Citrus Sinensis ID: 009230

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------54
Protein Sequence
MCFRAKCGWKGSTSALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDIV
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccHHHHHHccEEEcccccEEEEEcEEEcccEEEEEEEEccccccEEcccccccccccccccccccEEEEccHHHHHHHHHHccccEEEEcccccccccccccccHHHHHHHHHHHHHHHHHccccEEEEEEcccHHHHHHHHHHHHHHHHccEEEEEccccccccccccHHHHHHHcccHHHHHHHHHccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccEEEEEccccccHHHHHHHHHHHHHHHcccEEEEEEccccHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHccccEEEEEccccccccccccccHHHHHHHHHHHHHHHHHHcccEEEEEEcccccccccccccccccccccHHHHHcccEEEEEEEcccccccccccEEEEEEEEEcccccEEEEEEEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccHHHcccccccccccccccccccccccccccHHHHHHHHHccccHHHHHHcccEEEcccccEEEEEEEccccEEEEEEEEccccEEEEcccccccccccHHcccccEEEEEccHHHHHHHHHHccccEEEccccccccccccccccccccHHHccHHHHHHHHHcccEEEEEEccccHHHHHHHHHHHHcccccEEEEEccccccccccccHHHHHHHccHHHHHHHHHHcccccccccEcHHHHHHHHHHHHccccccccccccccccHHHHccccccEEEEEEccccccHHHHHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHcccEEEEEcccccccHHHHHHHHHHHHHHccccEEEEccHHHHHccccccccHHHHHHHHHHHHHHHHHHcccEEEEEEccccccccccccccEccEcccHHHHHHcccEEEEEEccccccccccccEEEEEEEEEccccccEEEEEEEcccccEEEEcc
Coil and Loop (DISEMBL)
mcfrakcgwkgstsalvdnnrsqsslKKFSKMKTIREITEDSLELEPLGNELRAYFAERLISAETLRRNRVMqkrhghevviafpywrngklvnckyrDFNKKFWQEKDTEKVFyglddiegesDIIIVEgemdklsmeeagflncvsvpdgapssvskknvpseeqdtkYQYLWNCKMYLKQASRIIlatdgdppgQALAEELARRVGrercwrvrwpkkndvdhfkdANEVLMYLGPGALKEVVEnaelypimglfnfrDYFDEIDAyyhrtsgdefgiSTGWRALNELYnvlpgeltivtgvpnsgkseWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKkpffeanyggsaermTVEEFEQGKAWLSNTFSlircendslpsiKWVLDLAKAAVLRHgvrglvidpyneldhqrpvsqTETEYVSQMLTMVKRFAQHHACHvwfvahprqlhnwvgeppnlydisgsahfinkcdngivihrnrdpeagpidrVQVCVRKVRNKVVGTIGEAFLSYnrvtgeymdiv
Flexible Loop (DISEMBL)
mcfrakcgwkgstsalvdnnrsqsslkkfskmkTIREitedsleleplgNELRAYFAERLISAETLRrnrvmqkrhghevviafpywrngklVNCKYRDFNKKFWQEKDTEKVfyglddiegESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPssvskknvpseeqdtKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELArrvgrercwrvrwpkkndvdhfkdANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIdpyneldhqrpvSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNrdpeagpidrvqvcVRKVRnkvvgtigeaflsynrvtgeymdiv
Low Complexity Region (SEG)
MCFRAKCGWKGSTSALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELArrvgrercwrvrwPKKNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDIV
Disordered region (IsUnstruct)
*********************************************EPLGNELRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVS*********************KYQYLWNCKMYLKQASRIILATDGD***QALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYM***
Disordered Region (DISOPRED)
MCFRAKCGWKGSTSALV***************************LEPLGNELRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYN*****************QMLTMVKRFAQHHACHVWFV*******************SGSAHFINKCDNGIVIHRNRDP*AGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDIV
Disordered Region (DISEMBL)
**********GSTSALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPD****************DTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDIV
Disordered Region (DISPRO)
*C**AKCGWKGST**********************REITEDSLELEPLGNELRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MCFRAKCGWKGSTSALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDIV
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	539	2.2.26 [Sep-21-2011]
P03692	566	DNA primase/helicase OS=E	no	no	0.812	0.773	0.244	8e-12
P20315	566	DNA primase/helicase OS=E	no	no	0.764	0.727	0.238	1e-09
Q8CIW5	685	Twinkle protein, mitochon	yes	no	0.794	0.624	0.221	1e-08
Q5ZIW1	669	Twinkle protein, mitochon	yes	no	0.797	0.642	0.208	1e-07
Q96RR1	684	Twinkle protein, mitochon	yes	no	0.847	0.668	0.209	1e-07

>sp|P03692|PRIM_BPT7 DNA primase/helicase OS=Enterobacteria phage T7 GN=4 PE=1 SV=1

 Score = 72.4 bits (176), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 122/500 (24%), Positives = 203/500 (40%), Gaps = 62/500 (12%)

Query: 56  FAERLISAETLRRNRV-MQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEK-V 113
              R IS ET ++    + K  G    +A    +NG +V+ K RD +K F      +   
Sbjct: 81  LTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDA 140

Query: 114 FYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQY 173
            +G     G   I++ EGE+D L++ E        V  G  +S +KK   +  +      
Sbjct: 141 LFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASAAKKTCAANYE------ 194

Query: 174 LWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEV 233
                 Y  Q  +IIL  D D  G+   EE A+ +   +      P        KDANE 
Sbjct: 195 ------YFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLP-------CKDANEC 241

Query: 234 LMYLGPGALKEVVENAELY---PIMGLFNFRDYFDEIDAYYHRTSGDEFGIS-TGWRALN 289
            +      + E V NA  +    ++   + R+   E     H +S +  G+  +G   +N
Sbjct: 242 HLNGHDREIMEQVWNAGPWIPDGVVSALSLRERIRE-----HLSSEESVGLLFSGCTGIN 296

Query: 290 E-LYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEK 348
           +       GE+ +VT     GKS ++           G K  L  +E  V E A  L+  
Sbjct: 297 DKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGL 356

Query: 349 HIKKPFFEANYGGSAERMTVE--EFEQ--GKAWLSNTFSLIRCENDSLPSIKWVLDLAKA 404
           H +    +++   S +R  +E  +F+Q   + + ++TF L     DS    +    LAK 
Sbjct: 357 HNRVRLRQSD---SLKREIIENGKFDQWFDELFGNDTFHLY----DSFAEAETDRLLAKL 409

Query: 405 AVLRHGVRGLVIDPYNELDHQRPV-----SQTETEYVSQMLTMVKRFAQHHACHVWFVAH 459
           A +R G+   VI     LDH   V        E + +  ++T +K FA+     +  + H
Sbjct: 410 AYMRSGLGCDVI----ILDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICH 465

Query: 460 PR-----QLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVR 514
            +     + H   G P ++ D+ GS       D  I + RN+  +   +    V VR ++
Sbjct: 466 LKNPDKGKAHE-EGRPVSITDLRGSGALRQLSDTIIALERNQQGDMPNL----VLVRILK 520

Query: 515 NKVVGTIGEA-FLSYNRVTG 533
            +  G  G A ++ YN+ TG
Sbjct: 521 CRFTGDTGIAGYMEYNKETG 540

DNA primase synthesizes RNA primers necessary for replication by DNA polymerase. It also functions as an ATP-dependent unwinding protein. Has a 5'->3' helicase activity; 4a also has a DNA primase activity.
Escherichia coli (taxid: 562)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

>sp|P20315|PRIM_BPT3 DNA primase/helicase OS=Enterobacteria phage T3 GN=4 PE=3 SV=1

 Score = 65.1 bits (157), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 110/461 (23%), Positives = 184/461 (39%), Gaps = 49/461 (10%)

Query: 88  RNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDI-EGESDIIIVEGEMDKLSMEEAGFLNC 146
           +NG +V+ K RD +K F      +     L  +  G   I++ EGE+D L++ E      
Sbjct: 113 QNGSIVSQKVRDKDKNFKTTGSHKSDALFLKHLWSGGKKIVVTEGEIDALTVMELQDCKY 172

Query: 147 VSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELAR 206
             V  G  +S +KK   +  +            Y  Q  +IIL  D D  G+   EE A+
Sbjct: 173 PVVSLGHGASAAKKTCAANYE------------YFDQFEQIILMFDMDDAGRKAVEEAAQ 220

Query: 207 RVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDE 266
            +   +      P        KDANE  +     A+ E V NA  +   G+ +     D 
Sbjct: 221 VLPAGKVRVAVLP-------CKDANECHIMGEDKAILEQVWNANPWVPDGVVSALSLKDR 273

Query: 267 IDAYYHRTSGDEFGIS-TGWRALNE-LYNVLPGELTIVTGVPNSGKSEWIDALICNINEH 324
           +      TS D  G+   G + LN+       GE+ +VT     GKS ++        + 
Sbjct: 274 VKEAM--TSEDAVGLLFDGCQGLNDRTLGARGGEVVMVTSGSGMGKSTFVRQQALAWGKR 331

Query: 325 AGWKFVLCSMENKVREHARKLLEKHIKKPFFEAN--YGGSAERMTVEEFEQGKAWLSNTF 382
            G +  L  +E  V +  + ++  + K    +++      AE    +E+   + +  +TF
Sbjct: 332 MGKRVGLAMLEESVEDTIQDMMGLNNKVRLRQSDEVKKAIAEDGRFDEWYD-ELFGDDTF 390

Query: 383 SLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPV-----SQTETEYVS 437
            L     DS    +    LAK A +R G+   VI     LDH   V        E + + 
Sbjct: 391 HLY----DSFAEAEADRLLAKLAYMRTGLGCDVI----VLDHISIVVSASEESDERKMID 442

Query: 438 QMLTMVKRFAQHHACHVWFVAHPRQLHNWV----GEPPNLYDISGSAHFINKCDNGIVIH 493
           +++T +K FA+     +  + H +          G   ++ D+ GS       D  I + 
Sbjct: 443 RLMTKLKGFAKSTGVVLVVICHLKNPEKGKAHEEGRAVSITDLRGSGALRQLSDTIIALE 502

Query: 494 RNRDPEAGPIDRVQVCVRKVRNKVVGTIGEA-FLSYNRVTG 533
           RN+  +   +    V VR ++ +  G  G A ++ YNR TG
Sbjct: 503 RNQQGDMPNL----VLVRLLKCRFTGDTGIAGYMEYNRETG 539

DNA primase synthesizes RNA primers necessary for replication by DNA polymerase. It also functions as an ATP-dependent unwinding protein. Has a 5'->3' helicase activity; 4a also has a DNA primase activity.

Escherichia coli (taxid: 562)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q8CIW5|PEO1_MOUSE Twinkle protein, mitochondrial OS=Mus musculus GN=Peo1 PE=2 SV=1

 Score = 62.0 bits (149), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 110/497 (22%), Positives = 196/497 (39%), Gaps = 69/497 (13%)

Query: 53  RAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYWRNG-------KLVNCKYRDFNKKFW 105
           R  F    ++ +TLRR  V   R    +V  FP++  G       KL+  + ++   ++ 
Sbjct: 178 RVMFGLTKVTDDTLRRFSVRYLRSARSLV--FPWFTPGSSGLRGLKLLGAEGQENGVQYV 235

Query: 106 QEKDTEKVFY----GLDDIEG-ESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKK 160
           +        Y    GL  I   ++++++   E+D L++ ++  L  +S+P G    +   
Sbjct: 236 ETTIPRPGVYHNLFGLPLISRRDTEVVVTSRELDSLALSQSTGLPTLSLPRGT-VCLPPA 294

Query: 161 NVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPK 220
            +P                YL+Q  RI+     D      A+  AR++  +RC  VR P 
Sbjct: 295 LLP----------------YLEQFRRIVFWLGDDLRSWEAAKLFARKLNPKRCSLVR-PG 337

Query: 221 KNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFG 280
                  +  N+ L      +L  ++  A       + +FR   +E+       S  E  
Sbjct: 338 NQQPRPLEALNQGL------SLPRILRTALPAWHKSIVSFRQLREEV---LGELSNVEQA 388

Query: 281 ISTGWRALNELYNVLPG----ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN 336
               W    +L  +L G    ELT+ TG   SGK+ +I     ++    G   +  S E 
Sbjct: 389 AGVRWSRFPDLNRLLKGHRKGELTVFTGPTGSGKTTFISEYALDLCTQ-GVNTLWGSFEI 447

Query: 337 KVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSN--TFSLIRCENDSLPS 394
                AR +L +             +  R+  E+ ++ + W        L         S
Sbjct: 448 SNVRLARVMLTQF------------AVTRLE-EQLDKYEEWADRFEDLPLYFMTFHGQQS 494

Query: 395 IKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHV 454
           I+ V+D  + AV  + V  +VID    +     +S         ++   ++FA  ++CHV
Sbjct: 495 IRSVIDTMQHAVYVYDVCHVVIDNLQFMMGHEQLSSDRIAAQDYIVGAFRKFATDNSCHV 554

Query: 455 WFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDR-VQVCVRKV 513
             V HPR+  +   +      I GSA    + DN ++I ++R    GP  R +QV     
Sbjct: 555 TLVIHPRKEDD--DKELQTASIFGSAKASQEADN-VLILQDRKLVTGPGKRYLQVS---- 607

Query: 514 RNKVVGTIGEAFLSYNR 530
           +N+  G +G   L +N+
Sbjct: 608 KNRFDGDVGVFPLEFNK 624

Involved in mitochondrial DNA (mtDNA) metabolism. Could function as an adenine nucleotide-dependent DNA helicase. Function infered to be critical for lifetime maintenance of mtDNA integrity. May be a key regulator of mtDNA copy number in mammals.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q5ZIW1|PEO1_CHICK Twinkle protein, mitochondrial OS=Gallus gallus GN=PEO1 PE=2 SV=1

 Score = 58.9 bits (141), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 104/499 (20%), Positives = 198/499 (39%), Gaps = 69/499 (13%)

Query: 53  RAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYW-------RNGKLVNCKYRDFNKKFW 105
           +A F    ++  TL+R  V   R    +V  FP++       R  KL+  + R     + 
Sbjct: 183 KAAFGIAPLADGTLKRFGVRYLRAAKALV--FPWFAPRDAALRGLKLLVAEQRGDAVSYT 240

Query: 106 QEK----DTEKVFYGLDDI-EGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKK 160
           +E     D  +  +GL  I   ++++++   E+D L++ +A  + C+++P GA + +   
Sbjct: 241 EETLPRFDAYRNLFGLPLIGRRDAEVVLTGSELDALALHQATGVPCLALPRGA-TILPPA 299

Query: 161 NVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPK 220
            +P                YL+Q  R+ L    D      ++  AR++  +RC  V+ P 
Sbjct: 300 LLP----------------YLEQFRRVTLWLGDDLRSWEASKLFARKLNPKRCSLVQ-PG 342

Query: 221 KNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFG 280
                  +  N  L       L +++  A       + +FR   +E+   +   +  E  
Sbjct: 343 DLQPRPLEALNRGL------NLTKILRAALPAGHKAIVSFRQLREEV---FGELANSEQV 393

Query: 281 ISTGWRALNELYNVLPG----ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN 336
               W    EL  +L G    ELT+ TG   SGK+ +I     ++         +C++  
Sbjct: 394 AGVKWARFPELNKLLKGHRRGELTVFTGPTGSGKTTFISEYALDLCTQG-----VCTLWG 448

Query: 337 KVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSN--TFSLIRCENDSLPS 394
               +  +L +  + +          A R   ++ E    W        L         +
Sbjct: 449 SFEINNIRLAKIMLTQ---------FATRRLEDQLELYDEWADRFEDLPLYFMTFHGQQN 499

Query: 395 IKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHV 454
           IK VLD  + AV  + +  +V+D    +     +S         ++   ++FA  + CH+
Sbjct: 500 IKTVLDTMQHAVYMYDITHVVVDNLQFMMGHEQLSADRLAAQDFIVGAFRKFATDNTCHI 559

Query: 455 WFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDR-VQVCVRKV 513
             V HPR+  +   +      I GSA    + DN ++I ++R    GP  R +QV     
Sbjct: 560 TLVIHPRKEDD--EKELQTASIFGSAKASQEADN-VLILQDRKLTTGPGKRYLQVS---- 612

Query: 514 RNKVVGTIGEAFLSYNRVT 532
           +N+  G +G   L +++ +
Sbjct: 613 KNRFDGDVGVFPLEFSKAS 631

Involved in mitochondrial DNA (mtDNA) metabolism. Could function as an adenine nucleotide-dependent DNA helicase. Function inferred to be critical for lifetime maintenance of mtDNA integrity.

Gallus gallus (taxid: 9031)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q96RR1|PEO1_HUMAN Twinkle protein, mitochondrial OS=Homo sapiens GN=PEO1 PE=1 SV=1

 Score = 58.5 bits (140), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 111/531 (20%), Positives = 206/531 (38%), Gaps = 74/531 (13%)

Query: 24  SSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERL-----ISAETLRRNRVMQKRHGH 78
           S   +F   + +R I   ++ L  L ++     A+ +     ++ +TL+R  V   R   
Sbjct: 143 SKAPEFEDSEEVRRIWNRAIPLWELPDQEEVQLADTMFGLTKVTDDTLKRFSVRYLRPAR 202

Query: 79  EVVIAFPYWRNG-------KLVNCKYR----DFNKKFWQEKDTEKVFYGLDDIEG-ESDI 126
            +V  FP++  G       KL+  K +     + +            +GL  I   ++++
Sbjct: 203 SLV--FPWFSPGGSGLRGLKLLEAKCQGDGVSYEETTIPRPSAYHNLFGLPLISRRDAEV 260

Query: 127 IIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASR 186
           ++   E+D L++ ++  L  +++P G  + +    +P                YL+Q  R
Sbjct: 261 VLTSRELDSLALNQSTGLPTLTLPRGT-TCLPPALLP----------------YLEQFRR 303

Query: 187 IILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVV 246
           I+     D      A+  AR++  +RC+ VR P        +  N      G   L  ++
Sbjct: 304 IVFWLGDDLRSWEAAKLFARKLNPKRCFLVR-PGDQQPRPLEALN------GGFNLSRIL 356

Query: 247 ENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPG----ELTIV 302
             A       + +FR   +E+       S  E      W    +L  +L G    ELT+ 
Sbjct: 357 RTALPAWHKSIVSFRQLREEV---LGELSNVEQAAGLRWSRFPDLNRILKGHRKGELTVF 413

Query: 303 TGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGS 362
           TG   SGK+ +I     ++    G   +  S E      AR +L +              
Sbjct: 414 TGPTGSGKTTFISEYALDLCSQ-GVNTLWGSFEISNVRLARVMLTQF------------- 459

Query: 363 AERMTVEEFEQGKAWLSN--TFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYN 420
           AE    ++ ++   W        L         SI+ V+D  + AV  + +  ++ID   
Sbjct: 460 AEGRLEDQLDKYDHWADRFEDLPLYFMTFHGQQSIRTVIDTMQHAVYVYDICHVIIDNLQ 519

Query: 421 ELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSA 480
            +     +S         ++ + ++FA  + CHV  V HPR+  +   +      I GSA
Sbjct: 520 FMMGHEQLSTDRIAAQDYIIGVFRKFATDNNCHVTLVIHPRKEDD--DKELQTASIFGSA 577

Query: 481 HFINKCDNGIVIHRNRDPEAGPIDR-VQVCVRKVRNKVVGTIGEAFLSYNR 530
               + DN ++I ++R    GP  R +QV     +N+  G +G   L +N+
Sbjct: 578 KASQEADN-VLILQDRKLVTGPGKRYLQVS----KNRFDGDVGVFPLEFNK 623

Involved in mitochondrial DNA (mtDNA) metabolism. Could function as an adenine nucleotide-dependent DNA helicase. Function inferred to be critical for lifetime maintenance of mtDNA integrity. In vitro, forms in combination with POLG, a processive replication machinery, which can use double-stranded DNA (dsDNA) as template to synthesize single-stranded DNA (ssDNA) molecules. May be a key regulator of mtDNA copy number in mammals.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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	539
225444145	705	PREDICTED: uncharacterized protein LOC10	0.998	0.763	0.773	0.0
356555942	678	PREDICTED: uncharacterized protein LOC10	0.985	0.783	0.790	0.0
224056777	658	predicted protein [Populus trichocarpa]	0.996	0.816	0.735	0.0
356532467	679	PREDICTED: uncharacterized protein LOC10	0.985	0.782	0.783	0.0
255564299	700	nucleic acid binding protein, putative [	0.979	0.754	0.746	0.0
449488512	679	PREDICTED: twinkle protein, mitochondria	0.970	0.770	0.762	0.0
413943393	736	hypothetical protein ZEAMMB73_832314 [Ze	0.992	0.726	0.709	0.0
302141745	696	unnamed protein product [Vitis vinifera]	0.979	0.758	0.717	0.0
242093886	770	hypothetical protein SORBIDRAFT_10g02699	0.992	0.694	0.694	0.0
27311757	709	Unknown protein [Arabidopsis thaliana]	0.981	0.746	0.677	0.0

>gi|225444145|ref|XP_002268852.1| PREDICTED: uncharacterized protein LOC100257655 [Vitis vinifera] gi|297740887|emb|CBI31069.3| unnamed protein product [Vitis vinifera]

 Score =  887 bits (2292), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/538 (77%), Positives = 464/538 (86%)

Query: 1   MCFRAKCGWKGSTSALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERL 60
           MC R KCG +G+  A V+++ S   L + +K+K  REITE+SL L+PL +EL AYF ER+
Sbjct: 162 MCHRGKCGSRGNIRAFVNDSSSYGRLNQITKIKPKREITEESLGLKPLCSELVAYFGERM 221

Query: 61  ISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDI 120
           IS +TL RN VMQK +G + +IAF Y RNG LV+CKYRD NK FWQEKDTEK+FYG+DDI
Sbjct: 222 ISEKTLARNSVMQKSYGDQFIIAFTYRRNGVLVSCKYRDVNKNFWQEKDTEKIFYGVDDI 281

Query: 121 EGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMY 180
           +  SDIIIVEGE+DKLSMEEAGF NCVSVPDGAP SVS K   S E+D KYQYLWNCK Y
Sbjct: 282 KEASDIIIVEGEIDKLSMEEAGFYNCVSVPDGAPPSVSTKVFESAEKDIKYQYLWNCKEY 341

Query: 181 LKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPG 240
           L++ASRIILATDGD PG ALAEELARR+GRERCWRV+WPKKN+V+HFKDANEVLMYLGP 
Sbjct: 342 LEKASRIILATDGDAPGLALAEELARRLGRERCWRVKWPKKNEVEHFKDANEVLMYLGPD 401

Query: 241 ALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELT 300
            LKEV+ENAE+YPI GLFNF  YF+EID YYH T G E G+STGWR LN LYNV+PGELT
Sbjct: 402 VLKEVIENAEIYPIQGLFNFSHYFNEIDGYYHHTLGFELGVSTGWRGLNGLYNVVPGELT 461

Query: 301 IVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYG 360
           +VTGVPNSGKSEWIDAL+CNIN   GW F LCSMENKVREHARKLLEKHIKKPFF+A YG
Sbjct: 462 VVTGVPNSGKSEWIDALLCNINRSVGWSFALCSMENKVREHARKLLEKHIKKPFFKAGYG 521

Query: 361 GSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYN 420
            S ERMTVEEFE GK WLS TF LIRCE DSLP+IKWVLDLAK+AVLRHGVRGLVIDPYN
Sbjct: 522 ESIERMTVEEFELGKKWLSETFYLIRCEKDSLPNIKWVLDLAKSAVLRHGVRGLVIDPYN 581

Query: 421 ELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSA 480
           ELDHQRP  QTETEYVSQMLTM+KRFAQHH+CHVWFVAHPRQLH W G PPN+YDISGSA
Sbjct: 582 ELDHQRPPGQTETEYVSQMLTMIKRFAQHHSCHVWFVAHPRQLHQWNGGPPNMYDISGSA 641

Query: 481 HFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI 538
           HFINKCDNGIVIHRNR+PEAGP+D+VQVCVRKVRNKVVGTIG+AFLSY+R++G Y DI
Sbjct: 642 HFINKCDNGIVIHRNRNPEAGPVDQVQVCVRKVRNKVVGTIGDAFLSYDRISGVYTDI 699

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356555942|ref|XP_003546288.1| PREDICTED: uncharacterized protein LOC100779625 [Glycine max]

 Score =  876 bits (2264), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 422/534 (79%), Positives = 469/534 (87%), Gaps = 3/534 (0%)

Query: 2   CFRAKCGWKGSTSALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERLI 61
           CFR KCGWKGST A      S S+  +   +K IR+ITE+ LELEPL +EL  YF+ERLI
Sbjct: 135 CFRGKCGWKGSTQAFAG---SSSARTQVDPVKKIRKITEEELELEPLCDELVVYFSERLI 191

Query: 62  SAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIE 121
           S +TL RN V Q+++  ++VIAFPY RNG L++CKYRD NK FWQE +TEK+FYGLDDI 
Sbjct: 192 SKQTLERNGVKQRKYDDQIVIAFPYRRNGGLISCKYRDINKMFWQEANTEKIFYGLDDIV 251

Query: 122 GESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYL 181
           G SDIIIVEGEMDKL+MEEAGFLNCVSVPDGAP S+S K +P +++D KYQYLWNCK  L
Sbjct: 252 GHSDIIIVEGEMDKLAMEEAGFLNCVSVPDGAPPSISSKELPPQDKDKKYQYLWNCKDEL 311

Query: 182 KQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGA 241
           K+A+R+ILATDGDPPGQALAEELARR+G+E+CWRVRWP+K+  D+ KDANEVLMYLGP A
Sbjct: 312 KKATRVILATDGDPPGQALAEELARRIGKEKCWRVRWPRKSRSDNCKDANEVLMYLGPDA 371

Query: 242 LKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELTI 301
           LKEV+ENAELYPI GLFNFRDYFDEIDAYYHRT G + GISTGW  LN+LYNV+PGELTI
Sbjct: 372 LKEVIENAELYPIRGLFNFRDYFDEIDAYYHRTLGYDIGISTGWNNLNDLYNVVPGELTI 431

Query: 302 VTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGG 361
           VTGVPNSGKSEWIDAL+CN+NE  GWKF LCSMENKVREHARKLLEKH+KKPFF   YG 
Sbjct: 432 VTGVPNSGKSEWIDALLCNLNEIVGWKFALCSMENKVREHARKLLEKHLKKPFFNERYGE 491

Query: 362 SAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNE 421
           S ERM+VEEFEQGK WLS+TFSLIRCE+DSLP+I WVLDLAKAAVLRHGVRGLVIDPYNE
Sbjct: 492 SVERMSVEEFEQGKLWLSDTFSLIRCEDDSLPNISWVLDLAKAAVLRHGVRGLVIDPYNE 551

Query: 422 LDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAH 481
           LDHQRP +QTETEYVSQMLT++KRFAQHH CHVWFVAHPRQLHNWVG PPNLYDISGSAH
Sbjct: 552 LDHQRPPNQTETEYVSQMLTLIKRFAQHHGCHVWFVAHPRQLHNWVGGPPNLYDISGSAH 611

Query: 482 FINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEY 535
           FINKCDNGIVIHRNRDPEAGPID+VQVCVRKVRNKV GTIGEA L YNRVTGEY
Sbjct: 612 FINKCDNGIVIHRNRDPEAGPIDQVQVCVRKVRNKVAGTIGEAILLYNRVTGEY 665

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224056777|ref|XP_002299018.1| predicted protein [Populus trichocarpa] gi|222846276|gb|EEE83823.1| predicted protein [Populus trichocarpa]

 Score =  872 bits (2254), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/563 (73%), Positives = 469/563 (83%), Gaps = 26/563 (4%)

Query: 2   CFRAKCGWKGSTSALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRA------- 54
           CFRAKCGW G T     +  +  +  K SK+K IREITE SLELEPL +E+ A       
Sbjct: 80  CFRAKCGWNGGTKPFAGSKSTYGTSLKLSKVKEIREITEQSLELEPLCDEVVALSFYLCV 139

Query: 55  -----------------YFAERLISAETLRRNRVMQKRHGH--EVVIAFPYWRNGKLVNC 95
                            YF ERLISAETL RN+VMQK +G   +V IAF Y RNG LV+C
Sbjct: 140 LILILSCMMLIWVMLVCYFKERLISAETLARNQVMQKGYGDRGQVAIAFTYRRNGVLVSC 199

Query: 96  KYRDFNKKFWQEKDTEKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPS 155
           KYRD NK+FWQEKDT+KVFYGLDDI+G  +IIIVEGEMDKL+MEEAGF NCVSVPDGAP 
Sbjct: 200 KYRDINKRFWQEKDTKKVFYGLDDIKGADEIIIVEGEMDKLAMEEAGFRNCVSVPDGAPP 259

Query: 156 SVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWR 215
           SVS K +P  ++DTKYQYLWNCK YL + SRIILATDGDPPGQALAEELARR+GRERCWR
Sbjct: 260 SVSPKELPPNQEDTKYQYLWNCKEYLDKVSRIILATDGDPPGQALAEELARRLGRERCWR 319

Query: 216 VRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTS 275
           V+WPKKN  +HFKDANEVLM+ GP AL++++ENAELYPI GLF F DYF EIDAYY+RT 
Sbjct: 320 VKWPKKNTDEHFKDANEVLMFSGPLALRDIIENAELYPIRGLFQFSDYFPEIDAYYNRTL 379

Query: 276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME 335
           G EFG STGW ALNE+YNV+PGELT+VTGVPNSGKSEWIDAL+CN+NE  GWKF LCSME
Sbjct: 380 GYEFGASTGWTALNEIYNVMPGELTLVTGVPNSGKSEWIDALLCNLNESVGWKFALCSME 439

Query: 336 NKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSI 395
           N VR+HARKLLEKH+KKPFF+A YG SAERM+ +E E+GK WLS+TF LIRCE+D+LP+I
Sbjct: 440 NNVRQHARKLLEKHMKKPFFDARYGESAERMSAKELEEGKQWLSDTFYLIRCEDDALPNI 499

Query: 396 KWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVW 455
           KWVLDLA+AAVLRHGVRGLVIDPYNELDHQRP + TETEYVSQMLT++KRFAQHHACHVW
Sbjct: 500 KWVLDLARAAVLRHGVRGLVIDPYNELDHQRPPNMTETEYVSQMLTLIKRFAQHHACHVW 559

Query: 456 FVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRN 515
            VAHPRQL NW G+PPNLYDISGSAHF+NKCDNGIVIHRNR+P AGPID+VQV VRKVRN
Sbjct: 560 LVAHPRQLQNWTGQPPNLYDISGSAHFVNKCDNGIVIHRNRNPNAGPIDQVQVLVRKVRN 619

Query: 516 KVVGTIGEAFLSYNRVTGEYMDI 538
           KV GTIG+AFLSYNRVTGE+M++
Sbjct: 620 KVAGTIGDAFLSYNRVTGEFMNV 642

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356532467|ref|XP_003534794.1| PREDICTED: uncharacterized protein LOC100804637 [Glycine max]

 Score =  870 bits (2249), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/535 (78%), Positives = 474/535 (88%), Gaps = 4/535 (0%)

Query: 2   CFRAKCGWKGSTSALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERLI 61
           CFR KCGWKGST A   +N +++ L   + +K IR+ITE+ LELEPL +EL  YF+ERLI
Sbjct: 135 CFRGKCGWKGSTQAFAGSNSARTQL---APVKKIRKITEEELELEPLCDELVTYFSERLI 191

Query: 62  SAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIE 121
           S +TL RN V Q+++  ++VIAFPY +NG L++CKYRD NK FWQE +TEK+FYGLDDI 
Sbjct: 192 SKQTLERNGVKQRKYDDQIVIAFPYHQNGGLISCKYRDINKMFWQEANTEKIFYGLDDIV 251

Query: 122 GESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVS-KKNVPSEEQDTKYQYLWNCKMY 180
           G +DIIIVEGEMDKL+MEEAGF NCVSVPDGAP SVS K+ +P +++D KYQYLWNCK  
Sbjct: 252 GHNDIIIVEGEMDKLAMEEAGFFNCVSVPDGAPPSVSSKEELPPQDKDKKYQYLWNCKDE 311

Query: 181 LKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPG 240
           LK+A+R+ILATDGDPPGQALAEELARR+G+E+CWRVRWP+K+  D+ KDANEVLMYLGP 
Sbjct: 312 LKKATRVILATDGDPPGQALAEELARRIGKEKCWRVRWPRKSRSDNCKDANEVLMYLGPD 371

Query: 241 ALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELT 300
           ALKEV+ENAELYPI GLFNFRDYFDEIDAYYHRT G + GISTGW  LN+LYNV+PGELT
Sbjct: 372 ALKEVIENAELYPIRGLFNFRDYFDEIDAYYHRTLGYDIGISTGWNNLNDLYNVVPGELT 431

Query: 301 IVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYG 360
           IVTGVPNSGKSEWIDAL+CN+NE AGWKF LCSMENKVREHARKLLEKH+KKPFF   YG
Sbjct: 432 IVTGVPNSGKSEWIDALLCNLNEIAGWKFALCSMENKVREHARKLLEKHLKKPFFNERYG 491

Query: 361 GSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYN 420
            S ERM+VEEFEQGK WLS+TFSLIRCE++SLP+I WVLDLAKAAVLRHGVRGLVIDPYN
Sbjct: 492 ESVERMSVEEFEQGKLWLSDTFSLIRCEDNSLPNISWVLDLAKAAVLRHGVRGLVIDPYN 551

Query: 421 ELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSA 480
           ELDHQRP +QTETEYVSQMLT++KRFAQHH CHVWFVAHPRQLHNWVG+PPNLYDISGSA
Sbjct: 552 ELDHQRPPNQTETEYVSQMLTLIKRFAQHHGCHVWFVAHPRQLHNWVGDPPNLYDISGSA 611

Query: 481 HFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEY 535
           HFINKCDNGIVIHRNRDPE+GPID+VQVCVRKVRNKV GTIGEA L YNRVTGEY
Sbjct: 612 HFINKCDNGIVIHRNRDPESGPIDQVQVCVRKVRNKVAGTIGEAMLLYNRVTGEY 666

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564299|ref|XP_002523146.1| nucleic acid binding protein, putative [Ricinus communis] gi|223537553|gb|EEF39177.1| nucleic acid binding protein, putative [Ricinus communis]

 Score =  863 bits (2230), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 403/540 (74%), Positives = 461/540 (85%), Gaps = 12/540 (2%)

Query: 2   CFRAKCGWKGSTSALVDNNRS------QSSLKKFSKMKTIREITEDSLELEPLGNELRAY 55
           CFR KCGW G T  L+  + +      +SS++   K+K  R+IT + L L+PL  E+  +
Sbjct: 155 CFRGKCGWNGGTKLLLVQSYAGRHSTYESSVQP-KKVKLTRKITVEGLGLQPLCTEILGF 213

Query: 56  FAERLISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFY 115
           FAERLISAETL RNRVMQ+ +G+++VIAF YWRNG+L +CKYRD NK FWQE DT+K+FY
Sbjct: 214 FAERLISAETLHRNRVMQRSYGNQIVIAFTYWRNGELTSCKYRDINKNFWQESDTDKIFY 273

Query: 116 GLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLW 175
           GLDDI+   DIIIVEGEMDKL+MEEAGF NCVSVPDGAP  VS+K +PS+EQDTKYQYLW
Sbjct: 274 GLDDIKETDDIIIVEGEMDKLAMEEAGFRNCVSVPDGAPGQVSQKELPSKEQDTKYQYLW 333

