss_pred             ccCCeEEEccHhhhhccC
Confidence            999999999999999987

>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=3.2e-34  Score=258.20  Aligned_cols=178  Identities=38%  Similarity=0.656  Sum_probs=160.4

Q ss_pred             cCcEeeCCCCCC--CCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        153 SGITVSGADPPY--PVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       153 ~~i~~~g~~~p~--p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      +.+.+.|...|.  ++.+|.+++|++.++++|.+.||..|+|+|.++++.+++|+|++++++||||||++|++|++.++.
T Consensus         7 ~~~~~~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~   86 (253)
T 1wrb_A            7 IPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLV   86 (253)
T ss_dssp             CCCCEECCSSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CceeeeCCCCCCCCccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHH
Confidence            346677888877  899999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             hcCCC----CCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHH
Q psy17644        231 DQKEL----EPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVK  306 (330)
Q Consensus       231 ~~~~~----~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~  306 (330)
                      .....    ....++++|||+|||+||.|+++.+++++...++++..++||.....+...+..+++|+|+||++|..++.
T Consensus        87 ~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~  166 (253)
T 1wrb_A           87 CQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIE  166 (253)
T ss_dssp             TTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHH
T ss_pred             hhccccccccccCCceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHH
Confidence            64321    12346899999999999999999999999888899999999998888888888889999999999999999


Q ss_pred             cCCCCCCCccEEEeecccccCcCC
Q psy17644        307 MGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       307 ~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      +....++++.+|||||||+|+++|
T Consensus       167 ~~~~~~~~~~~lViDEah~~~~~~  190 (253)
T 1wrb_A          167 KNKISLEFCKYIVLDEADRMLDMG  190 (253)
T ss_dssp             TTSBCCTTCCEEEEETHHHHHHTT
T ss_pred             cCCCChhhCCEEEEeCHHHHHhCc
Confidence            888889999999999999998875

>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=3.8e-34  Score=256.39  Aligned_cols=181  Identities=33%  Similarity=0.546  Sum_probs=157.6

Q ss_pred             HHHHHHHHcCcEeeCCCCCCCCCCCCCC----CCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHH
Q psy17644        145 EAQELRAKSGITVSGADPPYPVSSFGHF----GFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       145 ~~~~~r~~~~i~~~g~~~p~p~~~f~~~----~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a  220 (330)
                      ++..+|.++++.+.|..+|.|+.+|.++    ++++.+++++.+.||..|+|+|.++++.+++|++++++++||||||++
T Consensus         3 ~~~~~~~~~~i~~~~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~   82 (245)
T 3dkp_A            3 KINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLA   82 (245)
T ss_dssp             HHHHHHHHTTEEEESSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHH
T ss_pred             hHHHHHHhCceEecCCCCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHH
Confidence            4677899999999999999999999987    899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHH-HHHHhCCCeEEEEChH
Q psy17644        221 FIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ-SKALELGAEIVVGTPG  299 (330)
Q Consensus       221 ~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~-~~~l~~~~dIiV~TP~  299 (330)
                      |++|++.++....    ..++++|||+|||+||.|+++.+++++...+.++..+.|+...... ......+++|+|+||+
T Consensus        83 ~~l~~l~~l~~~~----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~  158 (245)
T 3dkp_A           83 FSIPILMQLKQPA----NKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPN  158 (245)
T ss_dssp             HHHHHHHHHCSCC----SSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHH
T ss_pred             HHHHHHHHHhhcc----cCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHH
Confidence            9999999885422    2578999999999999999999999998888888877765433222 1222446899999999


Q ss_pred             HHHHHHHcC--CCCCCCccEEEeecccccCcC
Q psy17644        300 RIIDMVKMG--ATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       300 ~L~~~l~~~--~~~l~~i~~lVvDEad~lld~  329 (330)
                      +|..++.+.  ...++++.+|||||||+|+++
T Consensus       159 ~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~  190 (245)
T 3dkp_A          159 RLIYLLKQDPPGIDLASVEWLVVDESDKLFED  190 (245)
T ss_dssp             HHHHHHHSSSCSCCCTTCCEEEESSHHHHHHH
T ss_pred             HHHHHHHhCCCCcccccCcEEEEeChHHhccc
Confidence            999999876  467899999999999999874

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=100.00  E-value=1.3e-33  Score=250.19  Aligned_cols=171  Identities=37%  Similarity=0.611  Sum_probs=146.7

Q ss_pred             CCCCCCCCCCCCC-CCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCC-CC
Q psy17644        159 GADPPYPVSSFGH-FGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKE-LE  236 (330)
Q Consensus       159 g~~~p~p~~~f~~-~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~-~~  236 (330)
                      +...|.|+.+|.+ +++++.+++++.+.||..|||+|.++++.+++|+|++++++||||||++|++|++.++..... ..
T Consensus        11 ~~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~   90 (228)
T 3iuy_A           11 KRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISRE   90 (228)
T ss_dssp             CCCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC-------
T ss_pred             cCcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhh
Confidence            4567999999999 899999999999999999999999999999999999999999999999999999998865421 11


Q ss_pred             CCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCcc
Q psy17644        237 PGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVT  316 (330)
Q Consensus       237 ~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~  316 (330)
                      ...++++|||+|||+||.|+++.+++++ ..++++..++||.....+...+..+++|+|+||++|..++.+....++++.
T Consensus        91 ~~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~  169 (228)
T 3iuy_A           91 QRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSIT  169 (228)
T ss_dssp             --CCCSEEEECSSHHHHHHHHHHHHHHC-CTTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTCC
T ss_pred             ccCCCcEEEEeCCHHHHHHHHHHHHHhc-ccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccce
Confidence            2367899999999999999999999986 457888999999988888888888999999999999999998888899999


Q ss_pred             EEEeecccccCcCC
Q psy17644        317 FLVLDEADRMFDMG  330 (330)
Q Consensus       317 ~lVvDEad~lld~G  330 (330)
                      +|||||||+|+++|
T Consensus       170 ~lViDEah~~~~~~  183 (228)
T 3iuy_A          170 YLVIDEADKMLDME  183 (228)
T ss_dssp             EEEECCHHHHHHTT
T ss_pred             EEEEECHHHHhccc
Confidence            99999999998875

>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=1.6e-32  Score=263.11  Aligned_cols=176  Identities=40%  Similarity=0.697  Sum_probs=160.7

Q ss_pred             cEeeCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCC
Q psy17644        155 ITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKE  234 (330)
Q Consensus       155 i~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~  234 (330)
                      +.+.|..+|.++.+|.+++|++.++++|...||..|||+|.++||.++.|+|++++++||||||++|++|++.++.....
T Consensus         3 ~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~   82 (417)
T 2i4i_A            3 VEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGP   82 (417)
T ss_dssp             EEEESTTCCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCC
T ss_pred             cccCCCcCCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccc
Confidence            56778999999999999999999999999999999999999999999999999999999999999999999999876432


Q ss_pred             C-------------CCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHH
Q psy17644        235 L-------------EPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI  301 (330)
Q Consensus       235 ~-------------~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L  301 (330)
                      .             ....++++|||+|||+||.|+++.+++++...++++..++||.....+...+..+++|+|+||++|
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l  162 (417)
T 2i4i_A           83 GEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRL  162 (417)
T ss_dssp             CHHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHH
T ss_pred             cchhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHH
Confidence            1             122458999999999999999999999998889999999999998888888888899999999999


Q ss_pred             HHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        302 IDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       302 ~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      ..++......++++.+|||||||+|+++|
T Consensus       163 ~~~l~~~~~~~~~~~~iViDEah~~~~~~  191 (417)
T 2i4i_A          163 VDMMERGKIGLDFCKYLVLDEADRMLDMG  191 (417)
T ss_dssp             HHHHHTTSBCCTTCCEEEESSHHHHHHTT
T ss_pred             HHHHHcCCcChhhCcEEEEEChhHhhccC
Confidence            99999888889999999999999998765

>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=3.9e-33  Score=258.03  Aligned_cols=166  Identities=30%  Similarity=0.508  Sum_probs=142.9

Q ss_pred             cEeeCCCCC---CCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCC--CcEEEEcCCCChhHHHHHHHHHHHH
Q psy17644        155 ITVSGADPP---YPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       155 i~~~g~~~p---~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g--~d~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      +.+.+.+++   .++.+|.+++|++.++++|.++||..||++|.++||.++.|  +|++++|+||||||++|++|++.++
T Consensus        77 v~v~~~~~~~p~~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l  156 (300)
T 3fmo_B           77 VEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV  156 (300)
T ss_dssp             EEEECSSTTCCCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             ceeccCCCCCCcCCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhh
Confidence            444444443   35788999999999999999999999999999999999987  9999999999999999999999987


Q ss_pred             HhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHc-
Q psy17644        230 MDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKM-  307 (330)
Q Consensus       230 ~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~-  307 (330)
                      ...     ..+|++|||+|||+||.|++..++.++... ++.+.+++||.......   ..+++||||||++|.+++.+ 
T Consensus       157 ~~~-----~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~TP~~l~~~l~~~  228 (300)
T 3fmo_B          157 EPA-----NKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKL  228 (300)
T ss_dssp             CTT-----SCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTT
T ss_pred             hcc-----CCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh---cCCCCEEEECHHHHHHHHHhc
Confidence            553     257899999999999999999999998764 67888888887653322   45689999999999999965 


Q ss_pred             CCCCCCCccEEEeecccccCc
Q psy17644        308 GATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       308 ~~~~l~~i~~lVvDEad~lld  328 (330)
                      +...++++.+|||||||+|++
T Consensus       229 ~~~~l~~l~~lVlDEad~l~~  249 (300)
T 3fmo_B          229 KFIDPKKIKVFVLDEADVMIA  249 (300)
T ss_dssp             CCCCGGGCSEEEETTHHHHHH
T ss_pred             CCCChhhceEEEEeCHHHHhh
Confidence            566789999999999999997

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=100.00  E-value=1.7e-32  Score=243.76  Aligned_cols=166  Identities=29%  Similarity=0.453  Sum_probs=143.6

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCC
Q psy17644        159 GADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPG  238 (330)
Q Consensus       159 g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~  238 (330)
                      +...|.+..+|.+++|++.+++++.+.||..|+++|.++++.+++|+|++++++||+|||++|++|++.++...     .
T Consensus        16 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~-----~   90 (230)
T 2oxc_A           16 GDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLE-----N   90 (230)
T ss_dssp             --------CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----S
T ss_pred             CCCCCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc-----C
Confidence            45567788899999999999999999999999999999999999999999999999999999999999887543     2


Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccE
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTF  317 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~  317 (330)
                      .++++|||+|||+|+.|+++.+++++... ++++..++||.....+...+. +++|+|+||++|..++......+.++++
T Consensus        91 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~  169 (230)
T 2oxc_A           91 LSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK-KCHIAVGSPGRIKQLIELDYLNPGSIRL  169 (230)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTT-SCSEEEECHHHHHHHHHTTSSCGGGCCE
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhcc-CCCEEEECHHHHHHHHhcCCcccccCCE
Confidence            46899999999999999999999998765 788888999988776655554 6899999999999999888778899999


Q ss_pred             EEeecccccCcCC
Q psy17644        318 LVLDEADRMFDMG  330 (330)
Q Consensus       318 lVvDEad~lld~G  330 (330)
                      |||||||+|+++|
T Consensus       170 lViDEah~~~~~~  182 (230)
T 2oxc_A          170 FILDEADKLLEEG  182 (230)
T ss_dssp             EEESSHHHHHSTT
T ss_pred             EEeCCchHhhcCc
Confidence            9999999998876

>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=9.5e-33  Score=246.58  Aligned_cols=167  Identities=31%  Similarity=0.510  Sum_probs=138.6

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCC
Q psy17644        159 GADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPG  238 (330)
Q Consensus       159 g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~  238 (330)
                      ..+.|.++.+|++++|++.+++++.+.||..|+++|.++++.+++|++++++++||||||++|++|++.++...     .
T Consensus        22 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~-----~   96 (237)
T 3bor_A           22 ESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIE-----F   96 (237)
T ss_dssp             -----CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTT-----S
T ss_pred             cCCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc-----C
Confidence            34567788999999999999999999999999999999999999999999999999999999999999886532     2


Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCC-CeEEEEChHHHHHHHHcCCCCCCCccE
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELG-AEIVVGTPGRIIDMVKMGATKLNRVTF  317 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~-~dIiV~TP~~L~~~l~~~~~~l~~i~~  317 (330)
                      .++++|||+|||+|+.|+++.+++++...+..+..++||.....+...+..+ ++|+|+||++|.+++.++...+.++.+
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~  176 (237)
T 3bor_A           97 KETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKM  176 (237)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCE
T ss_pred             CCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcE
Confidence            4689999999999999999999999988888999999998877666666655 899999999999999988888899999


Q ss_pred             EEeecccccCcCC
Q psy17644        318 LVLDEADRMFDMG  330 (330)
Q Consensus       318 lVvDEad~lld~G  330 (330)
                      |||||||+|+++|
T Consensus       177 lViDEah~~~~~~  189 (237)
T 3bor_A          177 FVLDEADEMLSRG  189 (237)
T ss_dssp             EEEESHHHHHHTT
T ss_pred             EEECCchHhhccC
Confidence            9999999998765

>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=5.4e-32  Score=241.04  Aligned_cols=181  Identities=33%  Similarity=0.495  Sum_probs=152.6

Q ss_pred             HHHHHHHHHHcCcEeeCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHH
Q psy17644        143 PQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFI  222 (330)
Q Consensus       143 ~~~~~~~r~~~~i~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~l  222 (330)
                      ..++..++..+.     ...+.++.+|.++++++.+++++.+.||..|+++|.++++.+++|++++++++||+|||++|+
T Consensus         6 ~~~~~~~~~~~~-----~~~~~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~   80 (236)
T 2pl3_A            6 RESISRLMQNYE-----KINVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFL   80 (236)
T ss_dssp             HHHHHHHHHTTT-----TCCGGGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH
T ss_pred             HhHHHHHHhccc-----cCCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHH
Confidence            344555665553     223567888999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHH
Q psy17644        223 WPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRII  302 (330)
Q Consensus       223 lp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~  302 (330)
                      +|++.++...+. ....++++|||+|||+||.|+++.+++++...++.+..++||.....+...+ .+++|+|+||++|.
T Consensus        81 ~~~l~~l~~~~~-~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~  158 (236)
T 2pl3_A           81 VPVLEALYRLQW-TSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLL  158 (236)
T ss_dssp             HHHHHHHHHTTC-CGGGCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHH
T ss_pred             HHHHHHHHhhcc-cccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHH
Confidence            999998876321 1235789999999999999999999999988889999999998876665555 46899999999999


Q ss_pred             HHHHcC-CCCCCCccEEEeecccccCcCC
Q psy17644        303 DMVKMG-ATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       303 ~~l~~~-~~~l~~i~~lVvDEad~lld~G  330 (330)
                      .++.+. ...+.++.+|||||||+|+++|
T Consensus       159 ~~l~~~~~~~~~~~~~lViDEah~~~~~~  187 (236)
T 2pl3_A          159 QHMDETVSFHATDLQMLVLDEADRILDMG  187 (236)
T ss_dssp             HHHHHCSSCCCTTCCEEEETTHHHHHHTT
T ss_pred             HHHHhcCCcccccccEEEEeChHHHhcCC
Confidence            988765 4668899999999999998875

>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=3.7e-32  Score=244.81  Aligned_cols=161  Identities=40%  Similarity=0.654  Sum_probs=148.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEE
Q psy17644        165 PVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGL  244 (330)
Q Consensus       165 p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vL  244 (330)
                      ++.+|.+++|++.+++++.+.||..|+++|.++++.+++|++++++++||||||++|++|++.++....     .++++|
T Consensus        41 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~-----~~~~~l  115 (249)
T 3ber_A           41 ETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETP-----QRLFAL  115 (249)
T ss_dssp             HHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSC-----CSSCEE
T ss_pred             ccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCC-----CCceEE
Confidence            467799999999999999999999999999999999999999999999999999999999999987643     468899


Q ss_pred             EEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHc-CCCCCCCccEEEeecc
Q psy17644        245 ILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKM-GATKLNRVTFLVLDEA  323 (330)
Q Consensus       245 il~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~-~~~~l~~i~~lVvDEa  323 (330)
                      ||+|||+||.|+++.+++++...++++.+++||.....+...+..+++|+|+||++|.+++.+ ....++++++||||||
T Consensus       116 il~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEa  195 (249)
T 3ber_A          116 VLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEA  195 (249)
T ss_dssp             EECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSH
T ss_pred             EEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcCh
Confidence            999999999999999999998888999999999998888888888899999999999999876 4567899999999999


Q ss_pred             cccCcCC
Q psy17644        324 DRMFDMG  330 (330)
Q Consensus       324 d~lld~G  330 (330)
                      |+|+++|
T Consensus       196 h~l~~~~  202 (249)
T 3ber_A          196 DRILNMD  202 (249)
T ss_dssp             HHHHHTT
T ss_pred             hhhhccC
Confidence            9998765

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.98  E-value=9e-32  Score=234.27  Aligned_cols=159  Identities=33%  Similarity=0.614  Sum_probs=145.4

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      .+|++++|++.+++++.+.||..|+|+|.++++.+++|+++++++|||+|||++|++|++.++...     ..++++||+
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~-----~~~~~~lil   77 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK-----KDNIQAMVI   77 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT-----SCSCCEEEE
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhccc-----CCCeeEEEE
Confidence            469999999999999999999999999999999999999999999999999999999999886442     246899999


Q ss_pred             cccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      +||++|+.|+++.+++++... +..+..++||.....+...+..+++|+|+||++|..++.++...++++.+|||||||+
T Consensus        78 ~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~  157 (206)
T 1vec_A           78 VPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADK  157 (206)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHH
T ss_pred             eCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEChHH
Confidence            999999999999999998876 7888899999988877777788899999999999999998888899999999999999


Q ss_pred             cCcCC
Q psy17644        326 MFDMG  330 (330)
Q Consensus       326 lld~G  330 (330)
                      |+++|
T Consensus       158 ~~~~~  162 (206)
T 1vec_A          158 LLSQD  162 (206)
T ss_dssp             HTSTT
T ss_pred             hHhhC
Confidence            98754

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.98  E-value=1.1e-32  Score=242.87  Aligned_cols=161  Identities=36%  Similarity=0.633  Sum_probs=143.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEE
Q psy17644        165 PVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGL  244 (330)
Q Consensus       165 p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vL  244 (330)
                      |..+|.+++|++.+++++.+.||..|+++|.++++.+++|++++++++||+|||++|++|++.++...     ..++++|
T Consensus         2 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~-----~~~~~~l   76 (219)
T 1q0u_A            2 AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE-----RAEVQAV   76 (219)
T ss_dssp             --CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT-----SCSCCEE
T ss_pred             CCCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhC-----cCCceEE
Confidence            45679999999999999999999999999999999999999999999999999999999999887543     2468999


Q ss_pred             EEcccHHHHHHHHHHHHHhccCC----CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEe
Q psy17644        245 ILAPTRELSQQIYNEAKRFGKGY----NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVL  320 (330)
Q Consensus       245 il~Ptr~La~Qi~~~~~~l~~~~----~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVv  320 (330)
                      ||+|||+|+.|+++.+++++...    ++.+..++||.....+...+..+++|+|+||++|.+++.++...++++.+|||
T Consensus        77 il~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lVi  156 (219)
T 1q0u_A           77 ITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVV  156 (219)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEE
T ss_pred             EEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEE
Confidence            99999999999999999998766    67888899988776665556667899999999999999988788899999999


Q ss_pred             ecccccCcCC
Q psy17644        321 DEADRMFDMG  330 (330)
Q Consensus       321 DEad~lld~G  330 (330)
                      ||||+|+++|
T Consensus       157 DEah~~~~~~  166 (219)
T 1q0u_A          157 DEADLMLDMG  166 (219)
T ss_dssp             CSHHHHHHTT
T ss_pred             cCchHHhhhC
Confidence            9999998775

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.98  E-value=6.6e-32  Score=238.28  Aligned_cols=165  Identities=33%  Similarity=0.553  Sum_probs=141.9

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCC
Q psy17644        160 ADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGD  239 (330)
Q Consensus       160 ~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~  239 (330)
                      ...+.++.+|.+++|++.+++++.+.||..|+|+|.++++.+++|++++++++||+|||++|++|++.++...     ..
T Consensus         7 ~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~-----~~   81 (224)
T 1qde_A            7 TNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----VK   81 (224)
T ss_dssp             BSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----CC
T ss_pred             cccCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhcc-----CC
Confidence            3457788999999999999999999999999999999999999999999999999999999999999887543     24


Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEE
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLV  319 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lV  319 (330)
                      ++++|||+|||+|+.|+++.+++++...++++..++||.....+...+.. ++|+|+||++|..++.+....++++.+||
T Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~-~~iiv~Tp~~l~~~~~~~~~~~~~~~~iV  160 (224)
T 1qde_A           82 APQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRD-AQIVVGTPGRVFDNIQRRRFRTDKIKMFI  160 (224)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CTT-CSEEEECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcCCC-CCEEEECHHHHHHHHHhCCcchhhCcEEE
Confidence            68999999999999999999999998888999999998877666555554 89999999999999998888899999999


Q ss_pred             eecccccCcCC
Q psy17644        320 LDEADRMFDMG  330 (330)
Q Consensus       320 vDEad~lld~G  330 (330)
                      |||||+|+++|
T Consensus       161 iDEah~~~~~~  171 (224)
T 1qde_A          161 LDEADEMLSSG  171 (224)
T ss_dssp             EETHHHHHHTT
T ss_pred             EcChhHHhhhh
Confidence            99999998765

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.97  E-value=1.1e-31  Score=243.55  Aligned_cols=163  Identities=35%  Similarity=0.537  Sum_probs=143.5

Q ss_pred             CCCCCCC--CCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEE
Q psy17644        167 SSFGHFG--FDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGL  244 (330)
Q Consensus       167 ~~f~~~~--l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vL  244 (330)
                      .+|.+++  +++.+++++...||..|+|+|.++++.++.|+|++++++||||||++|++|++..+...+. ....++++|
T Consensus        52 ~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~-~~~~~~~~l  130 (262)
T 3ly5_A           52 TSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRF-MPRNGTGVL  130 (262)
T ss_dssp             GCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTC-CGGGCCCEE
T ss_pred             CChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccc-cccCCceEE
Confidence            3466776  9999999999999999999999999999999999999999999999999999999876431 123578999


Q ss_pred             EEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcC-CCCCCCccEEEeecc
Q psy17644        245 ILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMG-ATKLNRVTFLVLDEA  323 (330)
Q Consensus       245 il~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~-~~~l~~i~~lVvDEa  323 (330)
                      ||+|||+||.|+++.+++++...+..+..++||.....+...+..+++|+||||++|..++.+. ...++++.+||||||
T Consensus       131 il~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEa  210 (262)
T 3ly5_A          131 ILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEA  210 (262)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSH
T ss_pred             EEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcCh
Confidence            9999999999999999999998899999999999988888888888999999999999988765 367899999999999


Q ss_pred             cccCcCC
Q psy17644        324 DRMFDMG  330 (330)
Q Consensus       324 d~lld~G  330 (330)
                      |+|+++|
T Consensus       211 h~l~~~~  217 (262)
T 3ly5_A          211 DRILDVG  217 (262)
T ss_dssp             HHHHHTT
T ss_pred             HHHhhhh
Confidence            9999876

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.97  E-value=7.4e-31  Score=231.08  Aligned_cols=165  Identities=32%  Similarity=0.540  Sum_probs=141.5

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCC
Q psy17644        159 GADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPG  238 (330)
Q Consensus       159 g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~  238 (330)
                      |...+....+|.+++|++.+++++.+.||..|+|+|.++++.+++|++++++++||+|||++|++|++.++...     .
T Consensus         6 ~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~-----~   80 (220)
T 1t6n_A            6 GSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-----T   80 (220)
T ss_dssp             --------CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC-----T
T ss_pred             CCcccccCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhcc-----C
Confidence            34445566789999999999999999999999999999999999999999999999999999999999876432     2


Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhC-CCeEEEEChHHHHHHHHcCCCCCCCcc
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALEL-GAEIVVGTPGRIIDMVKMGATKLNRVT  316 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~  316 (330)
                      .++++|||+||++|+.|+++.+++++... ++++..++||.....+...+.. .++|+|+||++|..++.+....+.++.
T Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~  160 (220)
T 1t6n_A           81 GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIK  160 (220)
T ss_dssp             TCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCC
T ss_pred             CCEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCC
Confidence            45799999999999999999999998776 7888899999887766666654 479999999999999998888899999


Q ss_pred             EEEeecccccCc
Q psy17644        317 FLVLDEADRMFD  328 (330)
Q Consensus       317 ~lVvDEad~lld  328 (330)
                      +|||||||+|++
T Consensus       161 ~lViDEah~~~~  172 (220)
T 1t6n_A          161 HFILDECDKMLE  172 (220)
T ss_dssp             EEEEESHHHHHS
T ss_pred             EEEEcCHHHHhc
Confidence            999999999976

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.97  E-value=6.1e-31  Score=228.98  Aligned_cols=159  Identities=45%  Similarity=0.692  Sum_probs=143.0

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc
Q psy17644        168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA  247 (330)
Q Consensus       168 ~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~  247 (330)
                      +|.+++|++.+++++.+.|+..|+|+|.++++.+++|++++++++||+|||++|++|++.++.....  ...++++||++
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~--~~~~~~~lil~   79 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQE--RGRKPRALVLT   79 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCC--TTCCCSEEEEC
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccc--cCCCCcEEEEE
Confidence            5899999999999999999999999999999999999999999999999999999999988764321  23578999999


Q ss_pred             ccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        248 PTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       248 Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      |||+|+.|+++.+++++..  +++..++||.....+...+..+++|+|+||++|..++.++...++++.+|||||||+|+
T Consensus        80 P~~~L~~q~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~  157 (207)
T 2gxq_A           80 PTRELALQVASELTAVAPH--LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEML  157 (207)
T ss_dssp             SSHHHHHHHHHHHHHHCTT--SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhc--ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhh
Confidence            9999999999999999764  67788899988777777777789999999999999998888889999999999999998


Q ss_pred             cCC
Q psy17644        328 DMG  330 (330)
Q Consensus       328 d~G  330 (330)
                      ++|
T Consensus       158 ~~~  160 (207)
T 2gxq_A          158 SMG  160 (207)
T ss_dssp             HTT
T ss_pred             ccc
Confidence            764

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.97  E-value=6.3e-30  Score=244.78  Aligned_cols=165  Identities=33%  Similarity=0.570  Sum_probs=151.1

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCC
Q psy17644        161 DPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG  240 (330)
Q Consensus       161 ~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~  240 (330)
                      ..+.+..+|.+++|++.+++++.+.||..|+|+|.++++.+++|++++++++||+|||++|++|++.++...     ..+
T Consensus        31 ~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~-----~~~  105 (410)
T 2j0s_A           31 EEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ-----VRE  105 (410)
T ss_dssp             TTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT-----SCS
T ss_pred             CCccCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhc-----cCC
Confidence            344567789999999999999999999999999999999999999999999999999999999999876432     246


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEe
Q psy17644        241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVL  320 (330)
Q Consensus       241 ~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVv  320 (330)
                      +++|||+|||+|+.|+++.+++++...++.+..++||.....+...+..+++|+|+||++|.+++.++...+.++.+|||
T Consensus       106 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vVi  185 (410)
T 2j0s_A          106 TQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVL  185 (410)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEE
T ss_pred             ceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEE
Confidence            89999999999999999999999988899999999999988888888888999999999999999988888899999999


Q ss_pred             ecccccCcCC
Q psy17644        321 DEADRMFDMG  330 (330)
Q Consensus       321 DEad~lld~G  330 (330)
                      ||||+|+++|
T Consensus       186 DEah~~~~~~  195 (410)
T 2j0s_A          186 DEADEMLNKG  195 (410)
T ss_dssp             ETHHHHTSTT
T ss_pred             ccHHHHHhhh
Confidence            9999998875

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.96  E-value=2.9e-28  Score=233.01  Aligned_cols=166  Identities=33%  Similarity=0.521  Sum_probs=149.6

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCC
Q psy17644        160 ADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGD  239 (330)
Q Consensus       160 ~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~  239 (330)
                      ...+..+.+|..+++++.+++.+.+.|+..|+++|.++++.+++|++++++++||+|||++|++|++.++...     ..
T Consensus        33 ~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~-----~~  107 (414)
T 3eiq_A           33 SNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD-----LK  107 (414)
T ss_dssp             CCCCCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTT-----SC
T ss_pred             CCccchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhc-----CC
Confidence            3445667889999999999999999999999999999999999999999999999999999999999886543     24


Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh-CCCeEEEEChHHHHHHHHcCCCCCCCccEE
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE-LGAEIVVGTPGRIIDMVKMGATKLNRVTFL  318 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~-~~~dIiV~TP~~L~~~l~~~~~~l~~i~~l  318 (330)
                      ++++|||+||++|+.|+++.+++++...+..+..++||.........+. .+++|+|+||++|.+++.+....+.++.+|
T Consensus       108 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~v  187 (414)
T 3eiq_A          108 ATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMF  187 (414)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEE
T ss_pred             ceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEE
Confidence            6889999999999999999999999888999999999998877766665 678999999999999999888888999999


Q ss_pred             EeecccccCcCC
Q psy17644        319 VLDEADRMFDMG  330 (330)
Q Consensus       319 VvDEad~lld~G  330 (330)
                      ||||||+|+++|
T Consensus       188 ViDEah~~~~~~  199 (414)
T 3eiq_A          188 VLDEADEMLSRG  199 (414)
T ss_dssp             EECSHHHHHHTT
T ss_pred             EEECHHHhhccC
Confidence            999999988764

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.96  E-value=2.5e-28  Score=232.73  Aligned_cols=160  Identities=33%  Similarity=0.583  Sum_probs=144.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeE
Q psy17644        164 YPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMG  243 (330)
Q Consensus       164 ~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~v  243 (330)
                      .+..+|++++|++.++++|.+.||..|+|+|.++++.+++|++++++++||+|||++|++|++.++...     ..++++
T Consensus        18 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~-----~~~~~~   92 (400)
T 1s2m_A           18 TKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK-----LNKIQA   92 (400)
T ss_dssp             ---CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT-----SCSCCE
T ss_pred             cccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhc-----cCCccE
Confidence            345679999999999999999999999999999999999999999999999999999999999886432     246789


Q ss_pred             EEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecc
Q psy17644        244 LILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEA  323 (330)
Q Consensus       244 Lil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEa  323 (330)
                      |||+||++|+.|+++.+++++...++.+..++|+.....+...+..+++|+|+||++|..++.+....+.++.+||||||
T Consensus        93 lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEa  172 (400)
T 1s2m_A           93 LIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEA  172 (400)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESH
T ss_pred             EEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCc
Confidence            99999999999999999999988899999999999887777777778999999999999999888888999999999999


Q ss_pred             cccCc
Q psy17644        324 DRMFD  328 (330)
Q Consensus       324 d~lld  328 (330)
                      |++++
T Consensus       173 H~~~~  177 (400)
T 1s2m_A          173 DKMLS  177 (400)
T ss_dssp             HHHSS
T ss_pred             hHhhh
Confidence            99875

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.95  E-value=4.8e-28  Score=229.73  Aligned_cols=163  Identities=33%  Similarity=0.562  Sum_probs=146.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCC
Q psy17644        162 PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGP  241 (330)
Q Consensus       162 ~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~  241 (330)
                      ...++.+|++++|++.+++++...||..|+|+|.++++.+++|++++++++||+|||++|++|++.++...     ..++
T Consensus        16 ~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~-----~~~~   90 (394)
T 1fuu_A           16 YDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----VKAP   90 (394)
T ss_dssp             SCCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTT-----CCSC
T ss_pred             cccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhcc-----CCCC
Confidence            34567789999999999999999999999999999999999999999999999999999999999886542     2478


Q ss_pred             eEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEee
Q psy17644        242 MGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLD  321 (330)
Q Consensus       242 ~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvD  321 (330)
                      ++|||+||++|+.|+++.+.+++...++++..++||.........+. +++|+|+||++|...+.+....+.++.+||||
T Consensus        91 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiD  169 (394)
T 1fuu_A           91 QALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILD  169 (394)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSSCCTTCCEEEEE
T ss_pred             CEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCCcchhhCcEEEEE
Confidence            99999999999999999999999888899999999988776655555 57999999999999998887888999999999


Q ss_pred             cccccCcCC
Q psy17644        322 EADRMFDMG  330 (330)
Q Consensus       322 Ead~lld~G  330 (330)
                      |||+++++|
T Consensus       170 Eah~~~~~~  178 (394)
T 1fuu_A          170 EADEMLSSG  178 (394)
T ss_dssp             THHHHHHTT
T ss_pred             ChHHhhCCC
Confidence            999987654

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.95  E-value=1.7e-27  Score=225.94  Aligned_cols=158  Identities=33%  Similarity=0.561  Sum_probs=140.9

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      .+|++++|++.++++|.+.||..|+|+|.++++.++.|++++++++||+|||++|++|++..+...     ..++++|||
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~-----~~~~~~lil   82 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-----TGQVSVLVM   82 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCC-----TTCCCEEEE
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhccc-----CCCeeEEEE
Confidence            569999999999999999999999999999999999999999999999999999999999876432     246799999


Q ss_pred             cccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhC-CCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD  324 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad  324 (330)
                      +||++|+.|+++.+++++... ++++..++||.........+.. .++|+|+||++|..++.+....+.++.+|||||||
T Consensus        83 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH  162 (391)
T 1xti_A           83 CHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECD  162 (391)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHH
T ss_pred             CCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHH
Confidence            999999999999999998776 7888999999887766665554 47999999999999998888889999999999999


Q ss_pred             ccCcC
Q psy17644        325 RMFDM  329 (330)
Q Consensus       325 ~lld~  329 (330)
                      +++++
T Consensus       163 ~~~~~  167 (391)
T 1xti_A          163 KMLEQ  167 (391)
T ss_dssp             HHTSS
T ss_pred             HHhhc
Confidence            99763

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.95  E-value=8e-28  Score=241.16  Aligned_cols=163  Identities=33%  Similarity=0.519  Sum_probs=139.0

Q ss_pred             CCCCCCC----CCHHHHHHHHHCCCCCCCHHHHHhhhhhc--CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCC
Q psy17644        167 SSFGHFG----FDEVLMKALRKCEYTSPTPIQAQAVPAAL--SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG  240 (330)
Q Consensus       167 ~~f~~~~----l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~--~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~  240 (330)
                      .+|.++.    |++.+++++...||..|||+|.++|+.++  .|+|++++||||+|||++|++|++.++...+. ....+
T Consensus        17 ~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~-~~~~~   95 (579)
T 3sqw_A           17 VTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF-DSQYM   95 (579)
T ss_dssp             CCHHHHHHTTSSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTT-SSTTS
T ss_pred             cCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccc-cccCC
Confidence            3455543    99999999999999999999999999999  78999999999999999999999999887542 12346


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHhcc----CCCceEEEEECCCchHHHHHHHh-CCCeEEEEChHHHHHHHHcC-CCCCCC
Q psy17644        241 PMGLILAPTRELSQQIYNEAKRFGK----GYNLSVVCCYGGGSKWDQSKALE-LGAEIVVGTPGRIIDMVKMG-ATKLNR  314 (330)
Q Consensus       241 ~~vLil~Ptr~La~Qi~~~~~~l~~----~~~~~~~~~~gg~~~~~~~~~l~-~~~dIiV~TP~~L~~~l~~~-~~~l~~  314 (330)
                      +++|||+|||+||.|++..+++++.    .....+..++||.....+...+. .+++||||||++|.+++.+. ...++.
T Consensus        96 ~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~  175 (579)
T 3sqw_A           96 VKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRF  175 (579)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTT
T ss_pred             CeEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhcccccccc
Confidence            8999999999999999999999863    23467888899988777766664 37899999999999988764 345788


Q ss_pred             ccEEEeecccccCcCC
Q psy17644        315 VTFLVLDEADRMFDMG  330 (330)
Q Consensus       315 i~~lVvDEad~lld~G  330 (330)
                      +.+|||||||+|++||
T Consensus       176 ~~~lViDEah~l~~~g  191 (579)
T 3sqw_A          176 VDYKVLDEADRLLEIG  191 (579)
T ss_dssp             CCEEEEETHHHHTSTT
T ss_pred             CCEEEEEChHHhhcCC
Confidence            9999999999999987

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=99.95  E-value=1.3e-27  Score=234.02  Aligned_cols=157  Identities=30%  Similarity=0.503  Sum_probs=134.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCC--CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCC
Q psy17644        164 YPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGP  241 (330)
Q Consensus       164 ~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g--~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~  241 (330)
                      .++.+|..++|++.++++|.++||..|||+|.++||.++.+  ++++++|+||||||++|++|++.++...     ..++
T Consensus        89 ~~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~-----~~~~  163 (479)
T 3fmp_B           89 YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA-----NKYP  163 (479)
T ss_dssp             CCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTT-----SCSC
T ss_pred             cCcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhc-----CCCC
Confidence            34778999999999999999999999999999999999987  9999999999999999999999876543     2467


Q ss_pred             eEEEEcccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHc-CCCCCCCccEEE
Q psy17644        242 MGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKM-GATKLNRVTFLV  319 (330)
Q Consensus       242 ~vLil~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~-~~~~l~~i~~lV  319 (330)
                      ++|||+|||+||.|++..+++++... ++.+.+..++......   ...+++|+||||++|.+++.+ +...++++.+||
T Consensus       164 ~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iV  240 (479)
T 3fmp_B          164 QCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFV  240 (479)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEE
T ss_pred             cEEEEeChHHHHHHHHHHHHHHHhhCCCceEEEEeCCcccccc---ccCCCCEEEECchHHHHHHHhcCCcCcccCCEEE
Confidence            99999999999999999999988754 5677777776654322   134579999999999999965 456689999999


Q ss_pred             eecccccCc
Q psy17644        320 LDEADRMFD  328 (330)
Q Consensus       320 vDEad~lld  328 (330)
                      |||||+|++
T Consensus       241 iDEah~~~~  249 (479)
T 3fmp_B          241 LDEADVMIA  249 (479)
T ss_dssp             ECCHHHHHT
T ss_pred             EECHHHHhh
Confidence            999999986

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.95  E-value=3.3e-27  Score=223.64  Aligned_cols=155  Identities=30%  Similarity=0.570  Sum_probs=137.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCC--CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCe
Q psy17644        165 PVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPM  242 (330)
Q Consensus       165 p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g--~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~  242 (330)
                      ...+|++++|++.+++++.+.||..|+|+|.++++.++.+  +++++++|||+|||++|++|++.++...     ..+++
T Consensus         3 ~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~-----~~~~~   77 (395)
T 3pey_A            3 MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPE-----DASPQ   77 (395)
T ss_dssp             -CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT-----CCSCC
T ss_pred             cccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccC-----CCCcc
Confidence            3578999999999999999999999999999999999988  9999999999999999999999886543     25789


Q ss_pred             EEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeec
Q psy17644        243 GLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDE  322 (330)
Q Consensus       243 vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDE  322 (330)
                      +|||+||++|+.|+++.+++++...++.+..++++......    ..+++|+|+||++|..++.+....+.++.+|||||
T Consensus        78 ~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDE  153 (395)
T 3pey_A           78 AICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK----QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDE  153 (395)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTTS----CBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEET
T ss_pred             EEEECCCHHHHHHHHHHHHHHhcccCeeEEEEecCchhhhc----cCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEC
Confidence            99999999999999999999998888888888877653321    23689999999999999988888899999999999


Q ss_pred             ccccCc
Q psy17644        323 ADRMFD  328 (330)
Q Consensus       323 ad~lld  328 (330)
                      ||++++
T Consensus       154 ah~~~~  159 (395)
T 3pey_A          154 ADNMLD  159 (395)
T ss_dssp             HHHHHH
T ss_pred             hhhhcC
Confidence            999875

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.95  E-value=4.4e-27  Score=220.64  Aligned_cols=158  Identities=38%  Similarity=0.676  Sum_probs=142.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCC-CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEE
Q psy17644        166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG-RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGL  244 (330)
Q Consensus       166 ~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g-~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vL  244 (330)
                      ..+|.+++|++.+++++.+.||..|+|+|.++++.++++ ++++++++||+|||++|++|++.++..      ..++++|
T Consensus         5 ~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~------~~~~~~l   78 (367)
T 1hv8_A            5 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE------NNGIEAI   78 (367)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS------SSSCCEE
T ss_pred             cCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcc------cCCCcEE
Confidence            356999999999999999999999999999999999988 799999999999999999999887543      2478999


Q ss_pred             EEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccc
Q psy17644        245 ILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD  324 (330)
Q Consensus       245 il~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad  324 (330)
                      ||+||++|+.|+++.+++++...++.+..++||.....+...+. +++|+|+||++|..++.+....+.++.+|||||||
T Consensus        79 il~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah  157 (367)
T 1hv8_A           79 ILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEAD  157 (367)
T ss_dssp             EECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHH
T ss_pred             EEcCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHcCCcccccCCEEEEeCch
Confidence            99999999999999999998888889999999998877666665 58999999999999998888889999999999999


Q ss_pred             ccCcCC
Q psy17644        325 RMFDMG  330 (330)
Q Consensus       325 ~lld~G  330 (330)
                      ++.++|
T Consensus       158 ~~~~~~  163 (367)
T 1hv8_A          158 EMLNMG  163 (367)
T ss_dssp             HHHTTT
T ss_pred             Hhhhhc
Confidence            988764

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.95  E-value=2.1e-27  Score=236.90  Aligned_cols=156  Identities=34%  Similarity=0.531  Sum_probs=134.5

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHhhhhhc--CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q psy17644        174 FDEVLMKALRKCEYTSPTPIQAQAVPAAL--SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE  251 (330)
Q Consensus       174 l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~--~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~  251 (330)
                      |++.+++++.+.||..|||+|.++|+.++  .|+|++++||||||||++|++|++.++...+.. ...++++|||+|||+
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~-~~~~~~~lil~Ptr~  157 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD-SQYMVKAVIVAPTRD  157 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTS-STTSCCEEEECSSHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhcccc-ccCCeeEEEEcCcHH
Confidence            99999999999999999999999999999  679999999999999999999999999875421 234679999999999


Q ss_pred             HHHHHHHHHHHhccC----CCceEEEEECCCchHHHHHHH-hCCCeEEEEChHHHHHHHHcC-CCCCCCccEEEeecccc
Q psy17644        252 LSQQIYNEAKRFGKG----YNLSVVCCYGGGSKWDQSKAL-ELGAEIVVGTPGRIIDMVKMG-ATKLNRVTFLVLDEADR  325 (330)
Q Consensus       252 La~Qi~~~~~~l~~~----~~~~~~~~~gg~~~~~~~~~l-~~~~dIiV~TP~~L~~~l~~~-~~~l~~i~~lVvDEad~  325 (330)
                      ||.|+++.+++++..    ....+..++||.....+...+ ..+++||||||++|.+++.+. ...++.+.+|||||||+
T Consensus       158 La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~  237 (563)
T 3i5x_A          158 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADR  237 (563)
T ss_dssp             HHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHH
T ss_pred             HHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHH
Confidence            999999999997542    245688889998877766555 447899999999999988764 33578899999999999


Q ss_pred             cCcCC
Q psy17644        326 MFDMG  330 (330)
Q Consensus       326 lld~G  330 (330)
                      |++||
T Consensus       238 l~~~~  242 (563)
T 3i5x_A          238 LLEIG  242 (563)
T ss_dssp             HTSTT
T ss_pred             Hhccc
Confidence            99987

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.95  E-value=3.4e-27  Score=225.22  Aligned_cols=160  Identities=30%  Similarity=0.506  Sum_probs=137.6

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCC--CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCC
Q psy17644        161 DPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPG  238 (330)
Q Consensus       161 ~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g--~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~  238 (330)
                      .++.++.+|.+++|++.+++++.+.||..|+|+|.++++.++++  +++++++|||+|||++|++|++.++...     .
T Consensus        19 ~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~-----~   93 (412)
T 3fht_A           19 SPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA-----N   93 (412)
T ss_dssp             STTCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT-----S
T ss_pred             CCccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhc-----C
Confidence            44566889999999999999999999999999999999999987  9999999999999999999999887543     2


Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHc-CCCCCCCcc
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKM-GATKLNRVT  316 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~-~~~~l~~i~  316 (330)
                      .++++|||+||++||.|+++.+++++... +..+....++......   ...+++|+|+||++|..++.+ ....+.++.
T Consensus        94 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~  170 (412)
T 3fht_A           94 KYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIK  170 (412)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCSSCGGGCC
T ss_pred             CCCCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhh---hcCCCCEEEECchHHHHHHHhcCCcChhhCc
Confidence            46799999999999999999999998764 5677777777654332   134579999999999999865 456688999


Q ss_pred             EEEeecccccCc
Q psy17644        317 FLVLDEADRMFD  328 (330)
Q Consensus       317 ~lVvDEad~lld  328 (330)
                      +|||||||+|++
T Consensus       171 ~iViDEah~~~~  182 (412)
T 3fht_A          171 VFVLDEADVMIA  182 (412)
T ss_dssp             EEEEETHHHHHS
T ss_pred             EEEEeCHHHHhh
Confidence            999999999876

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.94  E-value=2e-26  Score=213.89  Aligned_cols=145  Identities=36%  Similarity=0.622  Sum_probs=132.4

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q psy17644        174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELS  253 (330)
Q Consensus       174 l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La  253 (330)
                      |++.|.+++.++||..|+|+|.++++.+++|+++++++|||+|||++|++|++..           ++++|||+||++|+
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~-----------~~~~liv~P~~~L~   69 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL-----------GMKSLVVTPTRELT   69 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH-----------TCCEEEECSSHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh-----------cCCEEEEeCCHHHH
Confidence            5788999999999999999999999999999999999999999999999998864           57899999999999


Q ss_pred             HHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        254 QQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       254 ~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      .|+++.+++++...+..+..++||.....+...+.. ++|+|+||++|..++.+....+.++.+|||||||++.++|
T Consensus        70 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~  145 (337)
T 2z0m_A           70 RQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRN-ADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMG  145 (337)
T ss_dssp             HHHHHHHHHHTTTSCCCEEEECTTSCHHHHHHHHTT-CSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTT
T ss_pred             HHHHHHHHHHhhhcCCcEEEEECCcchHHHHhhcCC-CCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccc
Confidence            999999999998888999999999888776666654 8999999999999998877788999999999999988764

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.93  E-value=3.1e-26  Score=233.00  Aligned_cols=184  Identities=19%  Similarity=0.220  Sum_probs=148.7

Q ss_pred             chhhhhhhcCCCChhhhccCHHHHHHHHHHcCcEeeCCCCCCCCCCCCCCCCCHHHHHHHH--------HCCCCCCCHHH
Q psy17644        123 VYEEVEKNFYQPHEDIARLTPQEAQELRAKSGITVSGADPPYPVSSFGHFGFDEVLMKALR--------KCEYTSPTPIQ  194 (330)
Q Consensus       123 ~~~~~~~~f~~~~~~~~~~~~~~~~~~r~~~~i~~~g~~~p~p~~~f~~~~l~~~l~~~l~--------~~~~~~pt~iQ  194 (330)
                      .+.++...++...+++..++..++......+...+....           .|...+.+++.        ..|+ .|||+|
T Consensus        21 ~~~~~~~~in~~~~~~~~lsd~el~~~t~~~~~~~~~g~-----------~ld~~l~ea~a~vrea~~r~lG~-~pt~VQ   88 (844)
T 1tf5_A           21 RYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGA-----------TTDDLLVEAFAVVREASRRVTGM-FPFKVQ   88 (844)
T ss_dssp             HHHHHHHHHHHTTHHHHTCCHHHHHHHHHHHHHHHHTTC-----------CHHHHHHHHHHHHHHHHHHHHSC-CCCHHH
T ss_pred             HHHHHHHHHHhhhHHHHhCCHHHHHHHHHHHHHHHhcCC-----------ChHHHHHHHHHHHHHHHHHHcCC-CCcHHH
Confidence            467888888888899999999998776665543322111           12333444433        5799 999999


Q ss_pred             HHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEE
Q psy17644        195 AQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCC  274 (330)
Q Consensus       195 ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~  274 (330)
                      ..++|.++.|+  |+.++||+|||++|+||++.+.+        .++.|+||+|||+||.|+++++..++..+++++.++
T Consensus        89 ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL--------~g~~vlVltptreLA~qd~e~~~~l~~~lgl~v~~i  158 (844)
T 1tf5_A           89 LMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNAL--------TGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLN  158 (844)
T ss_dssp             HHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHT--------TSSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEEC
T ss_pred             HHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHH--------cCCCEEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEE
Confidence            99999999999  99999999999999999996654        367899999999999999999999999999999999


Q ss_pred             ECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcC------CCCCCCccEEEeecccccC-cCC
Q psy17644        275 YGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMG------ATKLNRVTFLVLDEADRMF-DMG  330 (330)
Q Consensus       275 ~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~------~~~l~~i~~lVvDEad~ll-d~G  330 (330)
                      +||.+...+..  ..++||+||||++| ++++...      ...++.+.++||||||+|| |+|
T Consensus       159 ~gg~~~~~r~~--~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea  220 (844)
T 1tf5_A          159 LNSMSKDEKRE--AYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEA  220 (844)
T ss_dssp             CTTSCHHHHHH--HHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTT
T ss_pred             eCCCCHHHHHH--hcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhcc
Confidence            99988654433  34689999999999 7777543      2457899999999999998 764

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.93  E-value=5.2e-26  Score=218.40  Aligned_cols=141  Identities=19%  Similarity=0.184  Sum_probs=119.8

Q ss_pred             HHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q psy17644        178 LMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIY  257 (330)
Q Consensus       178 l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~  257 (330)
                      +.+.+++.....|||+|.++++.+++|+|+++++|||||||++|++|++..+        ..++++|||+|||+||.|++
T Consensus        10 ~~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~--------~~~~~~lil~Pt~~L~~q~~   81 (414)
T 3oiy_A           10 FRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA--------RKGKKSALVFPTVTLVKQTL   81 (414)
T ss_dssp             HHHHHHHHHSSCCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHH--------TTTCCEEEEESSHHHHHHHH
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHh--------cCCCEEEEEECCHHHHHHHH
Confidence            4444554333489999999999999999999999999999999999988765        24789999999999999999


Q ss_pred             HHHHHhccCCCceEEEEECCCch---HHHHHHHhCC-CeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcC
Q psy17644        258 NEAKRFGKGYNLSVVCCYGGGSK---WDQSKALELG-AEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       258 ~~~~~l~~~~~~~~~~~~gg~~~---~~~~~~l~~~-~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~  329 (330)
                      +.+++++. .++++..++||...   ..+...+..+ ++|+|+||++|.+++..  ..+.++.+|||||||++++|
T Consensus        82 ~~~~~~~~-~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~iViDEaH~~~~~  154 (414)
T 3oiy_A           82 ERLQKLAD-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKA  154 (414)
T ss_dssp             HHHHHHCC-SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCCSEEEESCHHHHHHC
T ss_pred             HHHHHHcc-CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccccEEEEeChHhhhhc
Confidence            99999988 78999999999987   5555666665 99999999999988764  56779999999999876543

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=99.92  E-value=8.5e-25  Score=216.63  Aligned_cols=142  Identities=22%  Similarity=0.196  Sum_probs=120.2

Q ss_pred             CCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        186 EYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      +...|+|+|.++++.+++|++++++++||+|||++|++|++..+...+.   ..++++|||+||++|+.|++..+++++.
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~---~~~~~~lil~P~~~L~~q~~~~~~~~~~   80 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA---GRKAKVVFLATKVPVYEQQKNVFKHHFE   80 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS---SCCCCEEEECSSHHHHHHHHHHHHHHHG
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcc---cCCCeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            4568999999999999999999999999999999999999988876432   2378999999999999999999999998


Q ss_pred             CCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC-CCCCccEEEeecccccCcCC
Q psy17644        266 GYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT-KLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       266 ~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~-~l~~i~~lVvDEad~lld~G  330 (330)
                      ..++++..++|+.....+...+..+++|+|+||++|..++..... .+.++.+|||||||++.++|
T Consensus        81 ~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~  146 (556)
T 4a2p_A           81 RQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNH  146 (556)
T ss_dssp             GGTCCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTS
T ss_pred             ccCceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcc
Confidence            888999999999877666666666789999999999999988777 78999999999999998765

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.91  E-value=1.9e-24  Score=213.62  Aligned_cols=140  Identities=19%  Similarity=0.194  Sum_probs=124.6

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      .+|+|+|.++++.+++|++++++++||+|||++|++|++.++...+.   ..++++|||+||++|+.|++..+++++...
T Consensus         3 ~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~---~~~~~~lil~P~~~L~~q~~~~~~~~~~~~   79 (555)
T 3tbk_A            3 LKPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPC---GQKGKVVFFANQIPVYEQQATVFSRYFERL   79 (555)
T ss_dssp             CCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS---SCCCCEEEECSSHHHHHHHHHHHHHHHHTT
T ss_pred             CCCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhccc---CCCCEEEEEeCCHHHHHHHHHHHHHHhccC
Confidence            36999999999999999999999999999999999999998876432   247899999999999999999999999888


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC-CCCCccEEEeecccccCcCC
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT-KLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~-~l~~i~~lVvDEad~lld~G  330 (330)
                      ++++..++|+.....+...+..+++|+|+||++|..++..... .+.++.+|||||||++...|
T Consensus        80 ~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~  143 (555)
T 3tbk_A           80 GYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNH  143 (555)
T ss_dssp             TCCEEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTC
T ss_pred             CcEEEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcc
Confidence            9999999999877666666666789999999999999988776 68899999999999998754

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.91  E-value=4.4e-24  Score=217.86  Aligned_cols=146  Identities=18%  Similarity=0.185  Sum_probs=124.3

Q ss_pred             HHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q psy17644        180 KALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE  259 (330)
Q Consensus       180 ~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~  259 (330)
                      .++..+|+..|+|+|.++++.++.|+++|++++||+|||++|++|++.++...+.   ..++++|||+||++|+.|++..
T Consensus         4 ~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~---~~~~~~lvl~Pt~~L~~Q~~~~   80 (696)
T 2ykg_A            4 SDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQ---GQKGKVVFFANQIPVYEQNKSV   80 (696)
T ss_dssp             ---CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCT---TCCCCEEEECSSHHHHHHHHHH
T ss_pred             CcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCcc---CCCCeEEEEECCHHHHHHHHHH
Confidence            4556789999999999999999999999999999999999999999998876431   2347899999999999999999


Q ss_pred             HHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC-CCCCccEEEeecccccCc
Q psy17644        260 AKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT-KLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       260 ~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~-~l~~i~~lVvDEad~lld  328 (330)
                      +++++...++++..++||.....+...+..+++|+|+||++|.+++..... .++++.+|||||||++..
T Consensus        81 ~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~  150 (696)
T 2ykg_A           81 FSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSK  150 (696)
T ss_dssp             HHHHTTTTTCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCST
T ss_pred             HHHHhccCCceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccC
Confidence            999998888999999998876555555666799999999999999988766 688999999999999753

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.90  E-value=8e-24  Score=212.35  Aligned_cols=149  Identities=19%  Similarity=0.302  Sum_probs=124.8

Q ss_pred             CCCCC--CCCCCHHHHHHHHH-CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCe
Q psy17644        166 VSSFG--HFGFDEVLMKALRK-CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPM  242 (330)
Q Consensus       166 ~~~f~--~~~l~~~l~~~l~~-~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~  242 (330)
                      ...|.  .+++++.+...|++ .||..|+|+|.++|+.+++|+|+++++|||+|||++|++|++.+           .++
T Consensus        18 ~~~w~~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~-----------~g~   86 (591)
T 2v1x_A           18 PAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS-----------DGF   86 (591)
T ss_dssp             GGGGCCSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS-----------SSE
T ss_pred             hhccccccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc-----------CCc
Confidence            34454  57889999999998 69999999999999999999999999999999999999999752           468


Q ss_pred             EEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---H---hCCCeEEEEChHHHH------HHHHcCCC
Q psy17644        243 GLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---L---ELGAEIVVGTPGRII------DMVKMGAT  310 (330)
Q Consensus       243 vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l---~~~~dIiV~TP~~L~------~~l~~~~~  310 (330)
                      +|||+||++|+.|++..++++    ++.+..+.|+.........   +   ...++|||+||++|.      ..+.+ ..
T Consensus        87 ~lVisP~~~L~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~-~~  161 (591)
T 2v1x_A           87 TLVICPLISLMEDQLMVLKQL----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEK-AY  161 (591)
T ss_dssp             EEEECSCHHHHHHHHHHHHHH----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHH-HH
T ss_pred             EEEEeCHHHHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHh-hh
Confidence            999999999999999999987    6788888888876654332   2   346899999999874      22322 33


Q ss_pred             CCCCccEEEeecccccCcCC
Q psy17644        311 KLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       311 ~l~~i~~lVvDEad~lld~G  330 (330)
                      .+.++.+|||||||+|++||
T Consensus       162 ~~~~i~~iViDEAH~is~~g  181 (591)
T 2v1x_A          162 EARRFTRIAVDEVHCCSQWG  181 (591)
T ss_dssp             HTTCEEEEEEETGGGGSTTC
T ss_pred             hccCCcEEEEECcccccccc
Confidence            46789999999999999997

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.90  E-value=4.2e-25  Score=235.10  Aligned_cols=144  Identities=19%  Similarity=0.171  Sum_probs=124.8

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc
Q psy17644        168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA  247 (330)
Q Consensus       168 ~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~  247 (330)
                      .|..++++..+...+...++..|||+|.++|+.+.+|++++++|+||||||++|++|++..+.        +++++||++
T Consensus       163 ~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~--------~g~rvlvl~  234 (1108)
T 3l9o_A          163 NYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK--------NKQRVIYTS  234 (1108)
T ss_dssp             CCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHH--------TTCEEEEEE
T ss_pred             CcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHh--------cCCeEEEEc
Confidence            566777777766666677788899999999999999999999999999999999999998873        368999999


Q ss_pred             ccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        248 PTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       248 Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      |||+|+.|++..+++++.    .+..+.|+...       ..+++|+|+||++|.+++.+....++++.+|||||||+|+
T Consensus       235 PtraLa~Q~~~~l~~~~~----~VglltGd~~~-------~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~  303 (1108)
T 3l9o_A          235 PIKALSNQKYRELLAEFG----DVGLMTGDITI-------NPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMR  303 (1108)
T ss_dssp             SSHHHHHHHHHHHHHHTS----SEEEECSSCBC-------CCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTT
T ss_pred             CcHHHHHHHHHHHHHHhC----CccEEeCcccc-------CCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhcc
Confidence            999999999999999865    46667777663       3458999999999999998887778899999999999998


Q ss_pred             cCC
Q psy17644        328 DMG  330 (330)
Q Consensus       328 d~G  330 (330)
                      ++|
T Consensus       304 d~~  306 (1108)
T 3l9o_A          304 DKE  306 (1108)
T ss_dssp             SHH
T ss_pred             ccc
Confidence            764

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=99.90  E-value=3.7e-24  Score=217.38  Aligned_cols=133  Identities=18%  Similarity=0.164  Sum_probs=116.2

Q ss_pred             CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        185 CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .| ..|+++|..++|.++.|+  |+.++||+|||++|++|++.+.+        .++.|+||+|||+||.|++..+..++
T Consensus        71 lg-~~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l--------~g~~vlVltPTreLA~Q~~e~~~~l~  139 (853)
T 2fsf_A           71 FG-MRHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNAL--------TGKGVHVVTVNDYLAQRDAENNRPLF  139 (853)
T ss_dssp             HS-CCCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHT--------TSSCCEEEESSHHHHHHHHHHHHHHH
T ss_pred             cC-CCCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHH--------cCCcEEEEcCCHHHHHHHHHHHHHHH
Confidence            45 489999999999999998  99999999999999999997654        36789999999999999999999999


Q ss_pred             cCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcCC------CCCCCccEEEeecccccC-cCC
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMGA------TKLNRVTFLVLDEADRMF-DMG  330 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~~------~~l~~i~~lVvDEad~ll-d~G  330 (330)
                      ..+++++.+++||.+...  +.+..+++|+||||++| ++++..+.      ..++.+.++||||||+|| |+|
T Consensus       140 ~~lgl~v~~i~GG~~~~~--r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a  211 (853)
T 2fsf_A          140 EFLGLTVGINLPGMPAPA--KREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEA  211 (853)
T ss_dssp             HHTTCCEEECCTTCCHHH--HHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTT
T ss_pred             HhcCCeEEEEeCCCCHHH--HHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcC
Confidence            999999999999988643  33444689999999999 78887543      457899999999999999 654

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.90  E-value=4.3e-24  Score=211.68  Aligned_cols=149  Identities=18%  Similarity=0.247  Sum_probs=124.8

Q ss_pred             CCCCCCCCCHHHHHHHHH-CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        167 SSFGHFGFDEVLMKALRK-CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~-~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      .+|++++|++.+.+.|++ .||..|+|+|.++|+.+++|+|+++++|||+|||++|++|++..           .+++||
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~-----------~g~~lv   70 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL-----------NGLTVV   70 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS-----------SSEEEE
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh-----------CCCEEE
Confidence            579999999999999998 79999999999999999999999999999999999999999843           367999


Q ss_pred             EcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHH----HHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEee
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK----ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLD  321 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~----~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvD  321 (330)
                      |+|+++|+.|++..++.+    ++.+..+.|+........    .....++|+|+||++|............++.+||||
T Consensus        71 i~P~~aL~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViD  146 (523)
T 1oyw_A           71 VSPLISLMKDQVDQLQAN----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVD  146 (523)
T ss_dssp             ECSCHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEES
T ss_pred             ECChHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEe
Confidence            999999999999999886    667788888776554332    223458999999999963211112234789999999


Q ss_pred             cccccCcCC
Q psy17644        322 EADRMFDMG  330 (330)
Q Consensus       322 Ead~lld~G  330 (330)
                      |||++.+||
T Consensus       147 EaH~i~~~g  155 (523)
T 1oyw_A          147 EAHCISQWG  155 (523)
T ss_dssp             SGGGGCTTS
T ss_pred             CccccCcCC
Confidence            999999997

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.90  E-value=8.4e-24  Score=217.06  Aligned_cols=151  Identities=23%  Similarity=0.299  Sum_probs=132.3

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhh-hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPA-ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       168 ~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~-~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      +|.+++|++.+.+.+.+.||..|+|+|.++++. +..++++++++|||||||++|.+|++.++...       +.++||+
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~-------~~~~l~i   74 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ-------GGKAVYI   74 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH-------CSEEEEE
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC-------CCEEEEE
Confidence            588999999999999999999999999999998 88999999999999999999999999888752       6799999


Q ss_pred             cccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      +|||+||.|++..++++.. .++++..++|+......  . ...++|+|+||++|..++.+....++++.+|||||||++
T Consensus        75 ~P~raLa~q~~~~~~~l~~-~g~~v~~~~G~~~~~~~--~-~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l  150 (720)
T 2zj8_A           75 VPLKALAEEKFQEFQDWEK-IGLRVAMATGDYDSKDE--W-LGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLI  150 (720)
T ss_dssp             CSSGGGHHHHHHHTGGGGG-GTCCEEEECSCSSCCCG--G-GGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGG
T ss_pred             cCcHHHHHHHHHHHHHHHh-cCCEEEEecCCCCcccc--c-cCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCccc
Confidence            9999999999999976654 47888888887654332  1 235899999999999999887666899999999999999


Q ss_pred             CcC
Q psy17644        327 FDM  329 (330)
Q Consensus       327 ld~  329 (330)
                      .++
T Consensus       151 ~~~  153 (720)
T 2zj8_A          151 GSR  153 (720)
T ss_dssp             GCT
T ss_pred             CCC
Confidence            864

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=99.90  E-value=1.4e-23  Score=217.78  Aligned_cols=142  Identities=22%  Similarity=0.199  Sum_probs=120.4

Q ss_pred             CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        185 CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|+..|+|+|.++++.+++|++++++++||+|||++|++|++.++...+.   ..++++|||+||++|+.|++..+++++
T Consensus       244 ~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~---~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~  320 (797)
T 4a2q_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA---GRKAKVVFLATKVPVYEQQKNVFKHHF  320 (797)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS---SCCCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccc---cCCCeEEEEeCCHHHHHHHHHHHHHhc
Confidence            46789999999999999999999999999999999999999998876421   237899999999999999999999999


Q ss_pred             cCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC-CCCCccEEEeecccccCcC
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT-KLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~-~l~~i~~lVvDEad~lld~  329 (330)
                      ...++++..++||.....+...+..+++||||||++|..++.+... .+.++.+|||||||++...
T Consensus       321 ~~~~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~  386 (797)
T 4a2q_A          321 ERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGN  386 (797)
T ss_dssp             GGGTCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTT
T ss_pred             ccCCceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCC
Confidence            8888999999999977766666777899999999999999987766 6889999999999998764

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.90  E-value=1.3e-23  Score=215.38  Aligned_cols=152  Identities=22%  Similarity=0.295  Sum_probs=132.6

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhh-hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPA-ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~-~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      .+|.+++|++.+.+.+.+.||..|+|+|.++++. +.++++++++||||||||++|.++++.++..       ++.++||
T Consensus         8 ~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~-------~~~~il~   80 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLK-------NGGKAIY   80 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHH-------SCSEEEE
T ss_pred             CcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHH-------CCCeEEE
Confidence            5699999999999999999999999999999999 7899999999999999999999999988765       3679999


Q ss_pred             EcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      ++|||+||.|++..++++.. .++++..++|+......  .+ .+++|+|+||++|..++.+....++++.+|||||||.
T Consensus        81 i~P~r~La~q~~~~~~~~~~-~g~~v~~~~G~~~~~~~--~~-~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~  156 (715)
T 2va8_A           81 VTPLRALTNEKYLTFKDWEL-IGFKVAMTSGDYDTDDA--WL-KNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHY  156 (715)
T ss_dssp             ECSCHHHHHHHHHHHGGGGG-GTCCEEECCSCSSSCCG--GG-GGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGG
T ss_pred             EeCcHHHHHHHHHHHHHhhc-CCCEEEEEeCCCCCchh--hc-CCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhh
Confidence            99999999999999966543 47888888887654332  12 2589999999999999988766689999999999999


Q ss_pred             cCcC
Q psy17644        326 MFDM  329 (330)
Q Consensus       326 lld~  329 (330)
                      +.++
T Consensus       157 l~~~  160 (715)
T 2va8_A          157 LNDP  160 (715)
T ss_dssp             GGCT
T ss_pred             cCCc
Confidence            8764

>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=99.89  E-value=1.1e-23  Score=183.79  Aligned_cols=141  Identities=20%  Similarity=0.210  Sum_probs=107.2

Q ss_pred             CCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHH-HHHHHHHhc
Q psy17644        186 EYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQ-IYNEAKRFG  264 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Q-i~~~~~~l~  264 (330)
                      ....|+++|.++++.++++++++++++||+|||++|+++++.++...+.  ...++++|||+||++|+.| +.+.+.++.
T Consensus        30 ~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~--~~~~~~~lil~p~~~L~~q~~~~~~~~~~  107 (216)
T 3b6e_A           30 PELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKK--ASEPGKVIVLVNKVLLVEQLFRKEFQPFL  107 (216)
T ss_dssp             CCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHH--TTCCCCEEEEESSHHHHHHHHHHTHHHHH
T ss_pred             CCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhccc--ccCCCcEEEEECHHHHHHHHHHHHHHHHh
Confidence            4568999999999999999999999999999999999999987765321  1246789999999999999 777888886


Q ss_pred             cCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCC------CCCCCccEEEeecccccCcC
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGA------TKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~------~~l~~i~~lVvDEad~lld~  329 (330)
                      .. ++++..+.|+.........+..+++|+|+||++|..++....      ..+.++.+|||||||+++..
T Consensus       108 ~~-~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~  177 (216)
T 3b6e_A          108 KK-WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKE  177 (216)
T ss_dssp             TT-TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC------
T ss_pred             cc-CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccC
Confidence            54 677777877765444333444468999999999999887643      45788999999999999754

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=99.89  E-value=1.4e-23  Score=222.93  Aligned_cols=136  Identities=20%  Similarity=0.241  Sum_probs=118.9

Q ss_pred             HHHH-HCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        180 KALR-KCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       180 ~~l~-~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      +.+. ..||. | |+|.++||.+++|+|++++|+||||||+ |++|++.++..       .++++|||+|||+||.|+++
T Consensus        48 ~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~-------~~~~~lil~PtreLa~Q~~~  117 (1054)
T 1gku_B           48 EFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL-------KGKRCYVIFPTSLLVIQAAE  117 (1054)
T ss_dssp             HHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT-------TSCCEEEEESCHHHHHHHHH
T ss_pred             HHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh-------cCCeEEEEeccHHHHHHHHH
Confidence            3443 36898 9 9999999999999999999999999998 99999988765       47899999999999999999


Q ss_pred             HHHHhccCCCc----eEEEEECCCchHHH---HHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        259 EAKRFGKGYNL----SVVCCYGGGSKWDQ---SKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       259 ~~~~l~~~~~~----~~~~~~gg~~~~~~---~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      .+++++...++    ++.+++||.....+   ...+.. ++|+||||++|.+++.+    ++++.+|||||||+|++||
T Consensus       118 ~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~~~  191 (1054)
T 1gku_B          118 TIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILKAS  191 (1054)
T ss_dssp             HHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHTST
T ss_pred             HHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhhcc
Confidence            99999988888    88999999887663   344555 89999999999998765    6799999999999999854

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.89  E-value=6.9e-24  Score=217.14  Aligned_cols=151  Identities=21%  Similarity=0.264  Sum_probs=128.3

Q ss_pred             CCCCCC--CCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        168 SFGHFG--FDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       168 ~f~~~~--l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      +|++++  |++.+.+.+++.||..|+|+|.++++.+++++++++++|||||||++|.++++.++..        ++++||
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~--------~~~~l~   73 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK--------GGKSLY   73 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT--------TCCEEE
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh--------CCcEEE
Confidence            477888  9999999999999999999999999999999999999999999999999999988653        578999


Q ss_pred             EcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      ++|||+||.|++..++++. ..++++..++|+......   ....++|+|+||++|..++.+....++++.+|||||||.
T Consensus        74 i~P~r~La~q~~~~~~~~~-~~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~  149 (702)
T 2p6r_A           74 VVPLRALAGEKYESFKKWE-KIGLRIGISTGDYESRDE---HLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHL  149 (702)
T ss_dssp             EESSHHHHHHHHHHHTTTT-TTTCCEEEECSSCBCCSS---CSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGG
T ss_pred             EeCcHHHHHHHHHHHHHHH-hcCCEEEEEeCCCCcchh---hccCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeee
Confidence            9999999999999997654 347888888887654332   113689999999999999988766688999999999999


Q ss_pred             cCcCC
Q psy17644        326 MFDMG  330 (330)
Q Consensus       326 lld~G  330 (330)
                      |.+++
T Consensus       150 l~~~~  154 (702)
T 2p6r_A          150 LDSEK  154 (702)
T ss_dssp             GGCTT
T ss_pred             cCCCC
Confidence            98753

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=99.89  E-value=3.4e-23  Score=210.84  Aligned_cols=133  Identities=20%  Similarity=0.225  Sum_probs=116.1

Q ss_pred             HCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        184 KCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       184 ~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..|+ .||++|..++|.++.|+  |+.++||+|||++|+||++.+.+.        +..|+||+||++||.|+++++..+
T Consensus       107 ~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~--------g~~v~VvTpTreLA~Qdae~m~~l  175 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALA--------GNGVHIVTVNDYLAKRDSEWMGRV  175 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTT--------TSCEEEEESSHHHHHHHHHHHHHH
T ss_pred             HcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHh--------CCCeEEEeCCHHHHHHHHHHHHHH
Confidence            4687 99999999999999998  999999999999999999866553        568999999999999999999999


Q ss_pred             ccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcC------CCCCCCccEEEeecccccC-cC
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMG------ATKLNRVTFLVLDEADRMF-DM  329 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~------~~~l~~i~~lVvDEad~ll-d~  329 (330)
                      +..+|+++.+++||.+......  ..+|+|+||||++| ++++..+      ...++.+.++||||||+|| |+
T Consensus       176 ~~~lGLsv~~i~gg~~~~~r~~--~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDe  247 (922)
T 1nkt_A          176 HRFLGLQVGVILATMTPDERRV--AYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDE  247 (922)
T ss_dssp             HHHTTCCEEECCTTCCHHHHHH--HHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTG
T ss_pred             HhhcCCeEEEEeCCCCHHHHHH--hcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhc
Confidence            9999999999999988654333  33689999999999 8888654      3457899999999999998 54

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.88  E-value=8.1e-23  Score=217.47  Aligned_cols=132  Identities=20%  Similarity=0.199  Sum_probs=116.0

Q ss_pred             CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        185 CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|| .|||+|.++||.+++|+|++++|+||||||++|+++++..+        ..++++|||+|||+||.|+++.+++|+
T Consensus        75 ~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~--------~~~~~~Lil~PtreLa~Q~~~~l~~l~  145 (1104)
T 4ddu_A           75 FGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA--------RKGKKSALVFPTVTLVKQTLERLQKLA  145 (1104)
T ss_dssp             SSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHH--------TTTCCEEEEESSHHHHHHHHHHHHTTS
T ss_pred             cCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHH--------hcCCeEEEEechHHHHHHHHHHHHHhh
Confidence            566 69999999999999999999999999999998888877765        257899999999999999999999988


Q ss_pred             cCCCceEEEEECCCch---HHHHHHHhCC-CeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        265 KGYNLSVVCCYGGGSK---WDQSKALELG-AEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~---~~~~~~l~~~-~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                       ..++++..++||...   ..+...+..+ ++||||||++|.+++..  ..++++.+|||||||+++.
T Consensus       146 -~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l~~lViDEaH~l~~  210 (1104)
T 4ddu_A          146 -DEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLK  210 (1104)
T ss_dssp             -CTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCCSEEEESCHHHHTT
T ss_pred             -CCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCcCEEEEeCCCcccc
Confidence             778999999999987   6666777776 99999999999888764  5578999999999976553

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=99.88  E-value=7.3e-23  Score=215.41  Aligned_cols=142  Identities=22%  Similarity=0.199  Sum_probs=118.4

Q ss_pred             CCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        185 CEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .++..|+|+|.++++.+++|++++++++||+|||++|++|++.++...+.   ..++++|||+||++|+.|++..+++++
T Consensus       244 ~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~---~~~~~vLvl~Pt~~L~~Q~~~~~~~~~  320 (936)
T 4a2w_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA---GRKAKVVFLATKVPVYEQQKNVFKHHF  320 (936)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCS---SCCCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccc---cCCCeEEEEeCCHHHHHHHHHHHHHHh
Confidence            36788999999999999999999999999999999999999887755321   237889999999999999999999999


Q ss_pred             cCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC-CCCCccEEEeecccccCcC
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT-KLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~-~l~~i~~lVvDEad~lld~  329 (330)
                      ...++++..++|+.....+...+..+++|+|+||++|..++.+... .+.++.+|||||||++...
T Consensus       321 ~~~~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~  386 (936)
T 4a2w_A          321 ERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGN  386 (936)
T ss_dssp             HTTTCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTT
T ss_pred             cccCceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCC
Confidence            8888999999999876665555556789999999999999987766 6889999999999998764

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.88  E-value=2.5e-22  Score=204.05  Aligned_cols=131  Identities=17%  Similarity=0.168  Sum_probs=115.1

Q ss_pred             HCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        184 KCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       184 ~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..|+ .||++|..++|.+++|+  |+.++||+|||++|++|++.+.+.        +..|+||+||++||.|++..+..+
T Consensus        75 ~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~--------G~qv~VvTPTreLA~Qdae~m~~l  143 (997)
T 2ipc_A           75 YLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALT--------GKGVHVVTVNDYLARRDAEWMGPV  143 (997)
T ss_dssp             HTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT--------CSCCEEEESSHHHHHHHHHHHHHH
T ss_pred             HhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHh--------CCCEEEEeCCHHHHHHHHHHHHHH
Confidence            3688 99999999999999998  999999999999999999766543        568999999999999999999999


Q ss_pred             ccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcCC------CCCC---CccEEEeecccccC
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMGA------TKLN---RVTFLVLDEADRMF  327 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~~------~~l~---~i~~lVvDEad~ll  327 (330)
                      +..+++++.+++||.+.....  ...+++|+||||++| ++++..+.      ..++   .+.++||||||+||
T Consensus       144 ~~~lGLsv~~i~Gg~~~~~r~--~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmL  215 (997)
T 2ipc_A          144 YRGLGLSVGVIQHASTPAERR--KAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSIL  215 (997)
T ss_dssp             HHTTTCCEEECCTTCCHHHHH--HHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHT
T ss_pred             HHhcCCeEEEEeCCCCHHHHH--HHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHH
Confidence            999999999999998854433  334689999999999 89887653      3477   89999999999998

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.85  E-value=3.7e-21  Score=211.74  Aligned_cols=147  Identities=21%  Similarity=0.260  Sum_probs=122.3

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHhhhhhcC-CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q psy17644        174 FDEVLMKALRKCEYTSPTPIQAQAVPAALS-GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL  252 (330)
Q Consensus       174 l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~-g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~L  252 (330)
                      |+....+++...+|..++|+|.++++.++. +++++++||||||||++|.+|+++++...      .+.++|||+|||+|
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~------~~~kavyi~P~raL  984 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQS------SEGRCVYITPMEAL  984 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHC------TTCCEEEECSCHHH
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhC------CCCEEEEEcChHHH
Confidence            556677788888899999999999999975 56899999999999999999999998764      46789999999999


Q ss_pred             HHHHHHHHHH-hccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC--CCCCccEEEeecccccCcC
Q psy17644        253 SQQIYNEAKR-FGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT--KLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       253 a~Qi~~~~~~-l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~--~l~~i~~lVvDEad~lld~  329 (330)
                      |.|++..+++ |+...++++..++|+.....  +.+ .+++||||||++|..+++++..  .+++|.+||+||+|+|.+.
T Consensus       985 a~q~~~~~~~~f~~~~g~~V~~ltGd~~~~~--~~~-~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~ 1061 (1724)
T 4f92_B          985 AEQVYMDWYEKFQDRLNKKVVLLTGETSTDL--KLL-GKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGE 1061 (1724)
T ss_dssp             HHHHHHHHHHHHTTTSCCCEEECCSCHHHHH--HHH-HHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGST
T ss_pred             HHHHHHHHHHHhchhcCCEEEEEECCCCcch--hhc-CCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCC
Confidence            9999999875 66667889888888654332  222 3479999999999888876543  3789999999999988763

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=99.85  E-value=9.6e-22  Score=200.67  Aligned_cols=138  Identities=20%  Similarity=0.246  Sum_probs=111.8

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH-HHHHHHhccC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQI-YNEAKRFGKG  266 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi-~~~~~~l~~~  266 (330)
                      ..|+|+|.++++.+++|++++++++||+|||++|++|++.++...+.  ...+.++|||+||++|+.|+ +..+++++..
T Consensus         6 ~~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~--~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~   83 (699)
T 4gl2_A            6 LQLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKK--ASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK   83 (699)
T ss_dssp             -CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHH--HTCCCCBCCEESCSHHHHHHHHHTHHHHHTT
T ss_pred             CCccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccc--cCCCCeEEEEECCHHHHHHHHHHHHHHHcCc
Confidence            46999999999999999999999999999999999999988876421  12347899999999999999 9999998765


Q ss_pred             CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHH------HcCCCCCCCccEEEeecccccCc
Q psy17644        267 YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMV------KMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       267 ~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l------~~~~~~l~~i~~lVvDEad~lld  328 (330)
                       ++++..++|+.........+...++|||+||++|...+      ......+..+.+|||||||++..
T Consensus        84 -~~~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~  150 (699)
T 4gl2_A           84 -WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNK  150 (699)
T ss_dssp             -TSCEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBT
T ss_pred             -CceEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCc
Confidence             57888888887765555555567899999999999988      44456788999999999999853

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=99.84  E-value=1.8e-20  Score=192.77  Aligned_cols=136  Identities=20%  Similarity=0.271  Sum_probs=115.5

Q ss_pred             HHHHHHHHCCCCCCCHHHHHhhhhhcCC------CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q psy17644        177 VLMKALRKCEYTSPTPIQAQAVPAALSG------RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR  250 (330)
Q Consensus       177 ~l~~~l~~~~~~~pt~iQ~~~i~~~~~g------~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr  250 (330)
                      .+...+...+| .||++|.++|+.++++      ++++++|+||||||++|++|++..+..        +.++|||+||+
T Consensus       357 ~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~--------g~qvlvlaPtr  427 (780)
T 1gm5_A          357 LAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA--------GFQTAFMVPTS  427 (780)
T ss_dssp             HHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH--------TSCEEEECSCH
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc--------CCeEEEEeCcH
Confidence            34444567888 8999999999998865      699999999999999999999988743        68999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEECCCchHHH---HHHHhCC-CeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        251 ELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ---SKALELG-AEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       251 ~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~---~~~l~~~-~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      +||.|+++.+++++...++++..++|+......   ...+..+ ++|+|+||+.|..     ...+.++.+|||||||++
T Consensus       428 ~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l~lVVIDEaHr~  502 (780)
T 1gm5_A          428 ILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRF  502 (780)
T ss_dssp             HHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC
T ss_pred             HHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-----hhhccCCceEEecccchh
Confidence            999999999999998889999999999876553   3334444 8999999987754     356889999999999996

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=99.84  E-value=5.4e-20  Score=177.55  Aligned_cols=131  Identities=27%  Similarity=0.266  Sum_probs=113.3

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCC
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN  268 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~  268 (330)
                      .|+|+|.++++.++.+ ++++.++||+|||++++++++.++..       .+.++|||+||++|+.|+.+.+.+++...+
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~-------~~~~~liv~P~~~L~~q~~~~~~~~~~~~~   80 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTK-------YGGKVLMLAPTKPLVLQHAESFRRLFNLPP   80 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHH-------SCSCEEEECSSHHHHHHHHHHHHHHBCSCG
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhc-------CCCeEEEEECCHHHHHHHHHHHHHHhCcch
Confidence            6899999999999998 99999999999999999999887762       467899999999999999999999975445


Q ss_pred             ceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        269 LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       269 ~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      .++..+.|+.......... .+++|+|+||+.|...+.+....+.++.+|||||||++..
T Consensus        81 ~~v~~~~g~~~~~~~~~~~-~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~  139 (494)
T 1wp9_A           81 EKIVALTGEKSPEERSKAW-ARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVG  139 (494)
T ss_dssp             GGEEEECSCSCHHHHHHHH-HHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCST
T ss_pred             hheEEeeCCcchhhhhhhc-cCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCC
Confidence            5888888887766543333 3579999999999999988777889999999999999874

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.83  E-value=1.3e-20  Score=198.91  Aligned_cols=125  Identities=22%  Similarity=0.231  Sum_probs=109.7

Q ss_pred             CCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        186 EYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      +| .|+|+|.++++.+.+|++++++++||||||++|+++++..+.        .+.++||++||++|+.|++..+.+++.
T Consensus        84 ~f-~L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~--------~g~rvL~l~PtkaLa~Q~~~~l~~~~~  154 (1010)
T 2xgj_A           84 PF-TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK--------NKQRVIYTSPIKALSNQKYRELLAEFG  154 (1010)
T ss_dssp             SS-CCCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHH--------TTCEEEEEESSHHHHHHHHHHHHHHHS
T ss_pred             CC-CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhc--------cCCeEEEECChHHHHHHHHHHHHHHhC
Confidence            45 499999999999999999999999999999999999887763        368999999999999999999998765


Q ss_pred             CCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        266 GYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       266 ~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                          .+..++|+....       ..++|+|+||++|..++.++...++++.+|||||||+|.+++
T Consensus       155 ----~vglltGd~~~~-------~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~  208 (1010)
T 2xgj_A          155 ----DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKE  208 (1010)
T ss_dssp             ----CEEEECSSCEEC-------TTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTT
T ss_pred             ----CEEEEeCCCccC-------CCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccc
Confidence                566677776543       257999999999999998887888999999999999998864

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.83  E-value=1.3e-20  Score=207.38  Aligned_cols=140  Identities=24%  Similarity=0.280  Sum_probs=117.3