Query: 176 NCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLM 235
           NCK YL +ASRIILATDGDPPGQALAEE+ARR+GRERCWR+RWPKK+   HFKDANEVLM
Sbjct: 334 NCKEYLDKASRIILATDGDPPGQALAEEIARRIGRERCWRIRWPKKSKDTHFKDANEVLM 393

Query: 236 YLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVL 295
           YLGP AL+EV++NAELYPI GLFNF +YFDEIDAYYHRT G E+G STGW +L+ LYNV+
Sbjct: 394 YLGPTALREVIDNAELYPISGLFNFMEYFDEIDAYYHRTLGLEYGASTGWSSLDGLYNVM 453

Query: 296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFF 355
           PGELTIVTGVPNSGKSEWIDAL+CN+N   GWKF LCSMEN+VREHARKLLEK IKKPFF
Sbjct: 454 PGELTIVTGVPNSGKSEWIDALLCNLNRSVGWKFALCSMENRVREHARKLLEKRIKKPFF 513

Query: 356 EANY-----GGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHG 410
           +A Y     G   +RM VEEFE+GK WL++TF LIRCE+D LPS+ WVL LA+AAVLRHG
Sbjct: 514 DARYASDIDGQFVKRMNVEEFEEGKQWLADTFYLIRCEDDKLPSVDWVLKLARAAVLRHG 573

Query: 411 VRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEP 470
           VRGLVIDPYNELDHQRP+S TETEYVS+MLT++KRFAQHH CHVWFVAHPRQL NW G P
Sbjct: 574 VRGLVIDPYNELDHQRPISMTETEYVSRMLTLIKRFAQHHLCHVWFVAHPRQLQNWTGSP 633

Query: 471 PNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNR 530
           PNLYDISGSAHFINKCDNGIV+HRNRDPEAG ID+VQ+CVRKVRNKVVGTIG+AFLSYNR
Sbjct: 634 PNLYDISGSAHFINKCDNGIVVHRNRDPEAGAIDQVQICVRKVRNKVVGTIGDAFLSYNR 693

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449488512|ref|XP_004158064.1| PREDICTED: twinkle protein, mitochondrial-like [Cucumis sativus]

 Score =  855 bits (2209), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 399/523 (76%), Positives = 450/523 (86%)

Query: 15  ALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERLISAETLRRNRVMQK 74
           A  D   S   L + +  + IR+IT +SL+LEPL ++L  YFAERLIS +TL RN VMQK
Sbjct: 145 AFADGRSSYKHLGQVALKQNIRKITVESLQLEPLCDQLVDYFAERLISKQTLLRNSVMQK 204

Query: 75  RHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIEGESDIIIVEGEMD 134
           R  +++ +AF Y+R G L++CKYRD NKKFWQE +TE++FYG+DDI+G SDIIIVEGEMD
Sbjct: 205 RSDNQIAVAFTYYRGGALISCKYRDANKKFWQEPNTERIFYGIDDIDGASDIIIVEGEMD 264

Query: 135 KLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGD 194
           KLSM EAG  NCVSVPDGAP+SVS+K+VP  ++D K+Q+LWNCK YL +ASRIILATDGD
Sbjct: 265 KLSMAEAGIHNCVSVPDGAPASVSEKDVPPADKDKKFQFLWNCKDYLNKASRIILATDGD 324

Query: 195 PPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAELYPI 254
            PGQALAEE+ARRVGRERCWRV+WPKKN+VDHFKDANEVLMYLGP ALKEVV+NAELYPI
Sbjct: 325 TPGQALAEEIARRVGRERCWRVKWPKKNEVDHFKDANEVLMYLGPEALKEVVDNAELYPI 384

Query: 255 MGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWI 314
            GLF F+DYF EIDAYYH+  G+EFG+ TGWR LN+LYNV+PGELTIVTGVPNSGKSEWI
Sbjct: 385 SGLFRFKDYFHEIDAYYHKKFGNEFGVPTGWRCLNDLYNVVPGELTIVTGVPNSGKSEWI 444

Query: 315 DALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG 374
           DAL+CN+N  AGWKF LCSMENKVREH RKLLEKHIKKPFF   YGGS ER++ EE EQG
Sbjct: 445 DALLCNLNASAGWKFALCSMENKVREHGRKLLEKHIKKPFFVGRYGGSVERLSDEELEQG 504

Query: 375 KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETE 434
           K WL +TF L+R E DSLPSI WVLDLAKAAVLRHGV GLVIDPYNELDHQR  +QTETE
Sbjct: 505 KQWLDDTFFLLRSEKDSLPSISWVLDLAKAAVLRHGVSGLVIDPYNELDHQRLPNQTETE 564

Query: 435 YVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR 494
           YVSQMLT VKRFAQHH CHVWFVAHPRQL NW G PPN+YDISGSAHFINKCDNGIVIHR
Sbjct: 565 YVSQMLTKVKRFAQHHGCHVWFVAHPRQLQNWSGSPPNMYDISGSAHFINKCDNGIVIHR 624

Query: 495 NRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMD 537
           NRDPE+GPID VQVCVRKVRNKV GTIGEA+L YNRVTGE++D
Sbjct: 625 NRDPESGPIDLVQVCVRKVRNKVAGTIGEAYLEYNRVTGEFLD 667

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413943393|gb|AFW76042.1| hypothetical protein ZEAMMB73_832314 [Zea mays]

 Score =  818 bits (2113), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 388/547 (70%), Positives = 449/547 (82%), Gaps = 12/547 (2%)

Query: 2   CFRAKCGWKGSTSALVDNNRSQSSL-----------KKFSKMKTIREITEDSLELEPLGN 50
           CFR+KCGW+G   A    N SQ               K +  K  R+I+++ L LEPL +
Sbjct: 154 CFRSKCGWRGFVQADGVTNISQGKSGIESETDQEVEAKKAANKVYRKISDEDLNLEPLCD 213

Query: 51  ELRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDT 110
           EL  YFA R+ISAETLRRN+VMQ+   +++ IAF Y R+G LV CKYR  +K F QE +T
Sbjct: 214 ELVEYFATRMISAETLRRNKVMQRNWNNKISIAFTYRRDGALVGCKYRAVDKTFSQEANT 273

Query: 111 EKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTK 170
           EK+FYGLDDI+   D+IIVEGE+DKLSM+EAG+ NCVSVPDGAP  VS K +P +EQD K
Sbjct: 274 EKIFYGLDDIKRAHDVIIVEGEIDKLSMDEAGYRNCVSVPDGAPPKVSSK-IPDQEQDKK 332

Query: 171 YQYLWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDA 230
           Y YLWNCK YL  ASRIILATD D PGQALAEELARR+G+ERCWRV WPKKND D  KDA
Sbjct: 333 YSYLWNCKDYLDSASRIILATDNDRPGQALAEELARRLGKERCWRVNWPKKNDTDTCKDA 392

Query: 231 NEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNE 290
           NEVLM+LGP AL++V+E+AELYPI GLF+F  +F EID Y+    GDE GI TGW+++++
Sbjct: 393 NEVLMFLGPQALRKVIEDAELYPIRGLFSFEQFFPEIDNYFLGIHGDELGIHTGWKSMDD 452

Query: 291 LYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHI 350
           LY V+PGELT+VTGVPNSGKSEWIDAL+CNIN+ +GWKFVLCSMENKV+EHARKLLEKHI
Sbjct: 453 LYKVVPGELTVVTGVPNSGKSEWIDALLCNINKQSGWKFVLCSMENKVKEHARKLLEKHI 512

Query: 351 KKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHG 410
           +KPFF A YGGSA+RMT +EFE GK WL+ TF LIRCE+DSLPSI WVLDLAKAAVLRHG
Sbjct: 513 QKPFFNARYGGSAQRMTPDEFEAGKQWLNKTFHLIRCEDDSLPSINWVLDLAKAAVLRHG 572

Query: 411 VRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEP 470
           VRGLVIDPYNELDHQRP +QTETEYVSQ+LT +KRFAQHH+CHVWFVAHPRQL NW G P
Sbjct: 573 VRGLVIDPYNELDHQRPSNQTETEYVSQILTKIKRFAQHHSCHVWFVAHPRQLQNWNGGP 632

Query: 471 PNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNR 530
           PN+YDISGSAHFINKCDNGIVIHRNRDP AGP+D VQVCVRKVRNKVVG IG+AFL+Y+R
Sbjct: 633 PNIYDISGSAHFINKCDNGIVIHRNRDPNAGPLDTVQVCVRKVRNKVVGQIGDAFLTYDR 692

Query: 531 VTGEYMD 537
           VTGE+ D
Sbjct: 693 VTGEFKD 699

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302141745|emb|CBI18948.3| unnamed protein product [Vitis vinifera]

 Score =  807 bits (2084), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 386/538 (71%), Positives = 439/538 (81%), Gaps = 10/538 (1%)

Query: 2   CFRAKCGWKGSTSALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERLI 61
           C R KCGW+G T A  +   S   L + +K+K  REITE SL LEPL  EL AYF ER+I
Sbjct: 162 CHRGKCGWRGDTRAFANGRSSYGRLNQITKIKPKREITEKSLGLEPLCRELIAYFGERMI 221

Query: 62  SAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIE 121
           S +TL RN VMQK +G E +IAF Y RNG  V+CKYRD NK FWQE+DTEK+FYG+DDI+
Sbjct: 222 SEKTLARNSVMQKTYGDEFIIAFTYRRNGVFVSCKYRDVNKNFWQEEDTEKIFYGVDDIK 281

Query: 122 GESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYL 181
             SDIIIVEGE+DKLSMEEAGF NCVSVP+GAP+SVS K   S+E+DTKYQYLWNCK YL
Sbjct: 282 AASDIIIVEGEIDKLSMEEAGFYNCVSVPNGAPASVSTKVFKSDEEDTKYQYLWNCKEYL 341

Query: 182 KQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGA 241
           ++ASRIILATDGD PG ALAEELARR+GRERCWRV+WPKKN+VDHFKDANEVLMYLGP A
Sbjct: 342 EKASRIILATDGDSPGLALAEELARRLGRERCWRVKWPKKNEVDHFKDANEVLMYLGPDA 401

Query: 242 LKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLP-GELT 300
           LKEV+ENAELYPI GLFNF  YFDEIDAYYH+  G E G++TGWR LN LYNV     L 
Sbjct: 402 LKEVIENAELYPIQGLFNFSHYFDEIDAYYHQALGFELGVATGWRGLNGLYNVSTIFHLL 461

Query: 301 IVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYG 360
           + T +  SG  +    L+  I +          +   VREHARKLLEKHIKKPFF+A YG
Sbjct: 462 LFTMLVQSGAVDHWGILLERICQ---------KLSGLVREHARKLLEKHIKKPFFDAGYG 512

Query: 361 GSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYN 420
            S ERM++EEFE GK WLS TF LIRCENDSLP+IKWVLDLAKAAVLRHGVRGLVIDPYN
Sbjct: 513 ESIERMSIEEFELGKKWLSETFYLIRCENDSLPNIKWVLDLAKAAVLRHGVRGLVIDPYN 572

Query: 421 ELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSA 480
           ELDHQRP +QTETEYVSQMLT++KRFAQHH+CHVWFVAHPRQLH+W G PPN+YDISGSA
Sbjct: 573 ELDHQRPANQTETEYVSQMLTIIKRFAQHHSCHVWFVAHPRQLHHWDGGPPNMYDISGSA 632

Query: 481 HFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI 538
           HFINKCDNGIVIHRNR+P+AGP+D+VQVCVRKVRNKV+GT G+AFLSY+R+TG Y D+
Sbjct: 633 HFINKCDNGIVIHRNRNPDAGPVDQVQVCVRKVRNKVIGTTGDAFLSYDRITGVYTDV 690

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242093886|ref|XP_002437433.1| hypothetical protein SORBIDRAFT_10g026990 [Sorghum bicolor] gi|241915656|gb|EER88800.1| hypothetical protein SORBIDRAFT_10g026990 [Sorghum bicolor]

 Score =  804 bits (2076), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 386/556 (69%), Positives = 447/556 (80%), Gaps = 21/556 (3%)

Query: 2   CFRAKCGWKGSTSALVDNNRSQSSL-----------KKFSKMKTIREITEDSLELEPLGN 50
           CFR+KCGW+G   A    N SQ               K +  K  R++ E+ L LEPL +
Sbjct: 160 CFRSKCGWRGFIQADGVTNISQGKTDIESETDQEVESKKTANKVYRKVIEEDLNLEPLCD 219

Query: 51  ELRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDT 110
           EL  YF+ R+ISAETLRRN+VMQ+   +++ IAF Y R+G LV CKYR  +K F QE +T
Sbjct: 220 ELVEYFSTRMISAETLRRNKVMQRNWNNKISIAFTYRRDGVLVGCKYRAVDKTFSQEPNT 279

Query: 111 EKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTK 170
           EK+FYGLDDI+   D+IIVEGE+DKLSM+EAG+ NCVSVPDGAP  VS K +P +EQD K
Sbjct: 280 EKIFYGLDDIKRAHDVIIVEGEIDKLSMDEAGYRNCVSVPDGAPPKVSSK-IPDKEQDKK 338

Query: 171 YQYLWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDA 230
           Y YLWNCK YL  ASRIILATD D PGQALAEELARR+G+ERCWRV+WPKKND D  KDA
Sbjct: 339 YNYLWNCKDYLDSASRIILATDDDGPGQALAEELARRLGKERCWRVKWPKKNDTDTCKDA 398

Query: 231 NEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNE 290
           NEVLM+LGP AL++V+E+AELYPI GLF+F+D+F EID Y+    GDE GI TGW++L++
Sbjct: 399 NEVLMFLGPQALRKVIEDAELYPIRGLFSFKDFFPEIDNYFLGIHGDELGIHTGWKSLDD 458

Query: 291 LYN---------VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREH 341
           LY          V+PGELT+VTGVPNSGKSEWIDAL+CNIN   GWKFVLCSMENKV+EH
Sbjct: 459 LYKYHLNRLTWLVVPGELTVVTGVPNSGKSEWIDALLCNINTQCGWKFVLCSMENKVKEH 518

Query: 342 ARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDL 401
           ARKLLEK I KPFF+A YGG A+RMT ++FE GK WL+ TF LIRCE+DSLPSI WVLDL
Sbjct: 519 ARKLLEKRIGKPFFDARYGGDAQRMTPDDFEAGKEWLNETFHLIRCEDDSLPSINWVLDL 578

Query: 402 AKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPR 461
           AKAAVLRHGVRGLVIDPYNELDHQRP +QTETEYVSQ+LT VKRFAQHH+CHVWFVAHPR
Sbjct: 579 AKAAVLRHGVRGLVIDPYNELDHQRPSNQTETEYVSQILTKVKRFAQHHSCHVWFVAHPR 638

Query: 462 QLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTI 521
           QLHNW G PPN+YDISGSAHFINKCDNGIVIHRNRD  AGP+D VQVCVRKVRNKV+G I
Sbjct: 639 QLHNWNGGPPNMYDISGSAHFINKCDNGIVIHRNRDQNAGPLDVVQVCVRKVRNKVIGQI 698

Query: 522 GEAFLSYNRVTGEYMD 537
           G+AFL+Y+RVTG+Y D
Sbjct: 699 GDAFLTYDRVTGQYKD 714

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|27311757|gb|AAO00844.1| Unknown protein [Arabidopsis thaliana]

 Score =  790 bits (2040), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 364/537 (67%), Positives = 445/537 (82%), Gaps = 8/537 (1%)

Query: 2   CFRAKCGWKGSTSALVDNNRSQSSLKKFSKMKTI-REITEDSLELEPLGNELRAYFAERL 60
           CFR KCG KG         R+   L     ++ + R+IT + +ELEPL +E++ YFA R 
Sbjct: 164 CFRGKCGLKGGV-------RADGGLASADPIEKVERKITVEGIELEPLCDEIQDYFAARA 216

Query: 61  ISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDI 120
           IS +TL RNRVMQKR G E+VIAF YW+ G+LV+CKYR   K F+QE+ T ++ YGLDDI
Sbjct: 217 ISRKTLERNRVMQKRIGDEIVIAFTYWQRGELVSCKYRSLTKMFFQERKTRRILYGLDDI 276

Query: 121 EGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMY 180
           E  S++IIVEGE+DKL+MEEAGFLNCVSVPDGAP+ VS K +PSE++DTKY++LWNC  Y
Sbjct: 277 EKTSEVIIVEGEIDKLAMEEAGFLNCVSVPDGAPAKVSSKEIPSEDKDTKYKFLWNCNDY 336

Query: 181 LKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPG 240
           LK+ASRI++ATDGD PGQA+AEE+ARR+G+ERCWRV+WPKK++ +HFKDANEVLM  GP 
Sbjct: 337 LKKASRIVIATDGDGPGQAMAEEIARRLGKERCWRVKWPKKSEDEHFKDANEVLMSKGPH 396

Query: 241 ALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELT 300
            LKE + +AE YPI+GLF+F+D+FDEIDAYY RT G E+G+STGW+ L+ LY+V+PGELT
Sbjct: 397 LLKEAILDAEPYPILGLFSFKDFFDEIDAYYDRTHGHEYGVSTGWKNLDNLYSVVPGELT 456

Query: 301 IVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYG 360
           +VTG+PNSGKSEWIDA++CN+N   GWKF LCSMENKVR+HARKLLEKHIKKPFF+A+YG
Sbjct: 457 VVTGIPNSGKSEWIDAMLCNLNHSVGWKFALCSMENKVRDHARKLLEKHIKKPFFDADYG 516

Query: 361 GSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYN 420
            S +RM+VEE ++GK WL++TF  IRCE DSLPSI WVL+ AKAAVLR+G+RGLVIDPYN
Sbjct: 517 RSVQRMSVEEKDEGKKWLNDTFYPIRCEMDSLPSINWVLERAKAAVLRYGIRGLVIDPYN 576

Query: 421 ELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSA 480
           ELDHQR   QTETEYVSQMLT +KRF+QHH+CHVWFVAHP+QL +W G  PNLYDISGSA
Sbjct: 577 ELDHQRTPRQTETEYVSQMLTKIKRFSQHHSCHVWFVAHPKQLQHWDGGAPNLYDISGSA 636

Query: 481 HFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMD 537
           HFINKCDNGI++HRNRD  AGP+D VQ+ VRKVRNKV G IG+A+L Y+R TG Y D
Sbjct: 637 HFINKCDNGIIVHRNRDENAGPLDLVQIGVRKVRNKVAGQIGDAYLCYDRTTGSYSD 693

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	539
TAIR|locus:2204584	709	AT1G30680 [Arabidopsis thalian	0.983	0.747	0.662	1.2e-200
TAIR|locus:2204559	337	AT1G30660 "AT1G30660" [Arabido	0.454	0.727	0.581	2.9e-71
UNIPROTKB|Q1L7I7	765	Q1L7I7 "Mitochondrial helicase	0.619	0.436	0.239	7.6e-12
DICTYBASE|DDB_G0288209	772	DDB_G0288209 "T7-like mitochon	0.606	0.423	0.231	7.1e-11
UNIPROTKB|Q1L7I8	724	Q1L7I8 "Mitochondrial helicase	0.599	0.446	0.216	1.3e-06
UNIPROTKB|Q6NU50	679	MGC81247 "MGC81247 protein" [X	0.456	0.362	0.249	9.1e-05
UNIPROTKB|Q5ZIW1	669	PEO1 "Twinkle protein, mitocho	0.423	0.340	0.247	0.00085

TAIR|locus:2204584 AT1G30680 [Arabidopsis thaliana (taxid:3702)]

 Score = 1942 (688.7 bits), Expect = 1.2e-200, P = 1.2e-200
 Identities = 355/536 (66%), Positives = 433/536 (80%)

Query:     2 CFRAKCGWKGSTSALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERLI 61
             CFR KCG KG   A    +   +S     K++  R+IT + +ELEPL +E++ YFA R I
Sbjct:   164 CFRGKCGLKGGVRA----DGGLASADPIEKVE--RKITVEGIELEPLCDEIQDYFAARAI 217

Query:    62 SAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIE 121
             S +TL RNRVMQKR G E+VIAF YW+ G+LV+CKYR   K F+QE+ T ++ YGLDDIE
Sbjct:   218 SRKTLERNRVMQKRIGDEIVIAFTYWQRGELVSCKYRSLTKMFFQERKTRRILYGLDDIE 277

Query:   122 GESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYL 181
               S++IIVEGE+DKL+MEEAGFLNCVSVPDGAP+ VS K +PSE++DTKY++LWNC  YL
Sbjct:   278 KTSEVIIVEGEIDKLAMEEAGFLNCVSVPDGAPAKVSSKEIPSEDKDTKYKFLWNCNDYL 337

Query:   182 KQASRIILATDGDPPGQALAEELAXXXXXXXXXXXXXPKKNDVDHFKDANEVLMYLGPGA 241
             K+ASRI++ATDGD PGQA+AEE+A             PKK++ +HFKDANEVLM  GP  
Sbjct:   338 KKASRIVIATDGDGPGQAMAEEIARRLGKERCWRVKWPKKSEDEHFKDANEVLMSKGPHL 397

Query:   242 LKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPGELTI 301
             LKE + +AE YPI+GLF+F+D+FDEIDAYY RT G E+G+STGW+ L+ LY+V+PGELT+
Sbjct:   398 LKEAILDAEPYPILGLFSFKDFFDEIDAYYDRTHGHEYGVSTGWKNLDNLYSVVPGELTV 457

Query:   302 VTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGG 361
             VTG+PNSGKSEWIDA++CN+N   GWKF LCSMENKVR+HARKLLEKHIKKPFF+A+YG 
Sbjct:   458 VTGIPNSGKSEWIDAMLCNLNHSVGWKFALCSMENKVRDHARKLLEKHIKKPFFDADYGR 517

Query:   362 SAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNE 421
             S +RM+VEE ++GK WL++TF  IRCE DSLPSI WVL+ AKAAVLR+G+RGLVIDPYNE
Sbjct:   518 SVQRMSVEEKDEGKKWLNDTFYPIRCEMDSLPSIDWVLERAKAAVLRYGIRGLVIDPYNE 577

Query:   422 LDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAH 481
             LDHQR   QTETEYVSQMLT +KRF+QHH+CHVWFVAHP+QL +W G  PNLYDISGSAH
Sbjct:   578 LDHQRTPRQTETEYVSQMLTKIKRFSQHHSCHVWFVAHPKQLQHWDGGAPNLYDISGSAH 637

Query:   482 FINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMD 537
             FINKCDNGI++HRNRD  AGP+D VQ+ VRKVRNKV G IG+A+L Y+R TG Y D
Sbjct:   638 FINKCDNGIIVHRNRDENAGPLDLVQIGVRKVRNKVAGQIGDAYLCYDRTTGSYSD 693

GO:0003678 "DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0006260 "DNA replication" evidence=IEA

TAIR|locus:2204559 AT1G30660 "AT1G30660" [Arabidopsis thaliana (taxid:3702)]

 Score = 721 (258.9 bits), Expect = 2.9e-71, P = 2.9e-71
 Identities = 146/251 (58%), Positives = 180/251 (71%)

Query:     4 RAKCGWKGSTSALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERLISA 63
             R KCG KG     VD      S     K++  R+IT +S++LEPL +E++ +FA R IS 
Sbjct:    91 RRKCGLKGVLQ--VDGKLV--SKDPIGKVE--RKITVESIKLEPLCDEIQDFFAARAISG 144

Query:    64 ETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEKVFYGLDDIEGE 123
             +TL RNRVMQKR   E+VIAF YW+ G+LV+CKYR   KKF QE++T K+ YGLDDIE  
Sbjct:   145 KTLERNRVMQKRIDDEIVIAFTYWQRGELVSCKYRSLTKKFVQERNTRKILYGLDDIEET 204

Query:   124 SDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQ 183
             S+IIIVEGE DKL+MEEAGF NCVSVPDGAP +VS K +PSE +DT ++Y+WNC  YLK+
Sbjct:   205 SEIIIVEGEPDKLAMEEAGFFNCVSVPDGAPETVSSKEIPSESKDTAFKYIWNCNDYLKK 264

Query:   184 ASRIILATDGDPPGQALAEELAXXXXXXXXXXXXXPKKNDVDHFKDANEVLMYLGPGALK 243
             ASRI++ATDGD PGQALAEELA             PKK++ +HFKDANEVLM  GP  LK
Sbjct:   265 ASRIVIATDGDGPGQALAEELARRLGKERCWLVKWPKKSEDEHFKDANEVLMSKGPHLLK 324

Query:   244 EVVENAELYPI 254
             E + NAE YP+
Sbjct:   325 EAILNAEPYPL 335

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006304 "DNA modification" evidence=ISS

UNIPROTKB|Q1L7I7 Q1L7I7 "Mitochondrial helicase twinkle" [Acanthamoeba castellanii (taxid:5755)]

 Score = 156 (60.0 bits), Expect = 7.6e-12, Sum P(2) = 7.6e-12
 Identities = 88/367 (23%), Positives = 153/367 (41%)

Query:   181 LKQASRIILATDGDPPGQALAEELAXXXXXXXXXXXXXPKKNDVDHFKDANEVLMYLGPG 240
             L++  +I L  D D PGQ  A + A              K+ D +  KDAN+ L   G  
Sbjct:   381 LERFEKIYLWMDDDIPGQEGAAKFAQKLGIKRCLLVRT-KQGDPEGPKDANDALR-AGKD 438

Query:   241 ALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEF-GI-STGWRALNE-LYNVLPG 297
              L  +++ A   P   + +F+D  DE+  Y +  S DE  G+ S  + +L + L     G
Sbjct:   439 -LNAILKKAGRTPHQQVISFQDIADEV--YRNICSPDELAGVPSKMFPSLTKILKGHRKG 495

Query:   298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEA 357
             ELT+ TG    GK+  +  L  +     G + +  + E K    A+K+L ++  K   E 
Sbjct:   496 ELTVFTGPTGVGKTTLLSQLSLDFAMQ-GVRTLWGNFEIKNTYLAQKMLLQYAGKNLAEL 554

Query:   358 NYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVID 417
                   +R   +E    +A+       +R    +  S+  VLD    AV  H V  +V+D
Sbjct:   555 Q-----DRAQWDE--ASRAFSDLPLYWMRFHGST--SVDQVLDAMDYAVYVHDVEHVVLD 605

Query:   418 PYNEL------DHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPP 471
                 +        +   +  + +   + L   +RFA     H+  V HPR+  +    P 
Sbjct:   606 NLQFMLSGQAWGQEGVAAGNKFDIQDRALEEFRRFASTKNVHITLVIHPRKTED--DRPL 663

Query:   472 NLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRV 531
             N+  + GS     + DN +++  N+  +   ++     V K  N+  G +G   L +N+ 
Sbjct:   664 NVASVFGSVKATQEADNVLILQYNKGEDWKWLE-----VAK--NRFDGELGPIALQFNKR 716

Query:   532 TGEYMDI 538
                Y ++
Sbjct:   717 NKSYREM 723

GO:0003697 "single-stranded DNA binding" evidence=ISS

GO:0006264 "mitochondrial DNA replication" evidence=ISS

GO:0042645 "mitochondrial nucleoid" evidence=ISS

GO:0043139 "5'-3' DNA helicase activity" evidence=ISS

DICTYBASE|DDB_G0288209 DDB_G0288209 "T7-like mitochondrial DNA helicase" [Dictyostelium discoideum (taxid:44689)]

 Score = 151 (58.2 bits), Expect = 7.1e-11, Sum P(2) = 7.1e-11
 Identities = 84/363 (23%), Positives = 150/363 (41%)

Query:   181 LKQASRIILATDGDPPGQALAEELAXXXXXXXXXXXXXPKKNDVDHFKDANEVLMYLGPG 240
             L++  +I L  D D PG   A + +              K+ND +  KDAN+ L+  G  
Sbjct:   416 LERFEKIYLWMDDDVPGMEGAAKFSEKLGIQRTFIVST-KQNDPNGPKDANDALL-AGKD 473

Query:   241 ALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGI---STGW-RALNE-LYNVL 295
              LK ++  A   P   + +F D    + +  H    D   +    + W  + N+ L    
Sbjct:   474 -LKAILSTAANIPHDQICDFSD----VRSIIHNELKDPLSVIGKQSKWFPSFNKVLKGHR 528

Query:   296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFF 355
              GELTI +G    GK+  +  L  +     G + +  S E KV   ARK+L +     F 
Sbjct:   529 KGELTIFSGPTGIGKTSVLSQLSLDFCSQ-GTRTLWGSFELKVPRLARKMLSQ-----FS 582

Query:   356 EANYGGSAERMTVEEFEQGKAWLSNT-FSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGL 414
               N         VE +++     SN     +R    +   +  V+D  + AV    V  +
Sbjct:   583 NCNLDKH-----VENYQEIADNFSNMPMYFLRFFGST--QVDKVIDAMEYAVYVQDVEHI 635

Query:   415 VIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLY 474
             V+D    +   +       E +   +  +++FA     H+  V HPR+    + +  N+ 
Sbjct:   636 VLDNLQFMLGSQAKGIERFEIMDDSIEKLRKFASQKNVHITLVIHPRKQD--IDQVLNIN 693

Query:   475 DISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGE 534
             DI G+A    + DN I++  +++ +   +D     ++K  N+  G +G   LS+ + T  
Sbjct:   694 DIFGTAKATQEADNVIILQNSKNNQRY-LD-----IKK--NRFSGDLGIIPLSFEKETNR 745

Query:   535 YMD 537
             + +
Sbjct:   746 FSE 748

GO:0043139 "5'-3' DNA helicase activity" evidence=IEA;ISS

GO:0032508 "DNA duplex unwinding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA;ISS

GO:0003678 "DNA helicase activity" evidence=IEA

GO:0042645 "mitochondrial nucleoid" evidence=ISS

GO:0006264 "mitochondrial DNA replication" evidence=ISS

GO:0004386 "helicase activity" evidence=IEA

UNIPROTKB|Q1L7I8 Q1L7I8 "Mitochondrial helicase twinkle" [Vermamoeba vermiformis (taxid:5778)]

 Score = 113 (44.8 bits), Expect = 1.3e-06, Sum P(2) = 1.3e-06
 Identities = 80/369 (21%), Positives = 154/369 (41%)

Query:   181 LKQASRIILATDGDPPGQALAEELAXXXXXXXXXXXXXPKKNDVDHFKDANEVLMYLGPG 240
             L++  +I L  D D  GQ  A++ A              K       KDAN+ L   G  
Sbjct:   362 LERFDKIYLWLDDDVVGQQAAQKYALKLGRERCYLVST-KLGATTGPKDANDALRQ-GHD 419

Query:   241 ALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFG--ISTGWRALNELYNV-LPG 297
              L  +++ A   P   + NF +   E+  +    + D+        +  LN+L      G
Sbjct:   420 -LGTILKAARRLPHKQILNFNEIRSEV--FRELANPDQVAGRQMRSFPTLNKLLKGHRKG 476

Query:   298 ELTIVTGVPNSGKSEWIDAL---ICNINEHAGW-KFVLCSMENKVREHARKLLEKHIKKP 353
             EL+I+TG    GK+  I  +   +C+   +  W  F L    N VR  A+K+L +  +K 
Sbjct:   477 ELSILTGPTGIGKTTIISQISMDLCSQGVNTLWGSFEL----NNVRL-AKKMLNQFAQKN 531

Query:   354 FFEANYGGSAE-RMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVR 412
               E +    AE  +  ++F Q   +       +R    +   ++ VLD    AV  + V 
Sbjct:   532 L-EKHL---AEFDLWADKFSQVPLYF------MRFHGGT--EVEAVLDAMDYAVYVYDVE 579

Query:   413 GLVIDPYN---ELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGE 469
              +V+D      ++ H +   + +   +   +++ ++FA     H+  + HPR+  +  G+
Sbjct:   580 HIVLDNLQFMMQVGHFKGYERFDQ--LDSAISLFRKFATEKNVHITLIIHPRKEDD--GQ 635

Query:   470 PPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYN 529
               ++  + G+A    + DN I++ +      G   R    +   +N+  G +G     Y+
Sbjct:   636 ALSINSVFGTAKATQEADNVIIVQK------GKYYRY---LEVTKNRFSGDLGIVPYKYD 686

Query:   530 RVTGEYMDI 538
             + + +Y ++
Sbjct:   687 KESHKYFEL 695

GO:0003697 "single-stranded DNA binding" evidence=ISS

GO:0006264 "mitochondrial DNA replication" evidence=ISS

GO:0042645 "mitochondrial nucleoid" evidence=ISS

GO:0043139 "5'-3' DNA helicase activity" evidence=ISS

UNIPROTKB|Q6NU50 MGC81247 "MGC81247 protein" [Xenopus laevis (taxid:8355)]

 Score = 116 (45.9 bits), Expect = 9.1e-05, Sum P(2) = 9.1e-05
 Identities = 71/285 (24%), Positives = 118/285 (41%)

Query:   257 LFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPG----ELTIVTGVPNSGKSE 312
             + +FR   +E+  +    + D+      W    EL  +L G    ELT+ TG   SGK+ 
Sbjct:   385 IISFRQLREEV--FGQLENADQVA-GVKWNRFPELNKLLKGHRRGELTVFTGPTGSGKTT 441

Query:   313 WID--AL-ICNINEHAGW-KFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTV 368
             +I   AL +C    +  W  F L    N VR      L K +   F       + +R+  
Sbjct:   442 FISEYALDLCIQGINTLWGSFEL----NNVR------LAKIMLTQF-------ALQRLE- 483

Query:   369 EEFEQGKAWLSNTFSLIRC--ENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQR 426
             E+ ++   W      L  C        +IK V+D  + AV  + +  ++ID    +  Q 
Sbjct:   484 EQLDKYDEWADKFEDLPLCFMTFHGQQNIKAVMDTMQHAVYMYDITHVIIDNLQFMMGQE 543

Query:   427 PVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKC 486
              +          M+   ++FA  + CHV  V HPR+  +   +      I GSA    + 
Sbjct:   544 NIYSDRFAAQDYMVGAFRKFATVNNCHVTVVIHPRKEDD--DKELQTSSIFGSAKASQEA 601

Query:   487 DNGIVIHRNRDPEAGPIDR-VQVCVRKVRNKVVGTIGEAFLSYNR 530
             DN ++I ++R    G   R +QV     +N+  G +G   L +N+
Sbjct:   602 DN-VLILQDRKLVTGQGKRHLQVA----KNRFDGEVGVFSLEFNK 641

GO:0003697 "single-stranded DNA binding" evidence=ISS

GO:0006264 "mitochondrial DNA replication" evidence=ISS

GO:0042645 "mitochondrial nucleoid" evidence=ISS

GO:0043139 "5'-3' DNA helicase activity" evidence=ISS

UNIPROTKB|Q5ZIW1 PEO1 "Twinkle protein, mitochondrial" [Gallus gallus (taxid:9031)]

 Score = 102 (41.0 bits), Expect = 0.00085, Sum P(2) = 0.00085
 Identities = 65/263 (24%), Positives = 103/263 (39%)

Query:   257 LFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVLPG----ELTIVTGVPNSGKSE 312
             + +FR   +E+   +   +  E      W    EL  +L G    ELT+ TG   SGK+ 
Sbjct:   373 IVSFRQLREEV---FGELANSEQVAGVKWARFPELNKLLKGHRRGELTVFTGPTGSGKTT 429

Query:   313 WID--AL-ICNINEHAGWKFVLCSME-NKVREHARKLLEKHIKKPFFEANYGGSAERMTV 368
             +I   AL +C       W     S E N +R      L K +   F        A R   
Sbjct:   430 FISEYALDLCTQGVCTLWG----SFEINNIR------LAKIMLTQF--------ATRRLE 471

Query:   369 EEFEQGKAWLSN--TFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQR 426
             ++ E    W        L         +IK VLD  + AV  + +  +V+D    +    
Sbjct:   472 DQLELYDEWADRFEDLPLYFMTFHGQQNIKTVLDTMQHAVYMYDITHVVVDNLQFMMGHE 531