Q ss_pred             CCCCCCHHHHHhhhhhc-CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCC---CCCCCCeEEEEcccHHHHHHHHHHHH
Q psy17644        186 EYTSPTPIQAQAVPAAL-SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL---EPGDGPMGLILAPTRELSQQIYNEAK  261 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~-~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~---~~~~~~~vLil~Ptr~La~Qi~~~~~  261 (330)
                      ||..++++|++++|.++ +++|++++||||||||++|.+++++.+.+....   ....+.++|||+|||+||.|+++.++
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            78999999999999987 578999999999999999999999999875432   23457899999999999999999999


Q ss_pred             HhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCC--CCCCccEEEeecccccCc
Q psy17644        262 RFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGAT--KLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       262 ~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~--~l~~i~~lVvDEad~lld  328 (330)
                      +.....|+++..++|+......   ....++||||||++|..++++...  .++.|++|||||+|.|-|
T Consensus       156 ~~~~~~gi~V~~~tGd~~~~~~---~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d  221 (1724)
T 4f92_B          156 KRLATYGITVAELTGDHQLCKE---EISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD  221 (1724)
T ss_dssp             HHHTTTTCCEEECCSSCSSCCT---TGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGS
T ss_pred             HHHhhCCCEEEEEECCCCCCcc---ccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCC
Confidence            9888889999999998764322   123589999999999777765433  378999999999997753

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.82  E-value=2.1e-20  Score=197.38  Aligned_cols=125  Identities=20%  Similarity=0.212  Sum_probs=109.5

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCC
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN  268 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~  268 (330)
                      .|+|+|.++|+.+++|++++++++||||||++|+++++..+.        .++++||++||++|+.|+++.+++++.  +
T Consensus        39 ~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~--------~g~~vlvl~PtraLa~Q~~~~l~~~~~--~  108 (997)
T 4a4z_A           39 ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHR--------NMTKTIYTSPIKALSNQKFRDFKETFD--D  108 (997)
T ss_dssp             CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHH--------TTCEEEEEESCGGGHHHHHHHHHTTC----
T ss_pred             CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHh--------cCCeEEEEeCCHHHHHHHHHHHHHHcC--C
Confidence            589999999999999999999999999999999998877643        468999999999999999999998754  5


Q ss_pred             ceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        269 LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       269 ~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      +.+..++|+....       ..++|+|+||++|..++.+....+.++.+|||||||++.+||
T Consensus       109 ~~v~~l~G~~~~~-------~~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d~~  163 (997)
T 4a4z_A          109 VNIGLITGDVQIN-------PDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQD  163 (997)
T ss_dssp             CCEEEECSSCEEC-------TTSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTTC
T ss_pred             CeEEEEeCCCccC-------CCCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccccc
Confidence            6788888877543       347999999999999998877778999999999999999875

>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=99.81  E-value=3.1e-20  Score=169.55  Aligned_cols=127  Identities=21%  Similarity=0.148  Sum_probs=104.0

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      ..|+++|.++++.++.+++.+++++||+|||+++++++..++..       ...++|||+||++|+.|+++.+++++...
T Consensus       112 ~~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~-------~~~~~lil~Pt~~L~~q~~~~l~~~~~~~  184 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN-------YEGKILIIVPTTALTTQMADDFVDYRLFS  184 (282)
T ss_dssp             CCCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHH-------CSSEEEEECSSHHHHHHHHHHHHHHTSCC
T ss_pred             cCccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHc-------CCCeEEEEECCHHHHHHHHHHHHHhcccc
Confidence            37999999999999988899999999999999998887776543       23489999999999999999999998766


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      +..+..++||.....   ....+++|+|+||+.+...   ....+.++.+|||||||++.
T Consensus       185 ~~~~~~~~~~~~~~~---~~~~~~~I~v~T~~~l~~~---~~~~~~~~~~vIiDEaH~~~  238 (282)
T 1rif_A          185 HAMIKKIGGGASKDD---KYKNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLAT  238 (282)
T ss_dssp             GGGEEECSTTCSSTT---CCCTTCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCC
T ss_pred             cceEEEEeCCCcchh---hhccCCcEEEEchHHHHhh---HHHHHhhCCEEEEECCccCC
Confidence            778888888876532   1224589999999877533   22346789999999999985

>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=99.80  E-value=1.1e-19  Score=161.75  Aligned_cols=139  Identities=14%  Similarity=0.095  Sum_probs=104.4

Q ss_pred             HHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q psy17644        180 KALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE  259 (330)
Q Consensus       180 ~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~  259 (330)
                      ..+.......++++|.++++.+..|++++++|+||||||.+|.++++.++.....   ..++++|+++|||+|+.|+.+.
T Consensus        52 ~~~~~~~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~---~~~~~~l~~~p~~~la~q~~~~  128 (235)
T 3llm_A           52 AILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDR---AAECNIVVTQPRRISAVSVAER  128 (235)
T ss_dssp             HHHHHHHTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTC---GGGCEEEEEESSHHHHHHHHHH
T ss_pred             HHHHHHhcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCC---CCceEEEEeccchHHHHHHHHH
Confidence            3333334445789999999999999999999999999999999999888765432   2356899999999999999988


Q ss_pred             HHHhcc-CCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc-CcC
Q psy17644        260 AKRFGK-GYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM-FDM  329 (330)
Q Consensus       260 ~~~l~~-~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l-ld~  329 (330)
                      +..... ..+..+........     .....+++|+||||++|.+++.+   .++++++|||||||++ +++
T Consensus       129 ~~~~~~~~~~~~~g~~~~~~~-----~~~~~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~  192 (235)
T 3llm_A          129 VAFERGEEPGKSCGYSVRFES-----ILPRPHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINT  192 (235)
T ss_dssp             HHHTTTCCTTSSEEEEETTEE-----ECCCSSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHH
T ss_pred             HHHHhccccCceEEEeechhh-----ccCCCCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcch
Confidence            776433 33444433222111     11123579999999999999876   4889999999999986 543

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.79  E-value=1.9e-19  Score=177.18  Aligned_cols=128  Identities=21%  Similarity=0.147  Sum_probs=108.0

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccC
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKG  266 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~  266 (330)
                      ...|+|+|..+++.++++++++++++||+|||++|+++++..+..       .++++|||+||++|+.|+++.+++++..
T Consensus       111 ~~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~-------~~~~vlvl~P~~~L~~Q~~~~~~~~~~~  183 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN-------YEGKILIIVPTTALTTQMADDFVDYRLF  183 (510)
T ss_dssp             EECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHH-------CSSEEEEEESSHHHHHHHHHHHHHTTSS
T ss_pred             CCCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhC-------CCCeEEEEECcHHHHHHHHHHHHHhhcC
Confidence            347999999999999999999999999999999999988877653       2459999999999999999999999776


Q ss_pred             CCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        267 YNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       267 ~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      .+..+..++||.....+   +..+++|+|+||+.|..   .....+.++.+|||||||++.
T Consensus       184 ~~~~v~~~~~~~~~~~~---~~~~~~I~i~T~~~l~~---~~~~~~~~~~liIiDE~H~~~  238 (510)
T 2oca_A          184 SHAMIKKIGGGASKDDK---YKNDAPVVVGTWQTVVK---QPKEWFSQFGMMMNDECHLAT  238 (510)
T ss_dssp             CGGGEEECGGGCCTTGG---GCTTCSEEEEEHHHHTT---SCGGGGGGEEEEEEETGGGCC
T ss_pred             CccceEEEecCCccccc---cccCCcEEEEeHHHHhh---chhhhhhcCCEEEEECCcCCC
Confidence            67788888888776554   45568999999997653   223457789999999999985

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=99.77  E-value=5e-18  Score=181.63  Aligned_cols=141  Identities=23%  Similarity=0.282  Sum_probs=114.2

Q ss_pred             CCCCHHHHHHHHHC-CCCCCCHHHHHhhhhhcC----CC--cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEE
Q psy17644        172 FGFDEVLMKALRKC-EYTSPTPIQAQAVPAALS----GR--DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGL  244 (330)
Q Consensus       172 ~~l~~~l~~~l~~~-~~~~pt~iQ~~~i~~~~~----g~--d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vL  244 (330)
                      ++++....+.+... +| .|||+|.++++.++.    |+  |++++++||+|||.+|+++++..+.        .++++|
T Consensus       586 ~~~~~~~~~~~~~~f~~-~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~--------~g~~vl  656 (1151)
T 2eyq_A          586 FKHDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD--------NHKQVA  656 (1151)
T ss_dssp             CCCCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT--------TTCEEE
T ss_pred             CCCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHH--------hCCeEE
Confidence            45666777776554 55 579999999999885    66  9999999999999999999887653        367999


Q ss_pred             EEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHH---HHHHhC-CCeEEEEChHHHHHHHHcCCCCCCCccEEEe
Q psy17644        245 ILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ---SKALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVL  320 (330)
Q Consensus       245 il~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~---~~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVv  320 (330)
                      ||+||++||.|+++.+++++...++++..+.|.......   ...+.. .++|+|+||..|.     ....++++.+|||
T Consensus       657 vlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~-----~~~~~~~l~lvIi  731 (1151)
T 2eyq_A          657 VLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIV  731 (1151)
T ss_dssp             EECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEE
T ss_pred             EEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh-----CCccccccceEEE
Confidence            999999999999999998888778888888876665443   333444 4899999997663     3456889999999


Q ss_pred             eccccc
Q psy17644        321 DEADRM  326 (330)
Q Consensus       321 DEad~l  326 (330)
                      ||||++
T Consensus       732 DEaH~~  737 (1151)
T 2eyq_A          732 DEEHRF  737 (1151)
T ss_dssp             ESGGGS
T ss_pred             echHhc
Confidence            999995

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.77  E-value=1.9e-18  Score=172.12  Aligned_cols=129  Identities=19%  Similarity=0.069  Sum_probs=103.6

Q ss_pred             CCCHHHHHhhhh----hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        189 SPTPIQAQAVPA----ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       189 ~pt~iQ~~~i~~----~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|+|.|.+++..    +..|+++++.||||+|||++|++|++..           ++++||++||++|+.|+.+.+..+.
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~-----------~~~v~i~~pt~~l~~q~~~~~~~l~   71 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV-----------KPKVLFVVRTHNEFYPIYRDLTKIR   71 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHHH-----------CSEEEEEESSGGGHHHHHHHHTTCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHhC-----------CCeEEEEcCCHHHHHHHHHHHHHHh
Confidence            689999997765    4589999999999999999999999972           6899999999999999999999998


Q ss_pred             cCCCceEEEEECCCch---------------------------------HH------------------HHHHHhCCCeE
Q psy17644        265 KGYNLSVVCCYGGGSK---------------------------------WD------------------QSKALELGAEI  293 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~---------------------------------~~------------------~~~~l~~~~dI  293 (330)
                      +..++++..+.|+...                                 +.                  ..+....+++|
T Consensus        72 ~~~~~~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~~adI  151 (551)
T 3crv_A           72 EKRNITFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKADV  151 (551)
T ss_dssp             CSSCCCEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGGGCSE
T ss_pred             hhcCccEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhhcCCE
Confidence            7778888777663210                                 11                  12333457899


Q ss_pred             EEEChHHHHHHHHcCCCCC-CCccEEEeecccccCc
Q psy17644        294 VVGTPGRIIDMVKMGATKL-NRVTFLVLDEADRMFD  328 (330)
Q Consensus       294 iV~TP~~L~~~l~~~~~~l-~~i~~lVvDEad~lld  328 (330)
                      ||+||..|++...+....+ ....+|||||||+|.+
T Consensus       152 VV~~~~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          152 IALTYPYFFIDRYREFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             EEEETHHHHCHHHHTTSCCCSTTEEEEETTGGGGGG
T ss_pred             EEeCchHhcCHHHHHhcCCCcCCeEEEEecccchHH
Confidence            9999999998765443333 4678999999999986

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=99.75  E-value=1.1e-18  Score=169.81  Aligned_cols=121  Identities=15%  Similarity=0.121  Sum_probs=94.8

Q ss_pred             CCCCCCHHHHHhhhhhcCCCcE-EEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        186 EYTSPTPIQAQAVPAALSGRDI-IGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~~g~d~-i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      |+..|+|+|. +||.+++++++ +++++||||||++|++|++.++..       .++++||++|||+||.|++..+..+ 
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~-------~~~~~lvl~Ptr~La~Q~~~~l~g~-   71 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL-------RRLRTLILAPTRVVAAEMEEALRGL-   71 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTTTS-
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh-------cCCcEEEECCCHHHHHHHHHHhcCc-
Confidence            6788999985 79999999988 888999999999999999988776       4689999999999999999987532 


Q ss_pred             cCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                           .+....+....     ....+..|.++|++.|...+.+. ..++++.+|||||||++
T Consensus        72 -----~v~~~~~~~~~-----~~~~~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~  122 (451)
T 2jlq_A           72 -----PIRYQTPAVKS-----DHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT  122 (451)
T ss_dssp             -----CEEECCTTCSC-----CCCSSCCEEEEEHHHHHHHHHHC-SCCCCCSEEEEETTTCC
T ss_pred             -----eeeeeeccccc-----cCCCCceEEEEChHHHHHHhhCc-ccccCCCEEEEeCCccC
Confidence                 22211111110     11234579999999998877643 55889999999999986

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=99.74  E-value=9.3e-18  Score=163.56  Aligned_cols=115  Identities=23%  Similarity=0.124  Sum_probs=96.7

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      ..|+|+|.++++.++.+++++++++||+|||++|++++...           +.++|||+||++|+.|+++.+.+|    
T Consensus        92 ~~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~-----------~~~~Lvl~P~~~L~~Q~~~~~~~~----  156 (472)
T 2fwr_A           92 ISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL-----------STPTLIVVPTLALAEQWKERLGIF----  156 (472)
T ss_dssp             CCBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH-----------CSCEEEEESSHHHHHHHHHHGGGG----
T ss_pred             CCcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc-----------CCCEEEEECCHHHHHHHHHHHHhC----
Confidence            47999999999999999999999999999999999987754           468999999999999999999885    


Q ss_pred             Cce-EEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcC
Q psy17644        268 NLS-VVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       268 ~~~-~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~  329 (330)
                      ++. +..+.|+...         .++|+|+||+.+...+...   ..++.+|||||||++...
T Consensus       157 ~~~~v~~~~g~~~~---------~~~Ivv~T~~~l~~~~~~~---~~~~~liIvDEaH~~~~~  207 (472)
T 2fwr_A          157 GEEYVGEFSGRIKE---------LKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAE  207 (472)
T ss_dssp             CGGGEEEBSSSCBC---------CCSEEEEEHHHHHHTHHHH---TTTCSEEEEETGGGTTST
T ss_pred             CCcceEEECCCcCC---------cCCEEEEEcHHHHHHHHHh---cCCCCEEEEECCcCCCCh
Confidence            566 6666665542         4799999999998766421   246899999999998754

>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=99.73  E-value=4.1e-17  Score=145.45  Aligned_cols=115  Identities=23%  Similarity=0.113  Sum_probs=94.2

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      ..|+++|..++..++.+++++++++||+|||.+++.++...           +.++||++||++|+.|+.+.+.+|    
T Consensus        92 ~~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~-----------~~~~liv~P~~~L~~q~~~~~~~~----  156 (237)
T 2fz4_A           92 ISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL-----------STPTLIVVPTLALAEQWKERLGIF----  156 (237)
T ss_dssp             CCCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS-----------CSCEEEEESSHHHHHHHHHHHGGG----
T ss_pred             CCcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc-----------CCCEEEEeCCHHHHHHHHHHHHhC----
Confidence            57999999999999999999999999999999988776542           467999999999999999999885    


Q ss_pred             Cce-EEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcC
Q psy17644        268 NLS-VVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       268 ~~~-~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~  329 (330)
                      ++. +..+.|+..         ...+|+|+||+.+.......   ..++.+|||||||++.+.
T Consensus       157 ~~~~v~~~~g~~~---------~~~~i~v~T~~~l~~~~~~~---~~~~~llIiDEaH~l~~~  207 (237)
T 2fz4_A          157 GEEYVGEFSGRIK---------ELKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAE  207 (237)
T ss_dssp             CGGGEEEESSSCB---------CCCSEEEEEHHHHHHTHHHH---TTTCSEEEEECSSCCCTT
T ss_pred             CCCeEEEEeCCCC---------CcCCEEEEeHHHHHhhHHHh---cccCCEEEEECCccCCCh
Confidence            566 666665543         24799999999988765421   246899999999998753

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=99.70  E-value=3.3e-18  Score=172.30  Aligned_cols=135  Identities=16%  Similarity=0.107  Sum_probs=97.4

Q ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q psy17644        172 FGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE  251 (330)
Q Consensus       172 ~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~  251 (330)
                      +++++.+.+++... ...|+|+|++++|.+++|+|++++|+||||||++|++|++.++..       .++++|||+|||+
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~-------~~~~vLvl~Ptre  226 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK-------RRLRTLILAPTRV  226 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH-------TTCCEEEEESSHH
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh-------CCCeEEEEcChHH
Confidence            44555555554432 478999999999999999999999999999999999999999876       3689999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        252 LSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       252 La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      ||.|+++.++.+      .+. ..++...    .....+.-|.++|.+.|...+... ..++++++|||||||+|
T Consensus       227 La~Qi~~~l~~~------~v~-~~~~~l~----~~~tp~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~  289 (618)
T 2whx_A          227 VAAEMEEALRGL------PIR-YQTPAVK----SDHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT  289 (618)
T ss_dssp             HHHHHHHHTTTS------CEE-ECCTTSS----CCCCSSSCEEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC
T ss_pred             HHHHHHHHhcCC------cee-Eecccce----eccCCCceEEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC
Confidence            999999887632      222 1111100    001123467778888887765543 45889999999999998

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=99.69  E-value=1.1e-17  Score=168.29  Aligned_cols=114  Identities=17%  Similarity=0.106  Sum_probs=91.2

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCC
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN  268 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~  268 (330)
                      .+.+.|..+++.+..+++++++|+||||||++|.+|++.           .+.++||++|||+||.|+++.+.+..   +
T Consensus       217 P~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~-----------~g~~vLVl~PTReLA~Qia~~l~~~~---g  282 (666)
T 3o8b_A          217 PVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA-----------QGYKVLVLNPSVAATLGFGAYMSKAH---G  282 (666)
T ss_dssp             CSCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH-----------TTCCEEEEESCHHHHHHHHHHHHHHH---S
T ss_pred             CcHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH-----------CCCeEEEEcchHHHHHHHHHHHHHHh---C
Confidence            344566666667778899999999999999999998875           25689999999999999998776553   3


Q ss_pred             ceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        269 LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       269 ~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      ..+...+|+..       +..+++|+|+||++|   +.+....++++++|||||||.+
T Consensus       283 ~~vg~~vG~~~-------~~~~~~IlV~TPGrL---l~~~~l~l~~l~~lVlDEAH~l  330 (666)
T 3o8b_A          283 IDPNIRTGVRT-------ITTGAPVTYSTYGKF---LADGGCSGGAYDIIICDECHST  330 (666)
T ss_dssp             CCCEEECSSCE-------ECCCCSEEEEEHHHH---HHTTSCCTTSCSEEEETTTTCC
T ss_pred             CCeeEEECcEe-------ccCCCCEEEECcHHH---HhCCCcccCcccEEEEccchhc
Confidence            45566677654       355689999999998   4566777889999999999654

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.68  E-value=3.6e-17  Score=162.55  Aligned_cols=127  Identities=19%  Similarity=0.139  Sum_probs=88.5

Q ss_pred             CCCCCCCHHHHHhhhh----hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q psy17644        185 CEYTSPTPIQAQAVPA----ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEA  260 (330)
Q Consensus       185 ~~~~~pt~iQ~~~i~~----~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~  260 (330)
                      .|| .|+|+|.+++..    +..|+++++.+|||+|||++|++|++.+           ++++||++||++|+.|+++.+
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~-----------~~~~~~~~~t~~l~~q~~~~~   71 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL-----------KKKVLIFTRTHSQLDSIYKNA   71 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH-----------TCEEEEEESCHHHHHHHHHHH
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC-----------CCcEEEEcCCHHHHHHHHHHH
Confidence            356 799999998654    4589999999999999999999999764           579999999999999999988


Q ss_pred             HHhccCCCceEEEEECCCc-----------------------------------------------hHHHHHHHhCCCeE
Q psy17644        261 KRFGKGYNLSVVCCYGGGS-----------------------------------------------KWDQSKALELGAEI  293 (330)
Q Consensus       261 ~~l~~~~~~~~~~~~gg~~-----------------------------------------------~~~~~~~l~~~~dI  293 (330)
                      .++    ++++..+.|...                                               .....+....+++|
T Consensus        72 ~~l----~~~~~~l~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~~~~~Cpy~~~r~~~~~adi  147 (540)
T 2vl7_A           72 KLL----GLKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLKDKDV  147 (540)
T ss_dssp             GGG----TCCEEEC---------------------------------------------------------CTTGGGCSE
T ss_pred             Hhc----CCcEEEecCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhhhcCCChHHHHHHHhhcCCE
Confidence            875    333333332110                                               00011112335899


Q ss_pred             EEEChHHHHHHHHcCCC-------CCCCccEEEeecccccC
Q psy17644        294 VVGTPGRIIDMVKMGAT-------KLNRVTFLVLDEADRMF  327 (330)
Q Consensus       294 iV~TP~~L~~~l~~~~~-------~l~~i~~lVvDEad~ll  327 (330)
                      ||+|+..|++....+..       .+....+|||||||+|.
T Consensus       148 VV~n~~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~  188 (540)
T 2vl7_A          148 IAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLL  188 (540)
T ss_dssp             EEEETHHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGG
T ss_pred             EEEChHHhcCHHHHHhhCcccccccCcCCCEEEEEccccHH
Confidence            99999999885432211       24577899999999994

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*

Probab=99.63  E-value=4.7e-16  Score=164.01  Aligned_cols=140  Identities=19%  Similarity=0.184  Sum_probs=104.9

Q ss_pred             HHHHHHHHHCC-------CCCCCHHHHHhhhhhcC--------------CCcEEEEcCCCChhHHHHHHHHHHHHHhcCC
Q psy17644        176 EVLMKALRKCE-------YTSPTPIQAQAVPAALS--------------GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKE  234 (330)
Q Consensus       176 ~~l~~~l~~~~-------~~~pt~iQ~~~i~~~~~--------------g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~  234 (330)
                      ..+++.+...-       ...|+|+|..+++.++.              +++++++++||||||+++ ++++.. +... 
T Consensus       251 ~~ll~~l~~f~~~~~~~~~~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~l-l~~~-  327 (1038)
T 2w00_A          251 HTLLNVLVNYSVFDSSQTLLVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARL-ATEL-  327 (1038)
T ss_dssp             HHHHHHHHHSEEECTTCCEEECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHH-HTTC-
T ss_pred             HHHHHHHHhheeeccccccccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHH-HHhc-
Confidence            44555555432       23599999999999874              478999999999999997 556544 3321 


Q ss_pred             CCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh-CCCeEEEEChHHHHHHHHcCC--CC
Q psy17644        235 LEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE-LGAEIVVGTPGRIIDMVKMGA--TK  311 (330)
Q Consensus       235 ~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~-~~~dIiV~TP~~L~~~l~~~~--~~  311 (330)
                         ...+++||||||++|+.|+...+..++..      .+.++.+.......+. .+++|+|+||++|..++....  ..
T Consensus       328 ---~~~~rvLvlvpr~eL~~Q~~~~f~~f~~~------~v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~  398 (1038)
T 2w00_A          328 ---DFIDKVFFVVDRKDLDYQTMKEYQRFSPD------SVNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPV  398 (1038)
T ss_dssp             ---TTCCEEEEEECGGGCCHHHHHHHHTTSTT------CSSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGG
T ss_pred             ---CCCceEEEEeCcHHHHHHHHHHHHHhccc------ccccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhc
Confidence               23479999999999999999999998653      1235555555556664 468999999999999886542  23


Q ss_pred             CCCccEEEeecccccC
Q psy17644        312 LNRVTFLVLDEADRMF  327 (330)
Q Consensus       312 l~~i~~lVvDEad~ll  327 (330)
                      ++.+.+||+||||++.
T Consensus       399 ~~~~~lvIiDEAHrs~  414 (1038)
T 2w00_A          399 YNQQVVFIFDECHRSQ  414 (1038)
T ss_dssp             GGSCEEEEEESCCTTH
T ss_pred             cccccEEEEEccchhc
Confidence            5678999999999975

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=99.63  E-value=1.3e-15  Score=156.96  Aligned_cols=152  Identities=16%  Similarity=0.118  Sum_probs=110.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcC-CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCe
Q psy17644        164 YPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALS-GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPM  242 (330)
Q Consensus       164 ~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~-g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~  242 (330)
                      .++.+|..+++++.+.+.+...+ ..|+++|+++|+.++. +++++++|+||||||+  ++|++.......   ...+++
T Consensus        69 ~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~~---~~~g~~  142 (773)
T 2xau_A           69 GKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEMP---HLENTQ  142 (773)
T ss_dssp             SSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHCG---GGGTCE
T ss_pred             CCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhccc---cCCCce
Confidence            35678999999999999998887 7899999999998884 5679999999999997  566663222111   113678


Q ss_pred             EEEEcccHHHHHHHHHHHHHhc-cCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEee
Q psy17644        243 GLILAPTRELSQQIYNEAKRFG-KGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLD  321 (330)
Q Consensus       243 vLil~Ptr~La~Qi~~~~~~l~-~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvD  321 (330)
                      ++|++|||+||.|++..+.... ...+..+........      ......+|+|+||++|...+... ..+.++.+||||
T Consensus       143 ilvl~P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~------~~~~~~~I~v~T~G~l~r~l~~~-~~l~~~~~lIlD  215 (773)
T 2xau_A          143 VACTQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFEN------KTSNKTILKYMTDGMLLREAMED-HDLSRYSCIILD  215 (773)
T ss_dssp             EEEEESCHHHHHHHHHHHHHHTTCCBTTTEEEEETTEE------ECCTTCSEEEEEHHHHHHHHHHS-TTCTTEEEEEEC
T ss_pred             EEecCchHHHHHHHHHHHHHHhCCchhheecceecccc------ccCCCCCEEEECHHHHHHHHhhC-ccccCCCEEEec
Confidence            9999999999999998765543 222222221111111      01235799999999999877653 458899999999


Q ss_pred             cccc-cCc
Q psy17644        322 EADR-MFD  328 (330)
Q Consensus       322 Ead~-lld  328 (330)
                      |||. +++
T Consensus       216 Eah~R~ld  223 (773)
T 2xau_A          216 EAHERTLA  223 (773)
T ss_dssp             SGGGCCHH
T ss_pred             Cccccccc
Confidence            9995 654

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.63  E-value=1.7e-16  Score=159.17  Aligned_cols=128  Identities=20%  Similarity=0.171  Sum_probs=75.5

Q ss_pred             CCCCHHHHHhhhhhcC----C-CcEEEEcCCCChhHHHHHHHHHHHHHhcC--CCCCCCCCeEEEEcccHHHHHHHH-HH
Q psy17644        188 TSPTPIQAQAVPAALS----G-RDIIGVAKTGSGKTGAFIWPMLVHIMDQK--ELEPGDGPMGLILAPTRELSQQIY-NE  259 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~----g-~d~i~~a~TGsGKT~a~llp~l~~i~~~~--~~~~~~~~~vLil~Ptr~La~Qi~-~~  259 (330)
                      ..|+|+|.++++.++.    | ++++++++||+|||++++. ++..++...  ......++++|||+||++|+.|++ +.
T Consensus       177 ~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~-~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~  255 (590)
T 3h1t_A          177 YSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQ-ISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKT  255 (590)
T ss_dssp             --CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHHHHTTCCSSCSSSCCCEEEEEC-----------C
T ss_pred             CCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHH-HHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHH
Confidence            3699999999999875    4 6689999999999998654 444454432  001124689999999999999999 77


Q ss_pred             HHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHc----CCCCCCCccEEEeecccccCc
Q psy17644        260 AKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKM----GATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       260 ~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~----~~~~l~~i~~lVvDEad~lld  328 (330)
                      ++.++.    .+..+.++        ....+++|+|+||++|...+..    ..+....+.+|||||||++..
T Consensus       256 ~~~~~~----~~~~~~~~--------~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~  316 (590)
T 3h1t_A          256 FTPFGD----ARHKIEGG--------KVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSA  316 (590)
T ss_dssp             CTTTCS----SEEECCC----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC----
T ss_pred             HHhcch----hhhhhhcc--------CCCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccc
Confidence            776643    33333332        1234689999999999887652    233467799999999999875

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.62  E-value=1.4e-16  Score=161.72  Aligned_cols=125  Identities=14%  Similarity=0.140  Sum_probs=87.7

Q ss_pred             HHCCCC-----CCCHHHH-----Hhhhhhc------CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        183 RKCEYT-----SPTPIQA-----QAVPAAL------SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       183 ~~~~~~-----~pt~iQ~-----~~i~~~~------~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      ...||.     .||++|+     .+||.++      +|+|++++++||||||++|++|++.++..       +++++|||
T Consensus       204 ~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~-------~~~~~lil  276 (673)
T 2wv9_A          204 YGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ-------KRLRTAVL  276 (673)
T ss_dssp             EEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH-------TTCCEEEE
T ss_pred             eeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh-------CCCcEEEE
Confidence            345655     8999999     9999988      99999999999999999999999998765       46899999


Q ss_pred             cccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      +|||+||.|+++.++.+.    +.  . ..+ ...   .....+.-+-+.+.+.+...+... ..++++.+|||||||+|
T Consensus       277 aPTr~La~Q~~~~l~~~~----i~--~-~~~-~l~---~v~tp~~ll~~l~~~~l~~~l~~~-~~l~~l~lvViDEaH~~  344 (673)
T 2wv9_A          277 APTRVVAAEMAEALRGLP----VR--Y-LTP-AVQ---REHSGNEIVDVMCHATLTHRLMSP-LRVPNYNLFVMDEAHFT  344 (673)
T ss_dssp             ESSHHHHHHHHHHTTTSC----CE--E-CCC-------CCCCSCCCEEEEEHHHHHHHHHSS-SCCCCCSEEEEESTTCC
T ss_pred             ccHHHHHHHHHHHHhcCC----ee--e-ecc-ccc---ccCCHHHHHHHHHhhhhHHHHhcc-cccccceEEEEeCCccc
Confidence            999999999999887652    22  1 110 000   000011223344555554433332 56889999999999998

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=99.59  E-value=1.1e-15  Score=148.94  Aligned_cols=110  Identities=15%  Similarity=0.139  Sum_probs=80.3

Q ss_pred             hhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEEC
Q psy17644        197 AVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYG  276 (330)
Q Consensus       197 ~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~g  276 (330)
                      ...++.++++++++++||||||++|++|++.+++.       .++++|||+|||+||.|++..++.+      .+....+
T Consensus        14 ~~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~-------~~~~~lvl~Ptr~La~Q~~~~l~g~------~v~~~~~   80 (459)
T 2z83_A           14 SPNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ-------QRLRTAVLAPTRVVAAEMAEALRGL------PVRYQTS   80 (459)
T ss_dssp             -CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH-------TTCCEEEEECSHHHHHHHHHHTTTS------CEEECC-
T ss_pred             HHHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh-------CCCcEEEECchHHHHHHHHHHhcCc------eEeEEec
Confidence            35556789999999999999999999999998875       4689999999999999999988632      2222111


Q ss_pred             CCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        277 GGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       277 g~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      ....     .-..+.-+.++|.+.+...+... ..++++.+|||||||+
T Consensus        81 ~~~~-----~~t~~~~i~~~~~~~l~~~l~~~-~~l~~~~~iViDEaH~  123 (459)
T 2z83_A           81 AVQR-----EHQGNEIVDVMCHATLTHRLMSP-NRVPNYNLFVMDEAHF  123 (459)
T ss_dssp             ------------CCCSEEEEEHHHHHHHHHSC-C-CCCCSEEEESSTTC
T ss_pred             cccc-----CCCCCcEEEEEchHHHHHHhhcc-ccccCCcEEEEECCcc
Confidence            1110     01223457788888887766543 5588999999999998

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.58  E-value=6.9e-17  Score=156.63  Aligned_cols=100  Identities=20%  Similarity=0.248  Sum_probs=74.8

Q ss_pred             hhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCc
Q psy17644        200 AALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGS  279 (330)
Q Consensus       200 ~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~  279 (330)
                      ++++|+|++++++||||||++|++|++.++..       +++++|||+|||+||.|+++.++.+.    +  .. .++..
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~-------~~~~~lil~Ptr~La~Q~~~~l~~~~----v--~~-~~~~~   69 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECAR-------RRLRTLVLAPTRVVLSEMKEAFHGLD----V--KF-HTQAF   69 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTTTSC----E--EE-ESSCC
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHh-------cCCeEEEEcchHHHHHHHHHHHhcCC----e--EE-ecccc
Confidence            56789999999999999999999999998875       46899999999999999999887542    2  21 11110


Q ss_pred             hHHHHHHHhCCCeEEEEChHHHHHHHH--------cCCCCCCCccEEEeeccccc
Q psy17644        280 KWDQSKALELGAEIVVGTPGRIIDMVK--------MGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       280 ~~~~~~~l~~~~dIiV~TP~~L~~~l~--------~~~~~l~~i~~lVvDEad~l  326 (330)
                                   -+|+||+++.+++.        .....++++.+|||||||+|
T Consensus        70 -------------~~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~  111 (440)
T 1yks_A           70 -------------SAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL  111 (440)
T ss_dssp             -------------CCCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC
T ss_pred             -------------eeccCCccceeeecccchhHhhhCcccccCccEEEEECcccc
Confidence                         02566655433221        12345889999999999998

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.56  E-value=8.5e-15  Score=141.51  Aligned_cols=105  Identities=13%  Similarity=0.138  Sum_probs=77.7

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWD  282 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~  282 (330)
                      .|++++++++||||||++|++|++.++..       +++++|||+||++||.|++..+.      +..+....|+...  
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~-------~g~~~lvl~Pt~~La~Q~~~~~~------~~~v~~~~~~~~~--   65 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK-------KRLRTVILAPTRVVASEMYEALR------GEPIRYMTPAVQS--   65 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTT------TSCEEEC--------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh-------CCCCEEEECcHHHHHHHHHHHhC------CCeEEEEecCccc--
Confidence            47899999999999999999999987765       46899999999999999998775      3344433332111  


Q ss_pred             HHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        283 QSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       283 ~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                         .-..+.-+.+.|.+.+...+.. ...++++.+|||||||++
T Consensus        66 ---~~~~~~~~~~~~~~~l~~~l~~-~~~~~~l~~vViDEaH~~  105 (431)
T 2v6i_A           66 ---ERTGNEIVDFMCHSTFTMKLLQ-GVRVPNYNLYIMDEAHFL  105 (431)
T ss_dssp             ------CCCSEEEEEHHHHHHHHHH-TCCCCCCSEEEEESTTCC
T ss_pred             ---cCCCCceEEEEchHHHHHHHhc-CccccCCCEEEEeCCccC
Confidence               1112345677888888776555 456889999999999997

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.54  E-value=1e-14  Score=146.93  Aligned_cols=82  Identities=18%  Similarity=0.134  Sum_probs=68.9

Q ss_pred             CCCHHHHHhhhh----hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        189 SPTPIQAQAVPA----ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       189 ~pt~iQ~~~i~~----~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .|+|.|.+.+..    +.+|+++++.||||+|||++|++|++.++..       .+++++|++||++|+.|+++.+.++.
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~-------~~~kvli~t~T~~l~~Qi~~el~~l~   75 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSE-------RKLKVLYLVRTNSQEEQVIKELRSLS   75 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHH-------HTCEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhh-------cCCeEEEECCCHHHHHHHHHHHHHHh
Confidence            588999998864    4589999999999999999999999999865       36799999999999999999999987


Q ss_pred             cCCCceEEEEECC
Q psy17644        265 KGYNLSVVCCYGG  277 (330)
Q Consensus       265 ~~~~~~~~~~~gg  277 (330)
                      ...+++++.+.|+
T Consensus        76 ~~~~~~~~~l~gr   88 (620)
T 4a15_A           76 STMKIRAIPMQGR   88 (620)
T ss_dssp             HHSCCCEEECCCH
T ss_pred             hccCeEEEEEECC
Confidence            7666776666553

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=99.49  E-value=4.3e-14  Score=138.55  Aligned_cols=124  Identities=19%  Similarity=0.188  Sum_probs=91.2

Q ss_pred             CCCCHHHHHhhhhh----cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        188 TSPTPIQAQAVPAA----LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~----~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..|+|+|.+++..+    ..++++|++.+||+|||++++. ++..+...     ....++|||||+ .|+.||.++++++
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~-~i~~~~~~-----~~~~~~LIv~P~-~l~~qw~~e~~~~  108 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIA-VFSDAKKE-----NELTPSLVICPL-SVLKNWEEELSKF  108 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHH-HHHHHHHT-----TCCSSEEEEECS-TTHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHH-HHHHHHhc-----CCCCCEEEEccH-HHHHHHHHHHHHH
Confidence            46899999999876    3688999999999999988654 44444432     134679999995 6899999999999


Q ss_pred             ccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      +..  .++..+.|+...     .....++|+|+||+.|.....   .....+.+|||||||++..
T Consensus       109 ~~~--~~v~~~~g~~~~-----~~~~~~~ivi~t~~~l~~~~~---l~~~~~~~vIvDEaH~~kn  163 (500)
T 1z63_A          109 APH--LRFAVFHEDRSK-----IKLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKN  163 (500)
T ss_dssp             CTT--SCEEECSSSTTS-----CCGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSC
T ss_pred             CCC--ceEEEEecCchh-----ccccCCcEEEeeHHHHhccch---hcCCCcCEEEEeCccccCC
Confidence            753  455555554421     112347999999999976443   2234689999999999864

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.45  E-value=5.6e-14  Score=142.45  Aligned_cols=111  Identities=17%  Similarity=0.109  Sum_probs=79.6

Q ss_pred             HHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEE
Q psy17644        194 QAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVC  273 (330)
Q Consensus       194 Q~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~  273 (330)
                      |.......++|++++++||||||||+    +++..+...        +.+||++|||+||.|+++.+..+    ++.+..
T Consensus       145 ~~~p~ar~l~rk~vlv~apTGSGKT~----~al~~l~~~--------~~gl~l~PtR~LA~Qi~~~l~~~----g~~v~l  208 (677)
T 3rc3_A          145 NWYPDARAMQRKIIFHSGPTNSGKTY----HAIQKYFSA--------KSGVYCGPLKLLAHEIFEKSNAA----GVPCDL  208 (677)
T ss_dssp             GGCHHHHTSCCEEEEEECCTTSSHHH----HHHHHHHHS--------SSEEEEESSHHHHHHHHHHHHHT----TCCEEE
T ss_pred             hhCHHHHhcCCCEEEEEcCCCCCHHH----HHHHHHHhc--------CCeEEEeCHHHHHHHHHHHHHhc----CCcEEE
Confidence            33334456789999999999999997    445555442        34599999999999999999886    567788


Q ss_pred             EECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcCC
Q psy17644        274 CYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG  330 (330)
Q Consensus       274 ~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~G  330 (330)
                      ++|+....-  ..-....+++++|++.+.        ....+.+|||||||+|+++|
T Consensus       209 ltG~~~~iv--~TpGr~~~il~~T~e~~~--------l~~~v~lvVIDEaH~l~d~~  255 (677)
T 3rc3_A          209 VTGEERVTV--QPNGKQASHVSCTVEMCS--------VTTPYEVAVIDEIQMIRDPA  255 (677)
T ss_dssp             ECSSCEECC--STTCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGCTT
T ss_pred             EECCeeEEe--cCCCcccceeEecHhHhh--------hcccCCEEEEecceecCCcc
Confidence            888765410  000112578888874332        24678999999999998764

>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=99.35  E-value=6.8e-12  Score=127.06  Aligned_cols=134  Identities=18%  Similarity=0.181  Sum_probs=94.3

Q ss_pred             CCCHHHHHhhhhhc---------CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q psy17644        189 SPTPIQAQAVPAAL---------SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE  259 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~---------~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~  259 (330)
                      .++|+|.+++..+.         .++..|+..+||.|||+..+..+.. ++.+.........++|||||+ .|+.||.++
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~-l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E  132 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWT-LLKQSPDCKPEIDKVIVVSPS-SLVRNWYNE  132 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHH-HHHCCTTSSCSCSCEEEEECH-HHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHH-HHHhCccccCCCCcEEEEecH-HHHHHHHHH
Confidence            58899999998873         5677899999999999877655544 333322111123568999997 899999999


Q ss_pred             HHHhccCCCceEEEEECCCchHHH--HHH-HhC-----CCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        260 AKRFGKGYNLSVVCCYGGGSKWDQ--SKA-LEL-----GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       260 ~~~l~~~~~~~~~~~~gg~~~~~~--~~~-l~~-----~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      +.+++.. .+.++.+++|......  ... +..     ..+|+|+|++.+.....  .+....+.+||+||||++-
T Consensus       133 ~~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~--~l~~~~~~~vI~DEaH~ik  205 (644)
T 1z3i_X          133 VGKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLK  205 (644)
T ss_dssp             HHHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCC
T ss_pred             HHHHcCC-CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHH--HhhcCCccEEEEECceecC
Confidence            9999765 4566667776543221  111 111     37899999999876432  2334578899999999985

>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=99.34  E-value=5.7e-13  Score=140.59  Aligned_cols=130  Identities=18%  Similarity=0.059  Sum_probs=89.7

Q ss_pred             CCCCHHHHHhhhhhcC--CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        188 TSPTPIQAQAVPAALS--GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~--g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      ..|+|+|..++..++.  +..+|++++||+|||++++..+...+...      ...++|||||+ .|+.||..++.+.. 
T Consensus       152 ~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g------~~~rvLIVvP~-sLl~Qw~~E~~~~f-  223 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG------AAERVLIIVPE-TLQHQWLVEMLRRF-  223 (968)
T ss_dssp             SCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS------SCCCEEEECCT-TTHHHHHHHHHHHS-
T ss_pred             CCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC------CCCeEEEEeCH-HHHHHHHHHHHHHh-
Confidence            4699999999988875  45889999999999999877665554331      23479999999 99999999997654 


Q ss_pred             CCCceEEEEECCCchHHHHHH---HhCCCeEEEEChHHHHHHHHc-CCCCCCCccEEEeecccccCc
Q psy17644        266 GYNLSVVCCYGGGSKWDQSKA---LELGAEIVVGTPGRIIDMVKM-GATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       266 ~~~~~~~~~~gg~~~~~~~~~---l~~~~dIiV~TP~~L~~~l~~-~~~~l~~i~~lVvDEad~lld  328 (330)
                        +..+..+.|+ ........   .....+|+|+|+..|...... .......+.+|||||||++-.
T Consensus       224 --~l~v~v~~~~-~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn  287 (968)
T 3dmq_A          224 --NLRFALFDDE-RYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVW  287 (968)
T ss_dssp             --CCCCEECCHH-HHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCC
T ss_pred             --CCCEEEEccc-hhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcC
Confidence              4454444332 22111111   112469999999888532110 011245789999999999863

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.31  E-value=4.2e-12  Score=131.63  Aligned_cols=130  Identities=16%  Similarity=0.202  Sum_probs=93.9

Q ss_pred             CCCCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        188 TSPTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..++|+|..++..+.    .++++|++.+||.|||+..+..+...+...+     ....+||||| ..|+.||..++.++
T Consensus       235 ~~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~-----~~~~~LIV~P-~sll~qW~~E~~~~  308 (800)
T 3mwy_W          235 GELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARR-----QNGPHIIVVP-LSTMPAWLDTFEKW  308 (800)
T ss_dssp             SCCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHS-----CCSCEEEECC-TTTHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcC-----CCCCEEEEEC-chHHHHHHHHHHHH
Confidence            468999999998765    8899999999999999876655443333321     2456899999 67889999999999


Q ss_pred             ccCCCceEEEEECCCchHHHHHHH------------hCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        264 GKGYNLSVVCCYGGGSKWDQSKAL------------ELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       264 ~~~~~~~~~~~~gg~~~~~~~~~l------------~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      +.  ++.+.+++|+..........            ...++|+|+|++.+......  +....+.+|||||||++-
T Consensus       309 ~p--~~~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~--l~~~~w~~vIvDEaH~lk  380 (800)
T 3mwy_W          309 AP--DLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE--LGSIKWQFMAVDEAHRLK  380 (800)
T ss_dssp             ST--TCCEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH--HHTSEEEEEEETTGGGGC
T ss_pred             CC--CceEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH--HhcCCcceeehhhhhhhc
Confidence            74  45666666655444333322            12478999999999764321  112367899999999984

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=99.30  E-value=1.3e-11  Score=123.85  Aligned_cols=128  Identities=19%  Similarity=0.151  Sum_probs=102.3

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      -.|+++|....-.+..|+  |+...||+|||+++.+|++...+.        |..|.||+||+.||.|-++++..+...+
T Consensus        74 ~r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~--------G~~vhVvT~ndyLA~rdae~m~~l~~~L  143 (822)
T 3jux_A           74 MRPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALI--------GKGVHLVTVNDYLARRDALWMGPVYLFL  143 (822)
T ss_dssp             CCCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTT--------SSCEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             CCCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhc--------CCceEEEeccHHHHHhHHHHHHHHHHHh
Confidence            468899999888888887  889999999999999999877654        6779999999999999999999999999


Q ss_pred             CceEEEEECC--------------------------------------------------CchHHHHHHHhCCCeEEEEC
Q psy17644        268 NLSVVCCYGG--------------------------------------------------GSKWDQSKALELGAEIVVGT  297 (330)
Q Consensus       268 ~~~~~~~~gg--------------------------------------------------~~~~~~~~~l~~~~dIiV~T  297 (330)
                      |+++.+++..                                                  .+.......+  .|||+.+|
T Consensus       144 glsvg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~err~aY--~~DItYgT  221 (822)
T 3jux_A          144 GLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAY--LCDVTYGT  221 (822)
T ss_dssp             TCCEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCCHHHHH--HSSEEEEE
T ss_pred             CCEEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHHHHHHh--cCCCEEcc
Confidence            9999998872                                                  1222222222  37999999


Q ss_pred             hHHH-HHHHHcCC------CCCCCccEEEeecccccC
Q psy17644        298 PGRI-IDMVKMGA------TKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       298 P~~L-~~~l~~~~------~~l~~i~~lVvDEad~ll  327 (330)
                      ..-| +++|+.+-      .-...+.|.||||+|.||
T Consensus       222 n~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiL  258 (822)
T 3jux_A          222 NNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVL  258 (822)
T ss_dssp             HHHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHH
T ss_pred             CcchhhHhHHhhccCCHHHhccCCCCeEEEeccccee
Confidence            9876 44554321      124678999999999886

>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=98.87  E-value=1.1e-09  Score=110.07  Aligned_cols=72  Identities=22%  Similarity=0.210  Sum_probs=59.4

Q ss_pred             CHHHHHhhhhhcCCCcEEEEcCCCChhH--HHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCC
Q psy17644        191 TPIQAQAVPAALSGRDIIGVAKTGSGKT--GAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN  268 (330)
Q Consensus       191 t~iQ~~~i~~~~~g~d~i~~a~TGsGKT--~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~  268 (330)
                      ++.|+.+++.++.++.+++.|++|+|||  ++++++++..+..      ..+.++++++||+.+|.++.+.+..++..++
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~------~~~~~vll~APTg~AA~~L~e~~~~~~~~l~  224 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD------GERCRIRLAAPTGKAAARLTESLGKALRQLP  224 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS------SCCCCEEEEBSSHHHHHHHHHHHTHHHHHSS
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh------cCCCeEEEEeCChhHHHHHHHHHHHHHhcCC
Confidence            7899999999999999999999999999  6677777765321      2467899999999999999988877655443

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.26  E-value=1.8e-06  Score=87.25  Aligned_cols=68  Identities=24%  Similarity=0.256  Sum_probs=54.0

Q ss_pred             CCCCHHHHHhhhhhcCCCc-EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        188 TSPTPIQAQAVPAALSGRD-IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d-~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..+.+-|.+|+..+++.++ .|+.||.|+|||.+ +..++.++++       .+.++|+++||...+.++...+...
T Consensus       188 ~~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~t-i~~~I~~l~~-------~~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          188 TCLDTSQKEAVLFALSQKELAIIHGPPGTGKTTT-VVEIILQAVK-------QGLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             TTCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHH-HHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHhcCCCceEEECCCCCCHHHH-HHHHHHHHHh-------CCCeEEEEcCchHHHHHHHHHHHhc
Confidence            3578999999999987776 46669999999955 4455556665       3678999999999999998888664

>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=98.24  E-value=5.9e-06  Score=83.15  Aligned_cols=70  Identities=20%  Similarity=0.158  Sum_probs=55.7

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ...+++.|..++..++...-+++.||+|+|||.+. ..++.++...      .+.++|+++||...+.++...+.+.
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~-~~~i~~l~~~------~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQ------GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHH-HHHHHHHHTS------SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHH-HHHHHHHHHc------CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            45688999999999888777888999999999543 3445555432      3578999999999999999888764

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.13  E-value=1.2e-05  Score=83.03  Aligned_cols=70  Identities=17%  Similarity=0.188  Sum_probs=55.8

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      +..+++.|..++..++.+.-+++.||.|+|||.+. ..++.++...      .+.++|+++||...+.++...+.+.
T Consensus       358 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i-~~~i~~l~~~------~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTS-ATIVYHLSKI------HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHH-HHHHHHHHHH------HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHH-HHHHHHHHhC------CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            45688999999999988777889999999999543 3344454442      2568999999999999999988775

>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=98.09  E-value=1.6e-05  Score=82.11  Aligned_cols=70  Identities=20%  Similarity=0.158  Sum_probs=55.7

Q ss_pred             CCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        187 YTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       187 ~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ...+++.|..++..++.+.-+++.|++|+|||.+. ..++.++...      .+.++|+++||...+.++...+...
T Consensus       354 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti-~~~i~~l~~~------~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          354 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQ------GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             SCCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHH-HHHHHHHHTT------CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             ccCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHH-HHHHHHHHHc------CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            45688999999999888777889999999999543 3445555542      3578999999999999998887764

>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=98.03  E-value=1.7e-05  Score=76.75  Aligned_cols=70  Identities=13%  Similarity=0.150  Sum_probs=49.7

Q ss_pred             HCCCCCCCHHHHHhhhhhcC----CC-cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        184 KCEYTSPTPIQAQAVPAALS----GR-DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       184 ~~~~~~pt~iQ~~~i~~~~~----g~-d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      -+.|..+++-|+.++..++.    ++ .+++.|+.|||||. .+..++.++...      ....+++++||...|..+..
T Consensus        20 p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~-ll~~~~~~l~~~------~~~~il~~a~T~~Aa~~l~~   92 (459)
T 3upu_A           20 HMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATT-LTKFIIEALIST------GETGIILAAPTHAAKKILSK   92 (459)
T ss_dssp             -CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHH-HHHHHHHHHHHT------TCCCEEEEESSHHHHHHHHH
T ss_pred             CCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHH-HHHHHHHHHHhc------CCceEEEecCcHHHHHHHHh
Confidence            34577889999999987753    23 88888999999994 334455555543      12478999999988876655


Q ss_pred             HH
Q psy17644        259 EA  260 (330)
Q Consensus       259 ~~  260 (330)
                      .+
T Consensus        93 ~~   94 (459)
T 3upu_A           93 LS   94 (459)
T ss_dssp             HH
T ss_pred             hh
Confidence            44

>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=97.92  E-value=1.7e-05  Score=78.92  Aligned_cols=65  Identities=15%  Similarity=0.075  Sum_probs=49.8

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEA  260 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~  260 (330)
                      ..+++.|+.++..++.++.+++.|+.|+|||.+. ..++..+..       .+.++++++||...+..+.+.+
T Consensus       188 ~~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~-------~g~~Vl~~ApT~~Aa~~L~e~~  252 (574)
T 3e1s_A          188 KGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAES-------LGLEVGLCAPTGKAARRLGEVT  252 (574)
T ss_dssp             TTCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHh-------cCCeEEEecCcHHHHHHhHhhh
Confidence            4578999999999999999999999999999432 223333322       4678999999999988776543

>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=97.53  E-value=0.00038  Score=65.67  Aligned_cols=118  Identities=17%  Similarity=0.128  Sum_probs=77.2

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCC
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN  268 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~  268 (330)
                      .++|+|..++..+...|-+++..+-+.|||.+.+.-++..++..      .+..+++++||+..|..++..++.+....+
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 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN------KDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSS------SSCEEEEEESSHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhC------CCCeEEEEeCCHHHHHHHHHHHHHHHHhCh
Confidence            68999999998765556788889999999977666555544432      367899999999999999988887755332


Q ss_pred             --c--eEEEEECCCchHHHHHHHhCCCeEEEEC--hHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        269 --L--SVVCCYGGGSKWDQSKALELGAEIVVGT--PGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       269 --~--~~~~~~gg~~~~~~~~~l~~~~dIiV~T--P~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                        +  .+.. ....     ...+.+|+.|.+.+  |..+.         =.++.++|+||+|.+-
T Consensus       237 ~ll~~~~~~-~~~~-----~I~f~nGs~i~~lsa~~~slr---------G~~~~~viiDE~a~~~  286 (385)
T 2o0j_A          237 DFLQPGIVE-WNKG-----SIELDNGSSIGAYASSPDAVR---------GNSFAMIYIEDCAFIP  286 (385)
T ss_dssp             TTTSCCEEE-ECSS-----EEEETTSCEEEEEECSHHHHH---------TSCCSEEEEESGGGST
T ss_pred             Hhhhhhhcc-CCcc-----EEEeCCCCEEEEEECCCCCcc---------CCCCCEEEechhhhcC
Confidence              1  1111 1100     01123455554433  44443         1246899999999763

>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=97.37  E-value=0.00035  Score=70.68  Aligned_cols=68  Identities=26%  Similarity=0.349  Sum_probs=51.1

Q ss_pred             CCCCCCHHHHHhhhhhc----CCC-cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q psy17644        186 EYTSPTPIQAQAVPAAL----SGR-DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEA  260 (330)
Q Consensus       186 ~~~~pt~iQ~~~i~~~~----~g~-d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~  260 (330)
                      +| .|++.|..+|..+.    .|. ..++.+.||||||+++.- ++..+          +..+|||+|+..+|.|++..+
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~-~~~~~----------~~~~lvv~~~~~~A~ql~~el   73 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAK-VIEAL----------GRPALVLAPNKILAAQLAAEF   73 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH----------TCCEEEEESSHHHHHHHHHHH
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHH-HHHHh----------CCCEEEEecCHHHHHHHHHHH
Confidence            45 89999999887654    343 467789999999965442 22221          224899999999999999999


Q ss_pred             HHhcc
Q psy17644        261 KRFGK  265 (330)
Q Consensus       261 ~~l~~  265 (330)
                      +.|..
T Consensus        74 ~~~~~   78 (664)
T 1c4o_A           74 RELFP   78 (664)
T ss_dssp             HHHCT
T ss_pred             HHHCC
Confidence            99964

>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=97.30  E-value=0.00096  Score=66.54  Aligned_cols=118  Identities=16%  Similarity=0.120  Sum_probs=77.9

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCC
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN  268 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~  268 (330)
                      .++|+|..++..+...+-+++..+-|+|||.+...-++..++..      .+..+++++||+..|..++..++.+....+
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 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN------KDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS------SSCEEEEEESSHHHHHHHHHHHHHHHTTSC
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC------CCCeEEEEECCHHHHHHHHHHHHHHHHhCh
Confidence            58999999988775567788999999999977665555444432      356899999999999999988888766543


Q ss_pred             --ceEE-EEECCCchHHHHHHHhCCCeEEEE--ChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        269 --LSVV-CCYGGGSKWDQSKALELGAEIVVG--TPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       269 --~~~~-~~~gg~~~~~~~~~l~~~~dIiV~--TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                        +... .......     ..+.+|+.|.+.  +|..+.-         .++.++|+||+|.+
T Consensus       237 ~~~~~~~~~~~~~~-----i~~~nGs~i~~~s~~~~~lrG---------~~~~~~iiDE~~~~  285 (592)
T 3cpe_A          237 DFLQPGIVEWNKGS-----IELDNGSSIGAYASSPDAVRG---------NSFAMIYIEDCAFI  285 (592)
T ss_dssp             TTTSCCEEEECSSE-----EEETTSCEEEEEECCHHHHHH---------SCCSEEEEETGGGC
T ss_pred             HhhccccccCCccE-----EEecCCCEEEEEeCCCCCccC---------CCcceEEEehhccC
Confidence              1110 1011110     112345555443  3554431         14678999999975

>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=97.04  E-value=0.002  Score=64.47  Aligned_cols=72  Identities=18%  Similarity=0.180  Sum_probs=54.1

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      ..+++-|.+++..  ....+++.|+.|||||.+ ++.-+.+++....   ....++|+|++|+..+.++.+.+.++..
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~-l~~ri~~l~~~~~---~~~~~iL~ltft~~aa~e~~~rl~~~~~   79 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRV-LVHRIAWLMSVEN---CSPYSIMAVTFTNKAAAEMRHRIGQLMG   79 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHH-HHHHHHHHHHTSC---CCGGGEEEEESSHHHHHHHHHHHHHHHC
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHH-HHHHHHHHHHhCC---CChhhEEEEeccHHHHHHHHHHHHHHhc
Confidence            4688999999974  356799999999999954 3444455554321   1235899999999999999999888743

>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=96.49  E-value=0.0054  Score=61.90  Aligned_cols=71  Identities=18%  Similarity=0.120  Sum_probs=52.6

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      .+++-|++++...  +..+++.|+.|||||.+.+ .-+.+++....   ....++|+|+.|+..|.++.+.+.++..
T Consensus         2 ~L~~~Q~~av~~~--~~~~lV~AgaGSGKT~~l~-~ri~~ll~~~~---~~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A            2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVIT-NKIAHLIRGCG---YQARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             CCCHHHHHHHHCC--SSEEEECCCTTSCHHHHHH-HHHHHHHHHHC---CCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHhCC--CCCEEEEeCCCCChHHHHH-HHHHHHHHhcC---CCHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            4789999999763  5788999999999995433 33344443211   1345899999999999999999887654

>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=96.38  E-value=0.0087  Score=61.04  Aligned_cols=71  Identities=18%  Similarity=0.145  Sum_probs=52.9

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      ..+++-|++++...  ...+++.|+.|||||.+. +.-+.+++....   ....++|+|+.|+..|.++.+.+.++.
T Consensus        10 ~~Ln~~Q~~av~~~--~g~~lV~AgAGSGKT~vL-~~ri~~ll~~~~---~~p~~IL~vTFTnkAA~Em~~Rl~~~l   80 (724)
T 1pjr_A           10 AHLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVL-THRIAYLMAEKH---VAPWNILAITFTNKAAREMRERVQSLL   80 (724)
T ss_dssp             TTSCHHHHHHHHCC--SSCEEEEECTTSCHHHHH-HHHHHHHHHTTC---CCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHhCC--CCCEEEEEcCCCCHHHHH-HHHHHHHHHhcC---CCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            46889999998763  568999999999999543 334445554311   123579999999999999998887764

>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=96.19  E-value=0.01  Score=64.22  Aligned_cols=72  Identities=25%  Similarity=0.279  Sum_probs=53.8

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .++|+-|.++|..-  ++++++.|..|||||.+.+--++..+.....  .....++|+|++|+..|..+.+.+...
T Consensus         9 ~~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~--~~~~~~il~~Tft~~aa~e~~~ri~~~   80 (1232)
T 3u4q_A            9 STWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEEN--PIDVDRLLVVTFTNASAAEMKHRIAEA   80 (1232)
T ss_dssp             -CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSS--CCCGGGEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCC--CCCccceEEEeccHHHHHHHHHHHHHH
Confidence            35799999999765  8899999999999996655444444433211  113458999999999999999988774

>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=96.12  E-value=0.022  Score=47.04  Aligned_cols=17  Identities=35%  Similarity=0.534  Sum_probs=15.0

Q ss_pred             CCCcEEEEcCCCChhHH
Q psy17644        203 SGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~  219 (330)
                      .|+.+++.|++|+|||.
T Consensus        37 ~g~~~~l~G~~G~GKTt   53 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTH   53 (180)
T ss_dssp             GCCEEEECCSSSSSHHH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            47889999999999994

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=96.08  E-value=0.0073  Score=57.82  Aligned_cols=44  Identities=25%  Similarity=0.313  Sum_probs=31.1

Q ss_pred             cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        206 DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      =.++.|+.|+|||...     ..++.        ....+|++||++++..+.+.+.+
T Consensus       163 v~~I~G~aGsGKTt~I-----~~~~~--------~~~~lVlTpT~~aa~~l~~kl~~  206 (446)
T 3vkw_A          163 VVLVDGVPGCGKTKEI-----LSRVN--------FEEDLILVPGRQAAEMIRRRANA  206 (446)
T ss_dssp             EEEEEECTTSCHHHHH-----HHHCC--------TTTCEEEESCHHHHHHHHHHHTT
T ss_pred             EEEEEcCCCCCHHHHH-----HHHhc--------cCCeEEEeCCHHHHHHHHHHhhh
Confidence            3566799999999533     22222        12459999999999888877754

>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=95.72  E-value=0.018  Score=50.00  Aligned_cols=91  Identities=14%  Similarity=0.150  Sum_probs=50.7

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWD  282 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~  282 (330)
                      .|.=+++.|++|+|||.+.+ -++.++..       .+.+++|+.|...-  .   ....++...++..           
T Consensus        11 ~G~i~litG~mGsGKTT~ll-~~~~r~~~-------~g~kVli~~~~~d~--r---~~~~i~srlG~~~-----------   66 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELI-RRLHRLEY-------ADVKYLVFKPKIDT--R---SIRNIQSRTGTSL-----------   66 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHH-HHHHHHHH-------TTCCEEEEEECCCG--G---GCSSCCCCCCCSS-----------
T ss_pred             CcEEEEEECCCCCcHHHHHH-HHHHHHHh-------cCCEEEEEEeccCc--h---HHHHHHHhcCCCc-----------
Confidence            35556777999999995543 33444333       35678888775421  0   0011222222111           


Q ss_pred             HHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        283 QSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       283 ~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                              ..+-+.+...+...+..... -...++||||||+.+
T Consensus        67 --------~~~~~~~~~~i~~~i~~~~~-~~~~dvViIDEaQ~l  101 (223)
T 2b8t_A           67 --------PSVEVESAPEILNYIMSNSF-NDETKVIGIDEVQFF  101 (223)
T ss_dssp             --------CCEEESSTHHHHHHHHSTTS-CTTCCEEEECSGGGS
T ss_pred             --------cccccCCHHHHHHHHHHHhh-CCCCCEEEEecCccC
Confidence                    12335566667766654322 245789999999875

>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=95.71  E-value=0.015  Score=49.27  Aligned_cols=40  Identities=18%  Similarity=0.069  Sum_probs=26.4

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR  250 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr  250 (330)
                      .|+=.++.+++|+|||.+.+- ++.+...       .+.+++++.|..
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~-~a~r~~~-------~g~kV~v~k~~~   46 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIR-RIRRAKI-------AKQKIQVFKPEI   46 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHH-HHHHHHH-------TTCCEEEEEEC-
T ss_pred             CCEEEEEECCCCCcHHHHHHH-HHHHHHH-------CCCEEEEEEecc
Confidence            355567779999999965443 3333332       467899998873

>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=95.65  E-value=0.024  Score=57.18  Aligned_cols=66  Identities=26%  Similarity=0.367  Sum_probs=48.5

Q ss_pred             CCCHHHHHhhhhhc----CCC-cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        189 SPTPIQAQAVPAAL----SGR-DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~----~g~-d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .|+..|..+|..+.    .|. ..++.+-||||||++..- ++...          +..+|||+|+..+|.|++..++.|
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~-~~~~~----------~~~~lvv~~~~~~A~~l~~el~~~   80 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSN-LIKEV----------NKPTLVIAHNKTLAGQLYSEFKEF   80 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH----------CCCEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHH-HHHHh----------CCCEEEEECCHHHHHHHHHHHHHH
Confidence            68888988887554    343 467789999999954432 22221          124899999999999999999999


Q ss_pred             cc
Q psy17644        264 GK  265 (330)
Q Consensus       264 ~~  265 (330)
                      ..
T Consensus        81 ~~   82 (661)
T 2d7d_A           81 FP   82 (661)
T ss_dssp             CT
T ss_pred             cC
Confidence            64

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=95.55  E-value=0.13  Score=43.13  Aligned_cols=71  Identities=17%  Similarity=0.201  Sum_probs=52.0

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---h-CCCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---E-LGAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~-~~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      ++++||.|+|+..|..+...++..    ++.+..++|+.+...+...+   + ....|+|||.     .+. ..+++..+
T Consensus        54 ~~~~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~-----~~~-~Gldi~~v  123 (191)
T 2p6n_A           54 PPPVLIFAEKKADVDAIHEYLLLK----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATD-----VAS-KGLDFPAI  123 (191)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECH-----HHH-TTCCCCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcC-----chh-cCCCcccC
Confidence            468999999999999999988876    57788889988765543332   2 2578999993     333 35567777


Q ss_pred             cEEEe
Q psy17644        316 TFLVL  320 (330)
Q Consensus       316 ~~lVv  320 (330)
                      .+||.
T Consensus       124 ~~VI~  128 (191)
T 2p6n_A          124 QHVIN  128 (191)
T ss_dssp             SEEEE
T ss_pred             CEEEE
Confidence            77765

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=95.46  E-value=0.013  Score=49.19  Aligned_cols=40  Identities=18%  Similarity=0.097  Sum_probs=25.9

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR  250 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr  250 (330)
                      .|+=.++.+++|+|||...+- ++.....       .+.+++++.|..
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~-~~~~~~~-------~g~~v~~~~~~~   41 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLS-FVEIYKL-------GKKKVAVFKPKI   41 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHH-HHHHHHH-------TTCEEEEEEEC-
T ss_pred             ccEEEEEECCCCCCHHHHHHH-HHHHHHH-------CCCeEEEEeecc
Confidence            355567889999999965432 3333332       356788888873

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=95.17  E-value=0.15  Score=41.33  Aligned_cols=73  Identities=14%  Similarity=0.176  Sum_probs=52.5

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+..|..+...+...    +..+..++|+.+.......   ++. ...|||||.     .+ ...+++..
T Consensus        34 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~-~~Gld~~~  103 (163)
T 2hjv_A           34 NPDSCIIFCRTKEHVNQLTDELDDL----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD-----VA-ARGIDIEN  103 (163)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----GG-TTTCCCSC
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC-----hh-hcCCchhc
Confidence            3568999999999999999988875    6778888998876554333   333 478999993     22 23556777


Q ss_pred             ccEEEee
Q psy17644        315 VTFLVLD  321 (330)
Q Consensus       315 i~~lVvD  321 (330)
                      +.+||.-
T Consensus       104 ~~~Vi~~  110 (163)
T 2hjv_A          104 ISLVINY  110 (163)
T ss_dssp             CSEEEES
T ss_pred             CCEEEEe
Confidence            7777753

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=95.04  E-value=0.12  Score=42.35  Aligned_cols=72  Identities=14%  Similarity=0.094  Sum_probs=52.3

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+..|..+...+...    +..+..++|+.+.......   ++. ...|+|||.     .+ ...+++..
T Consensus        33 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~-----~~-~~Gid~~~  102 (175)
T 2rb4_A           33 TIGQAIIFCQTRRNAKWLTVEMIQD----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTN-----VC-ARGIDVKQ  102 (175)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECC-----SC-CTTTCCTT
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEec-----ch-hcCCCccc
Confidence            3568999999999999999888765    6678888998876554333   333 478999993     11 23456777


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      +.+||.
T Consensus       103 ~~~Vi~  108 (175)
T 2rb4_A          103 VTIVVN  108 (175)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence            888874

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=94.86  E-value=0.19  Score=40.67  Aligned_cols=73  Identities=11%  Similarity=0.238  Sum_probs=52.5

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.++|+..|..+...+...    +..+..++|+.+.......   ++. ...|+|||.     .+ ....++..
T Consensus        29 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~-~~G~d~~~   98 (165)
T 1fuk_A           29 SVTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----LL-ARGIDVQQ   98 (165)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----GG-TTTCCCCS
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcC-----hh-hcCCCccc
Confidence            3578999999999999999988875    5678888888876554333   333 478999993     22 23456777


Q ss_pred             ccEEEee
Q psy17644        315 VTFLVLD  321 (330)
Q Consensus       315 i~~lVvD  321 (330)
                      +.+||.=
T Consensus        99 ~~~Vi~~  105 (165)
T 1fuk_A           99 VSLVINY  105 (165)
T ss_dssp             CSEEEES
T ss_pred             CCEEEEe
Confidence            7777753

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=94.79  E-value=0.12  Score=47.14  Aligned_cols=18  Identities=11%  Similarity=-0.101  Sum_probs=15.2

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      .+.++++.|++|+|||++
T Consensus        44 ~~~~lli~GpPGTGKT~~   61 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQL   61 (318)
T ss_dssp             CCCEEEEECCCSHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHH
Confidence            456899999999999954

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=94.76  E-value=0.031  Score=45.13  Aligned_cols=17  Identities=29%  Similarity=0.393  Sum_probs=15.2

Q ss_pred             CCCcEEEEcCCCChhHH
Q psy17644        203 SGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~  219 (330)
                      .|+.+++.+++|+|||.
T Consensus        35 ~g~~~~l~G~~G~GKTt   51 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSH   51 (149)
T ss_dssp             CCSEEEEESSSTTTTCH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            68889999999999993

>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=94.69  E-value=0.16  Score=43.19  Aligned_cols=71  Identities=14%  Similarity=0.213  Sum_probs=52.0

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---hC-CCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---EL-GAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~~-~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      +.++||.|+|+.-+..++..+...    +..+..++|+.+...+...+   +. ..+|+|||.     ++ ...+++..+
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~-----~~-~~Gidi~~v  100 (212)
T 3eaq_A           31 PDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD-----VA-ARGLDIPQV  100 (212)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHH----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT-----TT-TCSSSCCCB
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC-----hh-hcCCCCccC
Confidence            568999999999999999988876    57788899998876654333   33 478999993     22 234556677


Q ss_pred             cEEEe
Q psy17644        316 TFLVL  320 (330)
Q Consensus       316 ~~lVv  320 (330)
                      .+||.
T Consensus       101 ~~Vi~  105 (212)
T 3eaq_A          101 DLVVH  105 (212)
T ss_dssp             SEEEE
T ss_pred             cEEEE
Confidence            77664

>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=94.44  E-value=0.034  Score=47.88  Aligned_cols=40  Identities=15%  Similarity=0.104  Sum_probs=25.5

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE  251 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~  251 (330)
                      |+=.+++++.|+|||.+.+--+.+. ..       .+-+++|+.|...
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~-~~-------~g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRT-QF-------AKQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHH-HH-------TTCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHH-HH-------CCCEEEEEEeccC
Confidence            4444567999999996554444333 22       4678999998753

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=94.44  E-value=0.06  Score=45.62  Aligned_cols=39  Identities=13%  Similarity=0.019  Sum_probs=27.4

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT  249 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt  249 (330)
                      .|+=.++.+++|+||| +.|+-++.+...       .+.+++++.|.
T Consensus        19 ~g~l~fiyG~MgsGKT-t~Ll~~i~n~~~-------~~~kvl~~kp~   57 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKS-TELMRRVRRFQI-------AQYKCLVIKYA   57 (195)
T ss_dssp             CCEEEEEEECTTSCHH-HHHHHHHHHHHH-------TTCCEEEEEET
T ss_pred             ceEEEEEECCCCCcHH-HHHHHHHHHHHH-------cCCeEEEEccc
Confidence            3555677799999999 455555555444       25788999887

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=94.37  E-value=0.083  Score=48.54  Aligned_cols=18  Identities=28%  Similarity=0.351  Sum_probs=15.1

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      .++.+++.|++|+|||..
T Consensus        43 ~~~~vll~G~~G~GKT~l   60 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAV   60 (387)
T ss_dssp             CCCCEEECBCTTSSHHHH
T ss_pred             CCCcEEEECCCCCCHHHH
Confidence            457899999999999943

>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=94.11  E-value=0.15  Score=46.08  Aligned_cols=17  Identities=29%  Similarity=0.247  Sum_probs=14.6

Q ss_pred             CCCcEEEEcCCCChhHH
Q psy17644        203 SGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~  219 (330)
                      .+..+++.|++|+|||.
T Consensus        36 ~~~~lll~G~~GtGKT~   52 (324)
T 1l8q_A           36 LYNPIFIYGSVGTGKTH   52 (324)
T ss_dssp             SCSSEEEECSSSSSHHH
T ss_pred             CCCeEEEECCCCCcHHH
Confidence            35789999999999994

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=94.09  E-value=0.26  Score=47.16  Aligned_cols=117  Identities=17%  Similarity=0.062  Sum_probs=56.7

Q ss_pred             hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCch
Q psy17644        201 ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSK  280 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~  280 (330)
                      +..|.=+++.|++|+||| +|++.++.++...      .+-.|+|+..-- -..|+...+........... ...|....
T Consensus       200 l~~G~liiI~G~pG~GKT-tl~l~ia~~~~~~------~g~~Vl~~s~E~-s~~~l~~r~~~~~~~~~~~~-l~~g~l~~  270 (454)
T 2r6a_A          200 FQRSDLIIVAARPSVGKT-AFALNIAQNVATK------TNENVAIFSLEM-SAQQLVMRMLCAEGNINAQN-LRTGKLTP  270 (454)
T ss_dssp             BCTTCEEEEECCTTSCHH-HHHHHHHHHHHHH------SSCCEEEEESSS-CHHHHHHHHHHHHHTCCHHH-HHTSCCCH
T ss_pred             CCCCCEEEEECCCCCCHH-HHHHHHHHHHHHh------CCCcEEEEECCC-CHHHHHHHHHHHHcCCCHHH-HhcCCCCH
Confidence            345667778899999999 4555555555432      244577766432 22344443321100111100 00111222


Q ss_pred             HHH------HHHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        281 WDQ------SKALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       281 ~~~------~~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      ...      ...+.. ..+.|.     |.+.+...+.+-.. -..+++||||+.+.|..
T Consensus       271 ~~~~~~~~a~~~l~~-~~l~i~d~~~~s~~~i~~~~~~l~~-~~~~~livID~l~~~~~  327 (454)
T 2r6a_A          271 EDWGKLTMAMGSLSN-AGIYIDDTPSIRVSDIRAKCRRLKQ-ESGLGMIVIDYLQLIQG  327 (454)
T ss_dssp             HHHHHHHHHHHHHHS-SCEEEECCTTCCHHHHHHHHHHHHT-TTCCCEEEEECGGGSCC
T ss_pred             HHHHHHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHH-HcCCCEEEEccHHHhcc
Confidence            111      111222 345553     45555554432111 13589999999998873

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=93.44  E-value=0.098  Score=52.53  Aligned_cols=59  Identities=19%  Similarity=0.224  Sum_probs=40.3

Q ss_pred             CCCHHHHHhhhhhcC--CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        189 SPTPIQAQAVPAALS--GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~--g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      .+|.-|.+++..++.  ..-.++.|.-|.|||.+.-+.+ ..+ .         ..++|.+||.+-+..+.+
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~-a~~-~---------~~~~vtAP~~~a~~~l~~  235 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLI-SRI-A---------GRAIVTAPAKASTDVLAQ  235 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHH-HHS-S---------SCEEEECSSCCSCHHHHH
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHH-HHH-H---------hCcEEECCCHHHHHHHHH
Confidence            689999999987774  2235777999999994433322 222 1         135999999887765444

>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=93.35  E-value=0.38  Score=39.32  Aligned_cols=72  Identities=11%  Similarity=0.039  Sum_probs=50.2

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+..|..++..+...    +..+..++|+.........   ++. ...|+|||..     + ...+++..
T Consensus        30 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~-----~-~~Gldi~~   99 (172)
T 1t5i_A           30 EFNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL-----F-GRGMDIER   99 (172)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC-----C-STTCCGGG
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhc----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCc-----h-hcCcchhh
Confidence            3568999999999999999988875    5678888888876554333   333 4789999931     1 12344556


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      +.+||.
T Consensus       100 ~~~Vi~  105 (172)
T 1t5i_A          100 VNIAFN  105 (172)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            666654

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=93.28  E-value=0.74  Score=41.59  Aligned_cols=17  Identities=29%  Similarity=0.223  Sum_probs=14.4

Q ss_pred             CCcEEEEcCCCChhHHH
Q psy17644        204 GRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a  220 (330)
                      ...+++.|++|+|||..
T Consensus        55 ~~~vll~G~~GtGKT~l   71 (338)
T 3pfi_A           55 LDHILFSGPAGLGKTTL   71 (338)
T ss_dssp             CCCEEEECSTTSSHHHH
T ss_pred             CCeEEEECcCCCCHHHH
Confidence            35799999999999943

>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=93.26  E-value=0.11  Score=45.71  Aligned_cols=17  Identities=24%  Similarity=0.122  Sum_probs=14.3

Q ss_pred             CCcEEEEcCCCChhHHH
Q psy17644        204 GRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a  220 (330)
                      .+.+++.|++|+|||..
T Consensus        64 ~~~vLl~G~~GtGKT~l   80 (272)
T 1d2n_A           64 LVSVLLEGPPHSGKTAL   80 (272)
T ss_dssp             EEEEEEECSTTSSHHHH
T ss_pred             CeEEEEECCCCCcHHHH
Confidence            35799999999999944

>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=93.18  E-value=1.1  Score=43.54  Aligned_cols=77  Identities=16%  Similarity=0.106  Sum_probs=56.0

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh----CCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE----LGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~----~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+.-|..++..++.... .+..+..++|+.........+.    ...+|||||.     .+ ...+++..
T Consensus       338 ~~~~~iVF~~s~~~~~~l~~~L~~~~~-~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~-----~~-~~GiDip~  410 (563)
T 3i5x_A          338 SNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----VG-ARGMDFPN  410 (563)
T ss_dssp             TCCEEEEECSCHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----GG-TSSCCCTT
T ss_pred             CCCcEEEEcCcHHHHHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcc-----hh-hcCCCccc
Confidence            467999999999999999999987643 2567888888887665443332    3579999994     22 24566777


Q ss_pred             ccEEEeec
Q psy17644        315 VTFLVLDE  322 (330)
Q Consensus       315 i~~lVvDE  322 (330)
                      +.+||.-.
T Consensus       411 v~~VI~~~  418 (563)
T 3i5x_A          411 VHEVLQIG  418 (563)
T ss_dssp             CCEEEEES
T ss_pred             CCEEEEEC
Confidence            88887544

>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=93.16  E-value=0.3  Score=40.52  Aligned_cols=72  Identities=13%  Similarity=0.185  Sum_probs=43.4

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHH---HHHh-CCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS---KALE-LGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~---~~l~-~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+..|..+...++..    ++.+..++|+.+.....   ..++ ....|||||.     .+. ..+++..
T Consensus        45 ~~~k~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~-~Gldi~~  114 (185)
T 2jgn_A           45 KDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----VAA-RGLDISN  114 (185)
T ss_dssp             CCSCEEEEESCHHHHHHHHHHHHHT----TCCEEEEC--------CHHHHHHHHTSSSEEEEEC------------CCCS
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHc----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcC-----hhh-cCCCccc
Confidence            4678999999999999999888775    56788888877654432   2222 3578999993     222 2345666


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      +.+||.
T Consensus       115 ~~~VI~  120 (185)
T 2jgn_A          115 VKHVIN  120 (185)
T ss_dssp             BSEEEE
T ss_pred             CCEEEE
Confidence            776664

>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=93.08  E-value=0.45  Score=39.42  Aligned_cols=15  Identities=27%  Similarity=0.441  Sum_probs=13.1

Q ss_pred             CcEEEEcCCCChhHH
Q psy17644        205 RDIIGVAKTGSGKTG  219 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~  219 (330)
                      ..+++.|++|+|||.
T Consensus        39 ~~~ll~G~~G~GKT~   53 (226)
T 2chg_A           39 PHLLFSGPPGTGKTA   53 (226)
T ss_dssp             CCEEEECSTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            459999999999994

>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=93.03  E-value=0.16  Score=44.27  Aligned_cols=40  Identities=13%  Similarity=0.041  Sum_probs=26.7

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTR  250 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr  250 (330)
                      .|+=.++.|+.|+|||.+.+--+.+.. .       .+-+++|+-|..
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~-~-------~g~kvli~kp~~   57 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQ-I-------AQYKCLVIKYAK   57 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHH-T-------TTCCEEEEEETT
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHH-H-------CCCeEEEEeecC
Confidence            355567779999999965444443332 2       467889988864

>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=93.00  E-value=0.55  Score=45.34  Aligned_cols=52  Identities=13%  Similarity=0.202  Sum_probs=38.8

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      .|....+.+-||||||++  +..+.   .+      .+..+|||+|+...|.|++..++.|..
T Consensus        13 ~~~~~~l~g~~gs~ka~~--~a~l~---~~------~~~p~lvv~~~~~~A~~l~~~l~~~~~   64 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATL--VAEIA---ER------HAGPVVLIAPDMQNALRLHDEISQFTD   64 (483)
T ss_dssp             TTCEEEEECCCTTHHHHH--HHHHH---HH------SSSCEEEEESSHHHHHHHHHHHHHTCS
T ss_pred             CCCeEEEeCCCchHHHHH--HHHHH---HH------hCCCEEEEeCCHHHHHHHHHHHHhhCC
Confidence            456778889999999943  22222   21      133479999999999999999999864

>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=92.87  E-value=0.24  Score=45.55  Aligned_cols=15  Identities=27%  Similarity=0.372  Sum_probs=13.1

Q ss_pred             cEEEEcCCCChhHHH
Q psy17644        206 DIIGVAKTGSGKTGA  220 (330)
Q Consensus       206 d~i~~a~TGsGKT~a  220 (330)
                      .+++.|++|+|||..
T Consensus        46 ~~li~G~~G~GKTtl   60 (389)
T 1fnn_A           46 RATLLGRPGTGKTVT   60 (389)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             eEEEECCCCCCHHHH
Confidence            789999999999943

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=92.86  E-value=0.34  Score=43.90  Aligned_cols=53  Identities=13%  Similarity=0.031  Sum_probs=32.5

Q ss_pred             hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      +..|.=+++.|++|+||| +|++-+..++..       ++..++|++-- .-..|+...+..
T Consensus        65 l~~G~l~li~G~pG~GKT-tl~l~ia~~~a~-------~g~~vl~~slE-~s~~~l~~R~~~  117 (315)
T 3bh0_A           65 YKRRNFVLIAARPSMGKT-AFALKQAKNMSD-------NDDVVNLHSLE-MGKKENIKRLIV  117 (315)
T ss_dssp             BCTTCEEEEECCTTSSHH-HHHHHHHHHHHT-------TTCEEEEEESS-SCHHHHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCHH-HHHHHHHHHHHH-------cCCeEEEEECC-CCHHHHHHHHHH
Confidence            345667888899999999 455555555543       23567777643 334455544443

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=92.84  E-value=0.18  Score=46.44  Aligned_cols=115  Identities=14%  Similarity=0.059  Sum_probs=55.8

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      ..|.=+++.|++|+||| +|++-+..++..       .+..|+|++.- .-..|+...+.......+... +..|..+..
T Consensus        44 ~~G~LiiIaG~pG~GKT-t~al~ia~~~a~-------~g~~Vl~fSlE-ms~~ql~~Rlls~~~~v~~~~-l~~g~Ls~~  113 (338)
T 4a1f_A           44 NKGSLVIIGARPSMGKT-SLMMNMVLSALN-------DDRGVAVFSLE-MSAEQLALRALSDLTSINMHD-LESGRLDDD  113 (338)
T ss_dssp             CTTCEEEEEECTTSCHH-HHHHHHHHHHHH-------TTCEEEEEESS-SCHHHHHHHHHHHHHCCCHHH-HHHTCCCHH
T ss_pred             CCCcEEEEEeCCCCCHH-HHHHHHHHHHHH-------cCCeEEEEeCC-CCHHHHHHHHHHHhhCCCHHH-HhcCCCCHH
Confidence            35556777799999999 455555555544       25567777642 233444444322211111110 001212221