Query:   427 PVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKC 486
              +S         ++   ++FA  + CH+  V HPR+  +   +      I GSA    + 
Sbjct:   532 QLSADRLAAQDFIVGAFRKFATDNTCHITLVIHPRKEDD--EKELQTASIFGSAKASQEA 589

Query:   487 DNGIVIHRNRDPEAGPIDR-VQV 508
             DN ++I ++R    GP  R +QV
Sbjct:   590 DN-VLILQDRKLTTGPGKRYLQV 611

GO:0005524 "ATP binding" evidence=IEA

GO:0002020 "protease binding" evidence=IEA

GO:0006268 "DNA unwinding involved in replication" evidence=IEA

GO:0006390 "transcription from mitochondrial promoter" evidence=IEA

GO:0034214 "protein hexamerization" evidence=IEA

GO:0051260 "protein homooligomerization" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=ISS

GO:0043139 "5'-3' DNA helicase activity" evidence=ISS

GO:0006264 "mitochondrial DNA replication" evidence=ISS

GO:0042645 "mitochondrial nucleoid" 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.12	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	539
cd01122	271	cd01122, GP4d_helicase, GP4d_helicase is a homohex	9e-16
pfam13662	81	pfam13662, Toprim_4, Toprim domain	1e-12
cd01029	79	cd01029, TOPRIM_primases, TOPRIM_primases: The top	2e-10
COG0358	568	COG0358, DnaG, DNA primase (bacterial type) [DNA r	4e-09
pfam13155	90	pfam13155, Toprim_2, Toprim-like	2e-08
cd00188	83	cd00188, TOPRIM, Topoisomerase-primase domain	2e-08
pfam01751	86	pfam01751, Toprim, Toprim domain	4e-07
smart00493	75	smart00493, TOPRIM, topoisomerases, DnaG-type prim	5e-07
cd03364	79	cd03364, TOPRIM_DnaG_primases, TOPRIM_DnaG_primase	1e-06
TIGR01391	415	TIGR01391, dnaG, DNA primase, catalytic core	1e-05
pfam13481	154	pfam13481, AAA_25, AAA domain	1e-05
COG0305	435	COG0305, DnaB, Replicative DNA helicase [DNA repli	3e-05
PRK07004	460	PRK07004, PRK07004, replicative DNA helicase; Prov	4e-05
TIGR00665	434	TIGR00665, DnaB, replicative DNA helicase	6e-04
PRK07773	886	PRK07773, PRK07773, replicative DNA helicase; Vali	8e-04
PRK05748	448	PRK05748, PRK05748, replicative DNA helicase; Prov	9e-04

>gnl|CDD|238542 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3' helicases

 Score = 77.1 bits (190), Expect = 9e-16
 Identities = 63/262 (24%), Positives = 114/262 (43%), Gaps = 17/262 (6%)

Query: 284 GWRALNE-LYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA 342
            +  LN+    +  GEL I+T     GK+ ++     ++    G +    S+E  V   A
Sbjct: 16  PFPVLNKLTKGLRKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEEPVVRTA 75

Query: 343 RKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRC---ENDSLPSIKWVL 399
           R+LL ++  K     +   +    T+EEF+   A         R    ++    S+  VL
Sbjct: 76  RRLLGQYAGKRL---HLPDTVFIYTLEEFD---AAFDEFEGTGRLFMYDSFGEYSMDSVL 129

Query: 400 DLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH 459
           +  +   + HG++ ++ID  + +      S  E + + +++T ++ FA  H  H+  V+H
Sbjct: 130 EKVRYMAVSHGIQHIIIDNLSIMVSDERASGDERKALDEIMTKLRGFATEHGIHITLVSH 189

Query: 460 PRQ----LHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRN 515
            R+      +  G   +L D  GSA      DN I + RN+   A   +R    +R ++N
Sbjct: 190 LRRPDGDKTHEEGGEVSLSDFRGSAAIGQLADNVIALERNQQ--AELDERNTTYLRILKN 247

Query: 516 KVVGTIGEAF-LSYNRVTGEYM 536
           +  G  G A  L Y++ TG   
Sbjct: 248 RFTGGTGVAGPLEYDKETGRLS 269

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands. Length = 271

>gnl|CDD|222298 pfam13662, Toprim_4, Toprim domain

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 28/84 (33%), Positives = 36/84 (42%), Gaps = 15/84 (17%)

Query: 124 SDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQ 183
           S I IVEG  D L++E+AG+   V+V  GA S +          D K             
Sbjct: 1   STICIVEGYADVLALEQAGYKGVVAVLGGALSPLDGIGPEDLNIDVK------------- 47

Query: 184 ASRIILATDGDPPGQALAEELARR 207
              +ILA DGD  G+  A  LA  
Sbjct: 48  --EVILAFDGDVAGEKAALRLAEL 69

The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation. Length = 81

>gnl|CDD|173779 cd01029, TOPRIM_primases, TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 30/94 (31%), Positives = 41/94 (43%), Gaps = 19/94 (20%)

Query: 126 IIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQAS 185
           +IIVEG MD L++ +AG  N V+    A          +EEQ    + L       + A 
Sbjct: 3   VIIVEGYMDVLALHQAGIKNVVAALGTA---------NTEEQL---RLLK------RFAR 44

Query: 186 RIILATDGDPPGQALAEELARRVGRERCWRVRWP 219
            +ILA D D  G+  A   A  +      RVR P
Sbjct: 45  TVILAFDNDEAGKK-AAARALELLLALGGRVRVP 77

Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme. Length = 79

>gnl|CDD|223435 COG0358, DnaG, DNA primase (bacterial type) [DNA replication, recombination, and repair]

 Score = 58.7 bits (142), Expect = 4e-09
 Identities = 53/245 (21%), Positives = 84/245 (34%), Gaps = 63/245 (25%)

Query: 37  EITEDSLELEPLGNELRAYFAERLISAETLRRNRVMQKRHGHEVV------IAFP-YWRN 89
            I    L   P  + L  + A++    E L     + KR   ++       I FP     
Sbjct: 143 LIAHFRLGYAPPNDSLLPFLAKKEYREEKLEDLG-LLKRKEGKIYDRFRNRIMFPIRDLR 201

Query: 90  GKLVNCKYRDFNKKFWQEK--------DTE-----KVFYGLD----DIEGESDIIIVEGE 132
           G ++      F  +   +         +TE     +  YGLD     I     II+VEG 
Sbjct: 202 GDVI-----GFGGRVLGDDKPKYLNSPETELFKKGEELYGLDPARKKIAKADQIIVVEGY 256

Query: 133 MDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATD 192
           MD +++ +AG  N V+    A          +EE           K+  +   ++IL  D
Sbjct: 257 MDVIALHKAGIKNAVASLGTA---------LTEEHI---------KLLSRGKKKVILCFD 298

Query: 193 GDPPGQALAEELARR------VGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVV 246
           GD  G+  A+   +       VG      +  P   D D            G  AL++ +
Sbjct: 299 GDRAGRKAAKRALQLVLPLDFVGVF---VILLPDGKDPDELIRKE------GAEALRKKL 349

Query: 247 ENAEL 251
            N  L
Sbjct: 350 PNERL 354

Length = 568

>gnl|CDD|221942 pfam13155, Toprim_2, Toprim-like

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 29/112 (25%), Positives = 44/112 (39%), Gaps = 26/112 (23%)

Query: 127 IIVEGEMDKLSMEEAGFLN--CVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQA 184
            + EG +D LS+ + G  N   V V     +++      +E Q          K+  + A
Sbjct: 1   YVFEGAIDALSLYQLGQENNKAVVV-----ATLG--TALTEAQA---------KLLKRYA 44

Query: 185 SRIILATDGDPPGQALAEELARRVGRE--RCWRVRWPKKNDVDHFKDANEVL 234
             +ILA D D  G+  AE L + +  E      V  P        KD N+ L
Sbjct: 45  KEVILAFDNDKAGRKAAERLQKILKEEGLEVKVVLLPDG------KDWNDYL 90

This is a family or Toprim-like proteins. Length = 90

>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 24/95 (25%), Positives = 41/95 (43%), Gaps = 17/95 (17%)

Query: 126 IIIVEGEMDKLSMEEAGFLNC-VSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQA 184
           +IIVEG  D L++ +AG     V    G   + +++ +                  L +A
Sbjct: 3   LIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRL---------------LGEA 47

Query: 185 SRIILATDGDPPGQALAEELARRVGRERCWRVRWP 219
             +I+ATD D  G+A+A  L   + +    +VR  
Sbjct: 48  KEVIIATDADREGEAIALRLL-ELLKSLGKKVRRL 81

This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 83

>gnl|CDD|216679 pfam01751, Toprim, Toprim domain

 Score = 47.7 bits (114), Expect = 4e-07
 Identities = 27/97 (27%), Positives = 39/97 (40%), Gaps = 16/97 (16%)

Query: 126 IIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQAS 185
           +IIVEG  D +++E+AG +   +V        +  +    E       +   K  LK A 
Sbjct: 2   LIIVEGPSDAIALEKAGGVLGGAV------VATSGHALDLEH------IKELKKALKGAK 49

Query: 186 RIILATDGDPPGQA----LAEELARRVGRERCWRVRW 218
            +ILATD D  G+A    L E L       R      
Sbjct: 50  EVILATDPDREGEAIALKLLELLKPLGPIGRVEISEL 86

This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks. Length = 86

>gnl|CDD|214695 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 20/86 (23%)

Query: 124 SDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQ 183
             +IIVEG  D +++E+AG      V  G    +  K                    LK+
Sbjct: 1   KVLIIVEGPADAIALEKAGGKRGNVVALG--GHLLSKEQIKL---------------LKK 43

Query: 184 ASR---IILATDGDPPGQALAEELAR 206
            ++   +ILATD D  G+A+A ELA 
Sbjct: 44  LAKKAEVILATDPDREGEAIAWELAE 69

Length = 75

>gnl|CDD|173784 cd03364, TOPRIM_DnaG_primases, TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 18/81 (22%)

Query: 126 IIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQAS 185
           +I+VEG MD +++ +AG  N V+   G           +EEQ          ++  + A 
Sbjct: 3   VILVEGYMDVIALHQAGIKNVVASL-GTAL--------TEEQ---------AELLKRLAK 44

Query: 186 RIILATDGDPPGQALAEELAR 206
            +ILA DGD  GQ  A     
Sbjct: 45  EVILAFDGDEAGQKAALRALE 65

Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme. Length = 79

>gnl|CDD|233392 TIGR01391, dnaG, DNA primase, catalytic core

 Score = 47.2 bits (113), Expect = 1e-05
 Identities = 67/311 (21%), Positives = 101/311 (32%), Gaps = 120/311 (38%)

Query: 16  LVDNNRSQSSLKKFSKMKTIREITE-------DSLELEPLGNELRAYFAERLISAETLR- 67
           L      Q   ++ SK K + E+ E       + L+  P       Y   R +S ET+  
Sbjct: 94  LPFEKDQQEKKEQKSKRKKLYELLELAAKFFKNQLKHTPENRAALDYLQSRGLSDETIDR 153

Query: 68  ----------------------------------------------RNRVM---QKRHGH 78
                                                         RNR+M       G 
Sbjct: 154 FELGYAPNNWDFLFDFLQNKKGFDLELLAEAGLLVKKENGKYYDRFRNRIMFPIHDPKGR 213

Query: 79  EVVIAFPYWRNGKLVN---CKY------RDFNKKFWQEKDTEKVFYGLD----DIEGESD 125
             V+ F     G+ +     KY        F K         ++ YGL     +I  E +
Sbjct: 214 --VVGF----GGRALGDEKPKYLNSPETPLFKKS--------ELLYGLHKARKEIRKEKE 259

Query: 126 IIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQAS 185
           +I+VEG MD +++ +AG  N V     A    +     +EE     + L       + A 
Sbjct: 260 LILVEGYMDVIALHQAGIKNAV-----ASLGTAL----TEEH---IKLLK------RYAD 301

Query: 186 RIILATDGDPPGQA-------LAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLG 238
            IIL  DGD  G+        L   L   V       ++ P        KD +E L   G
Sbjct: 302 EIILCFDGDKAGRKAALRAIELLLPLGINVK-----VIKLPGG------KDPDEYLRKEG 350

Query: 239 PGALKEVVENA 249
             ALK+++EN+
Sbjct: 351 VEALKKLLENS 361

Members of this family are DNA primase, a ubiquitous bacteria protein. Most members of this family contain nearly two hundred additional residues C-terminal to the region represented here, but conservation between species is poor and the C-terminal region was not included in the seed alignment. This protein contains a CHC2 zinc finger (pfam01807) and a Toprim domain (pfam01751) [DNA metabolism, DNA replication, recombination, and repair]. Length = 415

>gnl|CDD|222165 pfam13481, AAA_25, AAA domain

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 33/166 (19%), Positives = 46/166 (27%), Gaps = 47/166 (28%)

Query: 296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFF 355
            G LT++ G P +GKS     L   +    G  F    +     E  R L          
Sbjct: 32  RGGLTLLAGAPGTGKSTLALDLAAAVA--TGRPF----LGPFPVEPGRVL---------- 75

Query: 356 EANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLV 415
              Y            E  +A L                 + +  L +A     G   +V
Sbjct: 76  ---YLD---------GEDSEAGL----------------RRRLRALGEALEEIEGPDLVV 107

Query: 416 IDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPR 461
           IDP   L             V  +L  + R A+     V  V H  
Sbjct: 108 IDPLASLLGGDENDNAA---VGALLAALDRLARRTGAAVLLVHHTG 150

This AAA domain is found in a wide variety of presumed DNA repair proteins. Length = 154

>gnl|CDD|223382 COG0305, DnaB, Replicative DNA helicase [DNA replication, recombination, and repair]

 Score = 46.1 bits (110), Expect = 3e-05
 Identities = 70/307 (22%), Positives = 121/307 (39%), Gaps = 41/307 (13%)

Query: 243 KEVVENAELYPIMGLFNFRD----YFDEIDAYYHRTSGDEFGISTGWRALNELYNVL-PG 297
           K++ + AE        +  D      DEI+A +        G+ TG+  L+E+ +   PG
Sbjct: 139 KKIFDVAERKNSEDFVHIGDLLKETMDEIEARFENGG--LIGVPTGFTDLDEITSGFRPG 196

Query: 298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKF----VLCSMENKVREHARKLL----EKH 349
           +L IV   P  GK+    AL  NI  +A         + S+E    +   +LL       
Sbjct: 197 DLIIVAARPGMGKT----ALALNIALNAAADGRKPVAIFSLEMSEEQLVMRLLSSESGIE 252

Query: 350 IKKPFFEANYGGSAERMTVEEFEQ-GKAWLSNTFSLIRCENDSLPSIKWVLDL---AKAA 405
             K            R++ +E+E+  KA  ++  S      D  P +  + ++   A+  
Sbjct: 253 SSKL--------RTGRLSDDEWERLIKA--ASELSEAPIFIDDTPGLT-ITEIRSKARRL 301

Query: 406 VLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLH 464
            L+H +  +VID Y +L      S+   + VS++   +K  A+     V  ++   R + 
Sbjct: 302 KLKHNLGLIVID-YLQLMTGGKKSENRKQEVSEISRSLKGLAKELGVPVIALSQLNRSVE 360

Query: 465 NWVGEPPNLYDISGSAHFINKCDNGIVIHR--NRDPEAGPIDRVQVCVRKVRNKVVGTIG 522
               + P L D+  S       D  I +HR      +       +V V K RN   G  G
Sbjct: 361 QRTDKRPMLSDLRESGALEQDADIVIFLHRDEAYLKDTPDRGEAEVIVAKNRN---GPTG 417

Query: 523 EAFLSYN 529
              L+++
Sbjct: 418 TVKLAFD 424

Length = 435

>gnl|CDD|235907 PRK07004, PRK07004, replicative DNA helicase; Provisional

 Score = 45.7 bits (108), Expect = 4e-05
 Identities = 63/287 (21%), Positives = 110/287 (38%), Gaps = 39/287 (13%)

Query: 265 DEIDAYYHR-TSGDEFGISTGWRALNELYNVL-PGELTIVTGVPNSGKSEWIDALICNIN 322
           + ID  YH     D  G  TG+  L+ + + +  GEL IV G P+ GK+    A   NI 
Sbjct: 179 ERIDTLYHTANPSDVTGTPTGFVDLDRMTSGMHGGELIIVAGRPSMGKT----AFSMNIG 234

Query: 323 EHA----GWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKA-- 376
           E+     G    + SME    + A ++L              GS  R+       G+   
Sbjct: 235 EYVAVEYGLPVAVFSMEMPGTQLAMRML--------------GSVGRLDQHRMRTGRLTD 280

Query: 377 --WLSNTFSLIRCEN-----DSLPSIKWVLDLAKAAVLRH--GVRGLVIDPYNELDHQRP 427
             W   T ++ +        D    +  +   ++A  L    G  GL+I  Y +L     
Sbjct: 281 EDWPKLTHAVQKMSEAQLFIDETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMSGSS 340

Query: 428 VSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKC 486
             +     +S++   +K  A+     V  ++   R L     + P + D+  S       
Sbjct: 341 QGENRATEISEISRSLKSLAKELDVPVIALSQLNRGLEQRPNKRPVMSDLRESGAIEQDA 400

Query: 487 DNGIVIHRNR--DPEAGPIDRVQVCVRKVRNKVVGTIGEAFL-SYNR 530
           D  + I+R+   +P++      ++ + K RN  +G +   FL  Y +
Sbjct: 401 DVILFIYRDEVYNPDSPDKGTAEIIIGKQRNGPIGPVRLTFLGQYTK 447

Length = 460

>gnl|CDD|233080 TIGR00665, DnaB, replicative DNA helicase

 Score = 42.0 bits (100), Expect = 6e-04
 Identities = 29/103 (28%), Positives = 51/103 (49%), Gaps = 18/103 (17%)

Query: 236 YLGPGALKEVVENAE--LYPIM------GLFNFRD----YFDEIDAYYHRTSGDEFGIST 283
           Y   G ++E+++ AE  ++ I       G  + ++      +EI+  Y R  G   G+ T
Sbjct: 122 YDPEGDVEELLDEAEQKIFEIAESRTSGGFKSIKEVLKETVEEIEELYER-KGGITGVPT 180

Query: 284 GWRALNELYNVL-PGELTIVTGVPNSGKSEWIDALICNINEHA 325
           G+  L++L + L P +L I+   P+ GK+    A   NI E+A
Sbjct: 181 GFTDLDKLTSGLQPSDLIILAARPSMGKT----AFALNIAENA 219

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 434

>gnl|CDD|236093 PRK07773, PRK07773, replicative DNA helicase; Validated

 Score = 42.0 bits (99), Expect = 8e-04
 Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 2/84 (2%)

Query: 264 FDEIDAYYHRTSGDEFGISTGWRALNELYNVL-PGELTIVTGVPNSGKSEWIDALICNIN 322
           FDEIDA          G+ TG+  L+ + N L PG+L IV   P+ GK+ +      N  
Sbjct: 184 FDEIDAIASSGGLAR-GVPTGFTELDAMTNGLHPGQLIIVAARPSMGKTTFGLDFARNCA 242

Query: 323 EHAGWKFVLCSMENKVREHARKLL 346
                   + S+E    +   +LL
Sbjct: 243 IRHRLAVAIFSLEMSKEQLVMRLL 266

Length = 886

>gnl|CDD|180232 PRK05748, PRK05748, replicative DNA helicase; Provisional

 Score = 41.5 bits (98), Expect = 9e-04
 Identities = 33/105 (31%), Positives = 54/105 (51%), Gaps = 14/105 (13%)

Query: 229 DANEVLMYLGPGALKEVVENAELYPIMGLFNFRDY----FDEIDAYYHRTSGDEFGISTG 284
           DA+E+L      A K++ E +E     G  N +D     +D I+  +++T GD  GI TG
Sbjct: 135 DADEIL----DEAEKKIFEVSERRNKSGFKNIKDVLVKAYDRIEMLHNQT-GDITGIPTG 189

Query: 285 WRALNELYNVL-PGELTIVTGVPNSGKSEWIDALICNINEHAGWK 328
           +  L+++ + L P +L IV   P+ GK+    A   NI ++   K
Sbjct: 190 FTDLDKMTSGLQPNDLIIVAARPSVGKT----AFALNIAQNVATK 230

Length = 448

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	539
PRK08006	471	replicative DNA helicase; Provisional	100.0
PRK08840	464	replicative DNA helicase; Provisional	100.0
PRK07004	460	replicative DNA helicase; Provisional	100.0
PRK05636	505	replicative DNA helicase; Provisional	100.0
COG0305	435	DnaB Replicative DNA helicase [DNA replication, re	100.0
PRK08760	476	replicative DNA helicase; Provisional	100.0
PRK06321	472	replicative DNA helicase; Provisional	100.0
PRK06749	428	replicative DNA helicase; Provisional	100.0
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	100.0
PRK06904	472	replicative DNA helicase; Validated	100.0
PRK05595	444	replicative DNA helicase; Provisional	100.0
PRK08506	472	replicative DNA helicase; Provisional	100.0
PRK09165	497	replicative DNA helicase; Provisional	100.0
PHA02542	473	41 41 helicase; Provisional	100.0
TIGR00665	434	DnaB replicative DNA helicase. This model describe	100.0
KOG2373	514	consensus Predicted mitochondrial DNA helicase twi	100.0
PRK05748	448	replicative DNA helicase; Provisional	100.0
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	100.0
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	100.0
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	100.0
PRK07773	886	replicative DNA helicase; Validated	100.0
TIGR01391	415	dnaG DNA primase, catalytic core. This protein con	99.95
PRK05667	580	dnaG DNA primase; Validated	99.95
TIGR00646	218	MG010 DNA primase-related protein. The DNA primase	99.95
PHA02540	337	61 DNA primase; Provisional	99.92
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	99.91
PRK05973	237	replicative DNA helicase; Provisional	99.9
COG0358	568	DnaG DNA primase (bacterial type) [DNA replication	99.9
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	99.9
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	99.89
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	99.88
PRK11823	446	DNA repair protein RadA; Provisional	99.88
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	99.88
PHA02415	930	DNA primase domain-containing protein	99.86
PRK04328	249	hypothetical protein; Provisional	99.85
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	99.85
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	99.85
PHA02031	266	putative DnaG-like primase	99.85
cd01394	218	radB RadB. The archaeal protein radB shares simila	99.84
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	99.84
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	99.84
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	99.82
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	99.82
cd00983	325	recA RecA is a bacterial enzyme which has roles in	99.81
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	99.81
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	99.8
PRK09354	349	recA recombinase A; Provisional	99.8
PRK09302	509	circadian clock protein KaiC; Reviewed	99.8
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	99.8
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	99.8
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	99.79
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	99.79
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	99.79
TIGR02237	209	recomb_radB DNA repair and recombination protein R	99.78
PTZ00035	337	Rad51 protein; Provisional	99.78
PRK08624	373	hypothetical protein; Provisional	99.77
PRK04301	317	radA DNA repair and recombination protein RadA; Va	99.77
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	99.77
TIGR02236	310	recomb_radA DNA repair and recombination protein R	99.77
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	99.75
PRK09302	509	circadian clock protein KaiC; Reviewed	99.75
PRK06067	234	flagellar accessory protein FlaH; Validated	99.74
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	99.71
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	99.69
PRK08533	230	flagellar accessory protein FlaH; Reviewed	99.69
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	99.67
PRK09519	790	recA DNA recombination protein RecA; Reviewed	99.67
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	99.64
PF00154	322	RecA: recA bacterial DNA recombination protein; In	99.63
PF13155	96	Toprim_2: Toprim-like	99.53
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	99.49
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	99.47
PRK07078	759	hypothetical protein; Validated	99.43
COG3598	402	RepA RecA-family ATPase [DNA replication, recombin	99.39
cd03364	79	TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The top	99.38
KOG1564	351	consensus DNA repair protein RHP57 [Replication, r	99.3
PF13362	96	Toprim_3: Toprim domain	99.25
PF13662	81	Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B	99.22
KOG1434	335	consensus Meiotic recombination protein Dmc1 [Cell	99.22
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	99.21
cd01029	79	TOPRIM_primases TOPRIM_primases: The topoisomerase	99.14
PF07088	484	GvpD: GvpD gas vesicle protein; InterPro: IPR00978	99.12
smart00493	76	TOPRIM topoisomerases, DnaG-type primases, OLD fam	98.79
PF12965	130	DUF3854: Domain of unknown function (DUF3854); Int	98.78
cd01027	81	TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The to	98.6
PRK04031	408	DNA primase; Provisional	98.58
PRK04296	190	thymidine kinase; Provisional	98.58
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	98.54
PF08275	128	Toprim_N: DNA primase catalytic core, N-terminal d	98.44
KOG1433	326	consensus DNA repair protein RAD51/RHP55 [Replicat	98.42
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	98.32
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.3
COG4619	223	ABC-type uncharacterized transport system, ATPase	98.29
COG4604	252	CeuD ABC-type enterochelin transport system, ATPas	98.27
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	98.25
COG4643	366	Uncharacterized protein conserved in bacteria [Fun	98.22
PF13479	213	AAA_24: AAA domain	98.15
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	98.11
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.11
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	98.11
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	98.09
KOG2859	293	consensus DNA repair protein, member of the recA/R	98.07
COG1122	235	CbiO ABC-type cobalt transport system, ATPase comp	98.06
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	98.01
cd03115	173	SRP The signal recognition particle (SRP) mediates	98.0
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.99
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	97.98
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.98
smart00382	148	AAA ATPases associated with a variety of cellular	97.98
cd00188	83	TOPRIM Topoisomerase-primase domain. This is a nuc	97.96
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	97.95
PRK09544	251	znuC high-affinity zinc transporter ATPase; Review	97.93
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.92
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	97.92
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	97.91
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	97.9
PRK13634	290	cbiO cobalt transporter ATP-binding subunit; Provi	97.89
COG1127	263	Ttg2A ABC-type transport system involved in resist	97.89
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	97.89
TIGR01184	230	ntrCD nitrate transport ATP-binding subunits C and	97.89
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	97.88
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	97.88
TIGR01277	213	thiQ thiamine ABC transporter, ATP-binding protein	97.88
PRK11308	327	dppF dipeptide transporter ATP-binding subunit; Pr	97.87
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	97.87
TIGR02770	230	nickel_nikD nickel import ATP-binding protein NikD	97.87
cd03216	163	ABC_Carb_Monos_I This family represents the domain	97.84
KOG0061	613	consensus Transporter, ABC superfamily (Breast can	97.83
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	97.83
PRK10867	433	signal recognition particle protein; Provisional	97.83
cd03298	211	ABC_ThiQ_thiamine_transporter ABC-type thiamine tr	97.83
cd03267	236	ABC_NatA_like Similar in sequence to NatA, this is	97.83
PRK13646	286	cbiO cobalt transporter ATP-binding subunit; Provi	97.83
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	97.82
COG4107	258	PhnK ABC-type phosphonate transport system, ATPase	97.82
PRK15079	331	oligopeptide ABC transporter ATP-binding protein O	97.82
TIGR02315	243	ABC_phnC phosphonate ABC transporter, ATP-binding	97.81
PRK15112	267	antimicrobial peptide ABC system ATP-binding prote	97.81
PRK11153	343	metN DL-methionine transporter ATP-binding subunit	97.8
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.8
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	97.8
cd03220	224	ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transpo	97.79
TIGR03864	236	PQQ_ABC_ATP ABC transporter, ATP-binding subunit,	97.79
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	97.78
TIGR00959	428	ffh signal recognition particle protein. This mode	97.78
PRK11247	257	ssuB aliphatic sulfonates transport ATP-binding su	97.78
cd03215	182	ABC_Carb_Monos_II This family represents domain II	97.78
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	97.77
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	97.77
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	97.77
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	97.77
PRK09536	402	btuD corrinoid ABC transporter ATPase; Reviewed	97.76
COG3638	258	ABC-type phosphate/phosphonate transport system, A	97.76
PRK11022	326	dppD dipeptide transporter ATP-binding subunit; Pr	97.76
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	97.75
cd03219	236	ABC_Mj1267_LivG_branched The Mj1267/LivG ABC trans	97.75
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	97.74
PRK13636	283	cbiO cobalt transporter ATP-binding subunit; Provi	97.74
TIGR00968	237	3a0106s01 sulfate ABC transporter, ATP-binding pro	97.74
PRK14974	336	cell division protein FtsY; Provisional	97.74
cd03269	210	ABC_putative_ATPase This subfamily is involved in	97.74
PRK11248	255	tauB taurine transporter ATP-binding subunit; Prov	97.74
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	97.73
cd03257	228	ABC_NikE_OppD_transporters The ABC transporter sub	97.73
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	97.73
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	97.72
PRK13537	306	nodulation ABC transporter NodI; Provisional	97.72
PF13173	128	AAA_14: AAA domain	97.72
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	97.72
cd03300	232	ABC_PotA_N PotA is an ABC-type transporter and the	97.72
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	97.71
PRK13637	287	cbiO cobalt transporter ATP-binding subunit; Provi	97.71
TIGR03740	223	galliderm_ABC gallidermin-class lantibiotic protec	97.71
PRK10575	265	iron-hydroxamate transporter ATP-binding subunit;	97.71
TIGR02769	265	nickel_nikE nickel import ATP-binding protein NikE	97.7
PRK11432	351	fbpC ferric transporter ATP-binding subunit; Provi	97.7
PRK10771	232	thiQ thiamine transporter ATP-binding subunit; Pro	97.7
cd03295	242	ABC_OpuCA_Osmoprotection OpuCA is a the ATP bindin	97.7
cd03262	213	ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-	97.69
PRK13645	289	cbiO cobalt transporter ATP-binding subunit; Provi	97.69
PRK10418	254	nikD nickel transporter ATP-binding protein NikD;	97.69
PRK13633	280	cobalt transporter ATP-binding subunit; Provisiona	97.69
PRK10419	268	nikE nickel transporter ATP-binding protein NikE;	97.69
TIGR00064	272	ftsY signal recognition particle-docking protein F	97.69
PRK09473	330	oppD oligopeptide transporter ATP-binding componen	97.69
PRK11650	356	ugpC glycerol-3-phosphate transporter ATP-binding	97.68
PRK13652	277	cbiO cobalt transporter ATP-binding subunit; Provi	97.68
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	97.68
COG3840	231	ThiQ ABC-type thiamine transport system, ATPase co	97.68
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	97.68
PRK14250	241	phosphate ABC transporter ATP-binding protein; Pro	97.67
cd03296	239	ABC_CysA_sulfate_importer Part of the ABC transpor	97.67
PRK09452	375	potA putrescine/spermidine ABC transporter ATPase	97.67
TIGR03265	353	PhnT2 putative 2-aminoethylphosphonate ABC transpo	97.67
TIGR03258	362	PhnT 2-aminoethylphosphonate ABC transport system,	97.66
TIGR01188	302	drrA daunorubicin resistance ABC transporter ATP-b	97.66
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.66
cd03294	269	ABC_Pro_Gly_Bertaine This family comprises the gly	97.65
PRK13648	269	cbiO cobalt transporter ATP-binding subunit; Provi	97.65
PRK11701	258	phnK phosphonate C-P lyase system protein PhnK; Pr	97.65
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	97.65
PRK10908	222	cell division protein FtsE; Provisional	97.65
TIGR01288	303	nodI ATP-binding ABC transporter family nodulation	97.65
PRK13651	305	cobalt transporter ATP-binding subunit; Provisiona	97.64
COG4559	259	ABC-type hemin transport system, ATPase component	97.64
PRK13635	279	cbiO cobalt transporter ATP-binding subunit; Provi	97.64
PRK10619	257	histidine/lysine/arginine/ornithine transporter su	97.64
cd03235	213	ABC_Metallic_Cations ABC component of the metal-ty	97.64
cd03299	235	ABC_ModC_like Archeal protein closely related to M	97.63
PRK13536	340	nodulation factor exporter subunit NodI; Provision	97.63
COG1134	249	TagH ABC-type polysaccharide/polyol phosphate tran	97.63
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	97.63
PRK11000	369	maltose/maltodextrin transporter ATP-binding prote	97.63
COG4555	245	NatA ABC-type Na+ transport system, ATPase compone	97.63
PRK13643	288	cbiO cobalt transporter ATP-binding subunit; Provi	97.62
TIGR03005	252	ectoine_ehuA ectoine/hydroxyectoine ABC transporte	97.61
COG1123	539	ATPase components of various ABC-type transport sy	97.61
PRK13546	264	teichoic acids export protein ATP-binding subunit;	97.61
PRK11831	269	putative ABC transporter ATP-binding protein YrbF;	97.61
cd03297	214	ABC_ModC_molybdenum_transporter ModC is an ABC-typ	97.6
COG1123	539	ATPase components of various ABC-type transport sy	97.6
COG0410	237	LivF ABC-type branched-chain amino acid transport	97.6
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.6
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	97.59
COG4586	325	ABC-type uncharacterized transport system, ATPase	97.59
PRK10584	228	putative ABC transporter ATP-binding protein YbbA;	97.59
TIGR03771	223	anch_rpt_ABC anchored repeat-type ABC transporter,	97.59
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.59
PRK13545	549	tagH teichoic acids export protein ATP-binding sub	97.59
TIGR02142	354	modC_ABC molybdenum ABC transporter, ATP-binding p	97.59
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	97.59
PRK13641	287	cbiO cobalt transporter ATP-binding subunit; Provi	97.58
PRK11629	233	lolD lipoprotein transporter ATP-binding subunit;	97.58
TIGR02314	343	ABC_MetN D-methionine ABC transporter, ATP-binding	97.58
PRK11300	255	livG leucine/isoleucine/valine transporter ATP-bin	97.58
TIGR02323	253	CP_lyasePhnK phosphonate C-P lyase system protein	97.58
PRK11607	377	potG putrescine transporter ATP-binding subunit; P	97.58
PRK11264	250	putative amino-acid ABC transporter ATP-binding pr	97.58
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	97.57
PRK11144	352	modC molybdate transporter ATP-binding protein; Pr	97.57
PRK13548	258	hmuV hemin importer ATP-binding subunit; Provision	97.57
PRK10851	353	sulfate/thiosulfate transporter subunit; Provision	97.56
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	97.56
COG1117	253	PstB ABC-type phosphate transport system, ATPase c	97.56
PRK09984	262	phosphonate/organophosphate ester transporter subu	97.56
PRK10416	318	signal recognition particle-docking protein FtsY;	97.55
PRK10070	400	glycine betaine transporter ATP-binding subunit; P	97.55
PRK13647	274	cbiO cobalt transporter ATP-binding subunit; Provi	97.55
PRK12377	248	putative replication protein; Provisional	97.55
PRK10253	265	iron-enterobactin transporter ATP-binding protein;	97.54
PRK08181	269	transposase; Validated	97.54
cd03234	226	ABCG_White The White subfamily represents ABC tran	97.53
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	97.53
TIGR03410	230	urea_trans_UrtE urea ABC transporter, ATP-binding	97.53
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.53
cd03260	227	ABC_PstB_phosphate_transporter Phosphate uptake is	97.51
PRK15093	330	antimicrobial peptide ABC transporter ATP-binding	97.51
PRK13638	271	cbiO cobalt transporter ATP-binding subunit; Provi	97.51
TIGR03873	256	F420-0_ABC_ATP proposed F420-0 ABC transporter, AT	97.5
PRK09493	240	glnQ glutamine ABC transporter ATP-binding protein	97.5
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	97.5
PRK10261	623	glutathione transporter ATP-binding protein; Provi	97.5
PRK13639	275	cbiO cobalt transporter ATP-binding subunit; Provi	97.5
TIGR02211	221	LolD_lipo_ex lipoprotein releasing system, ATP-bin	97.5
PRK13649	280	cbiO cobalt transporter ATP-binding subunit; Provi	97.5
TIGR01978	243	sufC FeS assembly ATPase SufC. SufC is part of the	97.49
PRK13650	279	cbiO cobalt transporter ATP-binding subunit; Provi	97.49
PRK15134	529	microcin C ABC transporter ATP-binding protein Yej	97.49
cd03251	234	ABCC_MsbA MsbA is an essential ABC transporter, cl	97.49
cd03224	222	ABC_TM1139_LivF_branched LivF (TM1139) is part of	97.49
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	97.49
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.49
PRK13409	590	putative ATPase RIL; Provisional	97.49
PRK10938	490	putative molybdenum transport ATP-binding protein	97.48
PRK13631	320	cbiO cobalt transporter ATP-binding subunit; Provi	97.48
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	97.48
COG1118	345	CysA ABC-type sulfate/molybdate transport systems,	97.47
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.47
PRK11614	237	livF leucine/isoleucine/valine transporter ATP-bin	97.47
PF00004	132	AAA: ATPase family associated with various cellula	97.45
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	97.45
cd03249	238	ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6)	97.45
PRK11124	242	artP arginine transporter ATP-binding subunit; Pro	97.44
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	97.44
TIGR00955	617	3a01204 The Eye Pigment Precursor Transporter (EPP	97.43
COG4172	534	ABC-type uncharacterized transport system, duplica	97.43
PRK15177	213	Vi polysaccharide export ATP-binding protein VexC;	97.43
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	97.42
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	97.42
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	97.42
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	97.42
cd03253	236	ABCC_ATM1_transporter ATM1 is an ABC transporter t	97.41
cd03246	173	ABCC_Protease_Secretion This family represents the	97.41
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	97.41
PF13245	76	AAA_19: Part of AAA domain	97.41
cd03236	255	ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 o	97.41
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	97.4
COG0444	316	DppD ABC-type dipeptide/oligopeptide/nickel transp	97.4
PRK13640	282	cbiO cobalt transporter ATP-binding subunit; Provi	97.4
TIGR03411	242	urea_trans_UrtD urea ABC transporter, ATP-binding	97.38
PRK10895	241	lipopolysaccharide ABC transporter ATP-binding pro	97.38
PRK10261	623	glutathione transporter ATP-binding protein; Provi	97.38
PRK14258	261	phosphate ABC transporter ATP-binding protein; Pro	97.37
PF05729	166	NACHT: NACHT domain	97.36
PRK08116	268	hypothetical protein; Validated	97.36
TIGR01186	363	proV glycine betaine/L-proline transport ATP bindi	97.36
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	97.36
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	97.36
cd03254	229	ABCC_Glucan_exporter_like Glucan exporter ATP-bind	97.35
cd03248	226	ABCC_TAP TAP, the Transporter Associated with Anti	97.35
PRK10744	260	pstB phosphate transporter ATP-binding protein; Pr	97.35
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	97.35
PRK13547	272	hmuV hemin importer ATP-binding subunit; Provision	97.35
PRK14235	267	phosphate transporter ATP-binding protein; Provisi	97.35
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	97.34
COG0411	250	LivG ABC-type branched-chain amino acid transport	97.34
cd03250	204	ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.	97.34
PRK14269	246	phosphate ABC transporter ATP-binding protein; Pro	97.33
PRK07952	244	DNA replication protein DnaC; Validated	97.33
COG2401	593	ABC-type ATPase fused to a predicted acetyltransfe	97.32
PLN03211	659	ABC transporter G-25; Provisional	97.31
PRK03695	248	vitamin B12-transporter ATPase; Provisional	97.31
TIGR03269	520	met_CoM_red_A2 methyl coenzyme M reductase system,	97.31
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.31
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	97.31
TIGR02982	220	heterocyst_DevA ABC exporter ATP-binding subunit,	97.3
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	97.3
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	97.3
PRK14256	252	phosphate ABC transporter ATP-binding protein; Pro	97.29
PRK11231	255	fecE iron-dicitrate transporter ATP-binding subuni	97.29
TIGR03269	520	met_CoM_red_A2 methyl coenzyme M reductase system,	97.28
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	97.28
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	97.28
PRK15134	529	microcin C ABC transporter ATP-binding protein Yej	97.28
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	97.28
PRK13644	274	cbiO cobalt transporter ATP-binding subunit; Provi	97.28
COG3842	352	PotA ABC-type spermidine/putrescine transport syst	97.28
TIGR01189	198	ccmA heme ABC exporter, ATP-binding protein CcmA.	97.27
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	97.27
TIGR00972	247	3a0107s01c2 phosphate ABC transporter, ATP-binding	97.26
TIGR03415	382	ABC_choXWV_ATP choline ABC transporter, ATP-bindin	97.26
PRK13540	200	cytochrome c biogenesis protein CcmA; Provisional	97.26
PRK13642	277	cbiO cobalt transporter ATP-binding subunit; Provi	97.25
PLN03140	1470	ABC transporter G family member; Provisional	97.25
PRK15439	510	autoinducer 2 ABC transporter ATP-binding protein	97.25
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	97.25
PRK13768	253	GTPase; Provisional	97.25
PRK06921	266	hypothetical protein; Provisional	97.24
PRK13632	271	cbiO cobalt transporter ATP-binding subunit; Provi	97.24
cd03231	201	ABC_CcmA_heme_exporter CcmA, the ATP-binding compo	97.24
cd03252	237	ABCC_Hemolysin The ABC-transporter hemolysin B is	97.24
PRK09580	248	sufC cysteine desulfurase ATPase component; Review	97.24
PRK14237	267	phosphate transporter ATP-binding protein; Provisi	97.24
PRK14268	258	phosphate ABC transporter ATP-binding protein; Pro	97.24
PRK07773	886	replicative DNA helicase; Validated	97.24
PRK14267	253	phosphate ABC transporter ATP-binding protein; Pro	97.23
PRK14242	253	phosphate transporter ATP-binding protein; Provisi	97.23
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	97.23
PRK14274	259	phosphate ABC transporter ATP-binding protein; Pro	97.23
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	97.23
PRK14245	250	phosphate ABC transporter ATP-binding protein; Pro	97.22
PRK14247	250	phosphate ABC transporter ATP-binding protein; Pro	97.22
PRK10762	501	D-ribose transporter ATP binding protein; Provisio	97.22
PRK14240	250	phosphate transporter ATP-binding protein; Provisi	97.22
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	97.2
TIGR02324	224	CP_lyasePhnL phosphonate C-P lyase system protein	97.2
PRK14273	254	phosphate ABC transporter ATP-binding protein; Pro	97.17
PRK14241	258	phosphate transporter ATP-binding protein; Provisi	97.17
COG1658	127	Small primase-like proteins (Toprim domain) [DNA r	97.17
PRK14271	276	phosphate ABC transporter ATP-binding protein; Pro	97.17
PRK14259	269	phosphate ABC transporter ATP-binding protein; Pro	97.16
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	97.16
PTZ00293	211	thymidine kinase; Provisional	97.16
COG1135	339	AbcC ABC-type metal ion transport system, ATPase c	97.16
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.15
cd03114	148	ArgK-like The function of this protein family is u	97.15
KOG0065	1391	consensus Pleiotropic drug resistance proteins (PD	97.15
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	97.15
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.15
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	97.14
cd03279	213	ABC_sbcCD SbcCD and other Mre11/Rad50 (MR) complex	97.12
PRK14262	250	phosphate ABC transporter ATP-binding protein; Pro	97.12
TIGR00956	1394	3a01205 Pleiotropic Drug Resistance (PDR) Family p	97.12
PRK15056	272	manganese/iron transporter ATP-binding protein; Pr	97.12
PRK15439	510	autoinducer 2 ABC transporter ATP-binding protein	97.11
TIGR00956	1394	3a01205 Pleiotropic Drug Resistance (PDR) Family p	97.11
PRK14270	251	phosphate ABC transporter ATP-binding protein; Pro	97.11
PRK14244	251	phosphate ABC transporter ATP-binding protein; Pro	97.11
PRK14253	249	phosphate ABC transporter ATP-binding protein; Pro	97.11
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	97.1
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.1
PRK09700	510	D-allose transporter ATP-binding protein; Provisio	97.1
PRK14272	252	phosphate ABC transporter ATP-binding protein; Pro	97.09
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	97.09
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	97.08
PRK14252	265	phosphate ABC transporter ATP-binding protein; Pro	97.08
PRK14236	272	phosphate transporter ATP-binding protein; Provisi	97.08
PRK11288	501	araG L-arabinose transporter ATP-binding protein;	97.07
PRK14260	259	phosphate ABC transporter ATP-binding protein; Pro	97.07
PRK10762	501	D-ribose transporter ATP binding protein; Provisio	97.07
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	97.06
PRK14257	329	phosphate ABC transporter ATP-binding protein; Pro	97.06
PRK14255	252	phosphate ABC transporter ATP-binding protein; Pro	97.06
PRK09700	510	D-allose transporter ATP-binding protein; Provisio	97.06
PRK14251	251	phosphate ABC transporter ATP-binding protein; Pro	97.06
PRK06835	329	DNA replication protein DnaC; Validated	97.05
PRK10636	638	putative ABC transporter ATP-binding protein; Prov	97.05
PRK14249	251	phosphate ABC transporter ATP-binding protein; Pro	97.05
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	97.05
PF01751	100	Toprim: Toprim domain; InterPro: IPR006171 This is	97.04
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	97.04
PRK11288	501	araG L-arabinose transporter ATP-binding protein;	97.03
PRK14246	257	phosphate ABC transporter ATP-binding protein; Pro	97.03
PRK14243	264	phosphate transporter ATP-binding protein; Provisi	97.03
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	97.02
CHL00131	252	ycf16 sulfate ABC transporter protein; Validated	97.02
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.01
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	97.01
PRK14265	274	phosphate ABC transporter ATP-binding protein; Pro	97.0
PRK14238	271	phosphate transporter ATP-binding protein; Provisi	97.0
cd03244	221	ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.	97.0
PRK10982	491	galactose/methyl galaxtoside transporter ATP-bindi	97.0
PRK00889	175	adenylylsulfate kinase; Provisional	97.0
PRK10982	491	galactose/methyl galaxtoside transporter ATP-bindi	96.99
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	96.99
PF09807	249	DUF2348: Uncharacterized conserved protein (DUF234	96.98
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.98
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	96.98
COG1101	263	PhnK ABC-type uncharacterized transport system, AT	96.98
PRK14261	253	phosphate ABC transporter ATP-binding protein; Pro	96.98
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	96.98
TIGR02633	500	xylG D-xylose ABC transporter, ATP-binding protein	96.97
cd03278	197	ABC_SMC_barmotin Barmotin is a tight junction-asso	96.97
PRK09183	259	transposase/IS protein; Provisional	96.97
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	96.96
TIGR03797	686	NHPM_micro_ABC2 NHPM bacteriocin system ABC transp	96.96
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	96.96
PRK15064	530	ABC transporter ATP-binding protein; Provisional	96.95
PRK13549	506	xylose transporter ATP-binding subunit; Provisiona	96.95
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	96.94
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.94
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	96.94
TIGR03018	207	pepcterm_TyrKin exopolysaccharide/PEPCTERM locus t	96.93
PRK09435	332	membrane ATPase/protein kinase; Provisional	96.92
PRK10522	547	multidrug transporter membrane component/ATP-bindi	96.92
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	96.92
TIGR02204	576	MsbA_rel ABC transporter, permease/ATP-binding pro	96.92
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	96.89
PRK13549	506	xylose transporter ATP-binding subunit; Provisiona	96.89
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.88
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	96.88
PRK14266	250	phosphate ABC transporter ATP-binding protein; Pro	96.88
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	96.88
PRK14275	286	phosphate ABC transporter ATP-binding protein; Pro	96.86
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	96.86
PRK10263	1355	DNA translocase FtsK; Provisional	96.86
PRK14263	261	phosphate ABC transporter ATP-binding protein; Pro	96.86
TIGR01846	694	type_I_sec_HlyB type I secretion system ABC transp	96.85
PRK10790	592	putative multidrug transporter membrane\ATP-bindin	96.85
PLN03140	1470	ABC transporter G family member; Provisional	96.84
PRK10789	569	putative multidrug transporter membrane\ATP-bindin	96.84
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	96.84
PRK11160	574	cysteine/glutathione ABC transporter membrane/ATP-	96.83
cd03245	220	ABCC_bacteriocin_exporters ABC-type bacteriocin ex	96.82
COG4178	604	ABC-type uncharacterized transport system, permeas	96.82
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	96.82
TIGR01526	325	nadR_NMN_Atrans nicotinamide-nucleotide adenylyltr	96.82
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.82
PRK13409	590	putative ATPase RIL; Provisional	96.82
TIGR00957	1522	MRP_assoc_pro multi drug resistance-associated pro	96.81
TIGR01194	555	cyc_pep_trnsptr cyclic peptide transporter. This m	96.81
TIGR02857	529	CydD thiol reductant ABC exporter, CydD subunit. U	96.8
cd03290	218	ABCC_SUR1_N The SUR domain 1. The sulfonylurea rec	96.8
PRK04017	132	hypothetical protein; Provisional	96.8
TIGR03796	710	NHPM_micro_ABC1 NHPM bacteriocin system ABC transp	96.79
TIGR01192	585	chvA glucan exporter ATP-binding protein. This mod	96.78
PRK10938	490	putative molybdenum transport ATP-binding protein	96.77
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.77
cd03288	257	ABCC_SUR2 The SUR domain 2. The sulfonylurea recep	96.77
COG4148	352	ModC ABC-type molybdate transport system, ATPase c	96.76
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.76
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	96.76
cd01128	249	rho_factor Transcription termination factor rho is	96.75
TIGR02633	500	xylG D-xylose ABC transporter, ATP-binding protein	96.74
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	96.74
PF02492	178	cobW: CobW/HypB/UreG, nucleotide-binding domain; I	96.73
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.73
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	96.73
TIGR01193	708	bacteriocin_ABC ABC-type bacteriocin transporter.	96.73
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	96.72
COG4987	573	CydC ABC-type transport system involved in cytochr	96.71
cd03275	247	ABC_SMC1_euk Eukaryotic SMC1 proteins; SMC protein	96.7
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	96.7
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	96.69
COG4674	249	Uncharacterized ABC-type transport system, ATPase	96.68
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.68
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	96.68
COG4988	559	CydD ABC-type transport system involved in cytochr	96.68
KOG0066	807	consensus eIF2-interacting protein ABC50 (ABC supe	96.67
TIGR01271	1490	CFTR_protein cystic fibrosis transmembrane conduct	96.67