Q ss_pred             HHH------HHHhCCCeEEE-EC----hHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        282 DQS------KALELGAEIVV-GT----PGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       282 ~~~------~~l~~~~dIiV-~T----P~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                      ++.      ..+.. ..|.| .+    +..|...+++-......+.+||||-.+.|.
T Consensus       114 e~~~l~~a~~~l~~-~~l~I~d~~~~si~~i~~~ir~l~~~~gg~~lIVIDyLqlm~  169 (338)
T 4a1f_A          114 QWENLAKCFDHLSQ-KKLFFYDKSYVRIEQIRLQLRKLKSQHKELGIAFIDYLQLMS  169 (338)
T ss_dssp             HHHHHHHHHHHHHH-SCEEEECCTTCCHHHHHHHHHHHHHHCTTEEEEEEEEEECCC
T ss_pred             HHHHHHHHHHHHhc-CCeEEeCCCCCcHHHHHHHHHHHHHhcCCCCEEEEechHHhc
Confidence            111      11222 34555 33    444544443211111168999999988774

>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=92.76  E-value=0.46  Score=45.25  Aligned_cols=16  Identities=25%  Similarity=0.181  Sum_probs=14.3

Q ss_pred             CCcEEEEcCCCChhHH
Q psy17644        204 GRDIIGVAKTGSGKTG  219 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~  219 (330)
                      +..+++.|++|+|||.
T Consensus       130 ~~~lll~Gp~G~GKTt  145 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTH  145 (440)
T ss_dssp             SCCEEEECSSSSSHHH
T ss_pred             CCeEEEECCCCCCHHH
Confidence            5789999999999994

>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=92.64  E-value=0.14  Score=47.22  Aligned_cols=17  Identities=29%  Similarity=0.178  Sum_probs=14.1

Q ss_pred             CCcEEEEcCCCChhHHH
Q psy17644        204 GRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a  220 (330)
                      ++.+++.|++|+|||..
T Consensus        45 ~~~vll~G~~G~GKT~l   61 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFV   61 (384)
T ss_dssp             CCEEEEEECTTSSHHHH
T ss_pred             CCcEEEECCCCCCHHHH
Confidence            45689999999999943

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=92.56  E-value=0.98  Score=41.74  Aligned_cols=72  Identities=15%  Similarity=0.209  Sum_probs=53.4

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---h-CCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---E-LGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~-~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+..|..++..+...    +..+..++|+.....+...+   + ...+|||||.     .+. ...++..
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~-----~~~-~Gidip~  344 (417)
T 2i4i_A          275 KDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----VAA-RGLDISN  344 (417)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECH-----HHH-TTSCCCC
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHC----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECC-----hhh-cCCCccc
Confidence            4678999999999999999988875    56788888888765543332   2 3578999994     333 3566777


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      +.+||.
T Consensus       345 v~~Vi~  350 (417)
T 2i4i_A          345 VKHVIN  350 (417)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence            887775

>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=92.35  E-value=0.54  Score=42.68  Aligned_cols=59  Identities=20%  Similarity=0.167  Sum_probs=32.3

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH-HHHHHHHHHHh
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL-SQQIYNEAKRF  263 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~L-a~Qi~~~~~~l  263 (330)
                      .|+-+++.|++|+|||. +++.++..+..... ..+.+.+++++.-...+ ..++...+.++
T Consensus       106 ~G~i~~i~G~~GsGKT~-la~~la~~~~~~~~-~gg~~~~vlyi~~e~~~~~~~l~~~~~~~  165 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQ-LCHQLSVNVQLPPE-KGGLSGKAVYIDTEGTFRWERIENMAKAL  165 (324)
T ss_dssp             TTSEEEEEESTTSSHHH-HHHHHHHHTTSCGG-GTCCSCEEEEEESSSCCCHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHhH-HHHHHHHHHhcccc-cCCCCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            56778888999999994 44444433222110 00114577877654322 44555555544

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=92.33  E-value=0.13  Score=44.30  Aligned_cols=41  Identities=20%  Similarity=0.098  Sum_probs=26.1

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE  251 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~  251 (330)
                      .|.=.+++++.|+|||...+- .+.+...       .+.+++|+.|...
T Consensus        27 ~G~I~vitG~M~sGKTT~Llr-~~~r~~~-------~g~kvli~kp~~D   67 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEELIR-RLRRGIY-------AKQKVVVFKPAID   67 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHHHH-HHHHHHH-------TTCCEEEEEEC--
T ss_pred             CceEEEEECCCCCCHHHHHHH-HHHHHHH-------cCCceEEEEeccC
Confidence            355567789999999954433 3344333       3578899988643

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=92.19  E-value=0.47  Score=45.19  Aligned_cols=116  Identities=18%  Similarity=0.090  Sum_probs=56.7

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      ..|.=+++.|++|+||| +|++.+..++...      .+..|+|+..- .-..|+...+........... ...|.....
T Consensus       198 ~~G~l~ii~G~pg~GKT-~lal~ia~~~a~~------~g~~vl~~slE-~~~~~l~~R~~~~~~~i~~~~-l~~g~l~~~  268 (444)
T 2q6t_A          198 GPGSLNIIAARPAMGKT-AFALTIAQNAALK------EGVGVGIYSLE-MPAAQLTLRMMCSEARIDMNR-VRLGQLTDR  268 (444)
T ss_dssp             CTTCEEEEEECTTSCHH-HHHHHHHHHHHHT------TCCCEEEEESS-SCHHHHHHHHHHHHTTCCTTT-CCGGGCCHH
T ss_pred             CCCcEEEEEeCCCCCHH-HHHHHHHHHHHHh------CCCeEEEEECC-CCHHHHHHHHHHHHcCCCHHH-HhCCCCCHH
Confidence            35566777899999999 5555555555432      24457776542 223344444322111111100 001222222


Q ss_pred             HH------HHHHhCCCeEEEE-----ChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        282 DQ------SKALELGAEIVVG-----TPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       282 ~~------~~~l~~~~dIiV~-----TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      .+      ...+.. ..|.|.     |+..+...+.+-.. -..+++||||..+.|..
T Consensus       269 ~~~~~~~a~~~l~~-~~l~i~d~~~~s~~~l~~~~~~l~~-~~~~~lIvID~l~~~~~  324 (444)
T 2q6t_A          269 DFSRLVDVASRLSE-APIYIDDTPDLTLMEVRARARRLVS-QNQVGLIIIDYLQLMSG  324 (444)
T ss_dssp             HHHHHHHHHHHHHT-SCEEEECCTTCBHHHHHHHHHHHHH-HSCCCEEEEECGGGCBC
T ss_pred             HHHHHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHH-HcCCCEEEEcChhhcCC
Confidence            21      112222 345553     44555544332110 12588999999998863

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=92.13  E-value=1.8  Score=42.35  Aligned_cols=77  Identities=16%  Similarity=0.106  Sum_probs=55.9

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---h-CCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---E-LGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~-~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+..|..++..++.... .+..+..++|+.........+   + ....|||||-     .+ ...+++..
T Consensus       287 ~~~~~iVF~~t~~~~~~l~~~L~~~~~-~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~-----~~-~~GiDip~  359 (579)
T 3sqw_A          287 SNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----VG-ARGMDFPN  359 (579)
T ss_dssp             TCCEEEEECSSHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----GG-TSSCCCTT
T ss_pred             CCCcEEEECCcHHHHHHHHHHHHHhhc-CCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcc-----hh-hcCCCccc
Confidence            467899999999999999999987643 256788888888765543332   2 3579999994     22 23566777


Q ss_pred             ccEEEeec
Q psy17644        315 VTFLVLDE  322 (330)
Q Consensus       315 i~~lVvDE  322 (330)
                      +.+||.-.
T Consensus       360 v~~VI~~~  367 (579)
T 3sqw_A          360 VHEVLQIG  367 (579)
T ss_dssp             CCEEEEES
T ss_pred             CCEEEEcC
Confidence            88887644

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=92.09  E-value=1.1  Score=40.28  Aligned_cols=71  Identities=13%  Similarity=0.200  Sum_probs=51.7

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---h-CCCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---E-LGAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~-~~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      +.++||.|+|+.-+..++..+...    +..+..++|+.+...+...+   + ...+|+|||-     ++. ..+++..+
T Consensus        28 ~~~~LVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~-----va~-~Gidi~~v   97 (300)
T 3i32_A           28 PDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVATD-----VAA-RGLDIPQV   97 (300)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHTT----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECS-----TTT-CSTTCCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEec-----hhh-cCccccce
Confidence            578999999999999888887664    67888999998766554333   2 2478999992     222 34566777


Q ss_pred             cEEEe
Q psy17644        316 TFLVL  320 (330)
Q Consensus       316 ~~lVv  320 (330)
                      .+||.
T Consensus        98 ~~VI~  102 (300)
T 3i32_A           98 DLVVH  102 (300)
T ss_dssp             SEEEE
T ss_pred             eEEEE
Confidence            77764

>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=91.91  E-value=0.53  Score=44.95  Aligned_cols=86  Identities=17%  Similarity=0.201  Sum_probs=44.8

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHHHHHHHHHHHhccCCCceEEEEECCCchHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA--PTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWD  282 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~--Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~  282 (330)
                      +-+++++++|+|||.+.. -+..+ +..      .+.+++++.  |.|.-+.   ..++.++...++.+.....+.....
T Consensus       101 ~vIlivG~~G~GKTTt~~-kLA~~-l~~------~G~kVllv~~D~~R~aa~---eqL~~~~~~~gvpv~~~~~~~dp~~  169 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVA-KLARY-FQK------RGYKVGVVCSDTWRPGAY---HQLRQLLDRYHIEVFGNPQEKDAIK  169 (443)
T ss_dssp             EEEEEECCTTSSHHHHHH-HHHHH-HHT------TTCCEEEEECCCSSTHHH---HHHHHHHGGGTCEEECCTTCCCHHH
T ss_pred             eEEEEECcCCCCHHHHHH-HHHHH-HHH------CCCeEEEEeCCCcchhHH---HHHHHHHHhcCCcEEecCCCCCHHH
Confidence            456777999999994433 22223 332      355666665  4455443   3455555555666554433333221


Q ss_pred             ----HHHHH-hCCCeEEE-EChHHH
Q psy17644        283 ----QSKAL-ELGAEIVV-GTPGRI  301 (330)
Q Consensus       283 ----~~~~l-~~~~dIiV-~TP~~L  301 (330)
                          ..... ..++|+|| =||+++
T Consensus       170 i~~~al~~a~~~~~DvVIIDTaGrl  194 (443)
T 3dm5_A          170 LAKEGVDYFKSKGVDIIIVDTAGRH  194 (443)
T ss_dssp             HHHHHHHHHHHTTCSEEEEECCCCS
T ss_pred             HHHHHHHHHHhCCCCEEEEECCCcc
Confidence                11222 23577654 577754

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=91.90  E-value=0.17  Score=45.18  Aligned_cols=18  Identities=22%  Similarity=0.257  Sum_probs=15.0

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      .+..+++.|++|+|||..
T Consensus        66 ~~~~vll~G~~GtGKT~l   83 (309)
T 3syl_A           66 PTLHMSFTGNPGTGKTTV   83 (309)
T ss_dssp             CCCEEEEEECTTSSHHHH
T ss_pred             CCceEEEECCCCCCHHHH
Confidence            456799999999999944

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=91.65  E-value=0.25  Score=42.32  Aligned_cols=53  Identities=23%  Similarity=0.258  Sum_probs=32.5

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..|.-+++.|++|+|||. +++.++..+..       .+.+++++.- .....++...+..+
T Consensus        21 ~~G~~~~i~G~~GsGKTt-l~~~~~~~~~~-------~~~~v~~~~~-e~~~~~~~~~~~~~   73 (247)
T 2dr3_A           21 PERNVVLLSGGPGTGKTI-FSQQFLWNGLK-------MGEPGIYVAL-EEHPVQVRQNMAQF   73 (247)
T ss_dssp             ETTCEEEEEECTTSSHHH-HHHHHHHHHHH-------TTCCEEEEES-SSCHHHHHHHHHTT
T ss_pred             CCCcEEEEECCCCCCHHH-HHHHHHHHHHh-------cCCeEEEEEc-cCCHHHHHHHHHHc
Confidence            467788889999999994 33444444433       2446676653 33445666655544

>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=91.36  E-value=0.97  Score=40.56  Aligned_cols=14  Identities=36%  Similarity=0.579  Sum_probs=10.2

Q ss_pred             EEEEcCCCChhHHH
Q psy17644        207 IIGVAKTGSGKTGA  220 (330)
Q Consensus       207 ~i~~a~TGsGKT~a  220 (330)
                      +++.+++|+|||..
T Consensus        51 ~L~~G~~G~GKT~l   64 (324)
T 3u61_B           51 ILHSPSPGTGKTTV   64 (324)
T ss_dssp             EEECSSTTSSHHHH
T ss_pred             EEeeCcCCCCHHHH
Confidence            45557799999943

>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=90.60  E-value=1.5  Score=41.22  Aligned_cols=70  Identities=7%  Similarity=0.129  Sum_probs=51.2

Q ss_pred             CeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---hC-CCeEEEEChHHHHHHHHcCCCCCCCcc
Q psy17644        241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---EL-GAEIVVGTPGRIIDMVKMGATKLNRVT  316 (330)
Q Consensus       241 ~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~  316 (330)
                      .++||.|+|+.-|..++..+...    +..+..++|+.....+...+   +. ...|||||.     . -...+++..+.
T Consensus       301 ~~~lVF~~t~~~a~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~-----v-~~rGlDi~~v~  370 (434)
T 2db3_A          301 DGTIVFVETKRGADFLASFLSEK----EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATS-----V-ASRGLDIKNIK  370 (434)
T ss_dssp             TTEEEECSSHHHHHHHHHHHHHT----TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECG-----G-GTSSCCCTTCC
T ss_pred             CCEEEEEeCcHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEch-----h-hhCCCCcccCC
Confidence            34999999999999999988875    56788888888765544333   33 478999994     2 23456677788


Q ss_pred             EEEe
Q psy17644        317 FLVL  320 (330)
Q Consensus       317 ~lVv  320 (330)
                      +||.
T Consensus       371 ~VI~  374 (434)
T 2db3_A          371 HVIN  374 (434)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7774

>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=90.58  E-value=1.5  Score=39.92  Aligned_cols=75  Identities=12%  Similarity=0.182  Sum_probs=54.7

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.++++.-|..++..++..    +..+..++|+.....+...   ++. ...|||||.     .+ ....++..
T Consensus       242 ~~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~-~~Gidip~  311 (395)
T 3pey_A          242 TIGSSIIFVATKKTANVLYGKLKSE----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTN-----VL-ARGIDIPT  311 (395)
T ss_dssp             TSSEEEEECSCHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECG-----GG-SSSCCCTT
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhc----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECC-----hh-hcCCCccc
Confidence            4578999999999999999988875    5677888888876554333   333 478999994     22 34567778


Q ss_pred             ccEEEeecc
Q psy17644        315 VTFLVLDEA  323 (330)
Q Consensus       315 i~~lVvDEa  323 (330)
                      +.+||.-..
T Consensus       312 ~~~Vi~~~~  320 (395)
T 3pey_A          312 VSMVVNYDL  320 (395)
T ss_dssp             EEEEEESSC
T ss_pred             CCEEEEcCC
Confidence            888886443

>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=90.58  E-value=2.1  Score=39.28  Aligned_cols=71  Identities=13%  Similarity=0.128  Sum_probs=52.7

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---hC-CCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---EL-GAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~~-~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      +.++||.|+|+..|..++..+...    +..+..++|+.....+...+   +. ...|||||.     .+ ....++..+
T Consensus       266 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~-~~Gidip~~  335 (412)
T 3fht_A          266 IAQAMIFCHTRKTASWLAAELSKE----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTN-----VC-ARGIDVEQV  335 (412)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----GG-TSSCCCTTE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhC----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcC-----cc-ccCCCccCC
Confidence            568999999999999999998876    56778888888766554333   33 478999994     22 235667788


Q ss_pred             cEEEe
Q psy17644        316 TFLVL  320 (330)
Q Consensus       316 ~~lVv  320 (330)
                      .+||.
T Consensus       336 ~~Vi~  340 (412)
T 3fht_A          336 SVVIN  340 (412)
T ss_dssp             EEEEE
T ss_pred             CEEEE
Confidence            88774

>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=90.47  E-value=3.3  Score=34.30  Aligned_cols=15  Identities=27%  Similarity=0.302  Sum_probs=12.8

Q ss_pred             cEEEEcCCCChhHHH
Q psy17644        206 DIIGVAKTGSGKTGA  220 (330)
Q Consensus       206 d~i~~a~TGsGKT~a  220 (330)
                      .+++.|++|+|||..
T Consensus        47 ~~ll~G~~G~GKT~l   61 (250)
T 1njg_A           47 AYLFSGTRGVGKTSI   61 (250)
T ss_dssp             EEEEECSTTSCHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            578899999999943

>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=90.40  E-value=0.46  Score=42.59  Aligned_cols=18  Identities=22%  Similarity=0.235  Sum_probs=14.9

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      ..+.+++.|++|+|||..
T Consensus        37 ~~~~vll~G~~GtGKT~l   54 (324)
T 1hqc_A           37 PLEHLLLFGPPGLGKTTL   54 (324)
T ss_dssp             CCCCCEEECCTTCCCHHH
T ss_pred             CCCcEEEECCCCCCHHHH
Confidence            347899999999999943

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=90.34  E-value=0.29  Score=46.34  Aligned_cols=28  Identities=18%  Similarity=0.189  Sum_probs=20.3

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      ..+++++.|+||||||... .+++..++.
T Consensus        52 ~~~h~~i~G~tGsGKs~~~-~~li~~~~~   79 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL-RELAYTGLL   79 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHHHH
T ss_pred             CcceEEEECCCCCCHHHHH-HHHHHHHHH
Confidence            4578999999999999763 344444443

>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=90.30  E-value=1.5  Score=37.25  Aligned_cols=21  Identities=19%  Similarity=0.058  Sum_probs=16.4

Q ss_pred             hcCCCcEEEEcCCCChhHHHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTGAF  221 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~a~  221 (330)
                      +-.|.-+++.+++|+|||...
T Consensus        21 i~~G~~~~i~G~~GsGKTtl~   41 (243)
T 1n0w_A           21 IETGSITEMFGEFRTGKTQIC   41 (243)
T ss_dssp             EETTSEEEEECCTTSSHHHHH
T ss_pred             CcCCeEEEEECCCCCcHHHHH
Confidence            346677888999999999443

>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=90.26  E-value=1.4  Score=40.52  Aligned_cols=72  Identities=7%  Similarity=0.114  Sum_probs=51.2

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||+|+++..|..++..++..    +..+..++|+.....+...   ++. ...|||||.     .+ ....++..
T Consensus       257 ~~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~-----~~-~~Gidip~  326 (400)
T 1s2m_A          257 QINQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD-----LL-TRGIDIQA  326 (400)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESS-----CS-SSSCCCTT
T ss_pred             CCCcEEEEEecHHHHHHHHHHHHhc----CCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-----cc-ccCCCccC
Confidence            3568999999999999999998876    5677888888876554333   333 468999993     11 22455667


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      +.+||.
T Consensus       327 ~~~Vi~  332 (400)
T 1s2m_A          327 VNVVIN  332 (400)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence            777664

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=89.80  E-value=0.24  Score=42.45  Aligned_cols=53  Identities=23%  Similarity=0.396  Sum_probs=30.9

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .|.-+++.|++|+||| +|++.++.+...+      .+..++|++- ..-..++...+..+
T Consensus        29 ~G~l~~i~G~pG~GKT-~l~l~~~~~~~~~------~~~~v~~~s~-E~~~~~~~~~~~~~   81 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKT-TFAAQFIYKGAEE------YGEPGVFVTL-EERARDLRREMASF   81 (251)
T ss_dssp             TTCEEEEECCTTSSHH-HHHHHHHHHHHHH------HCCCEEEEES-SSCHHHHHHHHHTT
T ss_pred             CCeEEEEEeCCCCCHH-HHHHHHHHHHHHh------cCCCceeecc-cCCHHHHHHHHHHc
Confidence            4567888899999999 4555544433221      2345666653 23455555555543

>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=89.74  E-value=1.7  Score=39.01  Aligned_cols=72  Identities=13%  Similarity=0.217  Sum_probs=50.6

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||+|+|+.-|..+++.++..    +..+..++|+.+.......   ++. ...|+|||.     .+.. ..++..
T Consensus       237 ~~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~~~~-Gid~~~  306 (367)
T 1hv8_A          237 KEFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-----VMSR-GIDVND  306 (367)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-----THHH-HCCCSC
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhc----CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECC-----hhhc-CCCccc
Confidence            4678999999999999999988876    5678888888776554332   233 468999993     2221 345566


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      +.+||.
T Consensus       307 ~~~Vi~  312 (367)
T 1hv8_A          307 LNCVIN  312 (367)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            666664

>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=89.32  E-value=1.8  Score=42.84  Aligned_cols=72  Identities=15%  Similarity=0.144  Sum_probs=53.1

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---h-CCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---E-LGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~-~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+.-|.+++..+...    ++.+..++||.+.......+   . ....|||||-     .+ ...+++.+
T Consensus       266 ~~~~~IVf~~sr~~~e~la~~L~~~----g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~-----a~-~~GID~p~  335 (591)
T 2v1x_A          266 KGQSGIIYCFSQKDSEQVTVSLQNL----GIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATV-----AF-GMGIDKPD  335 (591)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECT-----TS-CTTCCCSC
T ss_pred             cCCCeEEEeCcHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEec-----hh-hcCCCccc
Confidence            4678999999999999999998875    67888899988766553332   2 3478999993     11 23456777


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      +++||.
T Consensus       336 V~~VI~  341 (591)
T 2v1x_A          336 VRFVIH  341 (591)
T ss_dssp             EEEEEE
T ss_pred             ccEEEE
Confidence            888774

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=89.29  E-value=0.55  Score=43.72  Aligned_cols=18  Identities=28%  Similarity=0.410  Sum_probs=15.2

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      ..+.+++.|++|+|||..
T Consensus       147 ~~~~vLL~GppGtGKT~l  164 (389)
T 3vfd_A          147 PARGLLLFGPPGNGKTML  164 (389)
T ss_dssp             CCSEEEEESSTTSCHHHH
T ss_pred             CCceEEEECCCCCCHHHH
Confidence            357899999999999943

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=89.23  E-value=1.4  Score=39.60  Aligned_cols=60  Identities=18%  Similarity=0.226  Sum_probs=31.8

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcC----CC-CCCCC----CeEEEEcccHHH-HHHHHHHHHHh
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQK----EL-EPGDG----PMGLILAPTREL-SQQIYNEAKRF  263 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~----~~-~~~~~----~~vLil~Ptr~L-a~Qi~~~~~~l  263 (330)
                      .|+-+++.+++|+|||. +++.++..+....    .. ....+    .+++|+.-...+ ..++...+.++
T Consensus        97 ~g~i~~i~G~~gsGKT~-la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~~~~~  166 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQ-IMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHA  166 (322)
T ss_dssp             TTEEEEEEESTTSSHHH-HHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHH-HHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHHHHHc
Confidence            45678888999999994 4433333321100    00 00112    577777654332 45555555554

>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=89.02  E-value=1.1  Score=41.00  Aligned_cols=74  Identities=11%  Similarity=0.070  Sum_probs=52.4

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||+++++..|..++..+...    +..+..++|+.........   ++. ...|||||.     .+ ....++..
T Consensus       249 ~~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~~-~~Gidi~~  318 (391)
T 1xti_A          249 EFNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN-----LF-GRGMDIER  318 (391)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESC-----CC-SSCBCCTT
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHhC----CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECC-----hh-hcCCCccc
Confidence            4578999999999999999988875    5678888888776554333   232 478999993     11 22455677


Q ss_pred             ccEEEeec
Q psy17644        315 VTFLVLDE  322 (330)
Q Consensus       315 i~~lVvDE  322 (330)
                      +.+||.-.
T Consensus       319 ~~~Vi~~~  326 (391)
T 1xti_A          319 VNIAFNYD  326 (391)
T ss_dssp             EEEEEESS
T ss_pred             CCEEEEeC
Confidence            77777543

>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=88.74  E-value=0.36  Score=44.08  Aligned_cols=18  Identities=33%  Similarity=0.414  Sum_probs=15.0

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      .++.+++.|++|+|||..
T Consensus        44 ~~~~vli~G~~G~GKTtl   61 (386)
T 2qby_A           44 KPNNIFIYGLTGTGKTAV   61 (386)
T ss_dssp             CCCCEEEEECTTSSHHHH
T ss_pred             CCCeEEEECCCCCCHHHH
Confidence            356899999999999943

>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=88.53  E-value=4.7  Score=37.03  Aligned_cols=71  Identities=10%  Similarity=0.183  Sum_probs=51.7

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---h-CCCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---E-LGAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~-~~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      ..++||.|+|+..|..++..+...    +..+..++|+.....+...+   + ....|||||.     .+ ...+++..+
T Consensus       276 ~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~-~~Gidi~~v  345 (410)
T 2j0s_A          276 ITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD-----VW-ARGLDVPQV  345 (410)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG-----GG-SSSCCCTTE
T ss_pred             CCcEEEEEcCHHHHHHHHHHHHhC----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECC-----hh-hCcCCcccC
Confidence            458999999999999999888875    56778888888765543332   2 2478999994     22 235667778


Q ss_pred             cEEEe
Q psy17644        316 TFLVL  320 (330)
Q Consensus       316 ~~lVv  320 (330)
                      .+||.
T Consensus       346 ~~Vi~  350 (410)
T 2j0s_A          346 SLIIN  350 (410)
T ss_dssp             EEEEE
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=88.38  E-value=1.4  Score=42.73  Aligned_cols=72  Identities=18%  Similarity=0.174  Sum_probs=52.3

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---Hh-CCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LE-LGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~-~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+||.-|..++..++..    ++.+..++|+.+.......   +. ....|||||.     .+ ...+++.+
T Consensus       235 ~~~~~IVf~~sr~~~e~l~~~L~~~----g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~-----a~-~~GiD~p~  304 (523)
T 1oyw_A          235 RGKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV-----AF-GMGINKPN  304 (523)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT-----TS-CTTTCCTT
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEec-----hh-hCCCCccC
Confidence            3568999999999999999998875    5678888898876554322   22 3578999994     11 23456777


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      +++||.
T Consensus       305 v~~VI~  310 (523)
T 1oyw_A          305 VRFVVH  310 (523)
T ss_dssp             CCEEEE
T ss_pred             ccEEEE
Confidence            887775

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=88.21  E-value=2  Score=34.40  Aligned_cols=17  Identities=24%  Similarity=0.393  Sum_probs=14.4

Q ss_pred             CCcEEEEcCCCChhHHH
Q psy17644        204 GRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a  220 (330)
                      ++.+++.|++|+|||..
T Consensus        43 ~~~~ll~G~~G~GKT~l   59 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAI   59 (195)
T ss_dssp             SCEEEEECCTTSCHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            46799999999999943

>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=88.17  E-value=2.3  Score=42.68  Aligned_cols=77  Identities=14%  Similarity=0.223  Sum_probs=56.9

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---Hh-CCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LE-LGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~-~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+..|..+...+...    ++.+..++|+.........   ++ ...+|+|||-     .+ ...+++..
T Consensus       444 ~~~~vlVf~~t~~~ae~L~~~L~~~----gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~-----~l-~~GlDip~  513 (661)
T 2d7d_A          444 RNERVLVTTLTKKMSEDLTDYLKEI----GIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN-----LL-REGLDIPE  513 (661)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESC-----CC-STTCCCTT
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHhc----CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecc-----hh-hCCcccCC
Confidence            4679999999999999999888876    5677778887765554433   33 2478999983     22 34566788


Q ss_pred             ccEEEeecccc
Q psy17644        315 VTFLVLDEADR  325 (330)
Q Consensus       315 i~~lVvDEad~  325 (330)
                      +.+||+=+++.
T Consensus       514 v~lVi~~d~d~  524 (661)
T 2d7d_A          514 VSLVAILDADK  524 (661)
T ss_dssp             EEEEEETTTTC
T ss_pred             CCEEEEeCccc
Confidence            99998887754

>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=88.04  E-value=1.3  Score=42.18  Aligned_cols=87  Identities=21%  Similarity=0.148  Sum_probs=42.6

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA--PTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~--Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      ++-+++++++|+|||....  .|...+..      .+.+++++.  +.|.-+.   +.+..++...++.+.....+....
T Consensus        97 ~~vI~lvG~~GsGKTTt~~--kLA~~l~~------~G~kVllv~~D~~r~~a~---eqL~~~~~~~gv~~~~~~~~~dp~  165 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAG--KLAYFYKK------RGYKVGLVAADVYRPAAY---DQLLQLGNQIGVQVYGEPNNQNPI  165 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHH--HHHHHHHH------TTCCEEEEEECCSCHHHH---HHHHHHHHTTTCCEECCTTCSCHH
T ss_pred             CeEEEEECCCCCCHHHHHH--HHHHHHHH------cCCeEEEEecCccchhHH---HHHHHHHHhcCCceeeccccCCHH
Confidence            4456777999999994433  22223332      355666655  3444332   334444444455544333333321


Q ss_pred             H----HHHHHh-CCCeE-EEEChHHH
Q psy17644        282 D----QSKALE-LGAEI-VVGTPGRI  301 (330)
Q Consensus       282 ~----~~~~l~-~~~dI-iV~TP~~L  301 (330)
                      .    ....+. .++++ ||=||+++
T Consensus       166 ~i~~~al~~a~~~~~DvvIIDTaGr~  191 (433)
T 3kl4_A          166 EIAKKGVDIFVKNKMDIIIVDTAGRH  191 (433)
T ss_dssp             HHHHHHHHHTTTTTCSEEEEEECCCS
T ss_pred             HHHHHHHHHHHhcCCCEEEEECCCCc
Confidence            1    112222 34555 45677763

>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=88.01  E-value=1.1  Score=40.68  Aligned_cols=15  Identities=20%  Similarity=0.383  Sum_probs=12.8

Q ss_pred             cEEEEcCCCChhHHH
Q psy17644        206 DIIGVAKTGSGKTGA  220 (330)
Q Consensus       206 d~i~~a~TGsGKT~a  220 (330)
                      .+++.|++|+|||..
T Consensus        38 ~~ll~Gp~G~GKTtl   52 (354)
T 1sxj_E           38 HLLLYGPNGTGKKTR   52 (354)
T ss_dssp             CEEEECSTTSSHHHH
T ss_pred             eEEEECCCCCCHHHH
Confidence            489999999999943

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=87.28  E-value=2.9  Score=33.35  Aligned_cols=17  Identities=29%  Similarity=0.372  Sum_probs=14.4

Q ss_pred             CCcEEEEcCCCChhHHH
Q psy17644        204 GRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a  220 (330)
                      .+.+++.|++|+|||..
T Consensus        43 ~~~vll~G~~G~GKT~l   59 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAI   59 (187)
T ss_dssp             SCEEEEESCGGGCHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            56789999999999943

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=87.18  E-value=0.49  Score=37.40  Aligned_cols=20  Identities=10%  Similarity=0.159  Sum_probs=16.8

Q ss_pred             hcCCCcEEEEcCCCChhHHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~a  220 (330)
                      ...+.++++.|++|+|||..
T Consensus        21 a~~~~~vll~G~~GtGKt~l   40 (145)
T 3n70_A           21 SETDIAVWLYGAPGTGRMTG   40 (145)
T ss_dssp             TTCCSCEEEESSTTSSHHHH
T ss_pred             hCCCCCEEEECCCCCCHHHH
Confidence            35678999999999999944

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=87.15  E-value=0.4  Score=37.85  Aligned_cols=19  Identities=16%  Similarity=0.052  Sum_probs=16.3

Q ss_pred             hcCCCcEEEEcCCCChhHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~  219 (330)
                      ...+.++++.+++|+|||.
T Consensus        24 ~~~~~~vll~G~~GtGKt~   42 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFET   42 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHH
T ss_pred             hCCCCcEEEECCCCccHHH
Confidence            4567899999999999994

>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=87.02  E-value=0.12  Score=42.26  Aligned_cols=55  Identities=13%  Similarity=0.187  Sum_probs=39.5

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---hC-CCeEEEEC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---EL-GAEIVVGT  297 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~~-~~dIiV~T  297 (330)
                      .+.++||.|+|+..|..+...+...    +..+..++|+.+.......+   +. ...|||||
T Consensus        29 ~~~~~iVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT   87 (170)
T 2yjt_D           29 EATRSIVFVRKRERVHELANWLREA----GINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVAT   87 (170)
Confidence            3568999999999999988887765    56777788876654433222   22 36789988

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=86.52  E-value=0.7  Score=41.73  Aligned_cols=17  Identities=18%  Similarity=0.192  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCChhHHH
Q psy17644        204 GRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a  220 (330)
                      ++.+++.|++|+|||..
T Consensus       152 ~~~lll~G~~GtGKT~L  168 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYL  168 (308)
T ss_dssp             CCEEEEECSTTSSHHHH
T ss_pred             CceEEEECCCCCCHHHH
Confidence            68899999999999943

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=85.49  E-value=1.5  Score=36.26  Aligned_cols=16  Identities=25%  Similarity=0.202  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCChhHHH
Q psy17644        205 RDIIGVAKTGSGKTGA  220 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a  220 (330)
                      +.+++.|++|+|||..
T Consensus        55 ~~~~l~G~~GtGKT~l   70 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYL   70 (202)
T ss_dssp             CEEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            7899999999999953

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=85.36  E-value=3.1  Score=46.90  Aligned_cols=41  Identities=17%  Similarity=0.181  Sum_probs=27.7

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE  251 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~  251 (330)
                      .|+.+++++|+|+|||...+. ++.....       +|.+++|+.....
T Consensus      1426 ~g~~vll~GppGtGKT~LA~a-la~ea~~-------~G~~v~Fi~~e~~ 1466 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQ-VIAAAQR-------EGKTCAFIDAEHA 1466 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHH-HHHHHHT-------TTCCEEEECTTSC
T ss_pred             CCeEEEEECCCCCCHHHHHHH-HHHHHHH-------cCCcEEEEEcccc
Confidence            478999999999999954432 2222222       4678888876543

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=85.23  E-value=1.8  Score=36.23  Aligned_cols=19  Identities=26%  Similarity=0.101  Sum_probs=15.4

Q ss_pred             hcCCCcEEEEcCCCChhHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~  219 (330)
                      +..|.-+.+++++|+|||.
T Consensus        22 i~~G~~~~l~G~nGsGKST   40 (231)
T 4a74_A           22 IETQAITEVFGEFGSGKTQ   40 (231)
T ss_dssp             EESSEEEEEEESTTSSHHH
T ss_pred             CCCCcEEEEECCCCCCHHH
Confidence            4466778888999999994

>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=85.21  E-value=2.5  Score=39.26  Aligned_cols=93  Identities=15%  Similarity=0.170  Sum_probs=56.4

Q ss_pred             CCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEEC--------CCchHHHH
Q psy17644        213 TGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYG--------GGSKWDQS  284 (330)
Q Consensus       213 TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~g--------g~~~~~~~  284 (330)
                      ..++|. ..+.-++...+..     ..+.++||.++++..+..+...+...    ++.+..+.|        +.+..++.
T Consensus       340 ~~~~k~-~~l~~~l~~~~~~-----~~~~k~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~~~~~~~~~r~  409 (494)
T 1wp9_A          340 LDHPKM-DKLKEIIREQLQR-----KQNSKIIVFTNYRETAKKIVNELVKD----GIKAKRFVGQASKENDRGLSQREQK  409 (494)
T ss_dssp             CSCHHH-HHHHHHHHHHHHH-----CTTCCEEEECSCHHHHHHHHHHHHHT----TCCEEEECCSSCC-------CCHHH
T ss_pred             CCChHH-HHHHHHHHHHhcc-----CCCCeEEEEEccHHHHHHHHHHHHHc----CCCcEEEeccccccccccCCHHHHH
Confidence            344554 3344445444422     14678999999999999999988876    667788888        55443332


Q ss_pred             ---HHHh-CCCeEEEEChHHHHHHHHcCCCCCCCccEEEee
Q psy17644        285 ---KALE-LGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLD  321 (330)
Q Consensus       285 ---~~l~-~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvD  321 (330)
                         ..++ ..+.|||||.     .+ ...+++..+.+||+=
T Consensus       410 ~~~~~F~~~~~~vLv~T~-----~~-~~Gldl~~~~~Vi~~  444 (494)
T 1wp9_A          410 LILDEFARGEFNVLVATS-----VG-EEGLDVPEVDLVVFY  444 (494)
T ss_dssp             HHHHHHHHTSCSEEEECG-----GG-GGGGGSTTCCEEEES
T ss_pred             HHHHHHhcCCceEEEECC-----cc-ccCCCchhCCEEEEe
Confidence               2222 2478999993     11 124456667777653

>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=85.06  E-value=1.4  Score=40.15  Aligned_cols=43  Identities=23%  Similarity=0.164  Sum_probs=28.7

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTREL  252 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~L  252 (330)
                      .| -+++.+++|+||| .+++.++....++     ..+.+++++..-..+
T Consensus        28 ~G-iteI~G~pGsGKT-tL~Lq~~~~~~~~-----g~g~~vlyId~E~s~   70 (333)
T 3io5_A           28 SG-LLILAGPSKSFKS-NFGLTMVSSYMRQ-----YPDAVCLFYDSEFGI   70 (333)
T ss_dssp             SE-EEEEEESSSSSHH-HHHHHHHHHHHHH-----CTTCEEEEEESSCCC
T ss_pred             CC-eEEEECCCCCCHH-HHHHHHHHHHHhc-----CCCceEEEEeccchh
Confidence            35 4677899999999 4555666555442     125688888765555

>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=85.03  E-value=1.3  Score=39.84  Aligned_cols=19  Identities=32%  Similarity=0.483  Sum_probs=15.1

Q ss_pred             CCCcEEEEcCCCChhHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAF  221 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~  221 (330)
                      .++-+++++++|+|||...
T Consensus       104 ~g~vi~lvG~~GsGKTTl~  122 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTL  122 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            5677888899999999443

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=84.86  E-value=1  Score=41.83  Aligned_cols=18  Identities=28%  Similarity=0.351  Sum_probs=15.5

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      .+.+++++|+||+|||..
T Consensus        34 ~~~~~~i~G~~G~GKs~~   51 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFT   51 (392)
T ss_dssp             CCCCEEEECCTTSSHHHH
T ss_pred             ccCceEEEcCCCCCHHHH
Confidence            567899999999999954

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=84.81  E-value=1.5  Score=42.80  Aligned_cols=17  Identities=29%  Similarity=0.349  Sum_probs=15.2

Q ss_pred             CCCcEEEEcCCCChhHH
Q psy17644        203 SGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~  219 (330)
                      .|..+++.+|+|+|||.
T Consensus       107 ~g~~vll~Gp~GtGKTt  123 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTS  123 (543)
T ss_dssp             CSCEEEEESSSSSSHHH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            57889999999999994

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=84.59  E-value=1  Score=39.64  Aligned_cols=19  Identities=32%  Similarity=0.239  Sum_probs=15.8

Q ss_pred             hcCCCcEEEEcCCCChhHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~  219 (330)
                      +..|.-+++++|||||||.
T Consensus        22 i~~g~~v~i~Gp~GsGKST   40 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKST   40 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHH
T ss_pred             hCCCCEEEEECCCCccHHH
Confidence            4567778889999999983

>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=84.50  E-value=1.5  Score=46.89  Aligned_cols=79  Identities=11%  Similarity=0.141  Sum_probs=58.3

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---Hh-CCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LE-LGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~-~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.+++|+|+++.-|..++..+++...  +.++..++|+.........   +. ...+|||||-     ++. ..+++.+
T Consensus       811 ~g~qvlvf~~~v~~~~~l~~~L~~~~p--~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~-----v~e-~GiDip~  882 (1151)
T 2eyq_A          811 RGGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----IIE-TGIDIPT  882 (1151)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----TTG-GGSCCTT
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHhCC--CCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECC-----cce-eeecccC
Confidence            467899999999999999999988743  4677888888776544322   33 3579999994     222 3567888


Q ss_pred             ccEEEeecccc
Q psy17644        315 VTFLVLDEADR  325 (330)
Q Consensus       315 i~~lVvDEad~  325 (330)
                      +.+||+..++.
T Consensus       883 v~~VIi~~~~~  893 (1151)
T 2eyq_A          883 ANTIIIERADH  893 (1151)
T ss_dssp             EEEEEETTTTS
T ss_pred             CcEEEEeCCCC
Confidence            99999877754

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=84.14  E-value=1.7  Score=40.98  Aligned_cols=54  Identities=7%  Similarity=-0.076  Sum_probs=38.9

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh-CCCeEEEECh
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE-LGAEIVVGTP  298 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~-~~~dIiV~TP  298 (330)
                      +.++||+|||+.-|..++..+++.    +.++..++|+. .......++ ...+|||||-
T Consensus       171 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~v~~lhg~~-r~~~~~~f~~g~~~vLVaT~  225 (431)
T 2v6i_A          171 DGRTVWFVHSIKQGAEIGTCLQKA----GKKVLYLNRKT-FESEYPKCKSEKWDFVITTD  225 (431)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHT----TCCEEEESTTT-HHHHTTHHHHSCCSEEEECG
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc----CCeEEEeCCcc-HHHHHHhhcCCCCeEEEECc
Confidence            457999999999999999998876    56777777763 222223333 3478898883

>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=84.09  E-value=4.7  Score=40.34  Aligned_cols=77  Identities=13%  Similarity=0.199  Sum_probs=55.5

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---HhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+..|..+...+...    ++.+..++|+.........   ++. ..+|+|||-     .+ ...+++..
T Consensus       438 ~~~~vlVf~~t~~~ae~L~~~L~~~----gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~-----~l-~~GlDip~  507 (664)
T 1c4o_A          438 RGERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN-----LL-REGLDIPE  507 (664)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC-----CC-CTTCCCTT
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhc----CCCceeecCCCCHHHHHHHHHHhhcCCceEEEccC-----hh-hcCccCCC
Confidence            3679999999999999999888876    5677778887765554433   333 478999982     22 23556778


Q ss_pred             ccEEEeecccc
Q psy17644        315 VTFLVLDEADR  325 (330)
Q Consensus       315 i~~lVvDEad~  325 (330)
                      +.+||+=+++.
T Consensus       508 v~lVI~~d~d~  518 (664)
T 1c4o_A          508 VSLVAILDADK  518 (664)
T ss_dssp             EEEEEETTTTS
T ss_pred             CCEEEEeCCcc
Confidence            88888766643

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=83.20  E-value=3.3  Score=37.30  Aligned_cols=18  Identities=33%  Similarity=0.353  Sum_probs=13.5

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      .++-+++++++|+|||..
T Consensus       103 ~~~vi~ivG~~GsGKTTl  120 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTS  120 (306)
T ss_dssp             SCEEEEEECCTTSSHHHH
T ss_pred             CCeEEEEEcCCCChHHHH
Confidence            345567789999999943

>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=83.18  E-value=10  Score=38.74  Aligned_cols=74  Identities=18%  Similarity=0.236  Sum_probs=54.7

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhc-------cCCCceEEEEECCCchHHHHHHHhC---------CCeEEEEChHHHHH
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFG-------KGYNLSVVCCYGGGSKWDQSKALEL---------GAEIVVGTPGRIID  303 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~-------~~~~~~~~~~~gg~~~~~~~~~l~~---------~~dIiV~TP~~L~~  303 (330)
                      +.++||.+|++.-|..++..+...+       ...++.+..++|+.+...+...+..         ...|||||.     
T Consensus       303 ~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~-----  377 (773)
T 2xau_A          303 AGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTN-----  377 (773)
T ss_dssp             SCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECT-----
T ss_pred             CCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCc-----
Confidence            5789999999999999999887532       2246788899999988776555432         358999994     


Q ss_pred             HHHcCCCCCCCccEEE
Q psy17644        304 MVKMGATKLNRVTFLV  319 (330)
Q Consensus       304 ~l~~~~~~l~~i~~lV  319 (330)
                      .+.. .+++..+.+||
T Consensus       378 iae~-GidIp~v~~VI  392 (773)
T 2xau_A          378 IAET-SLTIDGIVYVV  392 (773)
T ss_dssp             HHHH-TCCCTTEEEEE
T ss_pred             HHHh-CcCcCCeEEEE
Confidence            3332 55677888776

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=83.15  E-value=1.1  Score=37.49  Aligned_cols=19  Identities=32%  Similarity=0.221  Sum_probs=15.6

Q ss_pred             hcCCCcEEEEcCCCChhHH
Q psy17644        201 ALSGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~  219 (330)
                      +..|.-+++.+++|+|||.
T Consensus        20 i~~G~~~~i~G~~GsGKTt   38 (235)
T 2w0m_A           20 IPQGFFIALTGEPGTGKTI   38 (235)
T ss_dssp             EETTCEEEEECSTTSSHHH
T ss_pred             CcCCCEEEEEcCCCCCHHH
Confidence            4467778888999999994

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=82.85  E-value=2.2  Score=40.58  Aligned_cols=39  Identities=18%  Similarity=0.139  Sum_probs=26.9

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP  248 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P  248 (330)
                      ..|.=+++.|++|+||| +|++.++.++..+       +.+|+|++-
T Consensus       195 ~~G~liiIaG~pG~GKT-tlal~ia~~~a~~-------g~~vl~fSl  233 (444)
T 3bgw_A          195 KRRNFVLIAARPSMGKT-AFALKQAKNMSDN-------DDVVNLHSL  233 (444)
T ss_dssp             CSSCEEEEEECSSSSHH-HHHHHHHHHHHHT-------TCEEEEECS
T ss_pred             CCCcEEEEEeCCCCChH-HHHHHHHHHHHHc-------CCEEEEEEC
Confidence            35566777899999999 5666666665542       456777764

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=82.78  E-value=1.6  Score=36.67  Aligned_cols=18  Identities=22%  Similarity=0.091  Sum_probs=15.4

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      .++.+++.|++|+|||..
T Consensus        51 ~~~~~ll~G~~G~GKT~l   68 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHL   68 (242)
T ss_dssp             SCSEEEEECSTTSSHHHH
T ss_pred             CCCeEEEECCCCCCHHHH
Confidence            468899999999999943

>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=82.25  E-value=1.8  Score=41.00  Aligned_cols=68  Identities=10%  Similarity=0.085  Sum_probs=44.2

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhC-CCeEEEEChHHHHHHHHcCCCCCCCccEE
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFL  318 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~l  318 (330)
                      +.++||+|||+.-|..++..++..    +.++..++|. ........++. ..+|||||.     .+. ...++. +.+|
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~----~~~v~~lhg~-~R~~~~~~F~~g~~~vLVaT~-----v~e-~GiDip-v~~V  244 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRK-TFEREYPTIKQKKPDFILATD-----IAE-MGANLC-VERV  244 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSS-SCC--------CCCSEEEESS-----STT-CCTTCC-CSEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc----CCCEEEecch-hHHHHHhhhcCCCceEEEECC-----hhh-eeeccC-ceEE
Confidence            568999999999999999998876    5677777773 33333334443 479999993     222 344566 7776


Q ss_pred             E
Q psy17644        319 V  319 (330)
Q Consensus       319 V  319 (330)
                      |
T Consensus       245 I  245 (440)
T 1yks_A          245 L  245 (440)
T ss_dssp             E
T ss_pred             E
Confidence            6

>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=81.67  E-value=5.9  Score=35.75  Aligned_cols=40  Identities=15%  Similarity=0.243  Sum_probs=25.4

Q ss_pred             CHHHHHhhhhhc----CCC---cEEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        191 TPIQAQAVPAAL----SGR---DIIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       191 t~iQ~~~i~~~~----~g~---d~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      .|+|..++..+.    +|+   -+++.|+.|+|||... ..+...+..
T Consensus         4 ~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a-~~la~~l~~   50 (334)
T 1a5t_A            4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALI-YALSRYLLC   50 (334)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHH-HHHHHHHTC
T ss_pred             CCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHH-HHHHHHHhC
Confidence            477777665543    444   4888999999999433 334444443

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=81.37  E-value=1.6  Score=40.54  Aligned_cols=29  Identities=17%  Similarity=0.171  Sum_probs=21.2

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      -.|+-+++.+++|+||| ++++.++.++..
T Consensus        72 ~~G~li~I~G~pGsGKT-tlal~la~~~~~  100 (366)
T 1xp8_A           72 PRGRITEIYGPESGGKT-TLALAIVAQAQK  100 (366)
T ss_dssp             ETTSEEEEEESTTSSHH-HHHHHHHHHHHH
T ss_pred             cCCcEEEEEcCCCCChH-HHHHHHHHHHHH
Confidence            35677888899999999 566666666544

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=81.23  E-value=1.7  Score=40.14  Aligned_cols=39  Identities=18%  Similarity=0.190  Sum_probs=25.3

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP  248 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P  248 (330)
                      -.|+-+++.+++|+|||. +++.++..+...       +.+++|+..
T Consensus        61 ~~G~ii~I~G~pGsGKTt-Lal~la~~~~~~-------g~~vlyid~   99 (356)
T 1u94_A           61 PMGRIVEIYGPESSGKTT-LTLQVIAAAQRE-------GKTCAFIDA   99 (356)
T ss_dssp             ETTSEEEEECSTTSSHHH-HHHHHHHHHHHT-------TCCEEEEES
T ss_pred             cCCeEEEEECCCCCCHHH-HHHHHHHHHHHC-------CCeEEEEeC
Confidence            356778888999999994 445555554432       345566554

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=81.19  E-value=1.6  Score=40.09  Aligned_cols=29  Identities=24%  Similarity=0.151  Sum_probs=20.2

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      -.|+-+++.+++|+|||. +++.++..+..
T Consensus        59 ~~G~iv~I~G~pGsGKTt-Lal~la~~~~~   87 (349)
T 2zr9_A           59 PRGRVIEIYGPESSGKTT-VALHAVANAQA   87 (349)
T ss_dssp             ETTSEEEEEESTTSSHHH-HHHHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCHHH-HHHHHHHHHHh
Confidence            356778888999999994 44555544443

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=80.97  E-value=1.1  Score=37.39  Aligned_cols=61  Identities=16%  Similarity=0.138  Sum_probs=40.9

Q ss_pred             CHHHHHhhhhhcCCC--cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        191 TPIQAQAVPAALSGR--DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       191 t~iQ~~~i~~~~~g~--d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      ++-|..++..++..+  -.++.+.-|++||...+.-++ ++...      .|.+|.||+|+..-.....+
T Consensus        36 ~~~~~~a~~~l~~s~~~~~iv~g~ggs~~~~~~~a~L~-~~a~~------~Gr~V~vLAp~~~s~~~l~~   98 (189)
T 2l8b_A           36 TAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELV-MMARE------QGREVQIIAADRRSQMNMKQ   98 (189)
T ss_dssp             HHHHHHHHHHHHHHSCCEECCBCSSCSHHHHHHHHHHH-HHHHH------TTCCEEEECSTTHHHHHHSC
T ss_pred             CccchhHHHHHhccCCceEEEecccchHHHHHHHHHHH-HHHHh------cCeEEEEEcCchHHHHHHHh
Confidence            466888888887443  344458889999976433332 22222      68899999999887665444

>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=80.83  E-value=4.8  Score=38.04  Aligned_cols=88  Identities=23%  Similarity=0.240  Sum_probs=42.3

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHHHHHHHHHHHhccCCCceEEEEECCCch
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA--PTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSK  280 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~--Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~  280 (330)
                      .++-+++++++|+|||....  .|...+..      .+.+++++.  +.|..+......   ++...++.+.....+...
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~--~LA~~l~~------~g~~Vllvd~D~~r~aa~~qL~~---~~~~~gv~v~~~~~~~~p  165 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAA--KLALYYKG------KGRRPLLVAADTQRPAAREQLRL---LGEKVGVPVLEVMDGESP  165 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHH--HHHHHHHT------TTCCEEEEECCSSCHHHHHHHHH---HHHHHTCCEEECCTTCCH
T ss_pred             CCeEEEEECCCCCCHHHHHH--HHHHHHHH------cCCeEEEeeccccCchhHHHHHH---hcccCCccEEecCCCCCH
Confidence            44556777999999994433  22333332      245565554  344444332222   222234444332222222


Q ss_pred             H----HHHHHH-hCCCe-EEEEChHHH
Q psy17644        281 W----DQSKAL-ELGAE-IVVGTPGRI  301 (330)
Q Consensus       281 ~----~~~~~l-~~~~d-IiV~TP~~L  301 (330)
                      .    .....+ ..++| |||=||+++
T Consensus       166 ~~i~~~~l~~~~~~~~DvVIIDTaG~l  192 (425)
T 2ffh_A          166 ESIRRRVEEKARLEARDLILVDTAGRL  192 (425)
T ss_dssp             HHHHHHHHHHHHHTTCSEEEEECCCCS
T ss_pred             HHHHHHHHHHHHHCCCCEEEEcCCCcc
Confidence            1    122333 25666 566788764

>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=80.76  E-value=2.1  Score=42.95  Aligned_cols=67  Identities=16%  Similarity=0.232  Sum_probs=49.8

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEE
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFL  318 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~l  318 (330)
                      .+.++||.++|+.-|.++++.+++.    ++.+..++|+.....+   .+.+.+|||||-     .+.++. ++. +++|
T Consensus       395 ~~~~vLVFv~Tr~~ae~la~~L~~~----g~~v~~lHG~l~q~er---~~~~~~VLVATd-----VaerGI-DId-V~~V  460 (666)
T 3o8b_A          395 RGGRHLIFCHSKKKCDELAAKLSGL----GINAVAYYRGLDVSVI---PTIGDVVVVATD-----ALMTGY-TGD-FDSV  460 (666)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHTT----TCCEEEECTTSCGGGS---CSSSCEEEEECT-----THHHHC-CCC-BSEE
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHhC----CCcEEEecCCCCHHHH---HhCCCcEEEECC-----hHHccC-CCC-CcEE
Confidence            4578999999999999999988865    6788889998876542   234569999994     444333 354 8877


Q ss_pred             E
Q psy17644        319 V  319 (330)
Q Consensus       319 V  319 (330)
                      |
T Consensus       461 I  461 (666)
T 3o8b_A          461 I  461 (666)
T ss_dssp             E
T ss_pred             E
Confidence            7

>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=80.68  E-value=4.2  Score=36.53  Aligned_cols=15  Identities=13%  Similarity=-0.117  Sum_probs=12.7

Q ss_pred             cEEEEcCCCChhHHH
Q psy17644        206 DIIGVAKTGSGKTGA  220 (330)
Q Consensus       206 d~i~~a~TGsGKT~a  220 (330)
                      ..++.||.|+|||.+
T Consensus        20 ~~Lf~Gp~G~GKtt~   34 (305)
T 2gno_A           20 SILINGEDLSYPREV   34 (305)
T ss_dssp             EEEEECSSSSHHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            578889999999843

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=80.63  E-value=4.2  Score=38.81  Aligned_cols=94  Identities=15%  Similarity=0.113  Sum_probs=52.9

Q ss_pred             ChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEEC--------CCchHHH---
Q psy17644        215 SGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYG--------GGSKWDQ---  283 (330)
Q Consensus       215 sGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~g--------g~~~~~~---  283 (330)
                      ++|. ..+..+|...+...     .+.++||.|+++..|..+...+...+....+.+..++|        +.+..++   
T Consensus       370 ~~k~-~~l~~~l~~~~~~~-----~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~  443 (555)
T 3tbk_A          370 NPKL-RDLYLVLQEEYHLK-----PETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCV  443 (555)
T ss_dssp             CHHH-HHHHHHHHHHHHHC-----TTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC------------------
T ss_pred             CHHH-HHHHHHHHHHhccC-----CCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHH
Confidence            4554 33444454444321     35789999999999999999998865433344444444        4433333   


Q ss_pred             HHHHhC--CCeEEEEChHHHHHHHHcCCCCCCCccEEEe
Q psy17644        284 SKALEL--GAEIVVGTPGRIIDMVKMGATKLNRVTFLVL  320 (330)
Q Consensus       284 ~~~l~~--~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVv  320 (330)
                      ...++.  ..+|||||-     .+ ...+++..+.+||.
T Consensus       444 ~~~F~~~g~~~vLvaT~-----~~-~~GlDlp~v~~VI~  476 (555)
T 3tbk_A          444 LEAFRASGDNNILIATS-----VA-DEGIDIAECNLVIL  476 (555)
T ss_dssp             --------CCSEEEECC-----CT-TCCEETTSCSEEEE
T ss_pred             HHHHhcCCCeeEEEEcc-----hh-hcCCccccCCEEEE
Confidence            233333  368999993     22 23456778888875

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=80.62  E-value=10  Score=36.08  Aligned_cols=76  Identities=12%  Similarity=0.076  Sum_probs=48.5

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHH---HH-hCCCeEEEEChHHHHHHHHcCCCCCCCc
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK---AL-ELGAEIVVGTPGRIIDMVKMGATKLNRV  315 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~---~l-~~~~dIiV~TP~~L~~~l~~~~~~l~~i  315 (330)
                      +...+|++..+.-|..+.+.+...    +.++..+.|+........   .+ ....+|||||+..+-.     .+++..+
T Consensus       347 ~~~~~ivf~~~~~~~~l~~~L~~~----~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~-----GiDip~v  417 (510)
T 2oca_A          347 DENAFVMFKHVSHGKAIFDLIKNE----YDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFST-----GISVKNL  417 (510)
T ss_dssp             TCEEEEEESSHHHHHHHHHHHHTT----CSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHH-----SCCCCSE
T ss_pred             CCCeEEEEecHHHHHHHHHHHHHc----CCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhc-----ccccccC
Confidence            445555555566676666666654    347788888877554332   22 2346899999655542     4567788


Q ss_pred             cEEEeeccc
Q psy17644        316 TFLVLDEAD  324 (330)
Q Consensus       316 ~~lVvDEad  324 (330)
                      .+||+..+.
T Consensus       418 ~~vi~~~~~  426 (510)
T 2oca_A          418 HHVVLAHGV  426 (510)
T ss_dssp             EEEEESSCC
T ss_pred             cEEEEeCCC
Confidence            888876655

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=80.42  E-value=0.76  Score=40.37  Aligned_cols=52  Identities=19%  Similarity=0.229  Sum_probs=29.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCHHH-HHhhh--hhcCCCcEEEEcCCCChhHHH
Q psy17644        166 VSSFGHFGFDEVLMKALRKCEYTSPTPIQ-AQAVP--AALSGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       166 ~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ-~~~i~--~~~~g~d~i~~a~TGsGKT~a  220 (330)
                      -.+|.++.-....++.+...-..   +.+ ...+.  .+..++.+++.|++|+|||..
T Consensus        13 ~~~~~~i~G~~~~~~~l~~~~~~---~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~l   67 (285)
T 3h4m_A           13 NVRYEDIGGLEKQMQEIREVVEL---PLKHPELFEKVGIEPPKGILLYGPPGTGKTLL   67 (285)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTHH---HHHCHHHHHHHCCCCCSEEEEESSSSSSHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHH---HhhCHHHHHhcCCCCCCeEEEECCCCCcHHHH
Confidence            34588876666666655432100   000 01111  123567899999999999943

>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=80.30  E-value=3  Score=44.65  Aligned_cols=49  Identities=22%  Similarity=0.290  Sum_probs=31.1

Q ss_pred             EEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q psy17644        208 IGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR  262 (330)
Q Consensus       208 i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~  262 (330)
                      ++.|..|||||. .++.-+.+++.+.    ..+.++|+|||.. +..++...+..
T Consensus         5 lV~agAGSGKT~-~l~~ri~~ll~~~----~~~~~il~lVP~q-~TFt~~~rl~~   53 (1166)
T 3u4q_B            5 FLVGRSGSGKTK-LIINSIQDELRRA----PFGKPIIFLVPDQ-MTFLMEYELAK   53 (1166)
T ss_dssp             EEEECTTSSHHH-HHHHHHHHHHHHC----TTSSCEEEECCGG-GHHHHHHHHTC
T ss_pred             EEEeCCCCChHH-HHHHHHHHHHHhC----CCCCcEEEEecCc-ccHHHHHHHHH
Confidence            677999999995 4444455555542    1457899999976 33444444433

---

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	330
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	1e-41
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	2e-35
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	4e-34
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	1e-32
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	2e-32
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	8e-30
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	4e-28
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	1e-26
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	2e-26
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	2e-24
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	1e-21
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	3e-20
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	2e-17
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	3e-12
d1a1va1	136	c.37.1.14 (A:190-325) HCV helicase domain {Human h	0.001

>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 =  141 bits (357), Expect = 1e-41
 Identities = 60/164 (36%), Positives = 92/164 (56%), Gaps = 8/164 (4%)

Query: 168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGR-DIIGVAKTGSGKTGAFIWPML 226
           +F      + ++ A+R   +  PT IQ + +P  L+   +I+  A+TGSGKT +F  P++
Sbjct: 5   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 64

Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA 286
             + +       +G   +IL PTREL+ Q+ +E +      NL +   YGG + + Q KA
Sbjct: 65  ELVNEN------NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKA 118

Query: 287 LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           L+  A IVVGTPGRI+D +  G   L  V + +LDEAD M +MG
Sbjct: 119 LK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMG 161

>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 =  126 bits (317), Expect = 2e-35
 Identities = 67/181 (37%), Positives = 100/181 (55%), Gaps = 6/181 (3%)

Query: 155 ITVSGAD--PPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAK 212
           ++V+G D      + +F     D  +   +    Y  PTPIQ  A+PA L  RDI+  A+
Sbjct: 7   VSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQ 66

Query: 213 TGSGKTGAFIWPMLVHIMD----QKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN 268
           TGSGKT AF+ P++ H++     Q+       P  LILAPTREL+ QI +E+++F     
Sbjct: 67  TGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTP 126

Query: 269 LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD 328
           L     YGG     Q + +++G  ++V TPGR++D ++     L    ++VLDEADRM D
Sbjct: 127 LRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLD 186

Query: 329 M 329
           M
Sbjct: 187 M 187

>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 =  122 bits (307), Expect = 4e-34
 Identities = 54/178 (30%), Positives = 88/178 (49%), Gaps = 5/178 (2%)

Query: 153 SGITVSGADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAK 212
           + +    ++      +F   G  E L++ +    +  P+ IQ +A+   + GRD+I  ++
Sbjct: 3   TKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQ 62

Query: 213 TGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVV 272
           +G+GKT  F   +L  +  Q           LILAPTREL+ QI       G   N+   
Sbjct: 63  SGTGKTATFSISVLQCLDIQV-----RETQALILAPTRELAVQIQKGLLALGDYMNVQCH 117

Query: 273 CCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            C GG +  +  + L+ G  +V GTPGR+ DM++  + +   +  LVLDEAD M + G
Sbjct: 118 ACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG 175

>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 =  118 bits (297), Expect = 1e-32
 Identities = 54/168 (32%), Positives = 83/168 (49%), Gaps = 6/168 (3%)

Query: 163 PYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFI 222
              V  F     DE L++ +    +  P+ IQ +A+   + G D++  A++G+GKTG F 
Sbjct: 6   DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFS 65

Query: 223 WPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWD 282
              L  I           P  L+LAPTREL+ QI           ++ V  C GG S  +
Sbjct: 66  IAALQRIDTSV-----KAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVE 120

Query: 283 QSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
            ++ L   A+IVVGTPGR+ D ++    + +++   +LDEAD M   G
Sbjct: 121 DAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG 167

>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 =  118 bits (296), Expect = 2e-32
 Identities = 54/172 (31%), Positives = 80/172 (46%), Gaps = 6/172 (3%)

Query: 160 ADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTG 219
           ++    V SF      E L++ +    +  P+ IQ +A+   + G D+I  A++G+GKT 
Sbjct: 5   SNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTA 64

Query: 220 AFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGS 279
            F   +L  I              L+LAPTREL+QQI       G     S   C GG +
Sbjct: 65  TFAISILQQIELDL-----KATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTN 119

Query: 280 KWDQSKALELG-AEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
              + + L++    I+VGTPGR+ DM+         +   VLDEAD M   G
Sbjct: 120 VRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG 171

>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 =  110 bits (276), Expect = 8e-30
 Identities = 51/166 (30%), Positives = 80/166 (48%), Gaps = 7/166 (4%)

Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           S F  F     L++A+  C +  P+ +Q + +P A+ G D++  AK+G GKT  F+   L
Sbjct: 1   SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 60

Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGS--KWDQS 284
             +              L++  TREL+ QI  E +RF K      V  + GG   K D+ 
Sbjct: 61  QQLEPVT-----GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEE 115

Query: 285 KALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
              +    IVVGTPGRI+ + +  +  L  +   +LDE D+M +  
Sbjct: 116 VLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQL 161

>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 =  106 bits (264), Expect = 4e-28
 Identities = 54/164 (32%), Positives = 91/164 (55%), Gaps = 6/164 (3%)

Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           + F  +     L+  + +  +  P+PIQ +++P ALSGRDI+  AK G+GK+GA++ P+L
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62

Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSK 285
             +  +K     D    +++ PTREL+ Q+     +  K      V+   GG +  D   
Sbjct: 63  ERLDLKK-----DNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIM 117

Query: 286 ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM 329
            L+    +V+ TPGRI+D++K G  K++ V  +VLDEAD++   
Sbjct: 118 RLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQ 161

>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 =  102 bits (255), Expect = 1e-26
 Identities = 53/163 (32%), Positives = 85/163 (52%), Gaps = 5/163 (3%)

Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           ++F  F     L+  + +  +  P+PIQ +A+P A++GRDI+  AK G+GKT AF+ P L
Sbjct: 1   NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL 60

Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA 286
             +  +      +    LI+ PTREL+ Q     +  GK   +S +   GG +  D    
Sbjct: 61  EKVKPKL-----NKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILR 115

Query: 287 LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM 329
           L     I+VGTPGR++D+       L+  +  ++DEAD+M   
Sbjct: 116 LNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSR 158

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score =  102 bits (255), Expect = 2e-26
 Identities = 30/188 (15%), Positives = 53/188 (28%), Gaps = 20/188 (10%)

Query: 151 AKSGITVSGADPPYPVSSFGHFGFDEVL--MKALRKCEYTSPTPIQAQAVPAALSGRDII 208
           A +    + A      +S   F  D +L       +     P  IQ       L      
Sbjct: 3   AAAAAAAAAAAAAAAAASLCLFPEDFLLKEFVEFFRKCVGEPRAIQKMWAKRILRKESFA 62

Query: 209 GVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN 268
             A TG GKT   +   L   +  K           ++ PT  L  Q     +++ +   
Sbjct: 63  ATAPTGVGKTSFGLAMSLFLALKGK--------RCYVIFPTSLLVIQAAETIRKYAEKAG 114

Query: 269 LSVVCCYGGGSKWDQSKAL------ELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDE 322
           +      G        +            +IV+ T   +    +     L    F+ +D+
Sbjct: 115 VGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRE----LGHFDFIFVDD 170

Query: 323 ADRMFDMG 330
            D +    
Sbjct: 171 VDAILKAS 178

>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 = 96.6 bits (239), Expect = 2e-24
 Identities = 26/166 (15%), Positives = 55/166 (33%), Gaps = 12/166 (7%)

Query: 166 VSSFGHFGFDEVLMKALRKC-EYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWP 224
           ++       +    + L++   Y    P Q + +   LSGRD + V  TG GK+  +  P
Sbjct: 1   MAQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIP 60

Query: 225 MLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS 284
            L+              + ++++P   L +   ++ +  G                   +
Sbjct: 61  ALLLN-----------GLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMT 109

Query: 285 KALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
                   ++   P R++    +          L +DEA  +   G
Sbjct: 110 GCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWG 155

>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 = 89.3 bits (220), Expect = 1e-21
 Identities = 30/158 (18%), Positives = 60/158 (37%), Gaps = 12/158 (7%)

Query: 173 GFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQ 232
                 +  L++       P QA+AV    SG++++    T +GKT      M+   +  
Sbjct: 9   SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG 68

Query: 233 KELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAE 292
                      L + P R L+ + Y   K++ K      +      S+ +         +
Sbjct: 69  --------GKSLYVVPLRALAGEKYESFKKWEKIGLRIGISTGDYESRDEHLG----DCD 116

Query: 293 IVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDMG 330
           I+V T  +   +++  A+ +  V+ LV+DE   +    
Sbjct: 117 IIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEK 154

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 85.1 bits (209), Expect = 3e-20
 Identities = 46/163 (28%), Positives = 77/163 (47%), Gaps = 1/163 (0%)

Query: 167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPML 226
           + F  F F   +++A++   +  PT IQ + +P AL G  ++G ++TG+GKT A+    +
Sbjct: 1   TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAY-LLPI 59

Query: 227 VHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA 286
           +  +  +  E              ++  +     K   K   +   C  GG  K    + 
Sbjct: 60  MEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEK 119

Query: 287 LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM 329
           L +   IV+GTPGRI D ++  A  ++    LV+DEAD M DM
Sbjct: 120 LNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDM 162

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 78.8 bits (193), Expect = 2e-17
 Identities = 19/128 (14%), Positives = 41/128 (32%), Gaps = 19/128 (14%)

Query: 203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKR 262
             R  I     G+GKT  ++  ++   + +       G   LILAPTR ++ ++    + 
Sbjct: 8   KKRLTIMDLHPGAGKTKRYLPAIVREAIKR-------GLRTLILAPTRVVAAEMEEALRG 60

Query: 263 FGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDE 322
               Y    +     G +              +         + +   ++     +++DE
Sbjct: 61  LPIRYQTPAIRAEHTGREIV-----------DLMCHATFTMRL-LSPIRVPNYNLIIMDE 108

Query: 323 ADRMFDMG 330
           A       
Sbjct: 109 AHFTDPAS 116

>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 = 62.9 bits (151), Expect = 3e-12
 Identities = 38/148 (25%), Positives = 57/148 (38%), Gaps = 10/148 (6%)

Query: 182 LRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGP 241
           LR+ +   P   Q           + + V  TG GKT   +      +          G 
Sbjct: 3   LRR-DLIQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKY-------GG 53

Query: 242 MGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI 301
             L+LAPT+ L  Q     +R        +V   G  S  ++SKA    A+++V TP  I
Sbjct: 54  KVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWA-RAKVIVATPQTI 112

Query: 302 IDMVKMGATKLNRVTFLVLDEADRMFDM 329
            + +  G   L  V+ +V DEA R    
Sbjct: 113 ENDLLAGRISLEDVSLIVFDEAHRAVGN 140

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 136

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 = 36.4 bits (83), Expect = 0.001
 Identities = 19/128 (14%), Positives = 30/128 (23%), Gaps = 25/128 (19%)

Query: 199 PAALSGRDI-IGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIY 257
           PA      +    A TGSGK+                     G   L+L P+   +    
Sbjct: 2   PAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ-----------GYKVLVLNPSVAATLGF- 49

Query: 258 NEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTF 317
                  K + +      G  +    S            T       +  G         
Sbjct: 50  --GAYMSKAHGVDPNIRTGVRTITTGSP----------ITYSTYGKFLADGGCSGGAYDI 97

Query: 318 LVLDEADR 325
           ++ DE   
Sbjct: 98  IICDECHS 105

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	330
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.97
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.93
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.91
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.9
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.87
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.72
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.68
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.66
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.61
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.61
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.5
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.44
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.12
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.95
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.86
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.81
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.78
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.75
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.37
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	96.76
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.38
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.3
d1vmaa2	213	GTPase domain of the signal recognition particle r	95.93
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	95.58
d1ls1a2	207	GTPase domain of the signal sequence recognition p	95.55
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	95.36
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	95.24
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	95.11
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	95.02
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.01
d1okkd2	207	GTPase domain of the signal recognition particle r	94.93
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	94.82
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	94.46
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.3
d1j8yf2	211	GTPase domain of the signal sequence recognition p	94.3
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	93.96
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	93.93
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	93.64
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	93.62
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	93.4
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	92.99
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	92.37
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	92.13
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	92.12
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	91.8
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	91.7
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	91.07
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	91.06
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	90.12
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	89.37
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	89.19
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	87.86
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	87.72
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	87.51
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	87.35
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	87.3
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	86.63
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	86.45
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	85.67
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	85.18
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	84.19
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	83.66
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	83.54
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	83.44
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	83.36
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	83.36
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	83.18
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	82.71
d1vi2a1	182	Putative shikimate dehydrogenase YdiB {Escherichia	82.56
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	81.67
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	81.31
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	80.83
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	80.67
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	80.64
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	80.55
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	80.29
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	80.13

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.1e-39  Score=286.95  Aligned_cols=165  Identities=33%  Similarity=0.573  Sum_probs=154.7

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCC
Q psy17644        161 DPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDG  240 (330)
Q Consensus       161 ~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~  240 (330)
                      .-.....+|++++|++.|+++|.++||..|||+|+++||.+++|+|++++|+||||||+||++|+++++....     ..
T Consensus        11 ~~~~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~-----~~   85 (222)
T d2j0sa1          11 EEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV-----RE   85 (222)
T ss_dssp             TTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTS-----CS
T ss_pred             CCCCCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccc-----cC
Confidence            3345566899999999999999999999999999999999999999999999999999999999999876542     57


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEe
Q psy17644        241 PMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVL  320 (330)
Q Consensus       241 ~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVv  320 (330)
                      +++||++|||+||.|+++.++++++..++++.+++||.....+...++.+++||||||++|.+++.++...++++++||+
T Consensus        86 ~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVl  165 (222)
T d2j0sa1          86 TQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVL  165 (222)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEE
T ss_pred             ceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeee
Confidence            89999999999999999999999999999999999999999998889999999999999999999999999999999999


Q ss_pred             ecccccCcCC
Q psy17644        321 DEADRMFDMG  330 (330)
Q Consensus       321 DEad~lld~G  330 (330)
                      ||||+|+++|
T Consensus       166 DEaD~ll~~~  175 (222)
T d2j0sa1         166 DEADEMLNKG  175 (222)
T ss_dssp             ETHHHHTSTT
T ss_pred             cchhHhhhcC
Confidence            9999999987

>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=1.9e-37  Score=269.87  Aligned_cols=159  Identities=33%  Similarity=0.614  Sum_probs=147.2

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      ++|++++|++.|+++|.++||..|||+|+++||.+++|+|++++|+||||||+||++|+++++...     .+++++||+
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~-----~~~~~~lil   77 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK-----KDNIQAMVI   77 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT-----SCSCCEEEE
T ss_pred             CChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhccccc-----ccCcceEEE
Confidence            679999999999999999999999999999999999999999999999999999999999987554     367999999


Q ss_pred             cccHHHHHHHHHHHHHhccCC-CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGY-NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~-~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      +|||+||.|++..+..+.+.. +..+....|+.....+...++.+++||||||++|.+++.++...++++++||+||||+
T Consensus        78 ~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~  157 (206)
T d1veca_          78 VPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADK  157 (206)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHH
T ss_pred             eecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccccccceEEEecccc
Confidence            999999999999999887654 4677778888888888888889999999999999999999999999999999999999


Q ss_pred             cCcCC
Q psy17644        326 MFDMG  330 (330)
Q Consensus       326 lld~G  330 (330)
                      |+++|
T Consensus       158 ll~~~  162 (206)
T d1veca_         158 LLSQD  162 (206)
T ss_dssp             HTSTT
T ss_pred             ccccc
Confidence            99987

>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=1.5e-37  Score=276.27  Aligned_cols=170  Identities=38%  Similarity=0.666  Sum_probs=157.3

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCC----CC
Q psy17644        161 DPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKE----LE  236 (330)
Q Consensus       161 ~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~----~~  236 (330)
                      ..|.++.+|++++|++.|+++|.++||..|||+|+.+||.+++|+|++++|+||||||+||++|+|++++....    ..
T Consensus        15 ~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~   94 (238)
T d1wrba1          15 SATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYS   94 (238)
T ss_dssp             SCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------
T ss_pred             CCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhccccccccc
Confidence            45778999999999999999999999999999999999999999999999999999999999999999986532    22


Q ss_pred             CCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCcc
Q psy17644        237 PGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVT  316 (330)
Q Consensus       237 ~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~  316 (330)
                      ...+|++|||+||++||.|++..+..++...++++..++|+.....+.+....++|||||||++|..++..+...+++++
T Consensus        95 ~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~  174 (238)
T d1wrba1          95 KTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCK  174 (238)
T ss_dssp             CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             CCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceeccccc
Confidence            34679999999999999999999999999999999999999988888888889999999999999999999888999999


Q ss_pred             EEEeecccccCcCC
Q psy17644        317 FLVLDEADRMFDMG  330 (330)
Q Consensus       317 ~lVvDEad~lld~G  330 (330)
                      ++||||||+|+++|
T Consensus       175 ~lViDEaD~ll~~~  188 (238)
T d1wrba1         175 YIVLDEADRMLDMG  188 (238)
T ss_dssp             EEEEETHHHHHHTT
T ss_pred             eeeeehhhhhhhhc
Confidence            99999999999876

>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=1.4e-37  Score=272.91  Aligned_cols=166  Identities=32%  Similarity=0.501  Sum_probs=148.7

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCC
Q psy17644        160 ADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGD  239 (330)
Q Consensus       160 ~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~  239 (330)
                      ++.|.++.+|++++|++.++++|.+.||..|||+|+++||.++.|+|++++|+||||||++|++|+++++...     ..
T Consensus         5 ~~~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~-----~~   79 (218)
T d2g9na1           5 SNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD-----LK   79 (218)
T ss_dssp             CCCCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----CC
T ss_pred             CCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheeccc-----cc
Confidence            3467899999999999999999999999999999999999999999999999999999999999999998543     36


Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHH-HHhCCCeEEEEChHHHHHHHHcCCCCCCCccEE
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK-ALELGAEIVVGTPGRIIDMVKMGATKLNRVTFL  318 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~-~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~l  318 (330)
                      ++++||++|||+||.|++..+++++...+..+..++++.....+.. ....+++|||+||++|.+++.++...++++++|
T Consensus        80 ~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~l  159 (218)
T d2g9na1          80 ATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMF  159 (218)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEE
T ss_pred             CccEEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEE
Confidence            8999999999999999999999999999999988888776554432 333468999999999999999988999999999


Q ss_pred             EeecccccCcCC
Q psy17644        319 VLDEADRMFDMG  330 (330)
Q Consensus       319 VvDEad~lld~G  330 (330)
                      |+||||+|+++|
T Consensus       160 VlDEaD~ll~~~  171 (218)
T d2g9na1         160 VLDEADEMLSRG  171 (218)
T ss_dssp             EEESHHHHHHTT
T ss_pred             EeeecchhhcCc
Confidence            999999999876

>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=4e-37  Score=268.91  Aligned_cols=166  Identities=33%  Similarity=0.556  Sum_probs=146.2

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCC
Q psy17644        159 GADPPYPVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPG  238 (330)
Q Consensus       159 g~~~p~p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~  238 (330)
                      |.+.|.++.+|++|+|++.++++|.++||..|||+|+.+||.++.|+|++++|+||||||++|++|+++++...     .
T Consensus         2 ~~~~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~-----~   76 (212)
T d1qdea_           2 QTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----V   76 (212)
T ss_dssp             CBSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----C
T ss_pred             CCCCcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhcc-----C
Confidence            46788999999999999999999999999999999999999999999999999999999999999999987543     3


Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEE
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFL  318 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~l  318 (330)
                      .+|++||++||++||.|++..+..+..........+.++.....+...++ +++|+|+||++|..++..+..++++++++
T Consensus        77 ~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~IvI~TP~~l~~~~~~~~~~l~~l~~l  155 (212)
T d1qdea_          77 KAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMF  155 (212)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CT-TCSEEEECHHHHHHHHHTTSSCCTTCCEE
T ss_pred             CCcceEEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHhc-CCcEEEECCCccccccccCceecCcceEE
Confidence            68999999999999999999999999888889888888887777666554 58999999999999999999999999999


Q ss_pred             EeecccccCcCC
Q psy17644        319 VLDEADRMFDMG  330 (330)
Q Consensus       319 VvDEad~lld~G  330 (330)
                      |+||||+|+++|
T Consensus       156 VlDEad~lld~~  167 (212)
T d1qdea_         156 ILDEADEMLSSG  167 (212)
T ss_dssp             EEETHHHHHHTT
T ss_pred             eehhhhhhcccc
Confidence            999999999876

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.3e-36  Score=263.07  Aligned_cols=157  Identities=32%  Similarity=0.554  Sum_probs=142.7

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      ++|++|+|++.++++|.++||.+|||+|+++||.+++|+|++++|+||||||+||++|+++++...     ..++++||+
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~-----~~~~~~lil   75 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-----TGQVSVLVM   75 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC-----TTCCCEEEE
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeeccc-----CCCceEEEE
Confidence            469999999999999999999999999999999999999999999999999999999999886443     357899999


Q ss_pred             cccHHHHHHHHHHHHHhccCCC-ceEEEEECCCchHHHHHHH-hCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGYN-LSVVCCYGGGSKWDQSKAL-ELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD  324 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~-~~~~~~~gg~~~~~~~~~l-~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad  324 (330)
                      +|||+||.|+++.++.++...+ +++.+++||.....+...+ +.+++||||||++|.++++++..+++++++||+||||
T Consensus        76 ~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD  155 (207)
T d1t6na_          76 CHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECD  155 (207)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHH
T ss_pred             eccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhh
Confidence            9999999999999999988764 5677888888877766555 5679999999999999999988899999999999999


Q ss_pred             ccCc
Q psy17644        325 RMFD  328 (330)
Q Consensus       325 ~lld  328 (330)
                      +|++
T Consensus       156 ~ll~  159 (207)
T d1t6na_         156 KMLE  159 (207)
T ss_dssp             HHHS
T ss_pred             hhhh
Confidence            9997

>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=3.5e-35  Score=255.74  Aligned_cols=157  Identities=38%  Similarity=0.687  Sum_probs=145.2

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCC-cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGR-DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLI  245 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~-d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLi  245 (330)
                      .+|++++|++.|+++|.++||.+|||+|+++||.+++|+ |++++++||+|||++|++|++.+...      ..+|++||
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~------~~~~~~li   77 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE------NNGIEAII   77 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS------SSSCCEEE
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccc------ccCcceEE
Confidence            479999999999999999999999999999999999885 99999999999999999999987543      36899999


Q ss_pred             EcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccc
Q psy17644        246 LAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADR  325 (330)
Q Consensus       246 l~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~  325 (330)
                      |+||++||.|++..+..++...+.++..++|+.....+.+.++ +++||||||++|.++++++..+++++++|||||||+
T Consensus        78 l~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~  156 (208)
T d1hv8a1          78 LTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADE  156 (208)
T ss_dssp             ECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHH
T ss_pred             EeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-CCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHH
Confidence            9999999999999999999999999999999998888777665 589999999999999999888999999999999999


Q ss_pred             cCcCC
Q psy17644        326 MFDMG  330 (330)
Q Consensus       326 lld~G  330 (330)
                      |++.|
T Consensus       157 l~~~~  161 (208)
T d1hv8a1         157 MLNMG  161 (208)
T ss_dssp             HHTTT
T ss_pred             hhcCC
Confidence            98765

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.3e-34  Score=250.17  Aligned_cols=159  Identities=33%  Similarity=0.595  Sum_probs=150.2

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      .+|++|+|++.|+++|.++||..|||+|+++||.++.|+|+++.|+||||||++|++|++.++..+     .++++++++
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~-----~~~~~~~~~   75 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK-----LNKIQALIM   75 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT-----SCSCCEEEE
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccc-----cccccceee
Confidence            379999999999999999999999999999999999999999999999999999999999987554     357899999


Q ss_pred             cccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      +|+++++.|....+..++...++++..++|+.....+...+..+++||||||++|.++++.....++++++||+||||+|
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l  155 (206)
T d1s2ma1          76 VPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKM  155 (206)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHH
T ss_pred             ccchhhhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhhh
Confidence            99999999999999999999999999999999999888889999999999999999999998889999999999999999


Q ss_pred             CcCC
Q psy17644        327 FDMG  330 (330)
Q Consensus       327 ld~G  330 (330)
                      +++|
T Consensus       156 ~~~~  159 (206)
T d1s2ma1         156 LSRD  159 (206)
T ss_dssp             SSHH
T ss_pred             hhhh
Confidence            9864

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.97  E-value=5.9e-32  Score=234.94  Aligned_cols=159  Identities=36%  Similarity=0.644  Sum_probs=140.5

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      +.|++++|++.|+++|.+.||.+|||+|+++||.+++|+|++++|+||||||+||++|+++++...     ...+.++++
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~-----~~~~~~~~~   75 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE-----RAEVQAVIT   75 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT-----SCSCCEEEE
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccc-----ccccccccc
Confidence            469999999999999999999999999999999999999999999999999999999999887654     246888999