>PRK08006 replicative DNA helicase; Provisional

Probab=100.00  E-value=2.8e-46  Score=386.86  Aligned_cols=266  Identities=19%  Similarity=0.238  Sum_probs=228.8

Q ss_pred             hHHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHH
Q 009230          263 YFDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREH  341 (539)
Q Consensus       263 ~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~  341 (539)
                      +++.+++..+...+...|+||||+.||++++ |++|+|++|+|+||+|||+|++++|.++|.++|.+|+|||+||+.+++
T Consensus       189 ~~~~i~~~~~~~~~~~~Gi~TG~~~LD~~~~Gl~~G~LiiIaarPgmGKTafalnia~~~a~~~g~~V~~fSlEM~~~ql  268 (471)
T PRK08006        189 TVARIEQLFQQPHDGVTGVNTGYDDLNKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMLQDKPVLIFSLEMPGEQI  268 (471)
T ss_pred             HHHHHHHHHhcCCCCCCcccCCCHHHHHhhcCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCeEEEEeccCCHHHH
Confidence            3344444443334567899999999999998 999999999999999999999999999997569999999999999999


Q ss_pred             HHHHHHHhhCCCccccccCCCCCCCCHHHHHHHH---HHh-hccceeEeecCCCCCCHHHHHHHHHHHHHHc-CCcEEEE
Q 009230          342 ARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGK---AWL-SNTFSLIRCENDSLPSIKWVLDLAKAAVLRH-GVRGLVI  416 (539)
Q Consensus       342 ~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~---~~l-~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~-~~~~vvI  416 (539)
                      +.|+++..++++..+++.+    .+++++|.++.   ..+ ...+++|  ++.+..++++|.+.+++++.++ ++++|||
T Consensus       269 ~~Rlla~~~~v~~~~i~~~----~l~~~e~~~~~~a~~~~~~~~~l~I--~d~~~~t~~~i~~~~r~~~~~~~~~~lvvI  342 (471)
T PRK08006        269 MMRMLASLSRVDQTRIRTG----QLDDEDWARISGTMGILLEKRNMYI--DDSSGLTPTEVRSRARRIFREHGGLSLIMI  342 (471)
T ss_pred             HHHHHHHhcCCCHHHhhcC----CCCHHHHHHHHHHHHHHHhcCCEEE--ECCCCCCHHHHHHHHHHHHHhcCCCCEEEE
Confidence            9999999999999999865    79999987754   344 5567777  3356789999999999988887 6999999


Q ss_pred             ccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          417 DPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       417 D~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                      | |++++.......++.++++++++.||.||+++|||||+++| ||..+++.+++|.++|+++|++|+|.||.|++|+|+
T Consensus       343 D-YLqli~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~LsQLnR~~e~r~dkrP~lsDLreSG~IEqdAD~v~~l~R~  421 (471)
T PRK08006        343 D-YLQLMRVPSLSDNRTLEIAEISRSLKALAKELQVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIMFIYRD  421 (471)
T ss_pred             c-cHHHccCCCCCCCcHHHHHHHHHHHHHHHHHhCCeEEEEEecCccccccCCCCCchhhhhhcCcccccCCEEEEEecc
Confidence            9 99998754323567778999999999999999999999999 999998889999999999999999999999999998


Q ss_pred             CCC--CCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          496 RDP--EAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       496 ~~~--~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      +..  +...++..+++|.|||+|++|.+   .+.|+++++||.+.
T Consensus       422 ~~y~~~~~~~g~~elivaKnR~G~~G~v---~l~f~~~~~~f~~~  463 (471)
T PRK08006        422 EVYHENSDLKGIAEIIIGKQRNGPIGTV---RLTFNGQWSRFDNY  463 (471)
T ss_pred             cccccccCCCCceEEEEecccCCCCceE---EEEEccCcccccCC
Confidence            642  22234679999999999999875   79999999999875

>PRK08840 replicative DNA helicase; Provisional

Probab=100.00  E-value=7.8e-46  Score=382.90  Aligned_cols=265  Identities=18%  Similarity=0.241  Sum_probs=228.1

Q ss_pred             HHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH
Q 009230          264 FDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA  342 (539)
Q Consensus       264 ~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~  342 (539)
                      ++.++++.+...+...|+||||+.||.+++ |++|+|++|+|+||+|||+|++++|.++|.++|.+|+|||+||+.++++
T Consensus       183 ~~~i~~~~~~~~~~~~gi~TG~~~LD~~~~G~~~g~LiviaarPg~GKTafalnia~~~a~~~~~~v~~fSlEMs~~ql~  262 (464)
T PRK08840        183 LERIELLYKTPQDGVTGVDTGFTDLNKKTAGLQGSDLIIVAARPSMGKTTFAMNLCENAAMDQDKPVLIFSLEMPAEQLM  262 (464)
T ss_pred             HHHHHHHHhcCCCCCCCcCCCcHHHHHhhcCCCCCceEEEEeCCCCchHHHHHHHHHHHHHhCCCeEEEEeccCCHHHHH
Confidence            444544433223557899999999999997 9999999999999999999999999999876699999999999999999


Q ss_pred             HHHHHHhhCCCccccccCCCCCCCCHHHHHHH---HHHh-hccceeEeecCCCCCCHHHHHHHHHHHHHHc-CCcEEEEc
Q 009230          343 RKLLEKHIKKPFFEANYGGSAERMTVEEFEQG---KAWL-SNTFSLIRCENDSLPSIKWVLDLAKAAVLRH-GVRGLVID  417 (539)
Q Consensus       343 ~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~---~~~l-~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~-~~~~vvID  417 (539)
                      .|+++..++++..+++.+    .+++++|..+   .+++ ...++||  ++.+..++++|.+.+++++.++ ++++||||
T Consensus       263 ~Rlla~~s~v~~~~i~~~----~l~~~e~~~~~~a~~~l~~~~~l~I--~d~~~~ti~~i~~~~r~~~~~~~~~~lvvID  336 (464)
T PRK08840        263 MRMLASLSRVDQTKIRTG----QLDDEDWARISSTMGILMEKKNMYI--DDSSGLTPTEVRSRARRIAREHGGLSMIMVD  336 (464)
T ss_pred             HHHHHhhCCCCHHHHhcC----CCCHHHHHHHHHHHHHHHhcCCEEE--ECCCCCCHHHHHHHHHHHHHhcCCCCEEEEc
Confidence            999999999999998865    7999998775   4556 3456777  3356778999999999998887 49999999


Q ss_pred             cccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          418 PYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       418 ~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                       |++++...+...++.+++.++++.||.||+++|||||+++| ||..+++.+++|.++||+||++|+|.||+|++|+|++
T Consensus       337 -YLql~~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~LsQLnR~~e~r~~krP~lsDLreSG~IEqdAD~v~~l~R~~  415 (464)
T PRK08840        337 -YLQLMRVPALSDNRTLEIAEISRSLKALAKELNVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIMFIYRDE  415 (464)
T ss_pred             -cHHhcCCCCCCCchHHHHHHHHHHHHHHHHHhCCeEEEEEecCccccccCCCCCchHhhhhcccccccCCEEEEEeccc
Confidence             99999654323567788999999999999999999999999 9999988899999999999999999999999999986


Q ss_pred             CC--CCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          497 DP--EAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       497 ~~--~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      ..  +...++.++++|.|||||++|.+   .+.|+++++||.+.
T Consensus       416 ~y~~~~~~~~~~elivaKnR~G~~G~v---~l~f~~~~~~f~~~  456 (464)
T PRK08840        416 VYNPDSPLKGTAEIIIGKQRNGPIGSV---RLTFQGQYSRFDNY  456 (464)
T ss_pred             ccCCCcCCCCceEEEEecccCCCCceE---EEEEecCcccccCC
Confidence            42  22334679999999999999875   79999999999875

>PRK07004 replicative DNA helicase; Provisional

Probab=100.00  E-value=1.3e-45  Score=382.30  Aligned_cols=253  Identities=19%  Similarity=0.233  Sum_probs=225.4

Q ss_pred             CCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCc
Q 009230          276 GDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPF  354 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~  354 (539)
                      +...|+||||+.||++++ +++|+|++|+|+||+|||+|+++++.++|.++|.+|+|||+||+.++++.|+++..++++.
T Consensus       191 ~~~~gi~TG~~~LD~~t~G~~~g~liviaarpg~GKT~~al~ia~~~a~~~~~~v~~fSlEM~~~ql~~R~la~~~~v~~  270 (460)
T PRK07004        191 SDVTGTPTGFVDLDRMTSGMHGGELIIVAGRPSMGKTAFSMNIGEYVAVEYGLPVAVFSMEMPGTQLAMRMLGSVGRLDQ  270 (460)
T ss_pred             CCCCCccCCcHHhcccccCCCCCceEEEEeCCCCCccHHHHHHHHHHHHHcCCeEEEEeCCCCHHHHHHHHHHhhcCCCH
Confidence            456799999999999998 9999999999999999999999999999876799999999999999999999999999999


Q ss_pred             cccccCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcC-CcEEEEccccccccCCCCCC
Q 009230          355 FEANYGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHG-VRGLVIDPYNELDHQRPVSQ  430 (539)
Q Consensus       355 ~~i~~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~-~~~vvID~~~~l~~~~~~~~  430 (539)
                      .+++.+    .+++++|.++   .+++.+.+++|  ++.+..++.+|.+.+++++.+++ +++|||| |++++.......
T Consensus       271 ~~i~~g----~l~~~e~~~~~~a~~~l~~~~l~I--~d~~~~~~~~i~~~~r~l~~~~~~~~lviID-YLql~~~~~~~~  343 (460)
T PRK07004        271 HRMRTG----RLTDEDWPKLTHAVQKMSEAQLFI--DETGGLNPMELRSRARRLARQCGKLGLIIID-YLQLMSGSSQGE  343 (460)
T ss_pred             HHHhcC----CCCHHHHHHHHHHHHHHhcCCEEE--ECCCCCCHHHHHHHHHHHHHhCCCCCEEEEC-hhhhccCCCCCC
Confidence            998865    7999998765   46677777887  34567789999999999988764 8999999 999997543346


Q ss_pred             CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCC--CCCCCCcEE
Q 009230          431 TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDP--EAGPIDRVQ  507 (539)
Q Consensus       431 ~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~--~~~~~~~~~  507 (539)
                      ++.++++++++.||.||++++||||+++| ||..+++.+++|.++|||+|++|+|.||.|++|+|++..  +...++.++
T Consensus       344 ~r~~ei~~Isr~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~lsDLreSg~IeqdAD~v~~l~R~~~y~~~~~~~g~~e  423 (460)
T PRK07004        344 NRATEISEISRSLKSLAKELDVPVIALSQLNRGLEQRPNKRPVMSDLRESGAIEQDADVILFIYRDEVYNPDSPDKGTAE  423 (460)
T ss_pred             cHHHHHHHHHHHHHHHHHHhCCeEEEEeccChhhhccCCCCCChHHHhcchhhhhcCCEEEEeccccccCCCcCCCCceE
Confidence            78888999999999999999999999999 999988888999999999999999999999999998742  223346799


Q ss_pred             EEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          508 VCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       508 l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      +.|.|||||++|++   ++.|+++++||.+.
T Consensus       424 ~ivaKnR~G~~G~v---~l~f~~~~~~F~~~  451 (460)
T PRK07004        424 IIIGKQRNGPIGPV---RLTFLGQYTKFDNF  451 (460)
T ss_pred             EEEEccCCCCCceE---EEEEecCCCcccCC
Confidence            99999999999975   79999999999875

>PRK05636 replicative DNA helicase; Provisional

Probab=100.00  E-value=1.4e-45  Score=383.64  Aligned_cols=264  Identities=18%  Similarity=0.263  Sum_probs=230.1

Q ss_pred             HHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH
Q 009230          264 FDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA  342 (539)
Q Consensus       264 ~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~  342 (539)
                      +++++++.. ..+...|+||||+.||++++ |++|+|++|+|+||+|||+|+++++.++|.++|.+|+|||+||+.++++
T Consensus       232 ~~~i~~~~~-~~~~~~Gi~TG~~~LD~~t~Gl~~G~Liiiaarpg~GKT~~al~~a~~~a~~~g~~v~~fSlEMs~~ql~  310 (505)
T PRK05636        232 MDELEMLSS-QGGIATGIPTGFKDLDDLTNGLRGGQMIIVAARPGVGKSTLALDFMRSASIKHNKASVIFSLEMSKSEIV  310 (505)
T ss_pred             HHHHHHHHh-CCCCCCceecChHHHhhhcCCCCCCceEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEEeeCCHHHHH
Confidence            344444332 23556899999999999998 9999999999999999999999999999876789999999999999999


Q ss_pred             HHHHHHhhCCCccccccCCCCCCCCHHHHHHHH---HHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccc
Q 009230          343 RKLLEKHIKKPFFEANYGGSAERMTVEEFEQGK---AWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPY  419 (539)
Q Consensus       343 ~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~---~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~  419 (539)
                      .|+++..+++++.+++.+    .+++++|.++.   .++.+.+++|  ++....++++|.+.+++++.++++++|||| |
T Consensus       311 ~R~ls~~s~v~~~~i~~g----~l~~~e~~~~~~a~~~l~~~~l~I--~d~~~~ti~~I~~~~r~~~~~~~~~lvvID-Y  383 (505)
T PRK05636        311 MRLLSAEAEVRLSDMRGG----KMDEDAWEKLVQRLGKIAQAPIFI--DDSANLTMMEIRSKARRLKQKHDLKLIVVD-Y  383 (505)
T ss_pred             HHHHHHhcCCCHHHHhcC----CCCHHHHHHHHHHHHHHhcCCEEE--ECCCCCCHHHHHHHHHHHHHhcCCCEEEEc-c
Confidence            999999999999999865    79999987754   4566677887  346678899999999999999999999999 9


Q ss_pred             cccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCC
Q 009230          420 NELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDP  498 (539)
Q Consensus       420 ~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~  498 (539)
                      ++++.......++.+++.++++.||.||++++||||+++| ||..+++.+++|.++||++|++|+|.||.|++|+|++..
T Consensus       384 Lql~~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~lsQLnR~~e~r~dkrP~lsDLreSG~IEqdAD~vl~l~R~~~y  463 (505)
T PRK05636        384 LQLMSSGKRVESRQQEVSEFSRQLKLLAKELDVPLIAISQLNRGPESRTDKRPQLADLRESGSLEQDADMVMLLYRPDSQ  463 (505)
T ss_pred             hHhcCCCCCCCcHHHHHHHHHHHHHHHHHHhCCeEEEEeecCccccccCCCCCcHHHHhhcccccccCCEEEEEeccccc
Confidence            9998743334567788999999999999999999999999 999998888999999999999999999999999998743


Q ss_pred             --CCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          499 --EAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       499 --~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                        +...++.++|+|.|||||++|++   .+.|+++++||.+.
T Consensus       464 ~~~~~~~g~~elivaK~RnG~~Gtv---~l~f~~~~~rF~~~  502 (505)
T PRK05636        464 DKDDERAGEADIILAKHRGGPIDTV---QVAHQLHYSRFVDM  502 (505)
T ss_pred             CCccCCCCceEEEEecCCCCCCceE---EEEeecCccccccc
Confidence              22335689999999999999986   79999999999875

>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]

Probab=100.00  E-value=1.3e-45  Score=368.79  Aligned_cols=266  Identities=23%  Similarity=0.324  Sum_probs=240.2

Q ss_pred             cchHHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH
Q 009230          261 RDYFDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR  339 (539)
Q Consensus       261 ~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~  339 (539)
                      .++++++++.+.+. + ..|+||||+.||.+++ |++|+|++++|+||+|||+|++++|.++|...+.+|++||+||+.+
T Consensus       161 ~~~~~~i~~~~~~~-~-~~Gi~tgf~~LD~~t~G~~~~dLii~AaRP~mGKTafalnia~n~a~~~~~~v~iFSLEM~~e  238 (435)
T COG0305         161 KETMDEIEARFENG-G-LIGVPTGFTDLDEITSGFRPGDLIIVAARPGMGKTALALNIALNAAADGRKPVAIFSLEMSEE  238 (435)
T ss_pred             HHHHHHHHHHhccC-C-CcccccCchhhHHHhcCCccCCEEEEccCCCCChHHHHHHHHHHHHHhcCCCeEEEEccCCHH
Confidence            34566777776542 3 8999999999999998 9999999999999999999999999999998789999999999999


Q ss_pred             HHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEE
Q 009230          340 EHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVI  416 (539)
Q Consensus       340 ~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvI  416 (539)
                      +++.|+++..++++..+++.|    .+++++|..+   .+.+++.++||  ++.+..++.+|++.+++++.++++++|||
T Consensus       239 ql~~R~Ls~~s~v~~~kirtg----~l~~~d~~~l~~a~~~l~~~~i~I--dD~~~~si~eir~~aRrlk~~~~l~~i~i  312 (435)
T COG0305         239 QLVMRLLSSESGIESSKLRTG----RLSDDEWERLIKAASELSEAPIFI--DDTPGLTITEIRSKARRLKLKHNLGLIVI  312 (435)
T ss_pred             HHHHHhhccccccchhccccc----cccHHHHHHHHHHHHHHhhCCeee--cCCCcCCHHHHHHHHHHHHHhcCccEEEE
Confidence            999999999999999999977    7999998775   56777788887  55788899999999999999999999999


Q ss_pred             ccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          417 DPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       417 D~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                      | |.+++.+.....++.+.+.++++.||.||++++|||++++| +|..++|.+++|.++|+|+||+|+|.||.|+++||+
T Consensus       313 D-YLqLm~~~~~~~~r~qevs~iSr~LK~lAkEl~vpvialSQLsR~~E~R~dkrP~lSDLRESGsIEQDAD~VmflyRd  391 (435)
T COG0305         313 D-YLQLMTGGKKSENRKQEVSEISRSLKGLAKELGVPVIALSQLNRSVEQRTDKRPMLSDLRESGALEQDADIVIFLHRD  391 (435)
T ss_pred             E-EEEeecccccchhHHHHHHHHHHHHHHHHHhcCCcEEehhhhcccchhccccCCccccCccCCchhhhCCEEEEEech
Confidence            9 99999877655788899999999999999999999999999 999999999999999999999999999999999998


Q ss_pred             CCC--CCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          496 RDP--EAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       496 ~~~--~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      +..  +.+..+.++++|.|||||++|++   .+.|++++.+|.+.
T Consensus       392 e~y~~~~~~~g~aeiIi~K~RnGp~GtV---~l~f~~~~~~F~~~  433 (435)
T COG0305         392 EAYLKDTPDRGEAEVIVAKNRNGPTGTV---KLAFDPQFTKFKNL  433 (435)
T ss_pred             hhccCCCCCCceEEEEEEeccCCCCceE---EEEEeccccccccc
Confidence            743  22344789999999999999987   69999999999864

>PRK08760 replicative DNA helicase; Provisional

Probab=100.00  E-value=2.6e-45  Score=381.23  Aligned_cols=266  Identities=18%  Similarity=0.227  Sum_probs=230.4

Q ss_pred             chHHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHH
Q 009230          262 DYFDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVRE  340 (539)
Q Consensus       262 ~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~  340 (539)
                      ++++.+++.+.. .+...|+||||+.||++++ |++|+|++|+|+||+|||+|++++|.++|.++|.+|+|||+||+.++
T Consensus       194 ~~~~~~~~~~~~-~~~~~Gi~TG~~~LD~~t~G~~~G~LivIaarPg~GKTafal~iA~~~a~~~g~~V~~fSlEMs~~q  272 (476)
T PRK08760        194 DAFEELRNRFEN-GGNITGLPTGYNDFDAMTAGLQPTDLIILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSMEMSASQ  272 (476)
T ss_pred             HHHHHHHHHHhC-CCCCCcccCCcHHHHHHhcCCCCCceEEEEeCCCCChhHHHHHHHHHHHHhcCCceEEEeccCCHHH
Confidence            344455554433 4557899999999999998 99999999999999999999999999999766999999999999999


Q ss_pred             HHHHHHHHhhCCCccccccCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEc
Q 009230          341 HARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVID  417 (539)
Q Consensus       341 ~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID  417 (539)
                      ++.|+++..++++...++.+    .+++++|.++   .+++.+.+++|  ++....++++|...+++++.++++++||||
T Consensus       273 l~~Rl~a~~s~i~~~~i~~g----~l~~~e~~~~~~a~~~l~~~~l~I--~d~~~~t~~~I~~~~r~l~~~~~~~lVvID  346 (476)
T PRK08760        273 LAMRLISSNGRINAQRLRTG----ALEDEDWARVTGAIKMLKETKIFI--DDTPGVSPEVLRSKCRRLKREHDLGLIVID  346 (476)
T ss_pred             HHHHHHHhhCCCcHHHHhcC----CCCHHHHHHHHHHHHHHhcCCEEE--eCCCCCCHHHHHHHHHHHHHhcCCCEEEEe
Confidence            99999999999999988865    7888887654   56677777777  335667899999999999999999999999


Q ss_pred             cccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          418 PYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       418 ~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                       |++++.......++.+++.++++.||.||++++||||+++| ||..+++.+++|.++||++|++|+|.||.|++|||++
T Consensus       347 -yLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~lsDLreSg~IeqdAD~vl~l~R~~  425 (476)
T PRK08760        347 -YLQLMSVPGNSENRATEISEISRSLKGLAKELNVPVIALSQLNRSLETRTDKRPVMADLRESGAIEQDADMIVFIYRDD  425 (476)
T ss_pred             -cHHhcCCCCCCcccHHHHHHHHHHHHHHHHHhCCEEEEeeccCccccccCCCCCCHHHHhhccchhcCCCEEEEEechh
Confidence             88888654334567778999999999999999999999999 9999888889999999999999999999999999986