Q ss_pred             cccHHHHHHHHHHHHHhccCC----CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeec
Q psy17644        247 APTRELSQQIYNEAKRFGKGY----NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDE  322 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~----~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDE  322 (330)
                      +|++.++.+.+..+.......    ...+.++.++.....+....+.+++|+||||+++..++.++...+++++++||||
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDE  155 (209)
T d1q0ua_          76 APTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDE  155 (209)
T ss_dssp             CSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECS
T ss_pred             ccccchhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccceEEEEee
Confidence            999999999999887765543    3456666777766666666777899999999999999999888899999999999


Q ss_pred             ccccCcCC
Q psy17644        323 ADRMFDMG  330 (330)
Q Consensus       323 ad~lld~G  330 (330)
                      ||+|+++|
T Consensus       156 ad~ll~~~  163 (209)
T d1q0ua_         156 ADLMLDMG  163 (209)
T ss_dssp             HHHHHHTT
T ss_pred             cccccccc
Confidence            99999886

>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=5.8e-26  Score=200.53  Aligned_cols=150  Identities=17%  Similarity=0.186  Sum_probs=114.9

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      ..|.+..+.+.+.+ +.+.++.+|+++|+.+++.++.|+|++++||||+|||++|+++++....        .+.++|||
T Consensus        22 ~~~~~~~~~~~~~~-~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~--------~~~rvliv   92 (237)
T d1gkub1          22 CLFPEDFLLKEFVE-FFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLAL--------KGKRCYVI   92 (237)
T ss_dssp             SCCTTHHHHHHHHH-HHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHT--------TSCCEEEE
T ss_pred             ccCccchhHHHHHH-HHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHH--------hcCeEEEE
Confidence            33444444444444 4556788999999999999999999999999999999999999886653        36789999


Q ss_pred             cccHHHHHHHHHHHHHhccCCCceE----EEEECCCchHHHHHHHh--CCCeEEEEChHHHHHHHHcCCCCCCCccEEEe
Q psy17644        247 APTRELSQQIYNEAKRFGKGYNLSV----VCCYGGGSKWDQSKALE--LGAEIVVGTPGRIIDMVKMGATKLNRVTFLVL  320 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~~~~----~~~~gg~~~~~~~~~l~--~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVv  320 (330)
                      +||++|+.|+++.+++++...++.+    ....++.........+.  .+++|+|+||++|.+    ....++++++|||
T Consensus        93 ~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~----~~~~~~~~~~vVv  168 (237)
T d1gkub1          93 FPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSK----HYRELGHFDFIFV  168 (237)
T ss_dssp             ESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHH----CSTTSCCCSEEEE
T ss_pred             eccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHH----hhhhcCCCCEEEE
Confidence            9999999999999999988765543    33334444444333333  357999999998764    3345788999999


Q ss_pred             ecccccCcC
Q psy17644        321 DEADRMFDM  329 (330)
Q Consensus       321 DEad~lld~  329 (330)
                      ||||.|++.
T Consensus       169 DE~d~~l~~  177 (237)
T d1gkub1         169 DDVDAILKA  177 (237)
T ss_dssp             SCHHHHHTS
T ss_pred             EChhhhhhc
Confidence            999998764

>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=99.91  E-value=2.8e-25  Score=191.80  Aligned_cols=148  Identities=18%  Similarity=0.239  Sum_probs=119.4

Q ss_pred             CCCCCCCCHHHHHHHHHC-CCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        168 SFGHFGFDEVLMKALRKC-EYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       168 ~f~~~~l~~~l~~~l~~~-~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      ..+.++|.+.+.+.|+.. ||..++|+|.++|+++++|+|+++++|||||||++|.+|++.+           ..+++++
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~-----------~~~~~~v   71 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL-----------NGLTVVV   71 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS-----------SSEEEEE
T ss_pred             chhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc-----------cCceEEe
Confidence            467788999999999887 9999999999999999999999999999999999999998743           5689999


Q ss_pred             cccHHHHHHHHHHHHHhccCCCceEEEEECCCchH----HHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeec
Q psy17644        247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW----DQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDE  322 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~----~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDE  322 (330)
                      +||++|+.|+...++.++.    ......+.....    ..........+|+++||.++.............+.+||+||
T Consensus        72 ~P~~~L~~q~~~~l~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDE  147 (206)
T d1oywa2          72 SPLISLMKDQVDQLQANGV----AAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDE  147 (206)
T ss_dssp             CSCHHHHHHHHHHHHHTTC----CEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESS
T ss_pred             ccchhhhhhHHHHHHhhcc----cccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeeee
Confidence            9999999999999988753    333333333322    22233444689999999998765544445677899999999


Q ss_pred             ccccCcCC
Q psy17644        323 ADRMFDMG  330 (330)
Q Consensus       323 ad~lld~G  330 (330)
                      ||++.++|
T Consensus       148 aH~~~~~~  155 (206)
T d1oywa2         148 AHCISQWG  155 (206)
T ss_dssp             GGGGCTTS
T ss_pred             eeeeeccc
Confidence            99999886

>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=99.90  E-value=1.9e-24  Score=186.14  Aligned_cols=144  Identities=23%  Similarity=0.271  Sum_probs=117.8

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q psy17644        174 FDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELS  253 (330)
Q Consensus       174 l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La  253 (330)
                      ++..+...|.+.||..|+|+|.++++.+++|+++++++|||+|||.+++++++..+.+        ++++|||+||++|+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~--------~~~vl~l~P~~~L~   81 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK--------GGKSLYVVPLRALA   81 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT--------TCCEEEEESSHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc--------cCcceeecccHHHH
Confidence            5567888899999999999999999999999999999999999999999999887754        56899999999999


Q ss_pred             HHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcC
Q psy17644        254 QQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       254 ~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~  329 (330)
                      .|++..++++... ..++....|+.....   .....++|+++||..+..++.+....+.++.+||+||||++.+.
T Consensus        82 ~q~~~~~~~~~~~-~~~v~~~~~~~~~~~---~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~  153 (202)
T d2p6ra3          82 GEKYESFKKWEKI-GLRIGISTGDYESRD---EHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSE  153 (202)
T ss_dssp             HHHHHHHTTTTTT-TCCEEEECSSCBCCS---SCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCT
T ss_pred             HHHHHHHHHHhhc-cccceeeccCccccc---ccccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhccc
Confidence            9999999988654 344445555443221   12235899999999999999888878889999999999998754

>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=99.87  E-value=8.7e-22  Score=168.44  Aligned_cols=132  Identities=27%  Similarity=0.265  Sum_probs=112.6

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      -+|+++|..++..+. ++++|+++|||+|||+++++++..++.+       .+.++|||+||++|+.|+++.++++....
T Consensus         8 ~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~-------~~~~il~i~P~~~L~~q~~~~~~~~~~~~   79 (200)
T d1wp9a1           8 IQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTK-------YGGKVLMLAPTKPLVLQHAESFRRLFNLP   79 (200)
T ss_dssp             HCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHH-------SCSCEEEECSSHHHHHHHHHHHHHHBCSC
T ss_pred             CCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHh-------cCCcEEEEcCchHHHHHHHHHHHHhhccc
Confidence            479999999998876 5789999999999999999888776654       35689999999999999999999998888


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      +.++..+.++.........+. .++|+++||..+...+......++++.+||+||||++..
T Consensus        80 ~~~v~~~~~~~~~~~~~~~~~-~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~  139 (200)
T d1wp9a1          80 PEKIVALTGEKSPEERSKAWA-RAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVG  139 (200)
T ss_dssp             GGGEEEECSCSCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCST
T ss_pred             ccceeeeecccchhHHHHhhh-cccccccccchhHHHHhhhhhhccccceEEEEehhhhhc
Confidence            888887777777655444433 368999999999999988888899999999999998863

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=99.72  E-value=2.4e-18  Score=155.58  Aligned_cols=111  Identities=16%  Similarity=0.133  Sum_probs=84.1

Q ss_pred             hhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCc
Q psy17644        200 AALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGS  279 (330)
Q Consensus       200 ~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~  279 (330)
                      ++.+||++++.|+||||||++|+++++.+....       ++++||++|||+||.|+++.++.++.....    ...   
T Consensus         5 ~~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~-------~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~----~~~---   70 (305)
T d2bmfa2           5 IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR-------GLRTLILAPTRVVAAEMEEALRGLPIRYQT----PAI---   70 (305)
T ss_dssp             SSSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH-------TCCEEEEESSHHHHHHHHHHTTTSCCBCCC----------
T ss_pred             HhhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc-------CCEEEEEccHHHHHHHHHHHHhcCCcceee----eEE---
Confidence            456899999999999999999998988877763       678999999999999999988766432211    110   


Q ss_pred             hHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCcC
Q psy17644        280 KWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFDM  329 (330)
Q Consensus       280 ~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld~  329 (330)
                          .........|+++||+.|..++.. ...+.++++|||||||++..+
T Consensus        71 ----~~~~~~~~~i~~~t~~~l~~~~~~-~~~~~~~~~vViDE~H~~~~~  115 (305)
T d2bmfa2          71 ----RAEHTGREIVDLMCHATFTMRLLS-PIRVPNYNLIIMDEAHFTDPA  115 (305)
T ss_dssp             ---------CCCSEEEEEHHHHHHHHTS-SSCCCCCSEEEEESTTCCSHH
T ss_pred             ----eecccCccccccCCcHHHHHHHhc-CccccceeEEEeeeeeecchh
Confidence                112234568999999988877653 455788999999999998754

>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=99.68  E-value=1.2e-15  Score=132.83  Aligned_cols=141  Identities=22%  Similarity=0.238  Sum_probs=115.8

Q ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHhhhhhc----CC--CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE
Q psy17644        173 GFDEVLMKALRKCEYTSPTPIQAQAVPAAL----SG--RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL  246 (330)
Q Consensus       173 ~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~----~g--~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil  246 (330)
                      ..+....+.+.+.-...+|+-|..++..+.    ++  .+.+++|.||||||.+|+..++..+.        +|.+|++|
T Consensus        39 ~~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~--------~g~qv~~l  110 (233)
T d2eyqa3          39 KHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD--------NHKQVAVL  110 (233)
T ss_dssp             CCCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT--------TTCEEEEE
T ss_pred             CCCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH--------cCCceEEE
Confidence            455677777777666789999999998875    33  47899999999999999988877653        58899999


Q ss_pred             cccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHH---HHHhC-CCeEEEEChHHHHHHHHcCCCCCCCccEEEeec
Q psy17644        247 APTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS---KALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDE  322 (330)
Q Consensus       247 ~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDE  322 (330)
                      +||..|+.|.+..++++....++.+..++|+.+..+..   ..+.. ..+|||+|...+.     ....++++.++||||
T Consensus       111 ~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~-----~~~~f~~LgLiIiDE  185 (233)
T d2eyqa3         111 VPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDE  185 (233)
T ss_dssp             CSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEES
T ss_pred             ccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc-----cCCccccccceeeec
Confidence            99999999999999999888999999999988865543   23333 4799999987665     345678999999999


Q ss_pred             cccc
Q psy17644        323 ADRM  326 (330)
Q Consensus       323 ad~l  326 (330)
                      -|+.
T Consensus       186 eH~f  189 (233)
T d2eyqa3         186 EHRF  189 (233)
T ss_dssp             GGGS
T ss_pred             hhhh
Confidence            9975

>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=99.66  E-value=8.4e-16  Score=136.23  Aligned_cols=140  Identities=20%  Similarity=0.212  Sum_probs=110.6

Q ss_pred             CHHHHHHHHHCCCCCCCHHHHHhhhhhc------CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q psy17644        175 DEVLMKALRKCEYTSPTPIQAQAVPAAL------SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP  248 (330)
Q Consensus       175 ~~~l~~~l~~~~~~~pt~iQ~~~i~~~~------~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P  248 (330)
                      ...+.+.+.+.--..+|.-|..++..+.      ...+.+++|-||||||.+|+..++..+..        |.+|++++|
T Consensus        69 ~~~l~~~f~~~LPFeLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~--------g~q~~~m~P  140 (264)
T d1gm5a3          69 EGKLAEEFIKSLPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA--------GFQTAFMVP  140 (264)
T ss_dssp             CTHHHHHHHHHSSSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH--------TSCEEEECS
T ss_pred             ChHHHHHHHhhccccCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc--------ccceeEEee
Confidence            3445555544444579999999999885      23478999999999999999988877654        789999999


Q ss_pred             cHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHH---HHHhC-CCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccc
Q psy17644        249 TRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS---KALEL-GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD  324 (330)
Q Consensus       249 tr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~---~~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad  324 (330)
                      |..||.|.+..++++....++.+..+.|+.+..+..   ..+.. .++|||||..-+..     ...++++.++||||-|
T Consensus       141 t~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~-----~~~f~~LglviiDEqH  215 (264)
T d1gm5a3         141 TSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQH  215 (264)
T ss_dssp             CHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCC
T ss_pred             hHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC-----CCCccccceeeecccc
Confidence            999999999999999998899999999988765443   33333 48999999865552     3446789999999999


Q ss_pred             ccC
Q psy17644        325 RMF  327 (330)
Q Consensus       325 ~ll  327 (330)
                      +..
T Consensus       216 ~fg  218 (264)
T d1gm5a3         216 RFG  218 (264)
T ss_dssp             CC-
T ss_pred             ccc
Confidence            863

>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=99.61  E-value=9.9e-16  Score=131.47  Aligned_cols=113  Identities=26%  Similarity=0.193  Sum_probs=86.4

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCC
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYN  268 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~  268 (330)
                      +|+++|.+++..+++++..++.++||+|||++++..+ .+          -+.++|||||++.|+.|+.+.+.+++..  
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~-~~----------~~~~~Liv~p~~~L~~q~~~~~~~~~~~--  136 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI-NE----------LSTPTLIVVPTLALAEQWKERLGIFGEE--  136 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHH-HH----------SCSCEEEEESSHHHHHHHHHHHGGGCGG--
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHH-HH----------hcCceeEEEcccchHHHHHHHHHhhccc--
Confidence            6899999999999999999999999999998765432 22          1457899999999999999999887542  


Q ss_pred             ceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        269 LSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       269 ~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                       .+ ..+.|...        ....|+|+|...+.......   ..++.+||+||||++-
T Consensus       137 -~~-~~~~~~~~--------~~~~i~i~t~~~~~~~~~~~---~~~~~lvIiDEaH~~~  182 (206)
T d2fz4a1         137 -YV-GEFSGRIK--------ELKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLP  182 (206)
T ss_dssp             -GE-EEESSSCB--------CCCSEEEEEHHHHHHTHHHH---TTTCSEEEEECSSCCC
T ss_pred             -ch-hhcccccc--------cccccccceehhhhhhhHhh---CCcCCEEEEECCeeCC
Confidence             23 33443322        23589999998887655432   3468899999999873

>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=99.61  E-value=5.4e-16  Score=139.52  Aligned_cols=126  Identities=21%  Similarity=0.169  Sum_probs=95.9

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      -.|+++|..++..++..+..++.+|||+|||++.++.+ .++...      .+.++|||||+++|+.|+++.+.+++...
T Consensus       112 ~~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~-~~~~~~------~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~  184 (282)
T d1rifa_         112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLA-RYYLEN------YEGKILIIVPTTALTTQMADDFVDYRLFS  184 (282)
T ss_dssp             CCCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHH-HHHHHH------CSSEEEEECSSHHHHHHHHHHHHHHTSCC
T ss_pred             cccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHH-HHhhhc------ccceEEEEEcCchhHHHHHHHHHHhhccc
Confidence            46999999999999988899999999999997755433 333332      24589999999999999999999987665


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                      ...+..+++|......   ......|+|+|+..+..+.   ...++++.+||+||||++
T Consensus       185 ~~~~~~~~~g~~~~~~---~~~~~~i~i~t~qs~~~~~---~~~~~~f~~VIvDEaH~~  237 (282)
T d1rifa_         185 HAMIKKIGGGASKDDK---YKNDAPVVVGTWQTVVKQP---KEWFSQFGMMMNDECHLA  237 (282)
T ss_dssp             GGGEEECSTTCSSTTC---CCTTCSEEEECHHHHTTSC---GGGGGGEEEEEEETGGGC
T ss_pred             cccceeecceeccccc---ccccceEEEEeeehhhhhc---ccccCCCCEEEEECCCCC
Confidence            5666667776653221   2235789999987765432   234578999999999986

>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=99.50  E-value=1.6e-14  Score=114.59  Aligned_cols=108  Identities=17%  Similarity=0.127  Sum_probs=76.7

Q ss_pred             hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCch
Q psy17644        201 ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSK  280 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~  280 (330)
                      +.+|++++++++||+|||.+++..++.....       .+.++||++|++.++.|+++.+..+    +..+....+....
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~-------~~~~vli~~p~~~l~~q~~~~~~~~----~~~~~~~~~~~~~   72 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECAR-------RRLRTLVLAPTRVVLSEMKEAFHGL----DVKFHTQAFSAHG   72 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHH-------TTCCEEEEESSHHHHHHHHHHTTTS----CEEEESSCCCCCC
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhh-------cCceeeeeecchhHHHHHHHHhhhh----hhhhccccccccc
Confidence            4578999999999999998877776666655       3678999999999999998876543    2222211111111


Q ss_pred             HHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        281 WDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       281 ~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                             .....+.++|...+..... ....+.++++|||||||.+.
T Consensus        73 -------~~~~~~~~~~~~~l~~~~~-~~~~~~~~~lvIiDEaH~~~  111 (140)
T d1yksa1          73 -------SGREVIDAMCHATLTYRML-EPTRVVNWEVIIMDEAHFLD  111 (140)
T ss_dssp             -------CSSCCEEEEEHHHHHHHHT-SSSCCCCCSEEEETTTTCCS
T ss_pred             -------ccccchhhhhHHHHHHHHh-ccccccceeEEEEccccccC
Confidence                   1135678888887766543 34567899999999999874

>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=99.44  E-value=4.8e-14  Score=112.43  Aligned_cols=100  Identities=18%  Similarity=0.063  Sum_probs=70.9

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWD  282 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~  282 (330)
                      .++..++.+|||||||..+...+    ..       .+.++||++||+.|+.|+.+.+..+...   ......+|.... 
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~----~~-------~~~~vli~~P~~~l~~q~~~~~~~~~~~---~~~~~~~~~~~~-   71 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAY----AA-------QGYKVLVLNPSVAATLGFGAYMSKAHGV---DPNIRTGVRTIT-   71 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHH----HT-------TTCCEEEEESCHHHHHHHHHHHHHHHSC---CCEEECSSCEEC-
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHH----HH-------cCCcEEEEcChHHHHHHHHHHHHHHhhc---cccccccccccc-
Confidence            45677889999999996543222    22       3678999999999999999998887543   233344443321 


Q ss_pred             HHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeeccccc
Q psy17644        283 QSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRM  326 (330)
Q Consensus       283 ~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~l  326 (330)
                            ....++++|...+....   ...++++++|||||||++
T Consensus        72 ------~~~~~~~~~~~~~~~~~---~~~~~~~~~vIiDE~H~~  106 (136)
T d1a1va1          72 ------TGSPITYSTYGKFLADG---GCSGGAYDIIICDECHST  106 (136)
T ss_dssp             ------CCCSEEEEEHHHHHHTT---GGGGCCCSEEEEETTTCC
T ss_pred             ------cccceEEEeeeeecccc---chhhhcCCEEEEeccccc
Confidence                  13578899988765443   335778999999999986

>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=99.12  E-value=4.4e-10  Score=100.86  Aligned_cols=135  Identities=19%  Similarity=0.221  Sum_probs=89.1

Q ss_pred             CCCHHHHHhhhhhc---------CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q psy17644        189 SPTPIQAQAVPAAL---------SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNE  259 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~---------~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~  259 (330)
                      .+.|+|..++..+.         .+..+|+.-.+|.|||+..+ .++.+++.+.........++|||||.. |+.||.++
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qai-a~l~~l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~E  132 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCI-TLIWTLLKQSPDCKPEIDKVIVVSPSS-LVRNWYNE  132 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHH-HHHHHHHHCCTTSSCSCSCEEEEECHH-HHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHH-HHHHHHHHhcccccCCCCcEEEEccch-hhHHHHHH
Confidence            57899999997542         45678888899999996543 344455544322222345789999985 88999999


Q ss_pred             HHHhccCCCceEEEEECCCchHHHHHH---HhC-----CCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        260 AKRFGKGYNLSVVCCYGGGSKWDQSKA---LEL-----GAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       260 ~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~~-----~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      +.+++.. ...++.++|+.........   ...     ..+|+|+|...+.....  ...-.++.+||+||||++-.
T Consensus       133 i~k~~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~--~l~~~~~~~vI~DEaH~ikn  206 (298)
T d1z3ix2         133 VGKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKN  206 (298)
T ss_dssp             HHHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCT
T ss_pred             HHhhcCC-ceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchh--cccccceeeeeccccccccc
Confidence            9998764 3445555665543222111   111     35799999988775443  22233578999999999854

>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=98.95  E-value=5e-09  Score=91.07  Aligned_cols=128  Identities=22%  Similarity=0.231  Sum_probs=103.4

Q ss_pred             CCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCC
Q psy17644        188 TSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGY  267 (330)
Q Consensus       188 ~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~  267 (330)
                      .+|+++|...--.+..|  -|+...||-|||++..+|+....+.        |..|-||+..--||..=.+++..+.+.+
T Consensus        79 ~RhyDVQLiGgi~L~~G--~iaem~TGEGKTL~a~l~a~l~al~--------g~~vhvvTvNdyLA~RDae~m~~iy~~l  148 (273)
T d1tf5a3          79 MFPFKVQLMGGVALHDG--NIAEMKTGEGKTLTSTLPVYLNALT--------GKGVHVVTVNEYLASRDAEQMGKIFEFL  148 (273)
T ss_dssp             CCCCHHHHHHHHHHHTT--SEEECCTTSCHHHHHHHHHHHHHTT--------SSCEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             eEEehhHHHHHHHHHhh--hheeecCCCcchhHHHHHHHHHHhc--------CCCceEEecCccccchhhhHHhHHHHHc
Confidence            46777887766666666  4889999999999999998887765        5678899999999999999999999999


Q ss_pred             CceEEEEECCCchHHHHHHHhCCCeEEEEChHHH-HHHHHcCCC------CCCCccEEEeecccccC
Q psy17644        268 NLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRI-IDMVKMGAT------KLNRVTFLVLDEADRMF  327 (330)
Q Consensus       268 ~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L-~~~l~~~~~------~l~~i~~lVvDEad~ll  327 (330)
                      |+++.++..+.........+  .|||+.+|...| .++++.+..      ..+.+.+.||||+|.||
T Consensus       149 Glsvg~~~~~~~~~~r~~~Y--~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsil  213 (273)
T d1tf5a3         149 GLTVGLNLNSMSKDEKREAY--AADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSIL  213 (273)
T ss_dssp             TCCEEECCTTSCHHHHHHHH--HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHH
T ss_pred             CCCccccccccCHHHHHHHh--hCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhh
Confidence            99999998887776655555  379999999887 456654321      25678999999999886

>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=98.86  E-value=2.3e-09  Score=92.29  Aligned_cols=123  Identities=16%  Similarity=0.187  Sum_probs=82.4

Q ss_pred             CCCHHHHHhhhhhc----CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        189 SPTPIQAQAVPAAL----SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~----~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      .+.|+|.+++..+.    .+..+|+.-.+|.|||+..+. ++.++....     ...++|||||. .++.|+.+++.+++
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~-~~~~~~~~~-----~~~~~LIv~p~-~l~~~W~~e~~~~~   84 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIA-VFSDAKKEN-----ELTPSLVICPL-SVLKNWEEELSKFA   84 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHH-HHHHHHHTT-----CCSSEEEEECS-TTHHHHHHHHHHHC
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHH-hhhhhhhcc-----cccccceecch-hhhhHHHHHHHhhc
Confidence            57899999997653    556788889999999987643 444544432     24578999994 77799999999987


Q ss_pred             cCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccCc
Q psy17644        265 KGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMFD  328 (330)
Q Consensus       265 ~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~lld  328 (330)
                      ...  .+.. +++......    ....+|+|+|...+.....-   .--...+||+||||++-.
T Consensus        85 ~~~--~~~~-~~~~~~~~~----~~~~~vvi~~~~~~~~~~~l---~~~~~~~vI~DEah~~k~  138 (230)
T d1z63a1          85 PHL--RFAV-FHEDRSKIK----LEDYDIILTTYAVLLRDTRL---KEVEWKYIVIDEAQNIKN  138 (230)
T ss_dssp             TTS--CEEE-CSSSTTSCC----GGGSSEEEEEHHHHTTCHHH---HTCCEEEEEEETGGGGSC
T ss_pred             ccc--ccee-eccccchhh----ccCcCEEEeeHHHHHhHHHH---hcccceEEEEEhhhcccc
Confidence            543  3322 222211110    12368999999887653321   112568899999999854

>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=97.78  E-value=1.6e-05  Score=72.35  Aligned_cols=71  Identities=20%  Similarity=0.199  Sum_probs=53.2

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      ..+..|+.|+..++.++-+++.|+.|+|||.+. ..++..+....   ...+.++++++||..-|.++.+.+...
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i-~~~l~~l~~~~---~~~~~~I~l~ApTgkAA~~L~e~~~~~  218 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTV-AKLLAALIQMA---DGERCRIRLAAPTGKAAARLTESLGKA  218 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHH-HHHHHHHHHTC---SSCCCCEEEEBSSHHHHHHHHHHHTHH
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehH-HHHHHHHHHHH---hccCCeEEEecCcHHHHHHHHHHHHHH
Confidence            456789999999999998999999999999552 23334443321   125678999999999988887776553

>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=97.75  E-value=2.7e-05  Score=68.19  Aligned_cols=71  Identities=18%  Similarity=0.102  Sum_probs=51.8

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      +++|-|++++..  ....+++.|+.|||||.+. +.-+.+++.+..   ....++||+++|+.+|..+...+.++..
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l-~~rv~~ll~~~~---~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVI-TNKIAHLIRGCG---YQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHH-HHHHHHHHHHHC---CCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHH-HHHHHHHHHhcC---CChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            478999999965  2356889999999999653 334444444321   1235799999999999999888877654

>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=97.37  E-value=0.00023  Score=62.55  Aligned_cols=71  Identities=18%  Similarity=0.137  Sum_probs=51.8

Q ss_pred             CCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhcc
Q psy17644        189 SPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGK  265 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~  265 (330)
                      .+++-|.+++...  +..+++.|+.|||||.+. +.-+.+++.+..   ...-++|++++|+.++..+...+.....
T Consensus        11 ~L~~eQ~~~v~~~--~g~~lV~g~aGSGKTt~l-~~ri~~ll~~~~---~~p~~il~lt~t~~aa~~~~~~~~~~~~   81 (318)
T d1pjra1          11 HLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVL-THRIAYLMAEKH---VAPWNILAITFTNKAAREMRERVQSLLG   81 (318)
T ss_dssp             TSCHHHHHHHHCC--SSCEEEEECTTSCHHHHH-HHHHHHHHHTTC---CCGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             hCCHHHHHHHhCC--CCCEEEEecCCccHHHHH-HHHHHHHHHcCC---CCHHHeEeEeccHHHHHHHHHHHHhhcc
Confidence            4789999999753  356999999999999644 444444554321   1234799999999999999998876543

>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=96.38  E-value=0.012  Score=48.62  Aligned_cols=84  Identities=19%  Similarity=0.248  Sum_probs=46.7

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEE-ccc-HHHHHHHHHHHHHhccCCCceEEEEECCCchHHHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLIL-APT-RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQS  284 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil-~Pt-r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~  284 (330)
                      +++++|||+|||.+..=-+ .++.+       .+.++.++ +-| |.-|   ++.++.|++..++.+.....+.......
T Consensus        12 i~lvGptGvGKTTTiAKLA-~~~~~-------~g~kV~lit~Dt~R~gA---~eQL~~~a~~l~v~~~~~~~~~d~~~~l   80 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLA-RQFEQ-------QGKSVMLAAGDTFRAAA---VEQLQVWGQRNNIPVIAQHTGADSASVI   80 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HHHHT-------TTCCEEEECCCTTCHHH---HHHHHHHHHHTTCCEECCSTTCCHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHH-------CCCcEEEEecccccccc---hhhhhhhhhhcCCcccccccCCCHHHHH
Confidence            4567999999995544322 23322       23344444 444 5444   3445556666678877666666544332


Q ss_pred             HH-----HhCCCe-EEEEChHHH
Q psy17644        285 KA-----LELGAE-IVVGTPGRI  301 (330)
Q Consensus       285 ~~-----l~~~~d-IiV~TP~~L  301 (330)
                      ..     ..++++ |+|=|+||.
T Consensus        81 ~~~~~~a~~~~~d~ilIDTaGr~  103 (211)
T d2qy9a2          81 FDAIQAAKARNIDVLIADTAGRL  103 (211)
T ss_dssp             HHHHHHHHHTTCSEEEECCCCCG
T ss_pred             HHHHHHHHHcCCCEEEeccCCCc
Confidence            21     123455 567798853

>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=96.30  E-value=0.003  Score=57.79  Aligned_cols=66  Identities=29%  Similarity=0.371  Sum_probs=47.4

Q ss_pred             CCCHHHHHhhhhhc----CC-CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        189 SPTPIQAQAVPAAL----SG-RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       189 ~pt~iQ~~~i~~~~----~g-~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .|+.-|-++|..+.    .| +..++.|-||||||++  ++.+..   +      .+..+|||+|+..+|.|+++.++.|
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~--iA~l~~---~------~~rp~LVVt~n~~~A~qL~~dL~~~   79 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFT--ISNVIA---Q------VNKPTLVIAHNKTLAGQLYSELKEF   79 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHH--HHHHHH---H------HTCCEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHH--HHHHHH---H------hCCCEEEEeCCHHHHHHHHHHHHHH
Confidence            46666766665554    34 6788889999999943  333222   1      1234799999999999999999998


Q ss_pred             cc
Q psy17644        264 GK  265 (330)
Q Consensus       264 ~~  265 (330)
                      ..
T Consensus        80 l~   81 (413)
T d1t5la1          80 FP   81 (413)
T ss_dssp             CT
T ss_pred             cC
Confidence            64

>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=95.93  E-value=0.026  Score=46.52  Aligned_cols=84  Identities=24%  Similarity=0.305  Sum_probs=44.2

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc-HHHHHHHHHHHHHhccCCCceEEEEECCCchHHH--
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT-RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ--  283 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt-r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~--  283 (330)
                      +++++|||+|||.+..=-+ .++.++      +...+||-+-| |.-|.+   +++.|++..++.+.....+.....-  
T Consensus        14 i~lvGptGvGKTTTiAKLA-a~~~~~------~~kV~lit~Dt~R~gA~e---QL~~~a~~l~i~~~~~~~~~d~~~~~~   83 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLA-KMFVDE------GKSVVLAAADTFRAAAIE---QLKIWGERVGATVISHSEGADPAAVAF   83 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHH-HHHHHT------TCCEEEEEECTTCHHHHH---HHHHHHHHHTCEEECCSTTCCHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHC------CCceEEEeecccccchhH---HHHHHhhhcCccccccCCCCcHHHHHH
Confidence            4667999999995533222 233332      23344555554 555543   3444554556666655554443221  


Q ss_pred             ---HHHHhCCCe-EEEEChHH
Q psy17644        284 ---SKALELGAE-IVVGTPGR  300 (330)
Q Consensus       284 ---~~~l~~~~d-IiV~TP~~  300 (330)
                         .....++++ |||=|+||
T Consensus        84 ~~~~~~~~~~~d~ilIDTaGr  104 (213)
T d1vmaa2          84 DAVAHALARNKDVVIIDTAGR  104 (213)
T ss_dssp             HHHHHHHHTTCSEEEEEECCC
T ss_pred             HHHHHHHHcCCCEEEEecccc
Confidence               122233454 66779874

>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=95.58  E-value=0.043  Score=42.95  Aligned_cols=73  Identities=11%  Similarity=0.235  Sum_probs=54.6

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh----CCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE----LGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~----~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      ...++||.|.|+..|.+++..+...    +..+..++|+.+..+....++    ....|||||-     .+ ...+++..
T Consensus        26 ~~~k~iIF~~s~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Td-----v~-~rGiDi~~   95 (162)
T d1fuka_          26 SVTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----LL-ARGIDVQQ   95 (162)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----GG-TTTCCCCS
T ss_pred             CCCcEEEEEEEEchHHHHHHHHhhc----CceEEEeccCCchhhHHHHHHHHhhcccceeeccc-----cc-cccccCCC
Confidence            3568999999999999998887765    678888999888766544432    2578999995     22 34667888


Q ss_pred             ccEEEee
Q psy17644        315 VTFLVLD  321 (330)
Q Consensus       315 i~~lVvD  321 (330)
                      +.+||.=
T Consensus        96 v~~VI~~  102 (162)
T d1fuka_          96 VSLVINY  102 (162)
T ss_dssp             CSEEEES
T ss_pred             ceEEEEe
Confidence            8888753

>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=95.55  E-value=0.012  Score=48.56  Aligned_cols=84  Identities=26%  Similarity=0.271  Sum_probs=43.4

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc--cHHHHHHHHHHHHHhccCCCceEEEEECCCchHHH-
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP--TRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQ-  283 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P--tr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~-  283 (330)
                      ++++++||+|||.+..--+. ++.+       .+.++++++-  .|.-|.++   ++.+++..++.+...........- 
T Consensus        13 i~lvGp~GvGKTTTiaKLA~-~~~~-------~g~kV~lit~Dt~R~gA~eQ---L~~~a~~l~v~~~~~~~~~~~~~~~   81 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAKLAL-YYKG-------KGRRPLLVAADTQRPAAREQ---LRLLGEKVGVPVLEVMDGESPESIR   81 (207)
T ss_dssp             EEEECCTTTTHHHHHHHHHH-HHHH-------TTCCEEEEECCSSCHHHHHH---HHHHHHHHTCCEEECCTTCCHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHH-------CCCcEEEEecccccchHHHH---HHHHHHhcCCccccccccchhhHHH
Confidence            45579999999855332222 2222       2344555543  46655544   444444446666666555544322 


Q ss_pred             -----HHHHhCCCeEEEEChHHH
Q psy17644        284 -----SKALELGAEIVVGTPGRI  301 (330)
Q Consensus       284 -----~~~l~~~~dIiV~TP~~L  301 (330)
                           .......--|+|=|++|.
T Consensus        82 ~~~~~~~~~~~~d~vlIDTaGr~  104 (207)
T d1ls1a2          82 RRVEEKARLEARDLILVDTAGRL  104 (207)
T ss_dssp             HHHHHHHHHHTCCEEEEECCCCS
T ss_pred             HHHHHHHhhccCcceeecccccc
Confidence                 112223234567788753

>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=95.36  E-value=0.052  Score=43.15  Aligned_cols=77  Identities=12%  Similarity=0.177  Sum_probs=58.3

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---hC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---EL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|+|+.-|..+...+...    |+++..++|+.+..+....+   ++ ..+|||||-     + -...+++.+
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~-----v-~~~GiDip~   99 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN-----L-LREGLDIPE   99 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC-----C-CCTTCCCTT
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhc----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeee-----e-eeeeccCCC
Confidence            4678999999999999999988875    78899999998876654333   33 489999993     2 233566888


Q ss_pred             ccEEEeecccc
Q psy17644        315 VTFLVLDEADR  325 (330)
Q Consensus       315 i~~lVvDEad~  325 (330)
                      +.+||+=.++.
T Consensus       100 V~~Vi~~~~~~  110 (174)
T d1c4oa2         100 VSLVAILDADK  110 (174)
T ss_dssp             EEEEEETTTTS
T ss_pred             CcEEEEecccc
Confidence            98888755543

>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=95.24  E-value=0.062  Score=41.52  Aligned_cols=55  Identities=15%  Similarity=0.220  Sum_probs=42.3

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHH---hC-CCeEEEECh
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKAL---EL-GAEIVVGTP  298 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l---~~-~~dIiV~TP  298 (330)
                      +.++||.|+|+.-|.+++..++..    +..+..+.|+.+..+....+   +. ...|+|||-
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~~----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~   86 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD   86 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT
T ss_pred             CCCEEEEECchHHHHHHHhhhccc----ccccccccccchhhhhhhhhhhhhcccceeeeehh
Confidence            468999999999999999888875    67788888888766654333   23 468999983

>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=95.11  E-value=0.063  Score=42.91  Aligned_cols=77  Identities=13%  Similarity=0.255  Sum_probs=58.4

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh---C-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE---L-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~---~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      ++.++||.|+|+..+..+...+++.    |+.+..++|+.+..+....+.   + ..+|||||-     ++ ...+++..
T Consensus        30 ~~~~~iif~~~~~~~~~~~~~l~~~----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTd-----v~-~rGiDip~   99 (181)
T d1t5la2          30 RNERTLVTTLTKKMAEDLTDYLKEA----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN-----LL-REGLDIPE   99 (181)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESC-----CC-SSSCCCTT
T ss_pred             cCCeEEEEeehhhhhHHHHHHHHhC----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEehh-----HH-HccCCCCC
Confidence            3568999999999999888888765    789999999998766544433   2 589999993     22 23567888


Q ss_pred             ccEEEeecccc
Q psy17644        315 VTFLVLDEADR  325 (330)
Q Consensus       315 i~~lVvDEad~  325 (330)
                      +.+||.-.+..
T Consensus       100 v~~VI~~d~p~  110 (181)
T d1t5la2         100 VSLVAILDADK  110 (181)
T ss_dssp             EEEEEETTTTS
T ss_pred             CCEEEEecCCc
Confidence            99998766553

>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=95.02  E-value=0.028  Score=46.66  Aligned_cols=49  Identities=18%  Similarity=0.219  Sum_probs=30.8

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHH
Q psy17644        168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHI  229 (330)
Q Consensus       168 ~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i  229 (330)
                      +|+++-....+.+.|...--.            -.....+++.||.|+|||.+ +..+++.+
T Consensus         9 ~~~diig~~~~~~~L~~~~~~------------~~~~~~lll~Gp~G~GKTt~-~~~la~~l   57 (252)
T d1sxje2           9 SLNALSHNEELTNFLKSLSDQ------------PRDLPHLLLYGPNGTGKKTR-CMALLESI   57 (252)
T ss_dssp             SGGGCCSCHHHHHHHHTTTTC------------TTCCCCEEEECSTTSSHHHH-HHTHHHHH
T ss_pred             CHHHccCcHHHHHHHHHHHHc------------CCCCCeEEEECCCCCCHHHH-HHHHHHhh
Confidence            578887788887777543110            11223589999999999943 33344444

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.01  E-value=0.072  Score=41.88  Aligned_cols=73  Identities=7%  Similarity=0.028  Sum_probs=53.5

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh----CCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE----LGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~----~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|.|+.-|..++..+...    +..+..++|+....+....+.    ....|+|||..      -...+++..
T Consensus        31 ~~~k~iVF~~~~~~~~~l~~~L~~~----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~------~~~Gid~~~  100 (171)
T d1s2ma2          31 QINQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL------LTRGIDIQA  100 (171)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC------SSSSCCCTT
T ss_pred             CCCceEEEEeeeehhhHhHHhhhcc----cccccccccccchhhhhhhhhhcccCccccccchhH------hhhccccce
Confidence            3568999999999999999888876    678888888888665543332    25789999952      223556777


Q ss_pred             ccEEEee
Q psy17644        315 VTFLVLD  321 (330)
Q Consensus       315 i~~lVvD  321 (330)
                      +.+||.=
T Consensus       101 v~~VI~~  107 (171)
T d1s2ma2         101 VNVVINF  107 (171)
T ss_dssp             EEEEEES
T ss_pred             eEEEEec
Confidence            7777753

>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=94.93  E-value=0.13  Score=41.97  Aligned_cols=87  Identities=24%  Similarity=0.258  Sum_probs=45.9

Q ss_pred             CCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEc-cc-HHHHHHHHHHHHHhccCCCceEEEEECCCchH
Q psy17644        204 GRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILA-PT-RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKW  281 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~-Pt-r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~  281 (330)
                      ++=+++++|||+|||.+..=-+ .++..       .+.++.+++ -| |.-|.++.+.   |++.+++.+.....+....
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA-~~~~~-------~g~kV~lit~Dt~R~gA~eQL~~---~a~~l~i~~~~~~~~~d~~   74 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLG-RYYQN-------LGKKVMFCAGDTFRAAGGTQLSE---WGKRLSIPVIQGPEGTDPA   74 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHH-HHHHT-------TTCCEEEECCCCSSTTHHHHHHH---HHHHHTCCEECCCTTCCHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH-HHHHH-------CCCcEEEEEeccccccchhhHhh---cccccCceEEeccCCccHH
Confidence            3456778999999995543222 23322       234454444 33 6666544433   3334466666555555543


Q ss_pred             HHHHH-----HhCCCe-EEEEChHHH
Q psy17644        282 DQSKA-----LELGAE-IVVGTPGRI  301 (330)
Q Consensus       282 ~~~~~-----l~~~~d-IiV~TP~~L  301 (330)
                      .....     ..++++ |+|=|+|+.
T Consensus        75 ~~~~~~~~~~~~~~~d~ilIDTaGr~  100 (207)
T d1okkd2          75 ALAYDAVQAMKARGYDLLFVDTAGRL  100 (207)
T ss_dssp             HHHHHHHHHHHHHTCSEEEECCCCCC
T ss_pred             HHHHHHHHHHHHCCCCEEEcCccccc
Confidence            32211     122344 567798863

>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=94.82  E-value=0.052  Score=44.49  Aligned_cols=80  Identities=11%  Similarity=0.143  Sum_probs=61.5

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHH---HHhC-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK---ALEL-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~---~l~~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .|.+|.||||..+-+..++..++++..  +.++.+++|..+..+...   .+.. ..+|+|||.     .++ ...++.+
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~~p--~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt-----vIE-vGiDvpn  101 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----IIE-TGIDIPT  101 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----TTG-GGSCCTT
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHhCC--ceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh-----hhh-hccCCCC
Confidence            588999999999999999999888765  467888888777655433   3333 489999993     233 3456889


Q ss_pred             ccEEEeeccccc
Q psy17644        315 VTFLVLDEADRM  326 (330)
Q Consensus       315 i~~lVvDEad~l  326 (330)
                      ..++||..|+++
T Consensus       102 A~~iiI~~a~rf  113 (211)
T d2eyqa5         102 ANTIIIERADHF  113 (211)
T ss_dssp             EEEEEETTTTSS
T ss_pred             CcEEEEecchhc
Confidence            999999999985