Q ss_pred             CC--C-CCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          497 DP--E-AGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       497 ~~--~-~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      ..  + .+.++.++|+|.|||||++|.+   .+.|+++++||.+.
T Consensus       426 ~y~~~~~~~~~~~eliiaKnR~G~~g~~---~l~f~~~~~~f~~~  467 (476)
T PRK08760        426 YYNKENSPDKGLAEIIIGKHRGGPTGSC---KLKFFGEYTRFDNL  467 (476)
T ss_pred             hcccccccCCCceEEEEEccCCCCCceE---EEEEecCCCceecc
Confidence            32  2 2235679999999999999875   79999999999885

>PRK06321 replicative DNA helicase; Provisional

Probab=100.00  E-value=9.7e-45  Score=375.01  Aligned_cols=253  Identities=17%  Similarity=0.209  Sum_probs=223.1

Q ss_pred             CCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCc
Q 009230          276 GDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPF  354 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~  354 (539)
                      +...|+||||+.||++++ |++|+|++|+|+||+|||+|+++++.++|..+|.+|+|||+||+.++++.|+++..++++.
T Consensus       204 ~~~~Gi~tG~~~LD~~t~Gl~~G~LiiiaarPgmGKTafal~ia~~~a~~~g~~v~~fSLEMs~~ql~~Rlla~~s~v~~  283 (472)
T PRK06321        204 PMISGIPTHFIDLDKMINGFSPSNLMILAARPAMGKTALALNIAENFCFQNRLPVGIFSLEMTVDQLIHRIICSRSEVES  283 (472)
T ss_pred             CCCCccccCcHHHHHHhcCCCCCcEEEEEeCCCCChHHHHHHHHHHHHHhcCCeEEEEeccCCHHHHHHHHHHhhcCCCH
Confidence            456799999999999998 9999999999999999999999999999976699999999999999999999999999999


Q ss_pred             cccccCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCC---C
Q 009230          355 FEANYGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRP---V  428 (539)
Q Consensus       355 ~~i~~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~---~  428 (539)
                      .+++.+    .++.++|.++   ...+.+.+++|  ++.+..++++|.+.+++++.++++++|||| |++++....   .
T Consensus       284 ~~i~~~----~l~~~e~~~~~~a~~~l~~~~~~i--dd~~~~ti~~i~~~~r~~~~~~~~~lvvID-yLql~~~~~~~~~  356 (472)
T PRK06321        284 KKISVG----DLSGRDFQRIVSVVNEMQEHTLLI--DDQPGLKITDLRARARRMKESYDIQFLIID-YLQLLSGSGNLRN  356 (472)
T ss_pred             HHhhcC----CCCHHHHHHHHHHHHHHHcCCEEE--eCCCCCCHHHHHHHHHHHHHhcCCCEEEEc-chHHcCCCCccCC
Confidence            998865    7888888765   45566677877  335677899999999999999999999999 889886432   2


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCC-CCCCCcE
Q 009230          429 SQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPE-AGPIDRV  506 (539)
Q Consensus       429 ~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~-~~~~~~~  506 (539)
                      ..++..++.++++.||.||++++||||+++| ||+.+++.+++|.++|||+|++|+|.||.|++|+|++..+ ...++.+
T Consensus       357 ~~~r~~ei~~Isr~LK~lAkel~vpVi~lsQLnR~~e~r~~krP~lsDLReSG~IEqdAD~v~~l~R~~~y~~~~~~~~~  436 (472)
T PRK06321        357 SESRQTEISEISRMLKNLARELNIPILCLSQLSRKVEDRANHRPMMSDLRESGSIEQDSDLVMFLLRREYYDPNDKPGTA  436 (472)
T ss_pred             cchHHHHHHHHHHHHHHHHHHhCCcEEEEeecChhhhccCCCCCCHHHHhhcccccccCCEEEEEechhhcCCcCCCCce
Confidence            3456678999999999999999999999999 9999988889999999999999999999999999976422 1234679


Q ss_pred             EEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          507 QVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       507 ~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      ++.|.|||+|++|.+   .+.|++++.||.+.
T Consensus       437 elivaKnR~G~~G~v---~l~f~~~~~~f~~~  465 (472)
T PRK06321        437 ELIVAKNRHGSIGSV---PLVFEKEFARFRNY  465 (472)
T ss_pred             EEEEEecCCCCCceE---EEEEecCCCcccCc
Confidence            999999999999875   79999999999875

>PRK06749 replicative DNA helicase; Provisional

Probab=100.00  E-value=9.9e-45  Score=372.02  Aligned_cols=270  Identities=17%  Similarity=0.217  Sum_probs=227.6

Q ss_pred             cccchHHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          259 NFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       259 ~~~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      ++.+.++++.+......+...|+||||+.||++++ |++|+|++|+|+||+|||+|+++++.++|.+ |.+|+|||+||+
T Consensus       147 ~~~~~~~~~~~~~~~~~~~~~Gi~TG~~~LD~~t~Gl~~G~LiiIaarPgmGKTafal~ia~~~a~~-g~~v~~fSlEMs  225 (428)
T PRK06749        147 DLKDALVDLYEELHQDAKEITGIETGYTSLNKMTCGLQEGDFVVLGARPSMGKTAFALNVGLHAAKS-GAAVGLFSLEMS  225 (428)
T ss_pred             cHHHHHHHHHHHHHhcCCCCCCccCCcHHHHHHhCCCCCCcEEEEEeCCCCCchHHHHHHHHHHHhc-CCCEEEEEeeCC
Confidence            44454444322222234567899999999999998 9999999999999999999999999999975 999999999999


Q ss_pred             HHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcC--Cc
Q 009230          338 VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHG--VR  412 (539)
Q Consensus       338 ~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~--~~  412 (539)
                      .++++.|+++..++++..+++.+  ...+++++|.++   ...+.+.+++|  ++.+..++++|.+.+++++.+++  +.
T Consensus       226 ~~ql~~R~ls~~~~i~~~~l~~~--~~~l~~~e~~~~~~a~~~l~~~~i~i--~d~~~~t~~~I~~~~r~~~~~~~~~~~  301 (428)
T PRK06749        226 SKQLLKRMASCVGEVSGGRLKNP--KHRFAMEDWEKVSKAFAEIGELPLEI--YDNAGVTVQDIWMQTRKLKRKHGDKKI  301 (428)
T ss_pred             HHHHHHHHHHhccCCCHHHHhcC--cccCCHHHHHHHHHHHHHHhcCCEEE--ECCCCCCHHHHHHHHHHHHHhcCCCCc
Confidence            99999999999999999888753  125788887654   45666777877  34677889999999999998887  45


Q ss_pred             EEEEccccccccCC-CCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEE
Q 009230          413 GLVIDPYNELDHQR-PVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGI  490 (539)
Q Consensus       413 ~vvID~~~~l~~~~-~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl  490 (539)
                      +|||| |++++... ....++.++++.+++.||.||++++||||+++| ||..+++.+++|.++|||+|++|+|.||.|+
T Consensus       302 lvvID-yLqli~~~~~~~~~r~~ei~~isr~LK~lAkel~vpVi~lsQLnR~~e~r~~krP~lsDLR~SG~IEqdAD~vl  380 (428)
T PRK06749        302 LIIVD-YLQLITGDPKHKGNRFQEISEISRKLKLLARELNVCVVALSQLSRSVESRQDKRPLLSDLRETGQIEQDADVIM  380 (428)
T ss_pred             EEEEe-ChhhcCCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEEEecCccccccCCCCCchHhhhhcccccccCCEEE
Confidence            99999 99988643 223567788999999999999999999999999 9999888889999999999999999999999


Q ss_pred             EEEeCCCC--CCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceecc
Q 009230          491 VIHRNRDP--EAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMD  537 (539)
Q Consensus       491 ~l~r~~~~--~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~  537 (539)
                      +|+|++..  +...++.++++|.|||||++|.+   .+.|+++++||.+
T Consensus       381 ~l~R~~~y~~~~~~~~~~eliiaKnR~G~~G~v---~~~f~~~~~~f~~  426 (428)
T PRK06749        381 LMYREDYYDKETMQKEMTEIHVAKHRNGPVGSF---KLRFLKEFGRFVE  426 (428)
T ss_pred             EEeecccccccccCCCceEEEEecCCCCCCceE---EEEEecCcccccC
Confidence            99998742  22234679999999999999875   7999999999986

>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=100.00  E-value=2.7e-45  Score=356.65  Aligned_cols=249  Identities=24%  Similarity=0.341  Sum_probs=211.4

Q ss_pred             ccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccc
Q 009230          280 GISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEAN  358 (539)
Q Consensus       280 gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~  358 (539)
                      |+||||+.||++++ +++|+|++|+|+||+|||+|++|++.+++.++|.+|+|||+||+.+++..|+++..++++..+++
T Consensus         1 Gi~TG~~~LD~~lgG~~~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~~~~vly~SlEm~~~~l~~R~la~~s~v~~~~i~   80 (259)
T PF03796_consen    1 GIPTGFPALDRLLGGLRPGELTVIAARPGVGKTAFALQIALNAALNGGYPVLYFSLEMSEEELAARLLARLSGVPYNKIR   80 (259)
T ss_dssp             SB-SSTHHHHHHHSSB-TT-EEEEEESTTSSHHHHHHHHHHHHHHTTSSEEEEEESSS-HHHHHHHHHHHHHTSTHHHHH
T ss_pred             CCCCChHHHHHHhcCCCcCcEEEEEecccCCchHHHHHHHHHHHHhcCCeEEEEcCCCCHHHHHHHHHHHhhcchhhhhh
Confidence            79999999999998 99999999999999999999999999999975799999999999999999999999999999998


Q ss_pred             cCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHH-cCCcEEEEccccccccCCCCCCCHHH
Q 009230          359 YGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLR-HGVRGLVIDPYNELDHQRPVSQTETE  434 (539)
Q Consensus       359 ~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~-~~~~~vvID~~~~l~~~~~~~~~~~~  434 (539)
                      .+    .++++++.++   .+++.+..+++.  +.+..++++|.+.++.+..+ .++++|||| |++++.......++++
T Consensus        81 ~g----~l~~~e~~~~~~~~~~l~~~~l~i~--~~~~~~~~~i~~~i~~~~~~~~~~~~v~ID-yl~ll~~~~~~~~~~~  153 (259)
T PF03796_consen   81 SG----DLSDEEFERLQAAAEKLSDLPLYIE--DTPSLTIDDIESKIRRLKREGKKVDVVFID-YLQLLKSEDSSDNRRQ  153 (259)
T ss_dssp             CC----GCHHHHHHHHHHHHHHHHTSEEEEE--ESSS-BHHHHHHHHHHHHHHSTTEEEEEEE-EGGGSBTSCSSSCCHH
T ss_pred             cc----ccCHHHHHHHHHHHHHHhhCcEEEE--CCCCCCHHHHHHHHHHHHhhccCCCEEEec-hHHHhcCCCCCCCHHH
Confidence            65    6888877654   566777777763  25677999999999999988 889999999 8888877545667788


Q ss_pred             HHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCC--CCCCCcEEEEEE
Q 009230          435 YVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPE--AGPIDRVQVCVR  511 (539)
Q Consensus       435 ~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~--~~~~~~~~l~i~  511 (539)
                      .+..+++.||.+|+++|||||+++| ||..+++.+++|+++|++||+.|+|.||+||+|+|++..+  ....+..+|+|.
T Consensus       154 ~~~~i~~~Lk~lA~~~~i~vi~~sQlnr~~~~~~~~~p~l~dl~~sg~Ie~~AD~vl~l~r~~~~~~~~~~~~~~~l~v~  233 (259)
T PF03796_consen  154 EIGEISRELKALAKELNIPVIALSQLNREAEDREDKRPSLSDLRESGAIEQDADVVLFLHRDEKYDEDRDDKGEAELIVA  233 (259)
T ss_dssp             HHHHHHHHHHHHHHHHTSEEEEEEEBSGGGGGSSSCS--HHHHCSTSSHHHH-SEEEEEEEHCHCHCCSSCTTEEEEEEE
T ss_pred             HHHHHHHHHHHHHHHcCCeEEEccccChhhhcccccccchhhhhhhHHHHHHHhhhhhhccchhhccccCCCCeEEEEEE
Confidence            9999999999999999999999999 9988877788999999999999999999999999987432  223458999999


Q ss_pred             EeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          512 KVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       512 K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      |||+|++|.+   .+.|+++++||.|.
T Consensus       234 KnR~G~~g~v---~~~f~~~~~~f~~~  257 (259)
T PF03796_consen  234 KNRNGPTGTV---PLRFNPETSRFTDL  257 (259)
T ss_dssp             EESSS--EEE---EEEEETTTTEEEE-
T ss_pred             ecCCCCCceE---EEEEECCCCeEeec
Confidence            9999988865   79999999999985

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK06904 replicative DNA helicase; Validated

Probab=100.00  E-value=2.3e-44  Score=373.24  Aligned_cols=255  Identities=16%  Similarity=0.217  Sum_probs=221.5

Q ss_pred             CCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          275 SGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       275 ~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      .+...|+||||+.||++++ |++|+|++|+|+||+|||+|++++|.++|...|.+|+|||+||+.++++.|+++..++++
T Consensus       198 ~~~~~Gi~TG~~~LD~~t~Gl~~G~LiiIaarPg~GKTafalnia~~~a~~~g~~Vl~fSlEMs~~ql~~Rlla~~s~v~  277 (472)
T PRK06904        198 NNGVTGVTTGFTDLDKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMASEKPVLVFSLEMPAEQIMMRMLASLSRVD  277 (472)
T ss_pred             CCCCCCccCChHHHHHHHhccCCCcEEEEEeCCCCChHHHHHHHHHHHHHhcCCeEEEEeccCCHHHHHHHHHHhhCCCC
Confidence            3567899999999999998 999999999999999999999999999997669999999999999999999999999999


Q ss_pred             ccccccCCCCCCCCHHHHHHHH---HHhhc-cceeEeecCCCCCCHHHHHHHHHHHHHHc-CCcEEEEccccccccCCCC
Q 009230          354 FFEANYGGSAERMTVEEFEQGK---AWLSN-TFSLIRCENDSLPSIKWVLDLAKAAVLRH-GVRGLVIDPYNELDHQRPV  428 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~---~~l~~-~~~~i~~~~~~~~~~~~i~~~i~~~~~~~-~~~~vvID~~~~l~~~~~~  428 (539)
                      ..+++.+   ..++.++|.++.   ..+.. .+++|  ++.+..++++|.+.++++..++ ++++|||| |++|+.....
T Consensus       278 ~~~i~~g---~~l~~~e~~~~~~a~~~l~~~~~l~I--~d~~~~t~~~i~~~~r~~~~~~~~~~lvvID-YLqli~~~~~  351 (472)
T PRK06904        278 QTKIRTG---QNLDQQDWAKISSTVGMFKQKPNLYI--DDSSGLTPTELRSRARRVYRENGGLSLIMVD-YLQLMRAPGF  351 (472)
T ss_pred             HHHhccC---CCCCHHHHHHHHHHHHHHhcCCCEEE--ECCCCCCHHHHHHHHHHHHHhCCCCCEEEEe-cHHhcCCCCC
Confidence            9988754   158889887754   45543 34776  3356778999999999888776 69999999 9999975433


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCC--C-CCC
Q 009230          429 SQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEA--G-PID  504 (539)
Q Consensus       429 ~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~--~-~~~  504 (539)
                      ..++..+++++++.||.||+++|||||+++| ||..+++.+++|.++|||||++|+|.||.|++|+|++..+.  . .++
T Consensus       352 ~~~r~~ei~~isr~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~lsDLreSG~IEqdAD~v~~l~R~~~y~~~~~~~~~  431 (472)
T PRK06904        352 EDNRTLEIAEISRSLKALAKELKVPVVALSQLNRTLENRGDKRPVNSDLRESGSIEQDADLIMFIYRDEVYNETTEDNKG  431 (472)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhCCeEEEEEecCchhhccCCCCCchHHHhhcCccccCCcEEEEEeccccccCccccCCC
Confidence            3567778999999999999999999999999 99998888999999999999999999999999999864221  1 246


Q ss_pred             cEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          505 RVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       505 ~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      .+++.|.|||+|++|.+   .+.|+++++||.+.
T Consensus       432 ~~elivaKnR~G~~G~v---~l~f~~~~~~f~~~  462 (472)
T PRK06904        432 VAEIIIGKQRNGPIGRV---RLAFQGQYSRFDNL  462 (472)
T ss_pred             ceEEEEeccCCCCCceE---EEEEccCCCCcccc
Confidence            79999999999999875   79999999999875

>PRK05595 replicative DNA helicase; Provisional

Probab=100.00  E-value=1.3e-44  Score=376.48  Aligned_cols=265  Identities=19%  Similarity=0.294  Sum_probs=229.3

Q ss_pred             hHHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHH
Q 009230          263 YFDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREH  341 (539)
Q Consensus       263 ~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~  341 (539)
                      +++++++.+.+ .+...|+||||+.||++++ |++|+|++|+|+||+|||+|+++++.++|.++|.+|+|||+||+.+++
T Consensus       167 ~~~~~~~~~~~-~~~~~gi~tg~~~ld~~~~G~~~g~liviaarpg~GKT~~al~ia~~~a~~~g~~vl~fSlEms~~~l  245 (444)
T PRK05595        167 GFEQIENLFNN-KGETTGVASGFRELDAKTSGFQKGDMILIAARPSMGKTTFALNIAEYAALREGKSVAIFSLEMSKEQL  245 (444)
T ss_pred             HHHHHHHHHhC-CCCCCcccCChHHHHHhcCCCCCCcEEEEEecCCCChHHHHHHHHHHHHHHcCCcEEEEecCCCHHHH
Confidence            34445554443 4556799999999999998 999999999999999999999999999886569999999999999999


Q ss_pred             HHHHHHHhhCCCccccccCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcc
Q 009230          342 ARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDP  418 (539)
Q Consensus       342 ~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~  418 (539)
                      +.|+++..++++...++.+    .++.++|.++   .+.+.+.+++|  ++....++++|.+.+++++.++|+++|||| 
T Consensus       246 ~~R~~a~~~~v~~~~~~~~----~l~~~e~~~~~~~~~~l~~~~l~i--~d~~~~t~~~i~~~~r~~~~~~~~~~vvID-  318 (444)
T PRK05595        246 AYKLLCSEANVDMLRLRTG----NLEDKDWENIARASGPLAAAKIFI--DDTAGVSVMEMRSKCRRLKIEHGIDMILID-  318 (444)
T ss_pred             HHHHHHHhcCCCHHHHhcC----CCCHHHHHHHHHHHHHHhcCCEEE--ECCCCCCHHHHHHHHHHHHHhcCCCEEEEe-
Confidence            9999999999999988765    7888887665   45566677777  335678899999999999988999999999 


Q ss_pred             ccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC
Q 009230          419 YNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD  497 (539)
Q Consensus       419 ~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~  497 (539)
                      |++++.......++.+++.++++.||.||+++|||||+++| ||..+++.+++|.++||++|++|+|.||.||+|+|++.
T Consensus       319 ylql~~~~~~~~~r~~~v~~is~~LK~lAke~~i~vi~lsQLnR~~e~r~~~rP~lsdlr~Sg~Ieq~AD~vl~l~r~~~  398 (444)
T PRK05595        319 YLQLMSGGKGSESRQQEVSEISRSIKALAKEMECPVIALSQLSRAPEQRADHRPMLSDLRESGSIEQDADVVMFLYRDEY  398 (444)
T ss_pred             HHHhccCCCCCccHHHHHHHHHHHHHHHHHHhCCeEEEeeccCcchhccCCCCCchhhhhhhcccccCCCEEEEEecccc
Confidence            88998754334567788999999999999999999999999 99998888899999999999999999999999999874


Q ss_pred             C--CCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          498 P--EAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       498 ~--~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      .  +...++..++.|.|||+|++|.+   .+.|+++++||.+.
T Consensus       399 ~~~~~~~~~~~e~iv~K~R~G~~g~~---~~~~~~~~~~f~~~  438 (444)
T PRK05595        399 YNKETEDKNVAECIIAKQRNGPTGTV---KLAWLGQYSKFGNL  438 (444)
T ss_pred             cccccCCCCceEEEEEccCCCCCceE---EEEEecCCCccccc
Confidence            2  22345789999999999999875   79999999999874

>PRK08506 replicative DNA helicase; Provisional

Probab=100.00  E-value=3.4e-44  Score=373.48  Aligned_cols=252  Identities=19%  Similarity=0.251  Sum_probs=219.7

Q ss_pred             CCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCc
Q 009230          276 GDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPF  354 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~  354 (539)
                      ....|+||||+.||++++ |++|+|++|+|+||+|||+|+++++.+++.+ |.+|+|||+||++++++.|+++..+++++
T Consensus       170 ~~~~Gi~TG~~~LD~~~~G~~~G~LivIaarpg~GKT~fal~ia~~~~~~-g~~V~~fSlEMs~~ql~~Rlla~~s~v~~  248 (472)
T PRK08506        170 KDIIGLDTGFVELNKMTKGFNKGDLIIIAARPSMGKTTLCLNMALKALNQ-DKGVAFFSLEMPAEQLMLRMLSAKTSIPL  248 (472)
T ss_pred             CCCCcccCChHHHHhhcCCCCCCceEEEEcCCCCChHHHHHHHHHHHHhc-CCcEEEEeCcCCHHHHHHHHHHHhcCCCH
Confidence            456799999999999998 9999999999999999999999999999875 99999999999999999999999999999


Q ss_pred             cccccCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHc-CCcEEEEccccccccCCCCCC
Q 009230          355 FEANYGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRH-GVRGLVIDPYNELDHQRPVSQ  430 (539)
Q Consensus       355 ~~i~~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~-~~~~vvID~~~~l~~~~~~~~  430 (539)
                      .+++.+    .+++++|.++   .+.+.+.+++|  ++.+..++++|.+.+++++.++ ++++|||| |++++.......
T Consensus       249 ~~i~~~----~l~~~e~~~~~~a~~~l~~~~l~I--~d~~~~ti~~I~~~~r~l~~~~~~~~lvvID-yLql~~~~~~~~  321 (472)
T PRK08506        249 QNLRTG----DLDDDEWERLSDACDELSKKKLFV--YDSGYVNIHQVRAQLRKLKSQHPEIGLAVID-YLQLMSGSGNFK  321 (472)
T ss_pred             HHHhcC----CCCHHHHHHHHHHHHHHHcCCeEE--ECCCCCCHHHHHHHHHHHHHhCCCCCEEEEc-ChhhccCCCCCC
Confidence            998865    7898888654   46677777887  3356778999999999988775 59999999 888987543335


Q ss_pred             CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCC----------
Q 009230          431 TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPE----------  499 (539)
Q Consensus       431 ~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~----------  499 (539)
                      ++..++..+++.||.||+++|||||+++| ||..+++.+++|.++|||||++|+|.||+|++|||++..+          
T Consensus       322 ~r~~ev~~isr~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~lsDLreSg~IeqdAD~vl~l~R~~~y~~~~~~~~~~~  401 (472)
T PRK08506        322 DRHLQISEISRGLKLLARELDIPIIALSQLNRSLESRADKRPMLSDLRESGAIEQDADIILFVYRDDVYKEREEKEKEKK  401 (472)
T ss_pred             CHHHHHHHHHHHHHHHHHHhCCcEEEEeecCcchhhccCCCCChHHhhcchhhhhcCCEEEEEecccccccccccccccc
Confidence            67788999999999999999999999999 9999888889999999999999999999999999985211          


Q ss_pred             ---CC-----------CCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          500 ---AG-----------PIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       500 ---~~-----------~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                         .+           ..+.++++|.|||||++|++   .+.|++++.||.+.
T Consensus       402 ~~~~g~~~~~~~~~~~~~~~~eliiaKnR~G~~G~v---~l~f~~~~~~f~~~  451 (472)
T PRK08506        402 AKKEGKEERRIHFQNKSIEEAEIIIGKNRNGPTGTV---KLRFQKEFTRFVDK  451 (472)
T ss_pred             cccccccccccccccccccceEEEEecCCCCCCceE---EEEEecCCccccCC
Confidence               00           01248999999999998875   79999999999885

>PRK09165 replicative DNA helicase; Provisional

Probab=100.00  E-value=3.4e-44  Score=375.37  Aligned_cols=254  Identities=22%  Similarity=0.289  Sum_probs=222.4

Q ss_pred             CCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh--------------cCCeEEEEeCCCCHH
Q 009230          275 SGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEH--------------AGWKFVLCSMENKVR  339 (539)
Q Consensus       275 ~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~--------------~g~~vl~~s~E~~~~  339 (539)
                      .+...|+||||+.||++++ |.+|+|++|+|+||+|||+|+++++.++|.+              +|.+|+|||+||+++
T Consensus       194 ~~~~~gi~TG~~~LD~~~gG~~~g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSlEMs~~  273 (497)
T PRK09165        194 DGHLSGISTGLRDLDSKLGGLHPSDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSLEMSAE  273 (497)
T ss_pred             CCCCCcccCChHHHhhhcCCCCCCceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeCcCCHH
Confidence            4567899999999999998 9999999999999999999999999999875              268999999999999


Q ss_pred             HHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHH---HHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEE
Q 009230          340 EHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGK---AWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVI  416 (539)
Q Consensus       340 ~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~---~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvI  416 (539)
                      +++.|+++..++++...++.+    .++.+++.++.   ..+...+++|.  +.+..++++|.+.+++++.++++++|||
T Consensus       274 ql~~R~la~~s~v~~~~i~~~----~l~~~e~~~l~~a~~~l~~~~l~I~--d~~~~ti~~i~~~ir~l~~~~~~~lvvI  347 (497)
T PRK09165        274 QLATRILSEQSEISSSKIRRG----KISEEDFEKLVDASQELQKLPLYID--DTPALSISQLRARARRLKRQHGLDLLVV  347 (497)
T ss_pred             HHHHHHHHHhcCCCHHHHhcC----CCCHHHHHHHHHHHHHHhcCCeEEe--CCCCCCHHHHHHHHHHHHHhcCCCEEEE
Confidence            999999999999999988765    79999887654   45666778873  3567789999999999999999999999


Q ss_pred             ccccccccCCC--CCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEE
Q 009230          417 DPYNELDHQRP--VSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIH  493 (539)
Q Consensus       417 D~~~~l~~~~~--~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~  493 (539)
                      | |++++....  ...++.+++..+++.||.||+++|||||+++| ||..+++.+++|.++|||||++|+|.||.|++|+
T Consensus       348 D-yLqli~~~~~~~~~~r~~ev~~is~~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~lsDLr~Sg~IEqdAD~v~~l~  426 (497)
T PRK09165        348 D-YLQLIRGSSKRSSDNRVQEISEITQGLKALAKELNIPVIALSQLSRQVEQRDDKRPQLSDLRESGSIEQDADVVMFVY  426 (497)
T ss_pred             c-chHhccCCCCCCCCchHHHHHHHHHHHHHHHHHhCCeEEEeecccchhhccCCCCCchhhhhhccchhccCCEEEEEe
Confidence            9 888886442  23566678999999999999999999999999 9999888889999999999999999999999999


Q ss_pred             eCCCCCC-------------------CCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          494 RNRDPEA-------------------GPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       494 r~~~~~~-------------------~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      |++..+.                   ...+.+++.|.|||+|++|++   .+.|+++++||.+.
T Consensus       427 R~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~e~ivaKnR~G~~g~~---~~~f~~~~~~f~~~  487 (497)
T PRK09165        427 REEYYLKRKEPREGTPKHEEWQEKMEKVHNKAEVIIAKQRHGPTGTV---KLAFESEFTRFGDL  487 (497)
T ss_pred             ehhhhccccccccccchhhhhhhhhcccCCceEEEEeccCCCCCeeE---EEEEecCCCcccCc
Confidence            9753110                   013679999999999999875   79999999999885

>PHA02542 41 41 helicase; Provisional

Probab=100.00  E-value=1.1e-43  Score=366.82  Aligned_cols=267  Identities=16%  Similarity=0.195  Sum_probs=227.0

Q ss_pred             ccchHHHHHHHhhccCCCccccccCchhhhhhh-c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          260 FRDYFDEIDAYYHRTSGDEFGISTGWRALNELY-N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       260 ~~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~-~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.++++.++++.....+...|+||||+.||.++ | +.+|+|++|+|+||+|||+|++++|.+++.+ |.+|+|||+||+
T Consensus       151 ~~~~~~~ie~~~~~~~~~~~gi~TG~~~LD~~t~gGl~~G~LiiIaarPgmGKTtfalniA~~~a~~-g~~Vl~fSLEM~  229 (473)
T PHA02542        151 GHDYFEDYEERYDSYQSKANKIPFKLEILNKITKGGAERKTLNVLLAGVNVGKSLGLCSLAADYLQQ-GYNVLYISMEMA  229 (473)
T ss_pred             HHHHHHHHHHHHhhccCCCCccCCCcHHHHHhccCCCCCCcEEEEEcCCCccHHHHHHHHHHHHHhc-CCcEEEEeccCC
Confidence            356677777754322344789999999999999 6 9999999999999999999999999999964 999999999999


Q ss_pred             HHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHh---hccceeEeecCCCCCCHHHHHHHHHHHHHHcC--Cc
Q 009230          338 VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWL---SNTFSLIRCENDSLPSIKWVLDLAKAAVLRHG--VR  412 (539)
Q Consensus       338 ~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l---~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~--~~  412 (539)
                      .++++.|+++..+++++.+++      .+++++|.+..+.+   ...+++|..++.+..++.+|...++++..+++  ++
T Consensus       230 ~~ql~~Rl~a~~~~i~~~~l~------~l~~~~~~~~~~~~~~~~~~~l~I~~~d~~~lt~~~ir~~~rrlk~~~g~~~d  303 (473)
T PHA02542        230 EEVIAKRIDANLLDVSLDDID------DLSKAEYKAKMEKLRSKTQGKLIIKQYPTGGAHAGHFRALLNELKLKKNFKPD  303 (473)
T ss_pred             HHHHHHHHHHHHcCCCHHHHh------hcCHHHHHHHHHHHHHHhCCCceeecCCCCCCCHHHHHHHHHHHHHhcCCCCC
Confidence            999999999999999998875      37888887655443   33456554344677789999999999987776  89


Q ss_pred             EEEEccccccccCC---CCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccce
Q 009230          413 GLVIDPYNELDHQR---PVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       413 ~vvID~~~~l~~~~---~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      +|||| |++|+...   ....++.++++++++.||.||+++|||||+++| ||+.+++.+  |.++|+|||++|+|.||.
T Consensus       304 lVvID-YLqL~~~~~~~~~~~nr~~ei~~Isr~LK~lAkel~vpVi~lsQLnR~~e~r~d--P~lsDLreSG~IEqdAD~  380 (473)
T PHA02542        304 VIIVD-YLGICASSRLRVSSENSYTYVKAIAEELRGLAVEHDVVVWTAAQTTRSGWDSSD--VDMSDTAESAGLPATADF  380 (473)
T ss_pred             EEEEe-chhhccCCcccCCCCChHHHHHHHHHHHHHHHHHhCCeEEEEEeeCccccccCC--CcchhcccccchHhhcCE
Confidence            99999 99998632   123577888999999999999999999999999 999887654  999999999999999999


Q ss_pred             EEEEEeCCCCCCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          489 GIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       489 vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      |++|+|++..+  ..+.++++|.|||+|++|++|.+.+.|+++++||.++
T Consensus       381 vl~l~r~~~~~--~~~~~eliv~KnR~G~~g~~g~v~l~f~~~~~~F~~~  428 (473)
T PHA02542        381 MLAVIETEELA--QMGQQLVKQLKSRYGDKNKFNKFLMGVDKGNQRWYDV  428 (473)
T ss_pred             EEEEecCcccc--cCCeEEEEEecCCCCCCCCceEEEEEEECCcCccccc
Confidence            99999987542  2367999999999999998888999999999999885

>TIGR00665 DnaB replicative DNA helicase

Probab=100.00  E-value=2.2e-43  Score=368.35  Aligned_cols=266  Identities=21%  Similarity=0.308  Sum_probs=226.7

Q ss_pred             hHHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHH
Q 009230          263 YFDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREH  341 (539)
Q Consensus       263 ~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~  341 (539)
                      +++++++.... .+...|+||||+.||++++ |++|+|++|+|+||+|||+|+++++.+++..+|.+|+|||+||+++++
T Consensus       161 ~~~~~~~~~~~-~~~~~gi~tG~~~LD~~~~G~~~G~l~vi~g~pg~GKT~~~l~~a~~~a~~~g~~vl~~SlEm~~~~i  239 (434)
T TIGR00665       161 TVEEIEELYER-GGGITGVPTGFTDLDKLTSGLQPSDLIILAARPSMGKTAFALNIAENAAIKEGKPVAFFSLEMSAEQL  239 (434)
T ss_pred             HHHHHHHHHhC-CCCCCcccCCchhhHhhcCCCCCCeEEEEEeCCCCChHHHHHHHHHHHHHhCCCeEEEEeCcCCHHHH
Confidence            34445444332 3457899999999999998 999999999999999999999999999997669999999999999999


Q ss_pred             HHHHHHHhhCCCccccccCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcc
Q 009230          342 ARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDP  418 (539)
Q Consensus       342 ~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~  418 (539)
                      +.|+++..++++...++.+    .++.+++.++   .+.+.+.++++.  +.+..++++|.+.+++++.++|+++|||| 
T Consensus       240 ~~R~~~~~~~v~~~~~~~g----~l~~~~~~~~~~a~~~l~~~~l~i~--d~~~~~~~~i~~~i~~~~~~~~~~~vvID-  312 (434)
T TIGR00665       240 AMRMLSSESRVDSQKLRTG----KLSDEDWEKLTSAAGKLSEAPLYID--DTPGLTITELRAKARRLKREHGLGLIVID-  312 (434)
T ss_pred             HHHHHHHhcCCCHHHhccC----CCCHHHHHHHHHHHHHHhcCCEEEE--CCCCCCHHHHHHHHHHHHHhcCCCEEEEc-
Confidence            9999999999999888765    6888877554   456766777773  34567899999999999999999999999 


Q ss_pred             ccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC
Q 009230          419 YNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD  497 (539)
Q Consensus       419 ~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~  497 (539)
                      |++++.......++..++..+++.||.||+++|||||+++| ||..+++.+++|.++|++||+.|+|.||.||+|+|++.
T Consensus       313 ~l~~i~~~~~~~~r~~~i~~i~~~Lk~lA~e~~i~vi~lsqlnr~~~~r~~~~p~lsdlr~Sg~ieq~aD~vi~l~r~~~  392 (434)
T TIGR00665       313 YLQLMSGSGRSENRQQEVSEISRSLKALAKELNVPVIALSQLSRSVEQREDKRPQLSDLRESGSIEQDADIVMFLYRDEY  392 (434)
T ss_pred             chHhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEEeccCcchhccCCCCCChHHHhhccchhhcCCEEEEeccccc
Confidence            77777543323466678899999999999999999999999 99988777899999999999999999999999999873


Q ss_pred             --CCCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccCC
Q 009230          498 --PEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDIV  539 (539)
Q Consensus       498 --~~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~~  539 (539)
                        ++...++.+++.|.|||+|++|.+   .+.|+++++||.|.+
T Consensus       393 ~~~~~~~~~~~~l~v~KnR~G~~g~~---~l~~~~~~~~f~~~~  433 (434)
T TIGR00665       393 YNPDSEDKGIAEIIIAKQRNGPTGTV---KLAFQGEYTRFENLA  433 (434)
T ss_pred             cCCCcCCCCceEEEEecCCCCCCCeE---EEEEecCCCcccCCC
Confidence              222335679999999999988865   899999999999863

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.

>KOG2373 consensus Predicted mitochondrial DNA helicase twinkle [Replication, recombination and repair]

Probab=100.00  E-value=6.3e-44  Score=334.47  Aligned_cols=436  Identities=19%  Similarity=0.236  Sum_probs=341.6

Q ss_pred             hcCCCHHHHHHcCcccccC-CceeEEEEeEe----eCCE-EEEEE------eecCCCcccc-----cCCCCCcccccccc
Q 009230           58 ERLISAETLRRNRVMQKRH-GHEVVIAFPYW----RNGK-LVNCK------YRDFNKKFWQ-----EKDTEKVFYGLDDI  120 (539)
Q Consensus        58 ~Rgi~~~~~~~~~~~~~~~-~~~~~i~fP~~----~~G~-~~~~~------~R~~~~~~~~-----~~~~~~~l~g~~~~  120 (539)
                      --.|+.+++.+|.+++... ...+++.||.+    .++. +.+.|      .|....+|--     ......++||++.+
T Consensus        39 lt~i~~~tl~rf~Vry~~p~~~qp~~~FP~~~~~tp~~~~~~GlK~l~e~~~~~~g~~ye~~~~~~~r~a~~~~fGL~l~  118 (514)
T KOG2373|consen   39 LTNISFETLARFNVRYQTPTYGQPAILFPRYRGMTPRLRIPMGLKLLREVGDRMEGENYELPDETSVRQAFNGVFGLHLA  118 (514)
T ss_pred             cchhhhhhhccccccccCcccCCCccccccccccCccchhhhhhHHHHHhhhccccccCCCCcccchhhhhcceeceeec
Confidence            3677899999999876432 24569999933    2221 12333      2222223321     12567889999988


Q ss_pred             CC-CCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCccchH
Q 009230          121 EG-ESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQA  199 (539)
Q Consensus       121 ~~-~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~~G~~  199 (539)
                      .. ...|+||-.|.|++++.++....++++|-|...      +|..           .+++|++|++||+|+--|...++
T Consensus       119 ~rrd~~vVltsne~D~lal~~~t~~~t~~LP~g~~~------lP~~-----------~LPyLE~F~~i~fWl~~d~~sw~  181 (514)
T KOG2373|consen  119 TRRDRSVVLTSNERDALALYEATKALTFALPHGEIL------LPQL-----------VLPYLEEFDKIYFWLPVDHVSWS  181 (514)
T ss_pred             ccccceEEEeecchhHHHHhhhcCceEEEccccccc------CcHH-----------HHHHHHhhheEEEEecccccchH
Confidence            65 568999999999999999986668999988865      5532           36899999999999999999999


Q ss_pred             HHHHHHHHhcCCceEEEecCCCCCCCCCCChHHHHHhcCcchHHHHHHhccccCccccccccchHHHHHHHhhccCCCcc
Q 009230          200 LAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEF  279 (539)
Q Consensus       200 ~~~~~~~~l~~~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~~~~~~~A~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  279 (539)
                      ||+.++..|...+|..++ |....+      .-.....+.-.+..++..|.+..++++.++.++.++|..-+.+ -+.+.
T Consensus       182 aAk~fa~kLn~~rClLvr-p~e~~p------~p~~al~~rlnl~~il~~a~p~~hk~i~sf~~mRe~ilseL~N-~e~v~  253 (514)
T KOG2373|consen  182 AAKDFASKLNTLRCLLVR-PEERPP------EPVRALDHRLNLNSILNSAVPMRHKGIRSFTDMREGILSELLN-TERVV  253 (514)
T ss_pred             HHHHHHhhcCcceEEEEC-CCCCCc------chhhhhcccccHHHHHhhhchhhhhhhhhHHHHHHHHHHHHhh-hhhhh
Confidence            999999999999999998 543222      2222223455677888999999999999999999988777665 56778


Q ss_pred             cccc-Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCcccc
Q 009230          280 GIST-GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEA  357 (539)
Q Consensus       280 gi~t-g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i  357 (539)
                      |+.| .||.|+++++ .++|||++++|++|+|||||+...++.++.+ |.+++|.|+|++..+++..|+.+.+|.++.+-
T Consensus       254 G~~WkRFpvLNk~LkGhR~GElTvlTGpTGsGKTTFlsEYsLDL~~Q-GVnTLwgSFEi~n~rla~~mL~Qyagyrl~dr  332 (514)
T KOG2373|consen  254 GFQWKRFPVLNKYLKGHRPGELTVLTGPTGSGKTTFLSEYSLDLFTQ-GVNTLWGSFEIPNKRLAHWMLVQYAGYRLLDR  332 (514)
T ss_pred             ceeehhhhHHHHHhccCCCCceEEEecCCCCCceeEehHhhHHHHhh-hhhheeeeeecchHHHHHHHHHHHccCchHhh
Confidence            8887 6999999998 9999999999999999999999999999997 99999999999999999999999988755321


Q ss_pred             ccCCCCCCCCH-HHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHH
Q 009230          358 NYGGSAERMTV-EEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYV  436 (539)
Q Consensus       358 ~~~~~~~~l~~-~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~  436 (539)
                              +.. .-|..   .+...++|++.. .+...++.+++.|...+.-+++..|||||+..+|....-..++...+
T Consensus       333 --------l~~y~HWad---rFErlplyfmtf-hgqq~~~~vi~~i~ha~yV~di~HViIDNLQFmmg~~~~~~Drf~~Q  400 (514)
T KOG2373|consen  333 --------LNSYKHWAD---RFERLPLYFMTF-HGQQFMEKVINEIAHAIYVEDIQHVIIDNLQFMMGQGMMALDRFHLQ  400 (514)
T ss_pred             --------hhhhhHHHH---HHhccchHhhhh-cccchHHHHHHHHHHHHHHHhhhhhhhhhHHHHhccchhccchhhhH
Confidence                    110 11222   222334444321 46777889999999888889999999999998887654345677788


Q ss_pred             HHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCC
Q 009230          437 SQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNK  516 (539)
Q Consensus       437 ~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g  516 (539)
                      +.++..+++||.++||||.+|.|+||.++  ++....+++-||....|.||+||++.+.+...  .++...+.|.|||. 
T Consensus       401 D~iig~fR~fAT~nn~HvTlVvHPRKed~--d~El~t~s~fGsAkatQEADNVliiQdkrl~~--~rgkkyLqi~KNRy-  475 (514)
T KOG2373|consen  401 DRIIGYFRQFATQNNIHVTLVVHPRKEDG--DTELDTQSFFGSAKATQEADNVLIIQDKRLDR--DRGKKYLQILKNRY-  475 (514)
T ss_pred             HHHHHHHHHHhhccceeEEEEecccccCC--CceeeehhhccccccccccccEEEEeeccccc--ccchhhhhhhhhcc-
Confidence            89999999999999999999999999875  67788899999999999999999998766532  24567899999887 


Q ss_pred             CcceeeeEEEEEeCCCceecc
Q 009230          517 VVGTIGEAFLSYNRVTGEYMD  537 (539)
Q Consensus       517 ~~G~~~~~~l~fd~~~~rf~~  537 (539)
                       .|.+|..+|+|+.....|.-
T Consensus       476 -~Gdvg~~pLEf~kn~ltyS~  495 (514)
T KOG2373|consen  476 -YGDVGSDPLEFVKNPLTYSH  495 (514)
T ss_pred             -cCcccccceeeccCCccccc
Confidence             57888889999988877753

>PRK05748 replicative DNA helicase; Provisional

Probab=100.00  E-value=3e-43  Score=367.23  Aligned_cols=265  Identities=19%  Similarity=0.289  Sum_probs=226.8

Q ss_pred             HHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH
Q 009230          264 FDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA  342 (539)
Q Consensus       264 ~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~  342 (539)
                      ++.++..... .+...|+||||+.||++++ |++|+|++|+|+||+|||+|+++++.++|.++|.+|+|||+||++++++
T Consensus       170 ~~~l~~~~~~-~~~~~gi~TG~~~LD~~~~G~~~G~livIaarpg~GKT~~al~ia~~~a~~~g~~v~~fSlEms~~~l~  248 (448)
T PRK05748        170 YDRIEMLHNQ-TGDITGIPTGFTDLDKMTSGLQPNDLIIVAARPSVGKTAFALNIAQNVATKTDKNVAIFSLEMGAESLV  248 (448)
T ss_pred             HHHHHHHHhc-CCCCCCccCChHHHHHhcCCCCCCceEEEEeCCCCCchHHHHHHHHHHHHhCCCeEEEEeCCCCHHHHH
Confidence            3444443332 3566899999999999998 9999999999999999999999999999876699999999999999999


Q ss_pred             HHHHHHhhCCCccccccCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHc-CCcEEEEcc
Q 009230          343 RKLLEKHIKKPFFEANYGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRH-GVRGLVIDP  418 (539)
Q Consensus       343 ~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~-~~~~vvID~  418 (539)
                      .|+++..++++...++.+    .++.++|..+   ...+.+.+++|.  +.+..++++|.+.+++++.++ ++++|||| 
T Consensus       249 ~R~l~~~~~v~~~~i~~~----~l~~~e~~~~~~a~~~l~~~~~~i~--d~~~~ti~~i~~~~r~~~~~~~~~~~vvID-  321 (448)
T PRK05748        249 MRMLCAEGNIDAQRLRTG----QLTDDDWPKLTIAMGSLSDAPIYID--DTPGIKVTEIRARCRRLAQEHGGLGLILID-  321 (448)
T ss_pred             HHHHHHhcCCCHHHhhcC----CCCHHHHHHHHHHHHHHhcCCEEEE--CCCCCCHHHHHHHHHHHHHhcCCCCEEEEc-
Confidence            999999999998888765    7888887654   566777778873  355678999999999999888 79999999 


Q ss_pred             ccccccCCC-CCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          419 YNELDHQRP-VSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       419 ~~~l~~~~~-~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      |++++.... ...++.+.+..+++.||.||++++||||+++| ||..+++.+++|.++||+||++|+|.||.|++|+|++
T Consensus       322 yL~li~~~~~~~~~r~~~i~~i~~~LK~lAke~~i~vi~lsQlnr~~~~r~~k~p~lsdlr~Sg~Ieq~AD~v~~l~r~~  401 (448)
T PRK05748        322 YLQLIQGSGRSGENRQQEVSEISRSLKALAKELKVPVIALSQLSRGVEQRQDKRPVMSDIRESGSIEQDADIVAFLYRDD  401 (448)
T ss_pred             cchhcCCCCCCCcCHHHHHHHHHHHHHHHHHHhCCeEEEecccChhHhhcCCCCCChHHHHhhcchhcCCCEEEEEeccc
Confidence            888886432 23567778999999999999999999999999 9988878889999999999999999999999999987


Q ss_pred             CC--CCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccCC
Q 009230          497 DP--EAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDIV  539 (539)
Q Consensus       497 ~~--~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~~  539 (539)
                      ..  +...++.++++|.|||+|++|.+   .+.|++++.||.+.+
T Consensus       402 ~~~~~~~~~~~~e~~v~K~R~G~~g~~---~~~~~~~~~~f~~~~  443 (448)
T PRK05748        402 YYDEETENKNTIEIIIAKQRNGPVGTV---ELAFQKEYNKFVNLA  443 (448)
T ss_pred             ccCccccCCCceEEEEeccCCCCCceE---EEEEeCCCCcccccc
Confidence            42  22335689999999999999875   799999999998853

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=100.00  E-value=2.8e-42  Score=358.03  Aligned_cols=284  Identities=20%  Similarity=0.259  Sum_probs=227.7

Q ss_pred             CCChHHHHHhcCcchHHHHHHhccccCccccccccchHHH----HHHHhhccCCCccccccCchhhhhhhc-cCCCcEEE
Q 009230          227 FKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDE----IDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTI  301 (539)
Q Consensus       227 ~kD~nd~l~~~g~~~~~~~~~~A~~~~~~~~~~~~~~~~~----i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~  301 (539)
                      .+++.+.+..- ...+.++- ++......+..++.++.++    +++.... .+...|+||||+.||++++ |++|+|++
T Consensus       122 ~~~~~~~l~~~-~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~gi~tG~~~LD~~~~G~~~g~liv  198 (421)
T TIGR03600       122 GQTAEQKVEEA-QAALLALT-GMSDGQERGFVTFGEVLEDVVRDLDKRFNP-KGELTGLSTGLPKLDRLTNGLVKGDLIV  198 (421)
T ss_pred             CCCHHHHHHHH-HHHHHHhh-hhhccCcCCchhHHHHHHHHHHHHHHHhcC-CCCCcceeCCChhHHHHhcCCCCCceEE
Confidence            34777876542 11222222 1122233345555554443    4443322 3456899999999999997 99999999


Q ss_pred             EEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHH---HHHh
Q 009230          302 VTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG---KAWL  378 (539)
Q Consensus       302 i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~---~~~l  378 (539)
                      |+|+||+|||+|+++++.++|.++|.+|+|||+||++++++.|+++..++++...++.+    .++.+++.++   .+.+
T Consensus       199 iag~pg~GKT~~al~ia~~~a~~~g~~v~~fSlEm~~~~l~~Rl~~~~~~v~~~~~~~~----~l~~~~~~~~~~~~~~l  274 (421)
T TIGR03600       199 IGARPSMGKTTLALNIAENVALREGKPVLFFSLEMSAEQLGERLLASKSGINTGNIRTG----RFNDSDFNRLLNAVDRL  274 (421)
T ss_pred             EEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEECCCCHHHHHHHHHHHHcCCCHHHHhcC----CCCHHHHHHHHHHHHHH
Confidence            99999999999999999999965699999999999999999999999999999988765    7888887654   4566


Q ss_pred             hccceeEeecCCCCCCHHHHHHHHHHHHHHc-CCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEE
Q 009230          379 SNTFSLIRCENDSLPSIKWVLDLAKAAVLRH-GVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFV  457 (539)
Q Consensus       379 ~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~-~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~  457 (539)
                      .+.+++|  ++.+..++++|.+.+++++.++ ++++|||| |++++... ...++.+.+..+++.||.||++++||||++
T Consensus       275 ~~~~l~i--~d~~~~t~~~i~~~~r~~~~~~~~~~lvvID-yLql~~~~-~~~~~~~~~~~i~~~Lk~lAke~~i~Vi~l  350 (421)
T TIGR03600       275 SEKDLYI--DDTGGLTVAQIRSIARRIKRKKGGLDLIVVD-YIQLMAPT-RGRDRNEELGGISRGLKALAKELDVPVVLL  350 (421)
T ss_pred             hcCCEEE--ECCCCCCHHHHHHHHHHHHHhcCCCCEEEEe-cccccCCC-CCCCHHHHHHHHHHHHHHHHHHhCCcEEEe
Confidence            6667776  3356789999999999998887 79999999 88887653 345777889999999999999999999999


Q ss_pred             ec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCC--CCCCcEEEEEEEeeCCCccee
Q 009230          458 AH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEA--GPIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       458 ~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~--~~~~~~~l~i~K~R~g~~G~~  521 (539)
                      +| ||..+++.+++|.++||+||++|+|.||+|++|+|++..+.  ...+.+++.|.|||||++|.+
T Consensus       351 sQlnr~~~~r~~krp~lsdlr~Sg~Ieq~AD~v~~l~R~~~~~~~~~~~~~~el~v~K~R~G~~g~~  417 (421)
T TIGR03600       351 AQLNRGSEKRTDKRPIMSDLRDSGAIEQDADVIGLIHREGYYDAREPPAGVAELILAKNRHGPTGTV  417 (421)
T ss_pred             cccCcchhhcCCCCCChHHHhhcCCccccCcEEEEeccccccCCccCCCCceEEEEECCCCCCCceE
Confidence            99 99988888899999999999999999999999999875432  223679999999999999986

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.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=100.00  E-value=3.1e-36  Score=295.68  Aligned_cols=254  Identities=24%  Similarity=0.297  Sum_probs=203.7

Q ss_pred             ccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccc
Q 009230          278 EFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFE  356 (539)
Q Consensus       278 ~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~  356 (539)
                      ..++||||+.||++++ +++|++++|+|+||+|||+|++|++.+++.++|.+|+|||+||+.+++..|+++..+++++..
T Consensus        10 ~~~~~tg~~~Ld~~~gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~E~~~~~~~~r~~~~~~~~~~~~   89 (271)
T cd01122          10 NEEVWWPFPVLNKLTKGLRKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEEPVVRTARRLLGQYAGKRLHL   89 (271)
T ss_pred             ccCCCCCcceeeeeeEEEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEcccCHHHHHHHHHHHHhCCCccc
Confidence            3599999999999998 999999999999999999999999999988669999999999999999999999888887754


Q ss_pred             cccCCCCCCCCHHHHHHHHHHhhcc-ceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHH
Q 009230          357 ANYGGSAERMTVEEFEQGKAWLSNT-FSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEY  435 (539)
Q Consensus       357 i~~~~~~~~l~~~~~~~~~~~l~~~-~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~  435 (539)
                      ...   ....+.+++..+.+.+.+. .+++ .+..+..+++++++.++.++.++++++||||++..+........++...
T Consensus        90 ~~~---~~~~~~~~~~~~~~~~~~~~~l~i-~d~~~~~~~~~i~~~i~~~~~~~~~~~vvID~l~~l~~~~~~~~~~~~~  165 (271)
T cd01122          90 PDT---VFIYTLEEFDAAFDEFEGTGRLFM-YDSFGEYSMDSVLEKVRYMAVSHGIQHIIIDNLSIMVSDERASGDERKA  165 (271)
T ss_pred             CCc---cccccHHHHHHHHHHhcCCCcEEE-EcCCCccCHHHHHHHHHHHHhcCCceEEEECCHHHHhccCCCchhHHHH
Confidence            421   1235566666666666432 2333 2334455899999999999888999999999776665432123455566


Q ss_pred             HHHHHHHHHHHHHHhCcEEEEEec-CCCCCCC---CCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEE
Q 009230          436 VSQMLTMVKRFAQHHACHVWFVAH-PRQLHNW---VGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVR  511 (539)
Q Consensus       436 ~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~---~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~  511 (539)
                      +.+++..|+.+|++++|+|++++| ++....+   .+.+|+++|++||+.+++.||.||.|+++++.|...++...|.+.
T Consensus       166 ~~~~~~~L~~la~~~~vtvll~sq~~~~~~~~~~~~~~~~~~~d~~gs~~i~~~aD~vi~l~r~~~~e~~~~~~~~i~v~  245 (271)
T cd01122         166 LDEIMTKLRGFATEHGIHITLVSHLRRPDGDKTHEEGGEVSLSDFRGSAAIGQLADNVIALERNQQAELDERNTTYLRIL  245 (271)
T ss_pred             HHHHHHHHHHHHHHhCCEEEEEecccCccCCCccccCCCceEEeccCcHhHhhhccEEEEEEecCccccccCCcEEEEEE
Confidence            789999999999999999999999 6644332   246899999999999999999999999987643233467889999


Q ss_pred             EeeCC-CcceeeeEEEEEeCCCceecc
Q 009230          512 KVRNK-VVGTIGEAFLSYNRVTGEYMD  537 (539)
Q Consensus       512 K~R~g-~~G~~~~~~l~fd~~~~rf~~  537 (539)
                      |+|++ .+|..  +.+.||++|+||..
T Consensus       246 K~R~~~~~g~~--~~~~~~~~t~~~~~  270 (271)
T cd01122         246 KNRFTGGTGVA--GPLEYDKETGRLSP  270 (271)
T ss_pred             eeccCCCccce--eeEEEECCCceecC
Confidence            99985 55542  58999999999974

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=100.00  E-value=2.6e-36  Score=291.36  Aligned_cols=234  Identities=20%  Similarity=0.268  Sum_probs=196.0

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCC
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAER  365 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~  365 (539)
                      +||++++ +++|++++|+|+||+|||+|++|++.+++.++|.+|+|||+||++++++.|+++..++++...+..+    .
T Consensus         2 ~LD~~~~Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~E~~~~~~~~r~~~~~~~~~~~~~~~~----~   77 (242)
T cd00984           2 DLDNLTGGLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEMSKEQLLQRLLASESGISLSKLRTG----S   77 (242)
T ss_pred             chhhhhcCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeCCCCHHHHHHHHHHHhcCCCHHHHhcC----C
Confidence            5899998 9999999999999999999999999999997799999999999999999999999999998887755    5


Q ss_pred             CCHHHHHH---HHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHH
Q 009230          366 MTVEEFEQ---GKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTM  442 (539)
Q Consensus       366 l~~~~~~~---~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~  442 (539)
                      ++.+++..   +...+...++++.  ..+..++++|.+.++.++.++++++||||++..+.... ...++.+.+..+++.
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~i~--~~~~~~~~~l~~~i~~~~~~~~~~~vvID~l~~l~~~~-~~~~~~~~~~~~~~~  154 (242)
T cd00984          78 LSDEDWERLAEAIGELKELPIYID--DSSSLTVSDIRSRARRLKKEHGLGLIVIDYLQLMSGSK-KKGNRQQEVAEISRS  154 (242)
T ss_pred             CCHHHHHHHHHHHHHHhcCCEEEe--CCCCCCHHHHHHHHHHHHHhcCCCEEEEcCchhcCCCC-CCCCHHHHHHHHHHH
Confidence            66555443   3445555566653  24567899999999999999999999999665444322 245677889999999


Q ss_pred             HHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCC--CCCCCCcEEEEEEEeeCCCcc
Q 009230          443 VKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDP--EAGPIDRVQVCVRKVRNKVVG  519 (539)
Q Consensus       443 Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~--~~~~~~~~~l~i~K~R~g~~G  519 (539)
                      |+.||+++||+||+++| +|...++.+++|++++++||+.++|.||.||.|+|++..  +...++..+|.|.|||+|+.|
T Consensus       155 L~~la~~~~~~ii~~~q~~r~~~~~~~~~~~~~~~~gS~~i~~~aD~vi~l~~~~~~~~~~~~~~~~~l~v~KnR~G~~g  234 (242)
T cd00984         155 LKLLAKELNVPVIALSQLSRGVESRADKRPMLSDLRESGSIEQDADVVMFLYRDEYYNKESESKGIAEIIVAKNRNGPTG  234 (242)
T ss_pred             HHHHHHHhCCeEEEecccChhhhccCCCCCCHHHHhhhcccccCCCEEEEEecccccccccCCCCceEEEEECCCCCCCe
Confidence            99999999999999999 887655556789999999999999999999999998742  233467899999999998877


Q ss_pred             eeeeEEEEEeC
Q 009230          520 TIGEAFLSYNR  530 (539)
Q Consensus       520 ~~~~~~l~fd~  530 (539)
                      ++   .+.|+|
T Consensus       235 ~~---~l~~~~  242 (242)
T cd00984         235 TV---ELRFDG  242 (242)
T ss_pred             eE---EEEeeC
Confidence            64   788886

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.

>PRK07773 replicative DNA helicase; Validated

Probab=100.00  E-value=7e-32  Score=301.58  Aligned_cols=219  Identities=21%  Similarity=0.253  Sum_probs=190.4

Q ss_pred             hHHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHH
Q 009230          263 YFDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREH  341 (539)
Q Consensus       263 ~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~  341 (539)
                      +++++++..++ .+...|+||||+.||++++ |++|+|++|+|+||+|||+|++++|.++|.++|.+|+|||+||+.+++
T Consensus       183 ~~~~i~~~~~~-~~~~~Gi~TG~~~LD~l~~Gl~~G~livIagrPg~GKT~fal~ia~~~a~~~~~~V~~fSlEms~~ql  261 (886)
T PRK07773        183 TFDEIDAIASS-GGLARGVPTGFTELDAMTNGLHPGQLIIVAARPSMGKTTFGLDFARNCAIRHRLAVAIFSLEMSKEQL  261 (886)
T ss_pred             HHHHHHHHHhc-CCCCCCccCChhHhccccCCCCCCcEEEEEeCCCCCcHHHHHHHHHHHHHhcCCeEEEEecCCCHHHH
Confidence            34445554332 4557899999999999998 999999999999999999999999999998778999999999999999


Q ss_pred             HHHHHHHhhCCCccccccCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcc
Q 009230          342 ARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDP  418 (539)
Q Consensus       342 ~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~  418 (539)
                      +.|+++..++++..+++.+    .++.+++..+   ...+.+.+++|  ++.+..++++|.+.+++++.++++++|||| 
T Consensus       262 ~~R~~s~~~~i~~~~i~~g----~l~~~~~~~~~~a~~~l~~~~i~i--~d~~~~~i~~i~~~~r~~~~~~~~~lvvID-  334 (886)
T PRK07773        262 VMRLLSAEAKIKLSDMRSG----RMSDDDWTRLARAMGEISEAPIFI--DDTPNLTVMEIRAKARRLRQEANLGLIVVD-  334 (886)
T ss_pred             HHHHHHHhcCCCHHHHhcC----CCCHHHHHHHHHHHHHHhcCCEEE--ECCCCCCHHHHHHHHHHHHHhcCCCEEEEc-
Confidence            9999999999999999865    7888887654   45666777887  346677899999999999999999999999 


Q ss_pred             ccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceE
Q 009230          419 YNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNG  489 (539)
Q Consensus       419 ~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~v  489 (539)
                      |++++.......++.+.+.++++.||.||+++|||||+++| ||..+++.+++|.++|||+|+.+++.+-++
T Consensus       335 yLql~~~~~~~~~r~~ei~~isr~LK~lAkel~vpvi~lsQLnR~~e~r~~krP~lsDlres~~~~~d~~V~  406 (886)
T PRK07773        335 YLQLMTSGKKYENRQQEVSEISRHLKLLAKELEVPVVALSQLSRGVEQRTDKRPMLSDLRESGCLTGDTLIL  406 (886)
T ss_pred             chhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHCCcEEEecccCcchhccCCCCCCHHHHhhcCcccCcceEE
Confidence            88888754334677788999999999999999999999999 999998889999999999999999866554

>TIGR01391 dnaG DNA primase, catalytic core

Probab=99.95  E-value=8.4e-28  Score=246.67  Aligned_cols=181  Identities=28%  Similarity=0.390  Sum_probs=144.4

Q ss_pred             CCCcHHHHHHHHhcCCCHHHHHHcCcccccCC------------------------------------ceeEEEEeEe-e
Q 009230           46 EPLGNELRAYFAERLISAETLRRNRVMQKRHG------------------------------------HEVVIAFPYW-R   88 (539)
Q Consensus        46 ~p~~~~~~~Yl~~Rgi~~~~~~~~~~~~~~~~------------------------------------~~~~i~fP~~-~   88 (539)
                      .|.+..+.+||.+|||++++++.|++++...+                                    .+++|+||++ .
T Consensus       131 ~~~~~~a~~YL~~RGis~e~i~~f~lGyap~~~~~l~~~l~~k~~~~~~~l~~~Gl~~~~~~g~~~d~Fr~RiifPi~d~  210 (415)
T TIGR01391       131 TPENRAALDYLQSRGLSDETIDRFELGYAPNNWDFLFDFLQNKKGFDLELLAEAGLLVKKENGKYYDRFRNRIMFPIHDP  210 (415)
T ss_pred             CccchHHHHHHHHcCCCHHHHHHcCCCCCCCcHHHHHHHHHhccCCCHHHHHHCCCeEECCCCCeeeecCCeEEEEEECC
Confidence            34355678999999999999999987543211                                    1358999988 7


Q ss_pred             CCEEEEEEeecC---CCcccccCC-----CCCcccccccc----CCCCcEEEEechhhHHHHHHhCCCceEEcCCCCCCC
Q 009230           89 NGKLVNCKYRDF---NKKFWQEKD-----TEKVFYGLDDI----EGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSS  156 (539)
Q Consensus        89 ~G~~~~~~~R~~---~~~~~~~~~-----~~~~l~g~~~~----~~~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~  156 (539)
                      .|++++|.+|.+   .+||.+++.     +...+||++..    .+.++|+||||++||||++|+|+.++|++. |++. 
T Consensus       211 ~G~vvgf~gR~~~~~~pKYlNspet~~f~K~~~lygl~~a~~~~~~~~~viivEG~~Daisl~~~G~~~aVA~~-Gtal-  288 (415)
T TIGR01391       211 KGRVVGFGGRALGDEKPKYLNSPETPLFKKSELLYGLHKARKEIRKEKELILVEGYMDVIALHQAGIKNAVASL-GTAL-  288 (415)
T ss_pred             CCCEEEEEeeecCCCCCceeCCCCCCCccCCccccCHhHHHHhhccCCcEEEEecHHHHHHHHHCCCCcEEECC-CCCC-
Confidence            899999999988   467887653     47789999864    346789999999999999999999888865 5532 


Q ss_pred             CCCCCCCChhhhhhhHHHHhHHHHhcc-CCEEEEEecCCccchHHHHHHHHHhcC--CceEEEecCCCCCCCCCCChHHH
Q 009230          157 VSKKNVPSEEQDTKYQYLWNCKMYLKQ-ASRIILATDGDPPGQALAEELARRVGR--ERCWRVRWPKKNDVDHFKDANEV  233 (539)
Q Consensus       157 ~~~~~l~~~~~~~~~~~l~~~~~~l~~-~~~ivl~~DnD~~G~~~~~~~~~~l~~--~~~~~~~~p~~~~~~~~kD~nd~  233 (539)
                            .           ..++..|.+ .++||+|+|+|.||++|+.++++.+..  ..++++.+|      .+|||||+
T Consensus       289 ------t-----------~~~~~~l~r~~~~vvl~~D~D~aG~~aa~r~~~~l~~~g~~v~v~~lp------~gkDpdd~  345 (415)
T TIGR01391       289 ------T-----------EEHIKLLKRYADEIILCFDGDKAGRKAALRAIELLLPLGINVKVIKLP------GGKDPDEY  345 (415)
T ss_pred             ------c-----------HHHHHHHHhhCCeEEEEeCCCHHHHHHHHHHHHHHHHcCCeEEEEECC------CCCCHHHH
Confidence                  1           112344544 469999999999999999999888843  457788887      58999999


Q ss_pred             HHhcCcchHHHHHHhccc
Q 009230          234 LMYLGPGALKEVVENAEL  251 (539)
Q Consensus       234 l~~~g~~~~~~~~~~A~~  251 (539)
                      +++.|.+++.+++++|.+
T Consensus       346 l~~~g~~~~~~~l~~a~~  363 (415)
T TIGR01391       346 LRKEGVEALKKLLENSKS  363 (415)
T ss_pred             HHHhCHHHHHHHHhcCCC
Confidence            999999999999999875

This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).

>PRK05667 dnaG DNA primase; Validated

Probab=99.95  E-value=3e-27  Score=250.19  Aligned_cols=182  Identities=27%  Similarity=0.423  Sum_probs=146.9

Q ss_pred             CCCcHHHHHHHHhcCCCHHHHHHcCcccccCC------------------------------------ceeEEEEeEe-e
Q 009230           46 EPLGNELRAYFAERLISAETLRRNRVMQKRHG------------------------------------HEVVIAFPYW-R   88 (539)
Q Consensus        46 ~p~~~~~~~Yl~~Rgi~~~~~~~~~~~~~~~~------------------------------------~~~~i~fP~~-~   88 (539)
                      .|.++.+.+||.+|||++++++.|++++...+                                    .+++|+||++ .
T Consensus       127 ~~~~~~a~~YL~~RGls~~~i~~f~lGyap~~~~~L~~~l~~~~~~~~~l~~~GL~~~~~~~~~~yd~Fr~RimfPI~d~  206 (580)
T PRK05667        127 TPEGAEARQYLYKRGLSEETIERFGIGYAPDGWDALLKHLGGKGFSEKELEEAGLLIKNEDGGGPYDRFRNRIMFPIRDL  206 (580)
T ss_pred             CccchHHHHHHHHcCCCHHHHHHhCCccCCChHHHHHHHHHhcCCCHHHHHHCCceEecCCCCCcchhcCCeEEEEEECC
Confidence            45667789999999999999999988643211                                    1468999988 7


Q ss_pred             CCEEEEEEeecC---CCcccccC-----CCCCccccccccC----CCCcEEEEechhhHHHHHHhCCCceEEcCCCCCCC
Q 009230           89 NGKLVNCKYRDF---NKKFWQEK-----DTEKVFYGLDDIE----GESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSS  156 (539)
Q Consensus        89 ~G~~~~~~~R~~---~~~~~~~~-----~~~~~l~g~~~~~----~~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~  156 (539)
                      .|++++|.+|.+   .+||.+++     .++..+||++...    +.++|+||||++|+||++|+|+.++|++. |++. 
T Consensus       207 ~G~vigF~GR~l~~~~pKYlNSpet~iF~K~~~LYgl~~a~~~i~~~~~viivEG~~Dvisl~q~Gi~naVA~l-Gtal-  284 (580)
T PRK05667        207 RGRVIGFGGRVLGDDKPKYLNSPETPLFHKGRVLYGLDEARKAIAKKKQVIVVEGYMDVIALHQAGITNAVASL-GTAL-  284 (580)
T ss_pred             CCcEEEEEeeecCCCCCeeeCCCCCCCccCCccccCccHHHHhcccCCeEEEEeeHHHHHHHHHcCCCcEEEeC-CCCC-
Confidence            899999999988   37888866     3468899998754    46799999999999999999999988864 5532 


Q ss_pred             CCCCCCCChhhhhhhHHHHhHHHHhcc-CCEEEEEecCCccchHHHHHHHHH---h--cCCceEEEecCCCCCCCCCCCh
Q 009230          157 VSKKNVPSEEQDTKYQYLWNCKMYLKQ-ASRIILATDGDPPGQALAEELARR---V--GRERCWRVRWPKKNDVDHFKDA  230 (539)
Q Consensus       157 ~~~~~l~~~~~~~~~~~l~~~~~~l~~-~~~ivl~~DnD~~G~~~~~~~~~~---l--~~~~~~~~~~p~~~~~~~~kD~  230 (539)
                            .           ..++..|.+ ..+||+|+|+|.||++|+.++++.   +  .+..++++.+|      .+|||
T Consensus       285 ------t-----------~~~~~~L~r~~~~vil~~D~D~AG~~aa~r~~~~~~~l~~~g~~v~vv~lp------~gkDp  341 (580)
T PRK05667        285 ------T-----------EEHLKLLRRLTDEVILCFDGDKAGRKAALRALELALPLLKDGRQVRVAFLP------DGKDP  341 (580)
T ss_pred             ------C-----------HHHHHHHHhcCCeEEEEeCCCHHHHHHHHHHHHHHHHHHhCCceEEEEECC------CCCCh
Confidence                  1           122445554 358999999999999999998887   4  23467888888      58999


Q ss_pred             HHHHHhcCcchHHHHHHhcccc
Q 009230          231 NEVLMYLGPGALKEVVENAELY  252 (539)
Q Consensus       231 nd~l~~~g~~~~~~~~~~A~~~  252 (539)
                      ||+++++|.+++.+++++|.++
T Consensus       342 dd~l~~~G~~~~~~~i~~a~~~  363 (580)
T PRK05667        342 DDLVRKEGPEAFRALLEQAIPL  363 (580)
T ss_pred             HHHHHHhCHHHHHHHHHcCCCH
Confidence            9999999999999999998753

>TIGR00646 MG010 DNA primase-related protein

Probab=99.95  E-value=1.8e-26  Score=209.12  Aligned_cols=175  Identities=21%  Similarity=0.310  Sum_probs=140.7

Q ss_pred             HHHHHHHHhcCCCHHHHHHcCcccccCCceeEEEEeEe-eCCEEEEEEeecC--CCcccccC-----CCCCcccccccc-
Q 009230           50 NELRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYW-RNGKLVNCKYRDF--NKKFWQEK-----DTEKVFYGLDDI-  120 (539)
Q Consensus        50 ~~~~~Yl~~Rgi~~~~~~~~~~~~~~~~~~~~i~fP~~-~~G~~~~~~~R~~--~~~~~~~~-----~~~~~l~g~~~~-  120 (539)
                      ..+..||+++|++...+-..|....|.+...+|+||++ ..|++|+|.+|.+  .++|++++     .++..+||++.. 
T Consensus        28 ~~l~~~l~~~g~~~~~~~~~G~~~~y~~~~~RimFPI~d~~G~vvgFgGR~l~~~~KYlNspet~~f~K~~~Lygl~~~~  107 (218)
T TIGR00646        28 RCAMNYLKKRGFNLQDFLKVGGGLAYLGEKEWLNLPLYNFDGNLIGFLNRKVGFEKEFLYLPFNKPPSKSEAFLGLKELP  107 (218)
T ss_pred             HHHHHHHHHcCCCHHHHHHcCCCEEecccCCEEEEEEECCCCCEEEEeccCCCCCCCcccCCCCCCcccchhhcCcchhh
Confidence            45899999999999999999854456777789999988 8999999999999  58899866     457779998544 


Q ss_pred             CCCCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhcc--CCEEEEEecCCccch
Q 009230          121 EGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQ--ASRIILATDGDPPGQ  198 (539)
Q Consensus       121 ~~~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~--~~~ivl~~DnD~~G~  198 (539)
                      .+.+.++||||.||++|++|+|+.++|+. +|++-.                  ..++..|++  .++|+||+|+|.||+
T Consensus       108 ~k~~~vilvEGymDVIsl~qaGi~naVAs-lGTALT------------------~~q~~lLkr~~~~~Iil~~D~D~AG~  168 (218)
T TIGR00646       108 IEDNSIYLVEGDFDWLAFRKAGILNCLPL-CGLTIS------------------DKQMKFFKQKKIEKIFICFDNDFAGK  168 (218)
T ss_pred             cCCCEEEEEecHHHHHHHHHCCCCeEEEc-CchHhH------------------HHHHHHHhccCCCEEEEEeCCCHHHH
Confidence            44678999999999999999999998874 566521                  122455665  479999999999999


Q ss_pred             HHHHHHHHHhc--CCceEEEecCCCCCCCCCCChHHHHHhcCcchHHHHHHhc
Q 009230          199 ALAEELARRVG--RERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENA  249 (539)
Q Consensus       199 ~~~~~~~~~l~--~~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~~~~~~~A  249 (539)
                      +|+.++.+.+.  +..+.++.+|     ..+|||||+++..+ +...+++.++
T Consensus       169 ~Aa~r~~~~L~~~G~~v~vv~lP-----~~~KDwNEllk~~~-~~w~~~l~~~  215 (218)
T TIGR00646       169 NAAANLEEILKKAGFITKVIEIK-----AAAKDWNDLFLLNN-KNWAAALRDH  215 (218)
T ss_pred             HHHHHHHHHHHHCCCeEEEEeCC-----CcCCChhHHHHHhh-hhHHHHHHhh
Confidence            99999999883  4567888888     57899999999765 3345555553

The DNA primase DnaG of E. coli and its apparent orthologs in other eubacterial species are approximately 600 residues in length. Within this set, a conspicuous outlier in percent identity, as seen in a UPGMA difference tree, is the branch containing the Mycoplasmas. This lineage is also unique in containing the small, DNA primase-related protein modelled by this alignment, which is homologous to the central third of DNA primase. Several small regions of sequence similarity specifically to Mycoplasma sequences rather than to all DnaG homologs suggests that the divergence of this protein from DnaG post-dated the separation of bacterial lineages. The function of this DNA primase-related protein is unknown.