>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=94.46  E-value=0.11  Score=41.97  Aligned_cols=71  Identities=20%  Similarity=0.177  Sum_probs=51.1

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh----CCCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE----LGAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~----~~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.++|+..|..+...+...    ++.+..++|+.........+.    ...+|||||-     .+ ...+++..
T Consensus        29 ~~~~~IIF~~t~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd-----~~-~~GiD~p~   98 (200)
T d1oywa3          29 RGKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV-----AF-GMGINKPN   98 (200)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT-----TS-CTTTCCTT
T ss_pred             CCCCEEEEEeeehhhHHhhhhhccC----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecc-----hh-hhccCCCC
Confidence            3568999999999999998887775    678888899887665443332    2478999994     11 23455667


Q ss_pred             ccEEE
Q psy17644        315 VTFLV  319 (330)
Q Consensus       315 i~~lV  319 (330)
                      |++||
T Consensus        99 v~~VI  103 (200)
T d1oywa3          99 VRFVV  103 (200)
T ss_dssp             CCEEE
T ss_pred             CCEEE
Confidence            77776

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=94.30  E-value=0.0093  Score=52.60  Aligned_cols=20  Identities=40%  Similarity=0.566  Sum_probs=17.0

Q ss_pred             hhcCCCcEEEEcCCCChhHH
Q psy17644        200 AALSGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       200 ~~~~g~d~i~~a~TGsGKT~  219 (330)
                      ++..+++++++|+||||||.
T Consensus       162 ~v~~~~nili~G~tgSGKTT  181 (323)
T d1g6oa_         162 GIAIGKNVIVCGGTGSGKTT  181 (323)
T ss_dssp             HHHHTCCEEEEESTTSSHHH
T ss_pred             HHHhCCCEEEEeeccccchH
Confidence            34578899999999999993

>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=94.30  E-value=0.041  Score=45.19  Aligned_cols=84  Identities=24%  Similarity=0.223  Sum_probs=38.5

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc-HHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT-RELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSK  285 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt-r~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~  285 (330)
                      +++++|||+|||.+..=-+ .++..+      ....+||-+-| |.-+.   ++++.|++..++.+..............
T Consensus        15 i~lvGptGvGKTTTiAKLA-~~~~~~------g~kV~lit~Dt~R~ga~---eQL~~~a~~l~v~~~~~~~~~~~~~~~~   84 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLA-YFYKKK------GFKVGLVGADVYRPAAL---EQLQQLGQQIGVPVYGEPGEKDVVGIAK   84 (211)
T ss_dssp             EEEECSCCC----HHHHHH-HHHHHT------TCCEEEEECCCSSHHHH---HHHHHHHHHHTCCEECCTTCCCHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHC------CCceEEEEeeccccchh---HHHHHhccccCcceeecccchhhhHHHH
Confidence            5567999999995533222 233221      12334444444 55443   3444455545666665555444322111


Q ss_pred             -----HHhCCCe-EEEEChHH
Q psy17644        286 -----ALELGAE-IVVGTPGR  300 (330)
Q Consensus       286 -----~l~~~~d-IiV~TP~~  300 (330)
                           ....+++ |+|=|||+
T Consensus        85 ~a~~~~~~~~~d~IlIDTaGr  105 (211)
T d1j8yf2          85 RGVEKFLSEKMEIIIVDTAGR  105 (211)
T ss_dssp             HHHHHHHHTTCSEEEEECCCS
T ss_pred             HHHHHhhccCCceEEEecCCc
Confidence                 1223344 56668875

>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=93.96  E-value=0.22  Score=38.88  Aligned_cols=72  Identities=10%  Similarity=0.194  Sum_probs=53.4

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh---C-CCeEEEEChHHHHHHHHcCCCCCCC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE---L-GAEIVVGTPGRIIDMVKMGATKLNR  314 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~---~-~~dIiV~TP~~L~~~l~~~~~~l~~  314 (330)
                      .+.++||.|.|+.-|..+...++..    +..+..++|+....+....+.   . ..+|+|||-     ++ ...+++..
T Consensus        33 ~~~k~iiF~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td-----~~-~rGiDi~~  102 (168)
T d2j0sa2          33 TITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD-----VW-ARGLDVPQ  102 (168)
T ss_dssp             TSSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG-----GG-SSSCCCTT
T ss_pred             CCCceEEEeeeHHHHHHHHHHhhhc----ccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccc-----hh-cccccccC
Confidence            3578999999999999998888775    567788888888766544432   2 478999994     22 34666778


Q ss_pred             ccEEEe
Q psy17644        315 VTFLVL  320 (330)
Q Consensus       315 i~~lVv  320 (330)
                      +.+||.
T Consensus       103 v~~VIn  108 (168)
T d2j0sa2         103 VSLIIN  108 (168)
T ss_dssp             EEEEEE
T ss_pred             cceEEE
Confidence            887764

>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=93.93  E-value=0.13  Score=40.34  Aligned_cols=55  Identities=11%  Similarity=0.042  Sum_probs=42.7

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHh---C-CCeEEEEC
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALE---L-GAEIVVGT  297 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~---~-~~dIiV~T  297 (330)
                      .+.++||.|+|+.-+..+...+.+.    +..+..++|+.+..++...+.   . ...|||||
T Consensus        26 ~~~k~iIF~~~~~~~~~l~~~L~~~----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T   84 (168)
T d1t5ia_          26 EFNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVAT   84 (168)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEES
T ss_pred             CCCeEEEEEeeeecchhhhhhhccc----cccccccccccchhhhhhhhhhhccccceeeecc
Confidence            3568999999999999988888765    567888999888766554433   2 47899999

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=93.62  E-value=0.23  Score=39.99  Aligned_cols=32  Identities=13%  Similarity=0.084  Sum_probs=25.0

Q ss_pred             EEEEChHHHHHHHHcCCCCCCCccEEEeeccc
Q psy17644        293 IVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD  324 (330)
Q Consensus       293 IiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad  324 (330)
                      |.-|||..+..++++.....+++..|.|+|-+
T Consensus       155 IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~  186 (195)
T d1jbka_         155 VGATTLDEYRQYIEKDAALERRFQKVFVAEPS  186 (195)
T ss_dssp             EEEECHHHHHHHTTTCHHHHTTEEEEECCCCC
T ss_pred             EecCCHHHHHHHHHcCHHHHhcCCEeecCCCC
Confidence            44589999999988766667788888888864

>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=93.40  E-value=0.11  Score=39.53  Aligned_cols=88  Identities=16%  Similarity=0.135  Sum_probs=50.6

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA  286 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~  286 (330)
                      -++.||+.||||. .|+-.+++...       .+.+++++-|...-         +...    .+. ...|..       
T Consensus         5 ~~i~GpMfsGKTt-eLi~~~~~~~~-------~~~kv~~ikp~~D~---------R~~~----~i~-s~~g~~-------   55 (139)
T d2b8ta1           5 EFITGPMFAGKTA-ELIRRLHRLEY-------ADVKYLVFKPKIDT---------RSIR----NIQ-SRTGTS-------   55 (139)
T ss_dssp             EEEECSTTSCHHH-HHHHHHHHHHH-------TTCCEEEEEECCCG---------GGCS----SCC-CCCCCS-------
T ss_pred             EEEEccccCHHHH-HHHHHHHHHHH-------CCCcEEEEEEcccc---------cccc----eEE-cccCce-------
Confidence            3678999999994 44444444332       36688999997442         1111    111 111111       


Q ss_pred             HhCCCeEEEEChHHHHHHHHcCCCCCCCccEEEeecccccC
Q psy17644        287 LELGAEIVVGTPGRIIDMVKMGATKLNRVTFLVLDEADRMF  327 (330)
Q Consensus       287 l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad~ll  327 (330)
                        . ..+.+.+...+...+..... ..+.+++.||||+-+-
T Consensus        56 --~-~~~~~~~~~~~~~~~~~~~~-~~~~dvI~IDE~QFf~   92 (139)
T d2b8ta1          56 --L-PSVEVESAPEILNYIMSNSF-NDETKVIGIDEVQFFD   92 (139)
T ss_dssp             --S-CCEEESSTHHHHHHHHSTTS-CTTCCEEEECSGGGSC
T ss_pred             --e-eeEEeccchhhHHHHHhhcc-ccCcCEEEechhhhcc
Confidence              1 23455665666666654332 3578999999998764

>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=92.99  E-value=0.12  Score=46.74  Aligned_cols=67  Identities=27%  Similarity=0.377  Sum_probs=45.7

Q ss_pred             CCCHHHHHhhhhh----cCCC-cEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        189 SPTPIQAQAVPAA----LSGR-DIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       189 ~pt~iQ~~~i~~~----~~g~-d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .|+.-|-++|..+    -.|+ .+.+.|-+||+|+  |+++.+..-.         +..+|||+|+...|.++++.++.|
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka--~~~A~l~~~~---------~rp~LvVt~~~~~A~~l~~dL~~~   76 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKT--VTMAKVIEAL---------GRPALVLAPNKILAAQLAAEFREL   76 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHH--HHHHHHHHHH---------TCCEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHH--HHHHHHHHHh---------CCCEEEEeCCHHHHHHHHHHHHHh
Confidence            3444554455543    4555 4677899999999  3344333321         234789999999999999999998


Q ss_pred             ccC
Q psy17644        264 GKG  266 (330)
Q Consensus       264 ~~~  266 (330)
                      ...
T Consensus        77 l~~   79 (408)
T d1c4oa1          77 FPE   79 (408)
T ss_dssp             CTT
T ss_pred             cCc
Confidence            653

>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=92.37  E-value=0.27  Score=39.67  Aligned_cols=39  Identities=15%  Similarity=0.277  Sum_probs=24.9

Q ss_pred             CHHHHHhhhhhc----CCC---cEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        191 TPIQAQAVPAAL----SGR---DIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       191 t~iQ~~~i~~~~----~g~---d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      +|+|..++..+.    +++   -+++.||.|+|||.+. ..+...++
T Consensus         4 yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a-~~~a~~l~   49 (207)
T d1a5ta2           4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALI-YALSRYLL   49 (207)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHH-HHHHHHHT
T ss_pred             CcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHH-HHHHHhcc
Confidence            477776666543    443   4899999999999433 23344444

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=92.13  E-value=0.55  Score=39.56  Aligned_cols=32  Identities=13%  Similarity=0.074  Sum_probs=25.7

Q ss_pred             EEEEChHHHHHHHHcCCCCCCCccEEEeeccc
Q psy17644        293 IVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD  324 (330)
Q Consensus       293 IiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad  324 (330)
                      |.-|||..+..++++.....+++..|-|+|-+
T Consensus       151 IgatT~eey~~~~e~d~al~rrF~~I~V~Eps  182 (268)
T d1r6bx2         151 IGSTTYQEFSNIFEKDRALARRFQKIDITEPS  182 (268)
T ss_dssp             EEEECHHHHHCCCCCTTSSGGGEEEEECCCCC
T ss_pred             EEeCCHHHHHHHHhhcHHHHhhhcccccCCCC
Confidence            44579999998887777677889999998865

>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=92.12  E-value=0.083  Score=47.49  Aligned_cols=29  Identities=17%  Similarity=0.178  Sum_probs=21.0

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      ...++++++|+||||||.+ +..++..++.
T Consensus        48 ~~~~H~~I~G~tGsGKT~~-l~~li~~~~~   76 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVL-LRELAYTGLL   76 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHH-HHHHHHHHHH
T ss_pred             cccceEEEEeCCCCcHHHH-HHHHHHHHHh
Confidence            4457899999999999965 4445555554

>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=91.80  E-value=0.12  Score=46.60  Aligned_cols=50  Identities=16%  Similarity=0.234  Sum_probs=29.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCc--EEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        165 PVSSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRD--IIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       165 p~~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d--~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      +..++.++|+.+.                |.+.+..++....  +|++||||||||. .+..++.++..
T Consensus       133 ~~~~l~~LG~~~~----------------~~~~l~~l~~~~~GliLvtGpTGSGKST-Tl~~~l~~~~~  184 (401)
T d1p9ra_         133 TRLDLHSLGMTAH----------------NHDNFRRLIKRPHGIILVTGPTGSGKST-TLYAGLQELNS  184 (401)
T ss_dssp             TCCCGGGSCCCHH----------------HHHHHHHHHTSSSEEEEEECSTTSCHHH-HHHHHHHHHCC
T ss_pred             cchhhhhhcccHH----------------HHHHHHHHHhhhhceEEEEcCCCCCccH-HHHHHhhhhcC
Confidence            3445777776544                4444444443332  5666999999994 33345666543

>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=91.70  E-value=0.11  Score=40.02  Aligned_cols=26  Identities=23%  Similarity=0.276  Sum_probs=18.7

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHh
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMD  231 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~  231 (330)
                      |++++.|++|+|||. .+..++..+..
T Consensus         2 k~v~ItG~~GtGKTt-l~~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT-LIHKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHH-HHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHH-HHHHHHHHHHH
Confidence            789999999999994 33344455444

>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=91.07  E-value=0.15  Score=38.73  Aligned_cols=67  Identities=16%  Similarity=0.225  Sum_probs=48.3

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEEChHHHHHHHHcCCCCCCCccEE
Q psy17644        239 DGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTPGRIIDMVKMGATKLNRVTFL  318 (330)
Q Consensus       239 ~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP~~L~~~l~~~~~~l~~i~~l  318 (330)
                      .+.++||.|+|+.-|.+++..+++.    ++.+..++++.....+.   ....+|||||-     .+.++ ++ ..+.+|
T Consensus        34 ~~~k~IVFc~t~~~ae~la~~L~~~----G~~~~~~H~~~~~~~~~---~~~~~vlvaTd-----~~~~G-iD-~~v~~V   99 (138)
T d1jr6a_          34 KGGRHLIFCHSKKKCDELAAKLVAL----GINAVAYYRGLDVSVIP---TNGDVVVVATD-----ALMTG-FT-GDFDSV   99 (138)
T ss_dssp             TTSCEEEECSCHHHHHHHHHHHHHH----TCEEEEECTTCCSCCCT---TSSCEEEEESS-----SSCSS-SC-CCBSEE
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHhcc----ccchhhhhccchhhhhh---hhhcceeehhH-----HHHhc-cc-cccceE
Confidence            3568999999999999999999876    67888888887754432   34579999993     33333 33 356665


Q ss_pred             E
Q psy17644        319 V  319 (330)
Q Consensus       319 V  319 (330)
                      |
T Consensus       100 i  100 (138)
T d1jr6a_         100 I  100 (138)
T ss_dssp             E
T ss_pred             E
Confidence            4

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=91.06  E-value=0.14  Score=41.78  Aligned_cols=52  Identities=19%  Similarity=0.287  Sum_probs=32.6

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .|.-+++.|++|+||| .+++.++.+..+       ++.++++++-. +-..++.+.+..+
T Consensus        25 ~gsl~li~G~pGsGKT-~l~~qia~~~~~-------~~~~~~~is~e-~~~~~~~~~~~~~   76 (242)
T d1tf7a2          25 KDSIILATGATGTGKT-LLVSRFVENACA-------NKERAILFAYE-ESRAQLLRNAYSW   76 (242)
T ss_dssp             SSCEEEEEECTTSSHH-HHHHHHHHHHHT-------TTCCEEEEESS-SCHHHHHHHHHTT
T ss_pred             CCeEEEEEeCCCCCHH-HHHHHHHHHHHH-------hccccceeecc-CCHHHHHHHHHHc
Confidence            4577888899999999 455555555544       35667777643 2334444555444

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=90.12  E-value=0.2  Score=43.16  Aligned_cols=55  Identities=9%  Similarity=0.044  Sum_probs=39.4

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHHHhCCCeEEEECh
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKALELGAEIVVGTP  298 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~l~~~~dIiV~TP  298 (330)
                      ..++||+||+..-+.++...+++.    +.+++.++|.....++.+......+|||||.
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~----g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t~   90 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKTFEREYPTIKQKKPDFILATD   90 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSSCC--------CCCSEEEESS
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhc----CCeEEEEcCcCcHhHHhhhhcCCcCEEEEec
Confidence            567999999999999999998875    5578888888776666555555678999993

>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=89.37  E-value=0.21  Score=41.76  Aligned_cols=41  Identities=20%  Similarity=0.186  Sum_probs=27.2

Q ss_pred             hcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q psy17644        201 ALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP  248 (330)
Q Consensus       201 ~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P  248 (330)
                      +..|.=+++.|+||+||| +|++.++.++...      .+-+|+|++.
T Consensus        32 ~~~G~l~vi~G~~G~GKT-~~~~~la~~~a~~------~g~~v~~~s~   72 (277)
T d1cr2a_          32 ARGGEVIMVTSGSGMGKS-TFVRQQALQWGTA------MGKKVGLAML   72 (277)
T ss_dssp             BCTTCEEEEECSTTSSHH-HHHHHHHHHHHHT------SCCCEEEEES
T ss_pred             CCCCeEEEEEeCCCCCHH-HHHHHHHHhhhhh------cccceeEeee
Confidence            345667788899999999 4555555454332      3567788764

>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=89.19  E-value=0.48  Score=42.36  Aligned_cols=58  Identities=16%  Similarity=0.081  Sum_probs=38.1

Q ss_pred             cEEEEcCCCChhHHHHHHHHHHHHHhcCCCC----CCCCCeEEEEcccHHHHHHHHHHHHHh
Q psy17644        206 DIIGVAKTGSGKTGAFIWPMLVHIMDQKELE----PGDGPMGLILAPTRELSQQIYNEAKRF  263 (330)
Q Consensus       206 d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~----~~~~~~vLil~Ptr~La~Qi~~~~~~l  263 (330)
                      .+||.|.-|||||.+-+--++..++......    .-..-.+|+|+=|+.-|..+.+.+...
T Consensus        18 ~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~   79 (485)
T d1w36b1          18 ERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (485)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHH
Confidence            4788999999999665555555554432111    011235889999998888877776543

>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=87.86  E-value=0.11  Score=47.49  Aligned_cols=18  Identities=33%  Similarity=0.554  Sum_probs=15.5

Q ss_pred             CCCcEEEEcCCCChhHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a  220 (330)
                      ..+|+|++||||+|||+.
T Consensus        48 ~ksNILliGPTGvGKTlL   65 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTEI   65 (443)
T ss_dssp             CCCCEEEECCTTSSHHHH
T ss_pred             ccccEEEECCCCCCHHHH
Confidence            457999999999999954

>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=87.72  E-value=0.25  Score=40.24  Aligned_cols=27  Identities=22%  Similarity=0.203  Sum_probs=19.8

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      .|+=+++.|++|+||| +|++.++.+..
T Consensus        35 ~G~~~li~G~pGsGKT-~~~lq~~~~~~   61 (254)
T d1pzna2          35 TQAITEVFGEFGSGKT-QLAHTLAVMVQ   61 (254)
T ss_dssp             SSEEEEEEESTTSSHH-HHHHHHHHHTT
T ss_pred             CCEEEEEEcCCCCCHH-HHHHHHHHHhh
Confidence            4677888899999999 45555555543

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.51  E-value=0.38  Score=37.57  Aligned_cols=27  Identities=19%  Similarity=0.142  Sum_probs=19.5

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      .|+=+++.|++|+||| .+++.++.+..
T Consensus        22 ~G~v~~i~G~~GsGKT-~l~l~la~~~~   48 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKT-QICHTLAVTCQ   48 (242)
T ss_dssp             TTSEEEEECCTTSSHH-HHHHHHHHHTT
T ss_pred             CCEEEEEEeCCCCCHH-HHHHHHHHHHH
Confidence            5677888899999999 45555555543

>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=87.35  E-value=1.6  Score=34.83  Aligned_cols=39  Identities=18%  Similarity=0.275  Sum_probs=24.9

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCC--CcEEEEcCCCChhHHH
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG--RDIIGVAKTGSGKTGA  220 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g--~d~i~~a~TGsGKT~a  220 (330)
                      ++|.++-..+.+.+.|+..               +.++  .++++.||+|+|||.+
T Consensus        11 ~~~~divg~~~~~~~L~~~---------------i~~~~~~~lLl~Gp~G~GKttl   51 (227)
T d1sxjc2          11 ETLDEVYGQNEVITTVRKF---------------VDEGKLPHLLFYGPPGTGKTST   51 (227)
T ss_dssp             SSGGGCCSCHHHHHHHHHH---------------HHTTCCCCEEEECSSSSSHHHH
T ss_pred             CCHHHccCcHHHHHHHHHH---------------HHcCCCCeEEEECCCCCChhHH
Confidence            4567766666666665432               1111  2489999999999943

>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=87.30  E-value=7.4  Score=34.00  Aligned_cols=126  Identities=18%  Similarity=0.158  Sum_probs=59.5

Q ss_pred             Hhhhhhc--CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHH-----HHHHHHHHhc----
Q psy17644        196 QAVPAAL--SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQ-----QIYNEAKRFG----  264 (330)
Q Consensus       196 ~~i~~~~--~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~-----Qi~~~~~~l~----  264 (330)
                      +++..+.  ...+.+++|+.|.|||...- .+...+........-.+.+++.|-+.+-+|-     ++...++.+.    
T Consensus        33 ~~~~~L~r~~k~n~llvG~~GvGKtaiv~-~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~e~r~~~i~~~~~  111 (387)
T d1qvra2          33 RVIQILLRRTKNNPVLIGEPGVGKTAIVE-GLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVV  111 (387)
T ss_dssp             HHHHHHHCSSCCCCEEEECTTSCHHHHHH-HHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCCeEECCCCCCHHHHHH-HHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchhHHHHHHHHHHHhc
Confidence            3444443  33578999999999994322 2233444433222234455555555544432     3333333322    


Q ss_pred             cCCCceEEEE-------EC-CCch-H-H----HHHHHhCC-C-eEEEEChHHHHHHHHcCCCCCCCccEEEeeccc
Q psy17644        265 KGYNLSVVCC-------YG-GGSK-W-D----QSKALELG-A-EIVVGTPGRIIDMVKMGATKLNRVTFLVLDEAD  324 (330)
Q Consensus       265 ~~~~~~~~~~-------~g-g~~~-~-~----~~~~l~~~-~-dIiV~TP~~L~~~l~~~~~~l~~i~~lVvDEad  324 (330)
                      ...+ .++++       +| |... . .    ....+.+| . =|.-+||..+.. +.+.....+++..|-|+|-+
T Consensus       112 ~~~~-~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~rg~~~~I~~tT~~ey~~-~e~d~al~rrF~~v~v~ep~  185 (387)
T d1qvra2         112 QSQG-EVILFIDELHTVVGAGKAEGAVDAGNMLKPALARGELRLIGATTLDEYRE-IEKDPALERRFQPVYVDEPT  185 (387)
T ss_dssp             TTCS-SEEEEECCC-------------------HHHHHTTCCCEEEEECHHHHHH-HTTCTTTCSCCCCEEECCCC
T ss_pred             cCCC-ceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhCCCcceeeecCHHHHHH-hcccHHHHHhcccccCCCCc
Confidence            2212 22222       22 1110 0 0    11223333 3 355689999976 56655567788999988864

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=86.63  E-value=0.39  Score=36.31  Aligned_cols=34  Identities=18%  Similarity=0.234  Sum_probs=20.8

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP  248 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P  248 (330)
                      +.++|+.||||| +++-.++.++..       .|-++.++..
T Consensus         5 i~itG~~GSGKT-TL~~~L~~~l~~-------~g~~v~v~~~   38 (170)
T d1np6a_           5 LAFAAWSGTGKT-TLLKKLIPALCA-------RGIRPGLIKH   38 (170)
T ss_dssp             EEEECCTTSCHH-HHHHHHHHHHHH-------TTCCEEEEEE
T ss_pred             EEEEcCCCCCHH-HHHHHHHHHHHH-------CCCeEEEecc
Confidence            467799999999 444445544443       2455555543

>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=86.45  E-value=3.2  Score=33.40  Aligned_cols=48  Identities=19%  Similarity=0.144  Sum_probs=29.7

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCC---CcEEEEcCCCChhHHHHHHHHHHHHH
Q psy17644        167 SSFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSG---RDIIGVAKTGSGKTGAFIWPMLVHIM  230 (330)
Q Consensus       167 ~~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g---~d~i~~a~TGsGKT~a~llp~l~~i~  230 (330)
                      ++|.++-....+.+.|...               +.++   +.+|+.||+|+|||.+.. .+++.+.
T Consensus         9 ~~~~dlig~~~~~~~L~~~---------------i~~~~~~~~~Ll~Gp~G~GKtt~a~-~~~~~l~   59 (239)
T d1njfa_           9 QTFADVVGQEHVLTALANG---------------LSLGRIHHAYLFSGTRGVGKTSIAR-LLAKGLN   59 (239)
T ss_dssp             SSGGGSCSCHHHHHHHHHH---------------HHTTCCCSEEEEECSTTSSHHHHHH-HHHHHHH
T ss_pred             CCHHHccChHHHHHHHHHH---------------HHcCCCCeeEEEECCCCCcHHHHHH-HHHHHhc
Confidence            4677877677776665431               1122   347889999999995433 3444443

>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=85.67  E-value=0.54  Score=38.00  Aligned_cols=45  Identities=16%  Similarity=0.194  Sum_probs=26.7

Q ss_pred             CcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYN  258 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~  258 (330)
                      ..+++.|++|+|||  .++.++.+-+..      .+..++++ +...+..++..
T Consensus        37 n~l~l~G~~G~GKT--HLl~A~~~~~~~------~~~~~~~~-~~~~~~~~~~~   81 (213)
T d1l8qa2          37 NPIFIYGSVGTGKT--HLLQAAGNEAKK------RGYRVIYS-SADDFAQAMVE   81 (213)
T ss_dssp             SSEEEECSSSSSHH--HHHHHHHHHHHH------TTCCEEEE-EHHHHHHHHHH
T ss_pred             CcEEEECCCCCcHH--HHHHHHHHHhcc------CccceEEe-chHHHHHHHHH
Confidence            34889999999999  444444443332      24555554 55555554444

>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=85.18  E-value=0.33  Score=41.75  Aligned_cols=19  Identities=32%  Similarity=0.485  Sum_probs=16.0

Q ss_pred             CCCcEEEEcCCCChhHHHH
Q psy17644        203 SGRDIIGVAKTGSGKTGAF  221 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~  221 (330)
                      ..+.++++||||+|||...
T Consensus        48 ~~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            4588999999999999543

>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=84.19  E-value=0.83  Score=37.68  Aligned_cols=66  Identities=17%  Similarity=0.198  Sum_probs=37.5

Q ss_pred             hhhhhcCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCC---CCCCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy17644        197 AVPAALSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKEL---EPGDGPMGLILAPTRELSQQIYNEAKRFG  264 (330)
Q Consensus       197 ~i~~~~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~---~~~~~~~vLil~Ptr~La~Qi~~~~~~l~  264 (330)
                      +++-++.|.=+++.|++|+|||. |++.+..++......   ....+.++||+.- -.-..++...+..+.
T Consensus        22 li~G~~pg~~~~i~G~~G~GKS~-l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~-E~~~~~~~~Rl~~~~   90 (274)
T d1nlfa_          22 VLPNMVAGTVGALVSPGGAGKSM-LALQLAAQIAGGPDLLEVGELPTGPVIYLPA-EDPPTAIHHRLHALG   90 (274)
T ss_dssp             EETTEETTSEEEEEESTTSSHHH-HHHHHHHHHHTCCCTTCCCCCCCCCEEEEES-SSCHHHHHHHHHHHH
T ss_pred             HhCCccCCcEEEEEeCCCCCHHH-HHHHHHHHHHcCCCcccccccCCCceEEEec-cchHHHHHHHHHHHh
Confidence            45666778878888999999993 444444455443221   1123445676653 223444555555443

>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=83.66  E-value=0.34  Score=36.12  Aligned_cols=18  Identities=33%  Similarity=0.390  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCChhHHHH
Q psy17644        204 GRDIIGVAKTGSGKTGAF  221 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~  221 (330)
                      .|.++++|++|+|||...
T Consensus         2 ~k~I~l~G~~GsGKSTva   19 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIG   19 (169)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            368999999999999543

>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=83.54  E-value=0.49  Score=37.77  Aligned_cols=39  Identities=23%  Similarity=0.271  Sum_probs=23.6

Q ss_pred             CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q psy17644        203 SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP  248 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P  248 (330)
                      .|.-+++.|++|+|||. |++.++.+....      .+.+++++..
T Consensus        25 ~G~~~~I~G~~G~GKT~-la~~~~~~~~~~------~~~~~~~~s~   63 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTL-FSIQFLYNGIIE------FDEPGVFVTF   63 (242)
T ss_dssp             TTSEEEEEESTTSSHHH-HHHHHHHHHHHH------HCCCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHH-HHHHHHHHHHHh------cCCCcccccc
Confidence            56778888999999994 444433332222      2345666653

>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=83.44  E-value=1.1  Score=35.86  Aligned_cols=15  Identities=33%  Similarity=0.395  Sum_probs=13.0

Q ss_pred             cEEEEcCCCChhHHH
Q psy17644        206 DIIGVAKTGSGKTGA  220 (330)
Q Consensus       206 d~i~~a~TGsGKT~a  220 (330)
                      ++++.||+|+|||.+
T Consensus        38 ~~ll~Gp~G~GKTt~   52 (224)
T d1sxjb2          38 HMIISGMPGIGKTTS   52 (224)
T ss_dssp             CEEEECSTTSSHHHH
T ss_pred             eEEEECCCCCCchhh
Confidence            589999999999954

>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=83.36  E-value=0.66  Score=35.04  Aligned_cols=37  Identities=14%  Similarity=0.015  Sum_probs=24.9

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE  251 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~  251 (330)
                      -+++||+.|||| +.|+-.+++...       .+.+++++-|...
T Consensus        10 ~lI~GpMfSGKT-teLi~~~~~~~~-------~g~~vl~i~~~~D   46 (141)
T d1xx6a1          10 EVIVGPMYSGKS-EELIRRIRRAKI-------AKQKIQVFKPEID   46 (141)
T ss_dssp             EEEECSTTSSHH-HHHHHHHHHHHH-------TTCCEEEEEEC--
T ss_pred             EEEEeccccHHH-HHHHHHHHHhhh-------cCCcEEEEEeccc
Confidence            467899999999 445555544333       3668999999754

>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=83.36  E-value=1.8  Score=34.31  Aligned_cols=59  Identities=17%  Similarity=0.147  Sum_probs=37.1

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHhccCCC--------------------------ceEEEEECCCchHHHH---HHHhC-
Q psy17644        240 GPMGLILAPTRELSQQIYNEAKRFGKGYN--------------------------LSVVCCYGGGSKWDQS---KALEL-  289 (330)
Q Consensus       240 ~~~vLil~Ptr~La~Qi~~~~~~l~~~~~--------------------------~~~~~~~gg~~~~~~~---~~l~~-  289 (330)
                      +..+||.||||..|..+...+..+.....                          ..+.+.+||.+.....   ..+++ 
T Consensus        40 ~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f~~g  119 (201)
T d2p6ra4          40 NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRG  119 (201)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTT
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHHhCC
Confidence            45689999999888888777766432110                          1156677887765442   22333 


Q ss_pred             CCeEEEECh
Q psy17644        290 GAEIVVGTP  298 (330)
Q Consensus       290 ~~dIiV~TP  298 (330)
                      ...|||||.
T Consensus       120 ~i~vlvaT~  128 (201)
T d2p6ra4         120 NIKVVVATP  128 (201)
T ss_dssp             SCCEEEECS
T ss_pred             CceEEEech
Confidence            467888884

>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=83.18  E-value=0.67  Score=34.57  Aligned_cols=37  Identities=11%  Similarity=0.016  Sum_probs=25.8

Q ss_pred             EEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q psy17644        207 IIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRE  251 (330)
Q Consensus       207 ~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~  251 (330)
                      -+++||+.||||. .|+-.++....       .+.+++++-|...
T Consensus         5 ~li~GpMfsGKTt-~Li~~~~~~~~-------~g~~v~~ikp~~D   41 (133)
T d1xbta1           5 QVILGPMFSGKST-ELMRRVRRFQI-------AQYKCLVIKYAKD   41 (133)
T ss_dssp             EEEECCTTSCHHH-HHHHHHHHHHT-------TTCCEEEEEETTC
T ss_pred             EEEEecccCHHHH-HHHHHHHHHHH-------cCCcEEEEecccc
Confidence            4678999999994 55555554433       3567899988644

>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=82.71  E-value=1.3  Score=35.63  Aligned_cols=17  Identities=24%  Similarity=0.274  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCChhHHHH
Q psy17644        205 RDIIGVAKTGSGKTGAF  221 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a~  221 (330)
                      .++++.||+|+|||.+.
T Consensus        36 ~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             CCEEEESSTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            47999999999999543

>d1vi2a1 c.2.1.7 (A:107-288) Putative shikimate dehydrogenase YdiB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Aminoacid dehydrogenase-like, C-terminal domain
domain: Putative shikimate dehydrogenase YdiB
species: Escherichia coli [TaxId: 562]

Probab=82.56  E-value=1.7  Score=33.82  Aligned_cols=86  Identities=14%  Similarity=0.127  Sum_probs=47.3

Q ss_pred             cCCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcc-cHHHHHHHHHHHHHhccCCCceEEEEECCCch
Q psy17644        202 LSGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAP-TRELSQQIYNEAKRFGKGYNLSVVCCYGGGSK  280 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~P-tr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~  280 (330)
                      ++++.+++.+.-|+||..+|.+.-             .+++.|+|+. +.+-+......+.++....+..+.. ..-...
T Consensus        16 l~~k~vlIlGaGGaarai~~al~~-------------~g~~~i~i~nR~~~~~~~~~~l~~~~~~~~~~~~~~-~~~~~~   81 (182)
T d1vi2a1          16 IKGKTMVLLGAGGASTAIGAQGAI-------------EGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTV-TDLADQ   81 (182)
T ss_dssp             CTTCEEEEECCSHHHHHHHHHHHH-------------TTCSEEEEEECSSTTHHHHHHHHHHHHHHSSCEEEE-EETTCH
T ss_pred             cCCCEEEEECCcHHHHHHHHHHhh-------------cCCceEeeeccchHHHHHHHHHHHHHHhhcCcceEe-eecccc
Confidence            477899999888888876554322             2455555554 3444555555555655544443332 222222


Q ss_pred             HHHHHHHhCCCeEEE-EChHHHH
Q psy17644        281 WDQSKALELGAEIVV-GTPGRII  302 (330)
Q Consensus       281 ~~~~~~l~~~~dIiV-~TP~~L~  302 (330)
                      .. .......++||| |||-.+.
T Consensus        82 ~~-~~~~~~~~diiIN~Tp~G~~  103 (182)
T d1vi2a1          82 QA-FAEALASADILTNGTKVGMK  103 (182)
T ss_dssp             HH-HHHHHHTCSEEEECSSTTST
T ss_pred             cc-hhhhhcccceeccccCCccc
Confidence            22 222233478888 7885544

>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=81.67  E-value=3.1  Score=32.82  Aligned_cols=51  Identities=12%  Similarity=0.007  Sum_probs=30.0

Q ss_pred             HHHhhhhhc---CCCcEEEEcCCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q psy17644        194 QAQAVPAAL---SGRDIIGVAKTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPT  249 (330)
Q Consensus       194 Q~~~i~~~~---~g~d~i~~a~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Pt  249 (330)
                      |.+.+..+.   .+..+++.|+.|+|||..... +.+.+....    ...|-++++.|.
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~-l~~~i~~~~----~~h~D~~~i~~~   55 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLE-LPEYVEKFP----PKASDVLEIDPE   55 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHH-HHHHHHTSC----CCTTTEEEECCS
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHH-HHHHHhccc----cCCCCEEEEeCC
Confidence            334444443   345799999999999844332 223333221    235678888885

>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=81.31  E-value=0.45  Score=38.25  Aligned_cols=17  Identities=18%  Similarity=0.135  Sum_probs=14.7

Q ss_pred             CCCcEEEEcCCCChhHH
Q psy17644        203 SGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       203 ~g~d~i~~a~TGsGKT~  219 (330)
                      .|+-+++.|++|+|||.
T Consensus        33 ~G~~~li~G~pGsGKT~   49 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQ   49 (251)
T ss_dssp             SSSEEEEEESTTSSHHH
T ss_pred             CCeEEEEEcCCCCCHHH
Confidence            56788889999999994

>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=80.83  E-value=0.31  Score=37.20  Aligned_cols=18  Identities=33%  Similarity=0.518  Sum_probs=15.0

Q ss_pred             cCCCcEEEEcCCCChhHH
Q psy17644        202 LSGRDIIGVAKTGSGKTG  219 (330)
Q Consensus       202 ~~g~d~i~~a~TGsGKT~  219 (330)
                      +.|+=+++.|++|||||.
T Consensus         2 ~~g~iI~l~G~~GsGKST   19 (176)
T d1zp6a1           2 LGGNILLLSGHPGSGKST   19 (176)
T ss_dssp             CTTEEEEEEECTTSCHHH
T ss_pred             CCCeEEEEECCCCCCHHH
Confidence            456778888999999995

>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=80.67  E-value=3.8  Score=33.10  Aligned_cols=93  Identities=17%  Similarity=0.109  Sum_probs=55.5

Q ss_pred             CCCChhHHHHHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHhccCCCceEEEEECCCchHHHHHH---Hh
Q psy17644        212 KTGSGKTGAFIWPMLVHIMDQKELEPGDGPMGLILAPTRELSQQIYNEAKRFGKGYNLSVVCCYGGGSKWDQSKA---LE  288 (330)
Q Consensus       212 ~TGsGKT~a~llp~l~~i~~~~~~~~~~~~~vLil~Ptr~La~Qi~~~~~~l~~~~~~~~~~~~gg~~~~~~~~~---l~  288 (330)
                      ...|||.. .++-++..+..       +|.++||.+..+....-+...+.+.+   +..+..+.|+.+.......   +.
T Consensus        65 ~~~S~K~~-~l~~~l~~~~~-------~g~kviIFs~~~~~~~~l~~~l~~~~---~~~~~~i~G~~~~~~R~~~i~~F~  133 (244)
T d1z5za1          65 VRRSGKMI-RTMEIIEEALD-------EGDKIAIFTQFVDMGKIIRNIIEKEL---NTEVPFLYGELSKKERDDIISKFQ  133 (244)
T ss_dssp             STTCHHHH-HHHHHHHHHHH-------TTCCEEEEESCHHHHHHHHHHHHHHH---CSCCCEECTTSCHHHHHHHHHHHH
T ss_pred             hhhhhHHH-HHHHHHHhhcc-------cccceEEEeeceehHHHHHHHHHhhc---cceEEEEecccchhccchhhhhhh
Confidence            35688873 45556655544       46789999999887766655554432   4566677888876543322   22


Q ss_pred             C--CCeEEEEChHHHHHHHHcCCCCCCCccEEEe
Q psy17644        289 L--GAEIVVGTPGRIIDMVKMGATKLNRVTFLVL  320 (330)
Q Consensus       289 ~--~~dIiV~TP~~L~~~l~~~~~~l~~i~~lVv  320 (330)
                      .  ++.++|+|+...     ...+++.....+|+
T Consensus       134 ~~~~~~vll~~~~~~-----g~Glnl~~a~~vi~  162 (244)
T d1z5za1         134 NNPSVKFIVLSVKAG-----GFGINLTSANRVIH  162 (244)
T ss_dssp             HCTTCCEEEEECCTT-----CCCCCCTTCSEEEE
T ss_pred             ccccchhcccccccc-----ccccccchhhhhhh
Confidence            2  457888886321     12344555555553

>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=80.64  E-value=1.4  Score=35.69  Aligned_cols=16  Identities=25%  Similarity=0.331  Sum_probs=14.0

Q ss_pred             CcEEEEcCCCChhHHH
Q psy17644        205 RDIIGVAKTGSGKTGA  220 (330)
Q Consensus       205 ~d~i~~a~TGsGKT~a  220 (330)
                      ..+++.||+|+|||.+
T Consensus        44 ~~lll~GppGtGKT~l   59 (276)
T d1fnna2          44 PRATLLGRPGTGKTVT   59 (276)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             CceEEECCCCCCHHHH
Confidence            6799999999999944

>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=80.55  E-value=0.86  Score=40.04  Aligned_cols=18  Identities=39%  Similarity=0.418  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCChhHHHH
Q psy17644        204 GRDIIGVAKTGSGKTGAF  221 (330)
Q Consensus       204 g~d~i~~a~TGsGKT~a~  221 (330)
                      -.+++++||||.|||...
T Consensus        68 ~~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CcceeeeCCCCccHHHHH
Confidence            367999999999999443

>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=80.29  E-value=1.2  Score=35.69  Aligned_cols=40  Identities=23%  Similarity=0.278  Sum_probs=25.6

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCHHHHHhhhhhcCCCcEEEEcCCCChhHHH
Q psy17644        168 SFGHFGFDEVLMKALRKCEYTSPTPIQAQAVPAALSGRDIIGVAKTGSGKTGA  220 (330)
Q Consensus       168 ~f~~~~l~~~l~~~l~~~~~~~pt~iQ~~~i~~~~~g~d~i~~a~TGsGKT~a  220 (330)
                      +|.++-..+.+.+.|...       ++..      +-.++++.||+|+|||.+
T Consensus        22 ~~~diig~~~~~~~l~~~-------i~~~------~~~~lll~Gp~G~GKTtl   61 (231)
T d1iqpa2          22 RLDDIVGQEHIVKRLKHY-------VKTG------SMPHLLFAGPPGVGKTTA   61 (231)
T ss_dssp             STTTCCSCHHHHHHHHHH-------HHHT------CCCEEEEESCTTSSHHHH
T ss_pred             CHHHccCcHHHHHHHHHH-------HHcC------CCCeEEEECCCCCcHHHH
Confidence            577776666666665442       1111      123589999999999944

>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=80.13  E-value=0.39  Score=35.80  Aligned_cols=13  Identities=38%  Similarity=0.657  Sum_probs=11.1

Q ss_pred             EEEEcCCCChhHH
Q psy17644        207 IIGVAKTGSGKTG  219 (330)
Q Consensus       207 ~i~~a~TGsGKT~  219 (330)
                      ++++|++|||||.
T Consensus         5 Iii~G~pGsGKTT   17 (152)
T d1ly1a_           5 ILTIGCPGSGKST   17 (152)
T ss_dssp             EEEECCTTSSHHH
T ss_pred             EEEECCCCCCHHH
Confidence            5678999999985