>PHA02540 61 DNA primase; Provisional

Probab=99.92  E-value=4.8e-25  Score=214.76  Aligned_cols=175  Identities=19%  Similarity=0.312  Sum_probs=131.9

Q ss_pred             CCcHHHHHHHHhcCCCHHHHHHcCcccccC--------------CceeEEEEeEe-eCCEEEEEEeecCC----Cccccc
Q 009230           47 PLGNELRAYFAERLISAETLRRNRVMQKRH--------------GHEVVIAFPYW-RNGKLVNCKYRDFN----KKFWQE  107 (539)
Q Consensus        47 p~~~~~~~Yl~~Rgi~~~~~~~~~~~~~~~--------------~~~~~i~fP~~-~~G~~~~~~~R~~~----~~~~~~  107 (539)
                      |....+++||++|||++++++.++....+.              ..+++|+||++ ..|++++|.+|.++    +||.+.
T Consensus       125 ~~~~~a~~YL~~RGi~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~d~~RImFPI~d~~G~vigFgGR~l~~~~~pKYlNS  204 (337)
T PHA02540        125 PEDHPIIKYVENRCIPKDKWKLLYFTREWQKLVNSIKPDTYKKEKPEPRLVIPIFNKDGKIESFQGRALRKDAPQKYITI  204 (337)
T ss_pred             cccHHHHHHHHHcCCCHHHHHhcCCCccHHHHHHHHhhccCchhccCCeeEEEEECCCCCEEEEEeEECCCCCCCCeeeC
Confidence            455679999999999999999876422110              12489999988 89999999999993    588886


Q ss_pred             C--CCCCccccccccCCCCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCC
Q 009230          108 K--DTEKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQAS  185 (539)
Q Consensus       108 ~--~~~~~l~g~~~~~~~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~  185 (539)
                      +  .+...|||++.+.+.+.++||||.+|+++     +.|+|+. .|++-..       .              ...--+
T Consensus       205 p~f~K~~~LYGl~~a~~~~~vilvEGYmDvi~-----i~naVAt-lGTaLT~-------~--------------~~~~~~  257 (337)
T PHA02540        205 KADEEATKIYGLDRIDPGKTVYVVEGPIDSLF-----LPNSIAI-TGGDLDL-------N--------------EVPFKD  257 (337)
T ss_pred             CcccccccccChhHhccCCEEEEEeCCcceee-----eccceee-CccccCH-------h--------------HhCccc
Confidence            5  56788999999988899999999999997     4677874 4665321       1              111135


Q ss_pred             EEEEEecCCccchHHHHHHHHHhcCCceEEEecCCCCCCCCCCChHHHHHhcCc--chHHHHHHhccc
Q 009230          186 RIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGP--GALKEVVENAEL  251 (539)
Q Consensus       186 ~ivl~~DnD~~G~~~~~~~~~~l~~~~~~~~~~p~~~~~~~~kD~nd~l~~~g~--~~~~~~~~~A~~  251 (539)
                      +|||++||| +|.+|+-+..+.|-...+.++.||..  +.++|||||++++.|.  +++.++++++..
T Consensus       258 ~vvl~~D~D-a~~~at~r~~~~l~~~g~~v~v~~~~--~~~~kDpde~i~~~G~~~~~~~~~i~~n~~  322 (337)
T PHA02540        258 TRVWVLDNE-PRHPDTIKRISKLIDAGEKVVIWDKC--PWPSKDINDMIMKGGATPEDIMEYIKSNTY  322 (337)
T ss_pred             eEEEEECCc-hhHHHHHHHHHHHHHCCCeEEEecCC--CCCCcCHHHHHHhcCCCHHHHHHHHHHccc
Confidence            899999999 66677766667774445666777731  1257999999999875  888888887753

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=99.91  E-value=3.3e-23  Score=201.49  Aligned_cols=200  Identities=17%  Similarity=0.219  Sum_probs=158.6

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      .....++||+.+||+++|  +.||++++|+|.||.||||+++|++..+|.+ + +|||+|.|++..++..|...  +|++
T Consensus        70 ~~~~Ri~tg~~EldRVLGGG~V~Gs~iLIgGdPGIGKSTLLLQva~~lA~~-~-~vLYVsGEES~~QiklRA~R--L~~~  145 (456)
T COG1066          70 EEEPRISTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKR-G-KVLYVSGEESLQQIKLRADR--LGLP  145 (456)
T ss_pred             eecccccCChHHHHhhhcCCcccccEEEEccCCCCCHHHHHHHHHHHHHhc-C-cEEEEeCCcCHHHHHHHHHH--hCCC
Confidence            445689999999999997  9999999999999999999999999999986 6 99999999999999766532  3322


Q ss_pred             ccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCC-CCCCH
Q 009230          354 FFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRP-VSQTE  432 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~-~~~~~  432 (539)
                      ..                          .+++    -...++++|.+.++    +.+++++||||+..+....- +..-.
T Consensus       146 ~~--------------------------~l~l----~aEt~~e~I~~~l~----~~~p~lvVIDSIQT~~s~~~~SapGs  191 (456)
T COG1066         146 TN--------------------------NLYL----LAETNLEDIIAELE----QEKPDLVVIDSIQTLYSEEITSAPGS  191 (456)
T ss_pred             cc--------------------------ceEE----ehhcCHHHHHHHHH----hcCCCEEEEeccceeecccccCCCCc
Confidence            11                          1222    23456777776664    47899999999998876542 22233


Q ss_pred             HHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEE
Q 009230          433 TEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRK  512 (539)
Q Consensus       433 ~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K  512 (539)
                      -.++.+....|.++||+.|++++++.|..|..          .|.|-..+|...|+|+.++.+...     ..+.+.-.|
T Consensus       192 VsQVRe~t~~L~~~AK~~~i~~fiVGHVTKeG----------~IAGPrvLEHmVDtVlyFEGd~~~-----~~RiLR~vK  256 (456)
T COG1066         192 VSQVREVAAELMRLAKTKNIAIFIVGHVTKEG----------AIAGPRVLEHMVDTVLYFEGDRHS-----RYRILRSVK  256 (456)
T ss_pred             HHHHHHHHHHHHHHHHHcCCeEEEEEEEcccc----------cccCchheeeeeeEEEEEeccCCC-----ceeeeehhc
Confidence            45788999999999999999999999944432          367778899999999999876542     256677889


Q ss_pred             eeCCCcceeeeEEEEE
Q 009230          513 VRNKVVGTIGEAFLSY  528 (539)
Q Consensus       513 ~R~g~~G~~~~~~l~f  528 (539)
                      ||.|.++++|.+.|.=
T Consensus       257 NRFG~t~EiGvFeM~~  272 (456)
T COG1066         257 NRFGATNELGVFEMTE  272 (456)
T ss_pred             ccCCcccceeEEEEec
Confidence            9999999999777653

>PRK05973 replicative DNA helicase; Provisional

Probab=99.90  E-value=6.4e-23  Score=192.46  Aligned_cols=170  Identities=19%  Similarity=0.250  Sum_probs=129.1

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCC
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAE  364 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~  364 (539)
                      ...|+++| |++|++++|+|+||+|||+|++|++.+.+.+ |.+|+|||+||+++++..|+.+.  |++..         
T Consensus        52 ~p~~~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~-Ge~vlyfSlEes~~~i~~R~~s~--g~d~~---------  119 (237)
T PRK05973         52 TPAEELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKS-GRTGVFFTLEYTEQDVRDRLRAL--GADRA---------  119 (237)
T ss_pred             CCHHHhcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhc-CCeEEEEEEeCCHHHHHHHHHHc--CCChH---------
Confidence            34788888 9999999999999999999999999999986 99999999999999999999764  43322         


Q ss_pred             CCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHH
Q 009230          365 RMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVK  444 (539)
Q Consensus       365 ~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk  444 (539)
                           ++.       + .+.+..  .+..+.+.++   +++..++++++|||| +.+++...  .  +...+..++..|+
T Consensus       120 -----~~~-------~-~~~~d~--~d~~~~~~ii---~~l~~~~~~~lVVID-sLq~l~~~--~--~~~el~~~~~~Lk  176 (237)
T PRK05973        120 -----QFA-------D-LFEFDT--SDAICADYII---ARLASAPRGTLVVID-YLQLLDQR--R--EKPDLSVQVRALK  176 (237)
T ss_pred             -----Hhc-------c-ceEeec--CCCCCHHHHH---HHHHHhhCCCEEEEE-cHHHHhhc--c--cchhHHHHHHHHH
Confidence                 111       1 122211  2233455543   344556789999999 44544321  1  1123677788999


Q ss_pred             HHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          445 RFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       445 ~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      .+|+++|++||+++| +|..+.+.+++|.++|+|    +.+.+|..++.++
T Consensus       177 ~~Ak~~gitvIl~sQl~r~~e~~~~~~P~laDlR----~~~~~d~~~f~~~  223 (237)
T PRK05973        177 SFARERGLIIVFISQIDRSFDPSAKPLPDIRDVR----LPNPLDLSLFDKA  223 (237)
T ss_pred             HHHHhCCCeEEEEecCccccccCCCCCCChhhcC----CCChhhHHHhhhh
Confidence            999999999999999 999988888999999998    4668888777654

>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]

Probab=99.90  E-value=2.7e-23  Score=222.27  Aligned_cols=220  Identities=25%  Similarity=0.370  Sum_probs=161.7

Q ss_pred             CcccccCCCCCCccccccc----cccc----------------------hhhhhhcccchhhhcccccCCCCCCcHHHHH
Q 009230            1 MCFRAKCGWKGSTSALVDN----NRSQ----------------------SSLKKFSKMKTIREITEDSLELEPLGNELRA   54 (539)
Q Consensus         1 ~C~~~~cg~~~~~~~~~~~----~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~   54 (539)
                      +||  +||++|++..|+.+    .|.+                      ..............++...+.  |...++++
T Consensus        57 hCF--GCg~~Gd~i~Fl~~~~g~sf~eav~~La~~~gi~~~~~~~~~~~~~~~l~~~~~~~~~fy~~~L~--~~~~~a~~  132 (568)
T COG0358          57 HCF--GCGAGGDAIKFLMELLGLSFDEAVLQLAGRAGIELPYEKGKRIEKRQKLYDGKEEAAIFYQSSLD--PEGAAALK  132 (568)
T ss_pred             ecC--CCCCCccHHHHHHHhcCCCHHHHHHHHHHHhCCCCCccccccchhHHHHHHHHHHHHHHHHHHHH--hchHHHHH
Confidence            599  99999997766654    1211                      011111111222233334444  66677889


Q ss_pred             HHHhcCCCHHHHHHcCcccccC---------------------------------CceeEEEEeEe-eCCEEEEEEeecC
Q 009230           55 YFAERLISAETLRRNRVMQKRH---------------------------------GHEVVIAFPYW-RNGKLVNCKYRDF  100 (539)
Q Consensus        55 Yl~~Rgi~~~~~~~~~~~~~~~---------------------------------~~~~~i~fP~~-~~G~~~~~~~R~~  100 (539)
                      ||.+||++.++++.|++++...                                 ...++|+||++ ..|++++|.+|.+
T Consensus       133 yL~~Rgls~~~i~~f~iG~ap~~~~~~~~~~k~~~~~~~l~~~Gl~~~~~~~~ydrFr~RImfPI~d~~g~vigFggR~l  212 (568)
T COG0358         133 YLETRGLAAELIAHFRLGYAPPNDSLLPFLAKKEYREEKLEDLGLLKRKEGKIYDRFRNRIMFPIRDLRGDVIGFGGRVL  212 (568)
T ss_pred             HHHHcCCCHHHHHHhCCCCCCCchHHHHHHhcCCcCHHHHHHCCCeecCCCceeehhcCeeEEeccCCCCCEEeeecccc
Confidence            9999999999999998872211                                 02479999988 7899999999998


Q ss_pred             ---CCcccccC-----CCCCccccccccC----CCCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhh
Q 009230          101 ---NKKFWQEK-----DTEKVFYGLDDIE----GESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQD  168 (539)
Q Consensus       101 ---~~~~~~~~-----~~~~~l~g~~~~~----~~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~  168 (539)
                         .+||++++     .++..+||++...    +.+.++||||++|+++++++|+.+|||+ .|++..            
T Consensus       213 ~~~~~KYlNspet~if~Kg~~Lyg~~~a~~~~~~~~~iivVEGymDViaL~~aGi~naVA~-lGTalt------------  279 (568)
T COG0358         213 GDDKPKYLNSPETELFKKGEELYGLDPARKKIAKADQIIVVEGYMDVIALHKAGIKNAVAS-LGTALT------------  279 (568)
T ss_pred             CCCCCcccCCCCCcCccCcHHhhCHHHHHHhhccCCeEEEEechHHHHHHHHcCCcceeec-ccccCC------------
Confidence               47888866     4577889988753    3678999999999999999999999995 566531            


Q ss_pred             hhhHHHHhHHHHhcc-CCEEEEEecCCccchHHHHHHHHHh---cCCceEEEecCCCCCCCCCCChHHHHHhcCcchHHH
Q 009230          169 TKYQYLWNCKMYLKQ-ASRIILATDGDPPGQALAEELARRV---GRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKE  244 (539)
Q Consensus       169 ~~~~~l~~~~~~l~~-~~~ivl~~DnD~~G~~~~~~~~~~l---~~~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~~~  244 (539)
                            ..++..|.+ ..+|++|+|+|.||++|+.++.+..   ....+.++.+|      .+|||+|++++.|.+++..
T Consensus       280 ------~ehi~~L~r~~~~vil~fDgD~AG~~Aa~ral~~~~~~~~~~v~v~~~P------~GkDpDel~~k~g~~al~~  347 (568)
T COG0358         280 ------EEHIKLLSRGKKKVILCFDGDRAGRKAAKRALQLVLPLDFVGVFVILLP------DGKDPDELIRKEGAEALRK  347 (568)
T ss_pred             ------HHHHHHHHhcCCCEEEEeCChHHHHHHHHHHHHHhhhhccCCeEEEECC------CCCChHHHHHHhChHHHHH
Confidence                  123445555 4569999999999999977776643   22237888998      4699999999999999888


Q ss_pred             HHHhc
Q 009230          245 VVENA  249 (539)
Q Consensus       245 ~~~~A  249 (539)
                      .+.++
T Consensus       348 ~l~~~  352 (568)
T COG0358         348 KLPNE  352 (568)
T ss_pred             HHHhC
Confidence            88774

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=99.90  E-value=4e-22  Score=200.60  Aligned_cols=197  Identities=17%  Similarity=0.216  Sum_probs=149.8

Q ss_pred             CccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCc
Q 009230          277 DEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPF  354 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~  354 (539)
                      ....++||+++||++++  +.+|++++|+|+||+|||+|++|++.+++.. |.+|+|++.|++..++..|...  .+++.
T Consensus        60 ~~~ri~TGi~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~~a~~-g~~VlYvs~EEs~~qi~~Ra~r--lg~~~  136 (372)
T cd01121          60 EEERIPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKR-GGKVLYVSGEESPEQIKLRADR--LGIST  136 (372)
T ss_pred             ccCccccCCHHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHHHHhc-CCeEEEEECCcCHHHHHHHHHH--cCCCc
Confidence            45689999999999996  9999999999999999999999999999885 8899999999999988776532  22211


Q ss_pred             cccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCC-CCCCHH
Q 009230          355 FEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRP-VSQTET  433 (539)
Q Consensus       355 ~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~-~~~~~~  433 (539)
                                               +.+.++     ...+++.|.+.+    ...++++||||++..+..... +.....
T Consensus       137 -------------------------~~l~l~-----~e~~le~I~~~i----~~~~~~lVVIDSIq~l~~~~~~~~~g~~  182 (372)
T cd01121         137 -------------------------ENLYLL-----AETNLEDILASI----EELKPDLVIIDSIQTVYSSELTSAPGSV  182 (372)
T ss_pred             -------------------------ccEEEE-----ccCcHHHHHHHH----HhcCCcEEEEcchHHhhccccccCCCCH
Confidence                                     111222     233466666554    456899999999887754321 112234


Q ss_pred             HHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEe
Q 009230          434 EYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKV  513 (539)
Q Consensus       434 ~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~  513 (539)
                      .++.+++..|.++|+++++++++++|..+..          .+.|+..+++.+|+||.++.++..     ....+.+.|+
T Consensus       183 ~qvr~~~~~L~~lak~~~itvilvghvtk~g----------~~aG~~~leh~vD~Vi~le~~~~~-----~~R~Lri~Kn  247 (372)
T cd01121         183 SQVRECTAELMRFAKERNIPIFIVGHVTKEG----------SIAGPKVLEHMVDTVLYFEGDRHS-----EYRILRSVKN  247 (372)
T ss_pred             HHHHHHHHHHHHHHHHcCCeEEEEeeccCCC----------cccCcccchhhceEEEEEEcCCCC-----cEEEEEEEeC
Confidence            5678889999999999999999999943321          256777899999999999876531     2567899999


Q ss_pred             eCCCcceeeeEE
Q 009230          514 RNKVVGTIGEAF  525 (539)
Q Consensus       514 R~g~~G~~~~~~  525 (539)
                      |.|++++++.+.
T Consensus       248 R~g~~~ei~~F~  259 (372)
T cd01121         248 RFGSTNELGVFE  259 (372)
T ss_pred             CCCCCCCEEEEE
Confidence            999988876443

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.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=99.89  E-value=8.6e-22  Score=190.49  Aligned_cols=209  Identities=17%  Similarity=0.191  Sum_probs=146.7

Q ss_pred             cccccCchhhhhhh---------------c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH
Q 009230          279 FGISTGWRALNELY---------------N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA  342 (539)
Q Consensus       279 ~gi~tg~~~LD~~~---------------~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~  342 (539)
                      -|+|||+++||+++               | +++|.+++|+|+||+|||+|++|++.+.+.+ |.+|+|+|+|++++.+.
T Consensus         2 ~~~~tGi~glD~~l~~~~~~~~~~~~~~~GGip~gs~~lI~G~pGtGKT~l~~qf~~~~a~~-Ge~vlyis~Ee~~~~~~   80 (259)
T TIGR03878         2 FGVPTGVEGLDELFFKVEIEEGKIVRKPLGGIPAYSVINITGVSDTGKSLMVEQFAVTQASR-GNPVLFVTVESPANFVY   80 (259)
T ss_pred             CCccCCchhHHHhhccccccccccccccCCCeECCcEEEEEcCCCCCHHHHHHHHHHHHHhC-CCcEEEEEecCCchHHH
Confidence            37899999999997               6 9999999999999999999999999999986 99999999999988777


Q ss_pred             HHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCC--CCCHHHHHHHHHHHHHHcCCcEEEEcccc
Q 009230          343 RKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDS--LPSIKWVLDLAKAAVLRHGVRGLVIDPYN  420 (539)
Q Consensus       343 ~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~--~~~~~~i~~~i~~~~~~~~~~~vvID~~~  420 (539)
                      .++........            ++.+       .+.++++++......  ..+++++...+..++.++++++|||||++
T Consensus        81 ~~l~~~a~~~g------------~d~~-------~~~~~l~~id~~~~~~~~~~~~~l~~~l~~~i~~~~~~~vVIDSls  141 (259)
T TIGR03878        81 TSLKERAKAMG------------VDFD-------KIEENIILIDAASSTELRENVPNLLATLAYAIKEYKVKNTVIDSIT  141 (259)
T ss_pred             HHHHHHHHHcC------------CCHH-------HHhCCEEEEECCCchhhhhhHHHHHHHHHHHHHhhCCCEEEEcCch
Confidence            66643322111            1111       122344554221100  13567788888888888999999999998


Q ss_pred             ccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCC--
Q 009230          421 ELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDP--  498 (539)
Q Consensus       421 ~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~--  498 (539)
                      .+...     . .....+++..|..+++++++++++++|.+.....    ... +..+...++..+|.+|.|......  
T Consensus       142 ~l~~~-----~-~~~~r~~~~~L~~~lk~~~~t~ll~~e~~~~~~~----~~~-~~~~~~~~~~l~D~vI~L~~~~~~~~  210 (259)
T TIGR03878       142 GLYEA-----K-EMMAREIVRQLFNFMKKWYQTALFVSQKRSGHEE----LSA-EAAGGYAVSHIVDGTIVLAKQLIMSR  210 (259)
T ss_pred             Hhccc-----c-hHHHHHHHHHHHHHHHHcCCeEEEEeccccCccc----ccc-cccCCcceeEeeccEEEEeeeeccch
Confidence            77532     1 1335677888899999999999999994332110    111 233444588999999999853211  


Q ss_pred             -------CCCCCCcEEEEEEEeeCCCc
Q 009230          499 -------EAGPIDRVQVCVRKVRNKVV  518 (539)
Q Consensus       499 -------~~~~~~~~~l~i~K~R~g~~  518 (539)
                             +....-...+.|.|.|....
T Consensus       211 ~~~~~~~~~~~~~~R~l~I~KmRg~~h  237 (259)
T TIGR03878       211 FDASLYKKPIGEIVRLFRIDGCRMCGH  237 (259)
T ss_pred             hhhhhccccccceEEEEEEEEccCCCC
Confidence                   11112246689999998644

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR00416 sms DNA repair protein RadA

Probab=99.88  E-value=2.7e-21  Score=200.18  Aligned_cols=200  Identities=18%  Similarity=0.246  Sum_probs=149.6

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      ....+++||+++||++++  +.+|++++|+|+||+|||||++|++.+++.+ |.+|+|+|+|++..++..|...  .+++
T Consensus        71 ~~~~ri~TGi~~LD~vLgGGi~~GsvilI~G~pGsGKTTL~lq~a~~~a~~-g~kvlYvs~EEs~~qi~~ra~r--lg~~  147 (454)
T TIGR00416        71 EEVPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKN-QMKVLYVSGEESLQQIKMRAIR--LGLP  147 (454)
T ss_pred             cccCccccCcHHHHHHhcCCccCCeEEEEEcCCCCCHHHHHHHHHHHHHhc-CCcEEEEECcCCHHHHHHHHHH--cCCC
Confidence            345689999999999995  9999999999999999999999999999885 8899999999999988777542  1221


Q ss_pred             ccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCC-CCCCH
Q 009230          354 FFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRP-VSQTE  432 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~-~~~~~  432 (539)
                      .              +           ..+++     ...+++.|.+.+    .+.++++|||||+..+..... +....
T Consensus       148 ~--------------~-----------~l~~~-----~e~~~~~I~~~i----~~~~~~~vVIDSIq~l~~~~~~~~~g~  193 (454)
T TIGR00416       148 E--------------P-----------NLYVL-----SETNWEQICANI----EEENPQACVIDSIQTLYSPDISSAPGS  193 (454)
T ss_pred             h--------------H-----------HeEEc-----CCCCHHHHHHHH----HhcCCcEEEEecchhhcccccccCCCC
Confidence            1              0           11222     223456555444    457899999999888764321 11122


Q ss_pred             HHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEE
Q 009230          433 TEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRK  512 (539)
Q Consensus       433 ~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K  512 (539)
                      ..++.+++..|.++|+++|+++++++|..+..          .+.|+..+++.+|.||.|...+.     .....+.+.|
T Consensus       194 ~~q~r~~~~~L~~~ak~~giTvllt~hvtkeg----------~~aG~~~le~lvD~VI~Le~~~~-----~~~R~L~v~K  258 (454)
T TIGR00416       194 VSQVRECTAELMRLAKTRGIAIFIVGHVTKEG----------SIAGPKVLEHMVDTVLYFEGDRD-----SRFRILRSVK  258 (454)
T ss_pred             HHHHHHHHHHHHHHHHHhCCEEEEEeccccCC----------ccCCcccEeeeceEEEEEeccCC-----CcEEEEEEec
Confidence            34567888999999999999999999943321          35677789999999999987442     1246788999


Q ss_pred             eeCCCcceeeeEEEE
Q 009230          513 VRNKVVGTIGEAFLS  527 (539)
Q Consensus       513 ~R~g~~G~~~~~~l~  527 (539)
                      +|.|++++++.+.+.
T Consensus       259 ~R~g~~~e~~~f~it  273 (454)
T TIGR00416       259 NRFGATNEIGIFEMT  273 (454)
T ss_pred             CCCCCCCcEEEEEEe
Confidence            999998887655444

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)).

>PRK11823 DNA repair protein RadA; Provisional

Probab=99.88  E-value=3.2e-21  Score=199.74  Aligned_cols=199  Identities=18%  Similarity=0.206  Sum_probs=148.1

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      .....++||+++||++++  +.+|++++|+|+||+|||+|++|++.+.+.+ |.+|+|+++|++.+++..|+..  .|.+
T Consensus        57 ~~~~ri~TGi~~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~-g~~vlYvs~Ees~~qi~~ra~r--lg~~  133 (446)
T PRK11823         57 EEEPRISTGIGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAA-GGKVLYVSGEESASQIKLRAER--LGLP  133 (446)
T ss_pred             ccCCcccCCcHHHHHHhcCCccCCEEEEEECCCCCCHHHHHHHHHHHHHhc-CCeEEEEEccccHHHHHHHHHH--cCCC
Confidence            345689999999999996  9999999999999999999999999999875 8999999999999998777532  2322


Q ss_pred             ccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCC-CCCCH
Q 009230          354 FFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRP-VSQTE  432 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~-~~~~~  432 (539)
                      ..                         . +++    ....+++.+.+.+    .+.++++||||++..+....- +....
T Consensus       134 ~~-------------------------~-l~~----~~e~~l~~i~~~i----~~~~~~lVVIDSIq~l~~~~~~~~~g~  179 (446)
T PRK11823        134 SD-------------------------N-LYL----LAETNLEAILATI----EEEKPDLVVIDSIQTMYSPELESAPGS  179 (446)
T ss_pred             hh-------------------------c-EEE----eCCCCHHHHHHHH----HhhCCCEEEEechhhhccccccCCCCC
Confidence            11                         1 222    1233466655544    456899999999887764321 11223


Q ss_pred             HHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEE
Q 009230          433 TEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRK  512 (539)
Q Consensus       433 ~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K  512 (539)
                      ..++.+++..|.++|+++|+++++++|..+..          .+.|+..+++.+|.||.+..+..     ...+.+.+.|
T Consensus       180 ~~qvr~~~~~L~~~ak~~~itvilv~hvtk~~----------~~ag~~~lehlvD~Vi~le~~~~-----~~~R~l~i~K  244 (446)
T PRK11823        180 VSQVRECAAELMRLAKQRGIAVFLVGHVTKEG----------AIAGPRVLEHMVDTVLYFEGDRH-----SRYRILRAVK  244 (446)
T ss_pred             HHHHHHHHHHHHHHHHHcCCEEEEEeeccCCC----------CcCCcchhhhhCeEEEEEEcCCC-----CceEEEEEcc
Confidence            34577888999999999999999999933321          24566679999999999875321     1256789999


Q ss_pred             eeCCCcceeeeEEE
Q 009230          513 VRNKVVGTIGEAFL  526 (539)
Q Consensus       513 ~R~g~~G~~~~~~l  526 (539)
                      +|.|++++++.+.+
T Consensus       245 ~R~g~~~e~~~f~i  258 (446)
T PRK11823        245 NRFGATNEIGVFEM  258 (446)
T ss_pred             CCCCCCCceEEEEE
Confidence            99999887654433

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=99.88  E-value=6.1e-21  Score=182.68  Aligned_cols=212  Identities=15%  Similarity=0.223  Sum_probs=145.8

Q ss_pred             ccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCcccc
Q 009230          280 GISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEA  357 (539)
Q Consensus       280 gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i  357 (539)
                      .++||+++||++++  +++|++++|+|+||+|||+|++|++.+.+.+ |.+++|+|+|++++++.+++.+  .|.+....
T Consensus         2 ri~tGi~~LD~~l~GG~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~-ge~~lyvs~ee~~~~i~~~~~~--~g~~~~~~   78 (237)
T TIGR03877         2 RVKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQM-GEPGIYVALEEHPVQVRRNMAQ--FGWDVRKY   78 (237)
T ss_pred             ccccCcHhHHHHhcCCCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHc-CCcEEEEEeeCCHHHHHHHHHH--hCCCHHHH
Confidence            48999999999884  9999999999999999999999999998875 9999999999999999999754  34443222


Q ss_pred             ccCCCCCCCCH-HHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHH
Q 009230          358 NYGGSAERMTV-EEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYV  436 (539)
Q Consensus       358 ~~~~~~~~l~~-~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~  436 (539)
                      ...+   .+.- +..............++   .....+++++...++..+..+++++|||||+..+...     +. ...
T Consensus        79 ~~~g---~l~~~d~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~i~~~i~~~~~~~vVIDSls~l~~~-----~~-~~~  146 (237)
T TIGR03877        79 EEEG---KFAIVDAFTGGIGEAAEREKYV---VKDPTDVRELIDVLRQAIRDINAKRVVIDSVTTLYIT-----KP-AMA  146 (237)
T ss_pred             hhcC---CEEEEecccccccccccccccc---ccCcccHHHHHHHHHHHHHHhCCCEEEEcChhHhhcC-----Ch-HHH
Confidence            1100   0000 00000000000111111   0123467888888888888889999999999887532     11 123


Q ss_pred             HHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeC
Q 009230          437 SQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRN  515 (539)
Q Consensus       437 ~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~  515 (539)
                      .+++..|+.+++++|+++++++| +.....          +.+ ..+++.||.||.|...+...   .-...+.|.|.|.
T Consensus       147 r~~l~~l~~~lk~~~~t~llt~~~~~~~~~----------~~~-~~~~~~~D~vI~L~~~~~~~---~~~R~l~i~K~Rg  212 (237)
T TIGR03877       147 RSIVMQLKRVLSGLGCTSIFVSQVSVGERG----------FGG-PGVEHAVDGIIRLDLDEIDG---ELKRSLIVWKMRG  212 (237)
T ss_pred             HHHHHHHHHHHHhCCCEEEEEECccccccc----------ccc-cceEEEEeEEEEEEEEeeCC---ceEEEEEEEECCC
Confidence            36778889999999999999999 432110          111 23678999999998765422   1246799999998


Q ss_pred             CCcce
Q 009230          516 KVVGT  520 (539)
Q Consensus       516 g~~G~  520 (539)
                      .....
T Consensus       213 ~~~~~  217 (237)
T TIGR03877       213 TKHSM  217 (237)
T ss_pred             CCCCC
Confidence            76654

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.

>PHA02415 DNA primase domain-containing protein

Probab=99.86  E-value=2.8e-21  Score=200.34  Aligned_cols=190  Identities=21%  Similarity=0.300  Sum_probs=131.6

Q ss_pred             cHHHHHHHHhcCCCHHHHHH-cCcc-------------cccC--Ccee-EEEEeEeeCCEEEEEEeecCCCcccccC---
Q 009230           49 GNELRAYFAERLISAETLRR-NRVM-------------QKRH--GHEV-VIAFPYWRNGKLVNCKYRDFNKKFWQEK---  108 (539)
Q Consensus        49 ~~~~~~Yl~~Rgi~~~~~~~-~~~~-------------~~~~--~~~~-~i~fP~~~~G~~~~~~~R~~~~~~~~~~---  108 (539)
                      ...+.+||++|||++++++. +..+             +...  ++++ +++||+..+|+++.++.|...+.|....   
T Consensus       121 ~rrA~AYLK~RGIS~EVI~~cIk~GlIg~~~W~s~rv~agd~gygg~nAAFIVpf~rdGtvv~v~~Rg~d~afkG~vKan  200 (930)
T PHA02415        121 RERVREYLGGRGISAAAIDAAFAARSLGFNTWTSSKVAAGEVGHAGPAAAFIVREPADGRVVAVDMRYVDPALNGGVKTQ  200 (930)
T ss_pred             hHHHHHHHHhcCCCHHHHHHHHHcCcccccccccccccccccccCCCceEEEecccCCceEEEeeeccccccccCCcccc
Confidence            46699999999999999997 3331             1111  1233 4569999999999999998755554422   


Q ss_pred             -CCCCcccccccc----CCCCcEEEEechhhHHHHHHhCCCce--EEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHh
Q 009230          109 -DTEKVFYGLDDI----EGESDIIIVEGEMDKLSMEEAGFLNC--VSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYL  181 (539)
Q Consensus       109 -~~~~~l~g~~~~----~~~~~v~i~EG~~Dalsl~~~g~~~~--v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l  181 (539)
                       .+....|+|+..    ...++|+||||+|||||++++|++++  |+| +|..+...             .+    ++.+
T Consensus       201 f~Gs~~G~gW~~p~~~L~~a~eVwIvEGiIDAISL~q~Gi~avAaVAL-~GLan~~~-------------iD----~~~l  262 (930)
T PHA02415        201 TQGDKAGYGWTADARRLDKAKRVFIVESAINALSIDTCAMPGAAALAL-RGLANVDA-------------ID----FSSL  262 (930)
T ss_pred             CCCCCCCCccCCCccccCCCCEEEEEechHhHHHHHHcCchhHHHHHH-cCcCCCch-------------hh----chhh
Confidence             123344444433    33578999999999999999998753  444 34443210             00    1233


Q ss_pred             ccCCEEEEEecCCcc------------chHHHHHHHHHhcCC--ceEEEe---cCC-----CCCCCCCCChHHHHHhcCc
Q 009230          182 KQASRIILATDGDPP------------GQALAEELARRVGRE--RCWRVR---WPK-----KNDVDHFKDANEVLMYLGP  239 (539)
Q Consensus       182 ~~~~~ivl~~DnD~~------------G~~~~~~~~~~l~~~--~~~~~~---~p~-----~~~~~~~kD~nd~l~~~g~  239 (539)
                       ..++|++|+|||+|            |++|+.++.+.+...  .++++.   |-+     ........|+||+|+.+|.
T Consensus       263 -~~KrVvlcLDNDea~~~~~~~~g~rpG~eAA~~l~e~lta~~i~~~lvd~~~w~~~~~~~~~~~~~~~d~nd~l~~~g~  341 (930)
T PHA02415        263 -RGKQVVICLDNDEPFEDGHPRAGHRPGPEAAWALYERLASLNISAVLVDQAGWLADLADGETKQQPINDVNDYLQLRGP  341 (930)
T ss_pred             -cCceEEEEecCCccccccCcccccCccHHHHHHHHHHHhhcCCceEEeehhhhhhhcccccccccccccHHHHHHHhCH
Confidence             46899999999998            999999999999432  344443   211     0111345699999999999


Q ss_pred             chHHHHHHhccccCcccc
Q 009230          240 GALKEVVENAELYPIMGL  257 (539)
Q Consensus       240 ~~~~~~~~~A~~~~~~~~  257 (539)
                      +++...++.-++|-+.+.
T Consensus       342 ~~~~~~l~~~~~wli~g~  359 (930)
T PHA02415        342 EELARALEQLEPWLIAGL  359 (930)
T ss_pred             HHHHHHHHhccccccCCC
Confidence            999999999998876655

>PRK04328 hypothetical protein; Provisional

Probab=99.85  E-value=7.9e-20  Score=175.87  Aligned_cols=214  Identities=16%  Similarity=0.220  Sum_probs=144.7

Q ss_pred             cccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccc
Q 009230          279 FGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFE  356 (539)
Q Consensus       279 ~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~  356 (539)
                      ..++||+++||++++  +++|.+++|+|+||+|||+|++|++.+.+.+ |.+++|+|+|++++++.+++.+  .|.+...
T Consensus         3 ~rv~tGi~~LD~lL~GGip~gs~ili~G~pGsGKT~l~~~fl~~~~~~-ge~~lyis~ee~~~~i~~~~~~--~g~d~~~   79 (249)
T PRK04328          3 KRVKTGIPGMDEILYGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQM-GEPGVYVALEEHPVQVRRNMRQ--FGWDVRK   79 (249)
T ss_pred             ceecCCchhHHHHhcCCCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhc-CCcEEEEEeeCCHHHHHHHHHH--cCCCHHH
Confidence            358999999999995  9999999999999999999999999998886 9999999999999998877644  3444322


Q ss_pred             cccCCCCCCCCHHH-HHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHH
Q 009230          357 ANYGGSAERMTVEE-FEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEY  435 (539)
Q Consensus       357 i~~~~~~~~l~~~~-~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~  435 (539)
                      ....+   .+.--+ .............++ .  ....+++.+...+...+.+.++++|||||+..+...     +. ..
T Consensus        80 ~~~~~---~l~iid~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~~i~~~i~~~~~~~vVIDSlt~l~~~-----~~-~~  147 (249)
T PRK04328         80 YEEEG---KFAIVDAFTGGIGSAAKREKYV-V--KDPDDVRELIDVLRQAIKDIGAKRVVIDSVSTLYLT-----KP-AM  147 (249)
T ss_pred             HhhcC---CEEEEecccccccccccccccc-c--cCcccHHHHHHHHHHHHHhhCCCEEEEeChhHhhcC-----Ch-HH
Confidence            21100   000000 000000000000111 0  123356778888888888889999999999887532     11 22


Q ss_pred             HHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeC
Q 009230          436 VSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRN  515 (539)
Q Consensus       436 ~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~  515 (539)
                      ..+++..|..+++++|+++++++|......         .+.+ ..++..||.||.|...+...   .....+.|.|.|.
T Consensus       148 ~r~~~~~l~~~lk~~g~t~llt~e~~~~~~---------~~~~-~~~~~~~D~vI~L~~~~~~~---~~~R~l~I~K~Rg  214 (249)
T PRK04328        148 ARSIVMQLKRVLSGLGCTAIFVSQVSVGER---------GFGG-PGVEHAVDGIIRLDLDEIDG---ELKRSLIVWKMRG  214 (249)
T ss_pred             HHHHHHHHHHHHHhCCCEEEEEECcccccc---------ccCC-CCcEEEEEEEEEEEEEecCC---cEEEEEEEEEccC
Confidence            346678888888999999999999322110         0111 23678899999998765321   1246789999998


Q ss_pred             CCcce
Q 009230          516 KVVGT  520 (539)
Q Consensus       516 g~~G~  520 (539)
                      ...+.
T Consensus       215 ~~~~~  219 (249)
T PRK04328        215 TKHSM  219 (249)
T ss_pred             CCCCC
Confidence            76554

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=99.85  E-value=2.8e-20  Score=177.35  Aligned_cols=199  Identities=18%  Similarity=0.232  Sum_probs=141.3

Q ss_pred             cccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccc
Q 009230          281 ISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEAN  358 (539)
Q Consensus       281 i~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~  358 (539)
                      ++||+++||++++  +++|.+++|.|+||+|||+|++|++.+.+.+.|.+|+|+|+|++++++.+++.+  .|+++.+  
T Consensus         1 V~TGI~~LD~~l~GGip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~ee~~~~l~~~~~s--~g~d~~~--   76 (226)
T PF06745_consen    1 VPTGIPGLDELLGGGIPKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFEEPPEELIENMKS--FGWDLEE--   76 (226)
T ss_dssp             E--SSTTHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESSS-HHHHHHHHHT--TTS-HHH--
T ss_pred             CCCCchhHHHhhcCCCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEecCCHHHHHHHHHH--cCCcHHH--
Confidence            5899999999994  999999999999999999999999999988549999999999999999888753  2333221  


Q ss_pred             cCCCCCCCCHHHHHHHHHHhhccceeEeecCCC----CCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHH
Q 009230          359 YGGSAERMTVEEFEQGKAWLSNTFSLIRCENDS----LPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETE  434 (539)
Q Consensus       359 ~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~----~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~  434 (539)
                                     +.+  ...+.++......    ..+++.+...+...+...++++|||||+..+....    + ..
T Consensus        77 ---------------~~~--~g~l~~~d~~~~~~~~~~~~~~~l~~~i~~~i~~~~~~~vVIDsls~l~~~~----~-~~  134 (226)
T PF06745_consen   77 ---------------YED--SGKLKIIDAFPERIGWSPNDLEELLSKIREAIEELKPDRVVIDSLSALLLYD----D-PE  134 (226)
T ss_dssp             ---------------HHH--TTSEEEEESSGGGST-TSCCHHHHHHHHHHHHHHHTSSEEEEETHHHHTTSS----S-GG
T ss_pred             ---------------Hhh--cCCEEEEecccccccccccCHHHHHHHHHHHHHhcCCCEEEEECHHHHhhcC----C-HH
Confidence                           111  1123333221111    35788899999988888899999999999983221    1 12


Q ss_pred             HHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchh-ccceEEEEEeCCCCCCCCCCcEEEEEEE
Q 009230          435 YVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFIN-KCDNGIVIHRNRDPEAGPIDRVQVCVRK  512 (539)
Q Consensus       435 ~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~-~aD~vl~l~r~~~~~~~~~~~~~l~i~K  512 (539)
                      .+..++..|....+++++++++++| ......           .....++. .||.||.|...+...   .-...+.|.|
T Consensus       135 ~~r~~l~~l~~~l~~~~~t~llt~~~~~~~~~-----------~~~~~i~~~l~D~vI~L~~~~~~~---~~~R~l~I~K  200 (226)
T PF06745_consen  135 ELRRFLRALIKFLKSRGVTTLLTSEMPSGSED-----------DGTFGIEHYLADGVIELRYEEEGG---RIRRRLRIVK  200 (226)
T ss_dssp             GHHHHHHHHHHHHHHTTEEEEEEEEESSSSSS-----------SSSTSHHHHHSSEEEEEEEEEETT---EEEEEEEEEE
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEEEccccCccc-----------ccccchhhhcccEEEEEEEEeeCC---EEEEEEEEEE
Confidence            3556788888888999999999999 432211           12334666 999999999865432   2257899999


Q ss_pred             eeCCCcc
Q 009230          513 VRNKVVG  519 (539)
Q Consensus       513 ~R~g~~G  519 (539)
                      .|.....
T Consensus       201 ~Rg~~~~  207 (226)
T PF06745_consen  201 MRGSRHS  207 (226)
T ss_dssp             ETTS---
T ss_pred             cCCCCCC
Confidence            9987543

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 ....

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=99.85  E-value=4.7e-20  Score=175.96  Aligned_cols=206  Identities=18%  Similarity=0.186  Sum_probs=145.7

Q ss_pred             cccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC------CeEEEEeCCCC--HHHHHHHHHHHhh
Q 009230          281 ISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAG------WKFVLCSMENK--VREHARKLLEKHI  350 (539)
Q Consensus       281 i~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g------~~vl~~s~E~~--~~~~~~r~~~~~~  350 (539)
                      ++||++.||++++  +++|+++.|+|+||+|||+|+++++.+.+.+ +      ..|+|++.|.+  ++++......  .
T Consensus         1 i~tG~~~lD~~l~GG~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~-~~~~g~~~~v~yi~~e~~~~~~rl~~~~~~--~   77 (226)
T cd01393           1 ISTGSKALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLP-GELGGLEGKVVYIDTEGAFRPERLVQLAVR--F   77 (226)
T ss_pred             CCCCcHHHHHHhCCCCcCCcEEEEeCCCCCChhHHHHHHHHHhhcc-cccCCCcceEEEEecCCCCCHHHHHHHHHH--h
Confidence            5899999999984  9999999999999999999999999998875 6      89999999976  4333222111  1


Q ss_pred             CCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHH---HcCCcEEEEccccccccCCC
Q 009230          351 KKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVL---RHGVRGLVIDPYNELDHQRP  427 (539)
Q Consensus       351 ~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~---~~~~~~vvID~~~~l~~~~~  427 (539)
                      +.              ..       +.+.++..++     ...+.+++...++.+..   ..++++||||++..+.....
T Consensus        78 ~~--------------~~-------~~~~~~i~~~-----~~~~~~~~~~~l~~~~~~~~~~~~~lvVIDsis~l~~~~~  131 (226)
T cd01393          78 GL--------------DP-------EEVLDNIYVA-----RPYNGEQQLEIVEELERIMSSGRVDLVVVDSVAALFRKEF  131 (226)
T ss_pred             cc--------------ch-------hhhhccEEEE-----eCCCHHHHHHHHHHHHHHhhcCCeeEEEEcCcchhhhhhh
Confidence            11              00       1112333443     22356666666666544   67899999999988865321


Q ss_pred             CC----CCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCC
Q 009230          428 VS----QTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGP  502 (539)
Q Consensus       428 ~~----~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~  502 (539)
                      ..    ..+...+.+++..|+.+|++++|+|++++| +.......+. +.  --.|+..+.+.+|+.|.|.+.+....  
T Consensus       132 ~~~~~~~~~~~~l~~~~~~L~~~a~~~~~~vi~tnq~~~~~~~~~~~-~~--~p~~G~~~~~~~~~ri~l~~~~~~~~--  206 (226)
T cd01393         132 IGRGMLAERARLLSQALRKLLRLADKFNVAVVFTNQVRAKVDVMFGD-PE--TPAGGNALAHASTTRLDLRKGRGIIG--  206 (226)
T ss_pred             cCCchHHHHHHHHHHHHHHHHHHHHHhCcEEEEEEEEeeecccccCC-Cc--cccCchhhhCcccEEEEEEecCCccC--
Confidence            11    123356788999999999999999999999 5544321111 11  12467899999999999998775321  


Q ss_pred             CCcEEEEEEEeeCCCccee
Q 009230          503 IDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       503 ~~~~~l~i~K~R~g~~G~~  521 (539)
                       ....+.+.|++..+.|+.
T Consensus       207 -~~r~~~~~k~~~~~~~~~  224 (226)
T cd01393         207 -ERRIAKVVKSPALPEAEA  224 (226)
T ss_pred             -cEEEEEEEeCCCCCCccc
Confidence             356799999998888764

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.

>PHA02031 putative DnaG-like primase

Probab=99.85  E-value=7e-21  Score=176.69  Aligned_cols=163  Identities=14%  Similarity=0.054  Sum_probs=126.9

Q ss_pred             HHHHHHHHhcCCCHHHHHHcCcccccCCceeEEEEeEeeCCEEEEEEeecC---CCcccccCCCCCcccccccc-CCCCc
Q 009230           50 NELRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYWRNGKLVNCKYRDF---NKKFWQEKDTEKVFYGLDDI-EGESD  125 (539)
Q Consensus        50 ~~~~~Yl~~Rgi~~~~~~~~~~~~~~~~~~~~i~fP~~~~G~~~~~~~R~~---~~~~~~~~~~~~~l~g~~~~-~~~~~  125 (539)
                      ..+..||.++||+.+.+..-+. ..|+..+++|+||+.+     +|.+|.+   .+||.+.++....+||++.. ...+.
T Consensus        88 ~~L~~~L~~kG~~~~~l~~~~~-~~yDrFr~RimFPI~d-----gFgGR~l~~~~PKYLN~~SP~~~l~~~~~~~~~~~~  161 (266)
T PHA02031         88 QSLYGLLLSKGIDPNMMEPGLP-LEYSERQGRLIFRTDA-----GWLGRATADQQPKWVGYGYPAPDYVGWPPELSMPRP  161 (266)
T ss_pred             HHHHHHHHHCCCCHHHHHhcCC-cceeeeCCEEEEeecc-----ccccccCCCCCCCcCCCCCCcHHHhhchhhhccCCe
Confidence            5688999999999998876432 2356678999999986     6777776   57999955446678888754 35789


Q ss_pred             EEEEechhhHHHHHH---hCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccC--CEEEEEecCCccchHH
Q 009230          126 IIIVEGEMDKLSMEE---AGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQA--SRIILATDGDPPGQAL  200 (539)
Q Consensus       126 v~i~EG~~Dalsl~~---~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~--~~ivl~~DnD~~G~~~  200 (539)
                      +|||||.+|++++++   +|+.++|+. .|++-       .           ..++..|.++  ++|++|+|.|.||++|
T Consensus       162 vIlvEGYmDVI~l~~a~~aG~~naVA~-LGTAL-------T-----------~~q~~~L~r~~~~~Vil~fDgD~AG~~A  222 (266)
T PHA02031        162 VVLTEDYLSALKVRWACNKPEVFAVAL-LGTRL-------R-----------DRLAAILLQQTCPRVLIFLDGDPAGVDG  222 (266)
T ss_pred             EEEEcCcHHHHHHHHHHhcCcceEEEC-CcccC-------C-----------HHHHHHHHhcCCCCEEEEeCCCHHHHHH
Confidence            999999999999976   699999985 57753       2           1235566664  8999999999999999


Q ss_pred             HHHHHHHhc--CCceEEEecCCCCCCCCCCChHHHHHhcCcchHH
Q 009230          201 AEELARRVG--RERCWRVRWPKKNDVDHFKDANEVLMYLGPGALK  243 (539)
Q Consensus       201 ~~~~~~~l~--~~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~~  243 (539)
                      +.+..+.|.  ...+.++.+|      .++||+|++++.+.+.+.
T Consensus       223 a~ra~~~l~~~~~~v~vv~lP------~g~DPDd~ir~~i~eal~  261 (266)
T PHA02031        223 SAGAMRRLRPLLIEGQVIITP------DGFDPKDLEREQIRELLI  261 (266)
T ss_pred             HHHHHHHHHHcCCceEEEECC------CCCChHHHHHHHHHHHHh
Confidence            999888873  3467888988      689999999876555443

>cd01394 radB RadB

Probab=99.84  E-value=2.2e-19  Score=170.28  Aligned_cols=197  Identities=18%  Similarity=0.175  Sum_probs=133.0

Q ss_pred             cccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccc
Q 009230          281 ISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEAN  358 (539)
Q Consensus       281 i~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~  358 (539)
                      +|||+++||.+++  +++|++++|+|+||+|||+|+++++.+++.+ |.+|+|++.|....+-..++...          
T Consensus         1 i~TGi~~LD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~-g~~v~yi~~e~~~~~~~~~~~~~----------   69 (218)
T cd01394           1 LPTGCKGLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQ-GKKVAYIDTEGLSSERFRQIAGD----------   69 (218)
T ss_pred             CCcchhHHHHHhcCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhc-CCeEEEEECCCCCHHHHHHHHhH----------
Confidence            5899999999995  9999999999999999999999999999885 99999999997654332222211          


Q ss_pred             cCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHH---HHHHHHHHcCCcEEEEccccccccCCCCC----CC
Q 009230          359 YGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLD---LAKAAVLRHGVRGLVIDPYNELDHQRPVS----QT  431 (539)
Q Consensus       359 ~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~---~i~~~~~~~~~~~vvID~~~~l~~~~~~~----~~  431 (539)
                            .         .+.+..+.+++.     ..+++++..   .+.... ..++++|||||+..+.......    ..
T Consensus        70 ------~---------~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~-~~~~~lvvIDsi~~l~~~~~~~~~~~~~  128 (218)
T cd01394          70 ------R---------PERAASSIIVFE-----PMDFNEQGRAIQETETFA-DEKVDLVVVDSATALYRLELGDDDTTIK  128 (218)
T ss_pred             ------C---------hHhhhcCEEEEe-----CCCHHHHHHHHHHHHHHH-hcCCcEEEEechHHhhhHHhcCccchHH
Confidence                  0         011223333331     223344433   333322 2358999999998875321101    12


Q ss_pred             HHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEE
Q 009230          432 ETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCV  510 (539)
Q Consensus       432 ~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i  510 (539)
                      ....+.+++..|+.+|++++|+||+++| ++...+ ...+|     .|+..+++.+|.+|.|.+.+..      .....+
T Consensus       129 ~~~~l~~~~~~L~~~a~~~~~~vi~t~q~~~~~~~-~~~~p-----~~g~~~~~~~d~~i~l~~~~~~------~r~~~~  196 (218)
T cd01394         129 NYRELAKQLTFLLWLARKHDVAVVITNQVYSDVGS-GSVRP-----LGGHTLEHWSKVILRLEKLRVG------TRRAVL  196 (218)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCEEEEecCCEEcCCC-Ccccc-----cCCcchhcceeEEEEEEEcCCC------eEEEEE
Confidence            2335677888899999999999999999 654432 11222     2456789999999999987621      233346


Q ss_pred             EEeeCCCccee
Q 009230          511 RKVRNKVVGTI  521 (539)
Q Consensus       511 ~K~R~g~~G~~  521 (539)
                      .|+|..+.+..
T Consensus       197 ~~~~~~~~~~~  207 (218)
T cd01394         197 EKHRFRPEGSS  207 (218)
T ss_pred             eeCCCCCCCce
Confidence            67777776654

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=99.84  E-value=1.4e-19  Score=172.33  Aligned_cols=197  Identities=17%  Similarity=0.220  Sum_probs=135.3

Q ss_pred             ccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC-CCHHHHHHHHHHHhhCCCccc
Q 009230          280 GISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME-NKVREHARKLLEKHIKKPFFE  356 (539)
Q Consensus       280 gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E-~~~~~~~~r~~~~~~~~~~~~  356 (539)
                      .++||+++||++++  +++|.++.|+|+||+|||+|++|++.+.+.. |.+|+|+++| ++++++.+ +...    +   
T Consensus         4 ~i~tGi~~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~-~~~v~yi~~e~~~~~r~~~-~~~~----~---   74 (225)
T PRK09361          4 RLPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKN-GKKVIYIDTEGLSPERFKQ-IAGE----D---   74 (225)
T ss_pred             cccCCcHHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHHC-CCeEEEEECCCCCHHHHHH-HHhh----C---
Confidence            58999999999994  9999999999999999999999999999885 9999999999 45544322 1110    0   


Q ss_pred             cccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHH---HHHHHcCCcEEEEccccccccCC--C--CC
Q 009230          357 ANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAK---AAVLRHGVRGLVIDPYNELDHQR--P--VS  429 (539)
Q Consensus       357 i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~---~~~~~~~~~~vvID~~~~l~~~~--~--~~  429 (539)
                                    +.+   .+ ++.+++     ...+.+++...++   .+.. .++++||||++..+....  .  ..
T Consensus        75 --------------~~~---~~-~~~~~~-----~~~~~~~~~~~i~~~~~~~~-~~~~lvVIDsi~al~~~~~~~~~~~  130 (225)
T PRK09361         75 --------------FEE---LL-SNIIIF-----EPSSFEEQSEAIRKAEKLAK-ENVGLIVLDSATSLYRLELEDEEDN  130 (225)
T ss_pred             --------------hHh---Hh-hCeEEE-----eCCCHHHHHHHHHHHHHHHH-hcccEEEEeCcHHHhHHHhcCCccH
Confidence                          111   11 233333     1234444433333   3332 689999999998775431  1  11


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEE
Q 009230          430 QTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQV  508 (539)
Q Consensus       430 ~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l  508 (539)
                      ......+.+++..|+.+|+++|++|++++| .......     . ..-.|+..+++.+|.+|.|.+.+.      +...+
T Consensus       131 ~~~~~~l~~~l~~L~~~a~~~~v~vi~tnq~~~~~~~~-----~-~~~~gg~~~~~~~d~ii~l~~~~~------~~r~~  198 (225)
T PRK09361        131 SKLNRELGRQLTHLLKLARKHDLAVVITNQVYSDIDSD-----G-LRPLGGHTLEHWSKTILRLEKFRN------GKRRA  198 (225)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCEEEEEccceecCCCC-----c-ccCCCcchhhhhccEEEEEEEccC------CeEEE
Confidence            112345677778899999999999999999 4433211     1 112355678999999999988322      24566


Q ss_pred             EEEEeeCCCccee
Q 009230          509 CVRKVRNKVVGTI  521 (539)
Q Consensus       509 ~i~K~R~g~~G~~  521 (539)
                      .+.|+|..+.|..
T Consensus       199 ~i~k~~~~~~~~~  211 (225)
T PRK09361        199 TLEKHRSRPEGES  211 (225)
T ss_pred             EEEECCCCCCCCe
Confidence            7899988777654

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=99.84  E-value=4.2e-19  Score=169.68  Aligned_cols=198  Identities=18%  Similarity=0.124  Sum_probs=141.3

Q ss_pred             cccCchhhhhhh-c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccc
Q 009230          281 ISTGWRALNELY-N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEAN  358 (539)
Q Consensus       281 i~tg~~~LD~~~-~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~  358 (539)
                      ++||+++||+++ | +++|++++|.|+||+|||+|+++++.+.+.+ |.+|+|+++|++++++..++  ...|+++.++.
T Consensus         2 i~tGi~~LD~~l~GGi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~-g~~~~~is~e~~~~~i~~~~--~~~g~~~~~~~   78 (229)
T TIGR03881         2 LSTGVEGLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRD-GDPVIYVTTEESRESIIRQA--AQFGMDFEKAI   78 (229)
T ss_pred             cCCChhhHHHhhcCCCcCCeEEEEECCCCCChHHHHHHHHHHHHhc-CCeEEEEEccCCHHHHHHHH--HHhCCCHHHHh
Confidence            789999999998 4 9999999999999999999999999988875 99999999999999888773  33455544321


Q ss_pred             cCCCCCCCCHHHHHHHHHHhhccceeEee--------cCCCCCCHHHHHHHHHHHHHHc--CCcEEEEccccccccCCCC
Q 009230          359 YGGSAERMTVEEFEQGKAWLSNTFSLIRC--------ENDSLPSIKWVLDLAKAAVLRH--GVRGLVIDPYNELDHQRPV  428 (539)
Q Consensus       359 ~~~~~~~l~~~~~~~~~~~l~~~~~~i~~--------~~~~~~~~~~i~~~i~~~~~~~--~~~~vvID~~~~l~~~~~~  428 (539)
                      ..                   ....++..        ......+++++...++.+..++  ++++||||++..+....  
T Consensus        79 ~~-------------------~~l~i~d~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~vvIDsl~~l~~~~--  137 (229)
T TIGR03881        79 EE-------------------GKLVIIDALMKEKEDEWSLRELSIEELLNKVIEAKKYLGYGHARLVIDSMSAFWLDK--  137 (229)
T ss_pred             hc-------------------CCEEEEEccccccccccccccCCHHHHHHHHHHHHHhhccCceEEEecCchhhhccC--
Confidence            10                   01111100        0012457888999998887775  47799999877765321  


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEE
Q 009230          429 SQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQV  508 (539)
Q Consensus       429 ~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l  508 (539)
                         . ....+++..|+.+++++|+++++++|......    .+      ....++..||.||.|+..+...   .....+
T Consensus       138 ---~-~~~r~~~~~l~~~l~~~~~tvil~~~~~~~~~----~~------~~~~~~~l~D~vI~L~~~~~~~---~~~R~i  200 (229)
T TIGR03881       138 ---P-AMARKYSYYLKRVLNRWNFTILLTSQYAITTS----QA------FGFGIEHVADGIIRFRKVVVDG---ELRRYL  200 (229)
T ss_pred             ---h-HHHHHHHHHHHHHHHhCCCEEEEEecccccCC----CC------cccceEEEEeEEEEEEEeccCC---cEEEEE
Confidence               1 12356778899999999999999999322211    00      1124678999999999765422   124678


Q ss_pred             EEEEeeCCCcc
Q 009230          509 CVRKVRNKVVG  519 (539)
Q Consensus       509 ~i~K~R~g~~G  519 (539)
                      .|.|.|.....
T Consensus       201 ~i~K~R~~~~~  211 (229)
T TIGR03881       201 IVEKMRQTNHD  211 (229)
T ss_pred             EEEeccCCCCC
Confidence            99999986443

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.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=99.82  E-value=1.6e-18  Score=171.81  Aligned_cols=239  Identities=15%  Similarity=0.128  Sum_probs=161.9

Q ss_pred             cchHHHHHHhccccCccccccccchHHHHHHHhhccCCCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHH
Q 009230          239 PGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDA  316 (539)
Q Consensus       239 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~  316 (539)
                      .+.+.+++..|......+..+..++++.        ......++||++.||++++  +++|.+|.|+|+||+|||+|++|
T Consensus        74 ~~~~~ki~~~a~~~~~~~~~ta~~~~~~--------~~~~~~isTG~~~LD~lLgGGi~~G~ItEI~G~~GsGKTql~lq  145 (344)
T PLN03187         74 EAKVDKICEAAEKLLNQGFITGSDALLK--------RKSVVRITTGSQALDELLGGGIETRCITEAFGEFRSGKTQLAHT  145 (344)
T ss_pred             HHHHHHHHHHHHHhhcccCCcHHHHHhh--------hccCceecCCcHhHHhhcCCCCCCCeEEEEecCCCCChhHHHHH
Confidence            3556666766665444455555555332        1345679999999999996  99999999999999999999999


Q ss_pred             HHHHHHHh-----cCCeEEEEeCCC--CHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecC
Q 009230          317 LICNINEH-----AGWKFVLCSMEN--KVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCEN  389 (539)
Q Consensus       317 la~~~a~~-----~g~~vl~~s~E~--~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~  389 (539)
                      ++.+.+..     .+.+|+|+++|.  +++++.+....  .|.+.              ++      .+ +++++.    
T Consensus       146 lav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~ia~~--~g~d~--------------~~------~l-~~I~~~----  198 (344)
T PLN03187        146 LCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPIAER--FGMDA--------------DA------VL-DNIIYA----  198 (344)
T ss_pred             HHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHHHHHH--cCCCh--------------hh------hc-CeEEEe----
Confidence            99887642     136999999998  68877665432  23221              11      12 223333    


Q ss_pred             CCCCCHHHHHHHH---HHHHHHcCCcEEEEccccccccCC--CCC--CCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CC
Q 009230          390 DSLPSIKWVLDLA---KAAVLRHGVRGLVIDPYNELDHQR--PVS--QTETEYVSQMLTMVKRFAQHHACHVWFVAH-PR  461 (539)
Q Consensus       390 ~~~~~~~~i~~~i---~~~~~~~~~~~vvID~~~~l~~~~--~~~--~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r  461 (539)
                       ...+.+++...+   .....+.++++|||||+..+....  +.+  ..+.+.+.+++..|+.+|+++|++|+++.| ..
T Consensus       199 -~~~~~e~~~~~l~~l~~~i~~~~~~LvVIDSital~r~~~~~rg~l~~rq~~L~~~~~~L~~lA~~~~vavvvTNqv~~  277 (344)
T PLN03187        199 -RAYTYEHQYNLLLGLAAKMAEEPFRLLIVDSVIALFRVDFTGRGELAERQQKLAQMLSRLTKIAEEFNVAVYMTNQVIA  277 (344)
T ss_pred             -cCCCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHhhhccccCccchHHHHHHHHHHHHHHHHHHHHcCCEEEEEecEEE
Confidence             334555544433   334556789999999999886542  111  123345788999999999999999999999 44


Q ss_pred             CCCCC-CCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCCCccee
Q 009230          462 QLHNW-VGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       462 ~~~~~-~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~G~~  521 (539)
                      +.... ....|  ..-.|+..+...+++.+.|.+.+.      ..+.+.+.|+++.+.+..
T Consensus       278 ~~~~~~~~~~~--~~pagG~~~~h~~~~Rl~l~k~~~------~~R~~~v~ksp~lp~~~~  330 (344)
T PLN03187        278 DPGGGMFISDP--KKPAGGHVLAHAATIRLMLRKGKG------EQRVCKVFDAPNLPEAEA  330 (344)
T ss_pred             cCCcccccCCC--CCCCCchhhheeeeEEEEEEcCCC------CeEEEEEEECCCCCCceE
Confidence            33211 00111  122456788899999999987542      246789999999888764

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=99.82  E-value=1.6e-18  Score=170.93  Aligned_cols=239  Identities=13%  Similarity=0.104  Sum_probs=158.5

Q ss_pred             cchHHHHHHhccccCccccccccchHHHHHHHhhccCCCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHH
Q 009230          239 PGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDA  316 (539)
Q Consensus       239 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~  316 (539)
                      .+.+.++++.|......+..+..++.+.        ......++||.+.||++++  +++|.++.|+|+||+|||+|++|
T Consensus        44 ~~~~~~i~~~~~~~~~~~~~ta~~~~~~--------~~~~~~isTG~~~LD~lLgGGi~~G~iteI~G~~GsGKTql~lq  115 (313)
T TIGR02238        44 EAKVDKIKEAASKIINPGFITAFEISQK--------RKKVLKITTGSQALDGILGGGIESMSITEVFGEFRCGKTQLSHT  115 (313)
T ss_pred             HHHHHHHHHHHHhhhcccCccHHHHHHh--------hccCceeCCCCHHHHHHhCCCCcCCeEEEEECCCCCCcCHHHHH
Confidence            3556667766655433344444444211        2445679999999999996  99999999999999999999999


Q ss_pred             HHHHHHHh-----cCCeEEEEeCCCC--HHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecC
Q 009230          317 LICNINEH-----AGWKFVLCSMENK--VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCEN  389 (539)
Q Consensus       317 la~~~a~~-----~g~~vl~~s~E~~--~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~  389 (539)
                      ++.+....     .+.+|+|+++|.+  ++++.++...  .+++.              ++       +-++.++.    
T Consensus       116 la~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~~a~~--~g~d~--------------~~-------~l~~i~~~----  168 (313)
T TIGR02238       116 LCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAER--FGVDP--------------DA-------VLDNILYA----  168 (313)
T ss_pred             HHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHHHHHH--cCCCh--------------HH-------hcCcEEEe----
Confidence            99887642     2579999999985  7877665432  23221              11       11223333    


Q ss_pred             CCCCCHHHHHHHHH---HHHHHcCCcEEEEccccccccCCCC--C-CC-HHHHHHHHHHHHHHHHHHhCcEEEEEec-CC
Q 009230          390 DSLPSIKWVLDLAK---AAVLRHGVRGLVIDPYNELDHQRPV--S-QT-ETEYVSQMLTMVKRFAQHHACHVWFVAH-PR  461 (539)
Q Consensus       390 ~~~~~~~~i~~~i~---~~~~~~~~~~vvID~~~~l~~~~~~--~-~~-~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r  461 (539)
                       ...+.++..+.+.   ....+.++++|||||+..+....-.  + .. +.+.+.+++..|+.+|+++|++|+++.| ..
T Consensus       169 -~~~~~e~~~~~l~~l~~~i~~~~~~LvVIDSisal~r~~~~~~g~~~~r~~~l~~~~~~L~~la~~~~vavvitNqv~~  247 (313)
T TIGR02238       169 -RAYTSEHQMELLDYLAAKFSEEPFRLLIVDSIMALFRVDFSGRGELSERQQKLAQMLSRLNKISEEFNVAVFVTNQVQA  247 (313)
T ss_pred             -cCCCHHHHHHHHHHHHHHhhccCCCEEEEEcchHhhhhhccCccchHHHHHHHHHHHHHHHHHHHHcCcEEEEECceEe
Confidence             2334444443333   3344568999999999988653211  1 11 2234778999999999999999999999 44


Q ss_pred             CCCCC--CCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCCCccee
Q 009230          462 QLHNW--VGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       462 ~~~~~--~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~G~~  521 (539)
                      +....  ....|  ..-.|+..++..+++.|.|.+.+.      +.+.+.|.|.++-+.+..
T Consensus       248 ~~~~~~~~~~~~--~~p~gG~~~~h~~~~Rl~l~k~~~------~~R~~~~~~sp~~p~~~~  301 (313)
T TIGR02238       248 DPGATMTFIADP--KKPIGGHVLAHASTTRILLRKGRG------EERVAKLYDSPDMPEAEA  301 (313)
T ss_pred             cCCcccccCCCC--ccCcchhhhhhheeEEEEEEecCC------CeEEEEEeeCCCCCCeEE
Confidence            43210  00001  011356788999999999997643      246788899988887764

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.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=99.81  E-value=2e-18  Score=169.05  Aligned_cols=219  Identities=16%  Similarity=0.093  Sum_probs=155.8

Q ss_pred             CCccccccCchhhhhhhc---cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCC
Q 009230          276 GDEFGISTGWRALNELYN---VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKK  352 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~---l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~  352 (539)
                      .....+|||++.||.+++   +++|.++.|+|+||+|||+|+++++.+++.. |.+|+|+++|.+...-  +  +...|+
T Consensus        31 ~~~~~isTGi~~LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal~~~~~~~~~-g~~~vyId~E~~~~~~--~--a~~lGv  105 (325)
T cd00983          31 QDVEVIPTGSLSLDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKL-GGTVAFIDAEHALDPV--Y--AKKLGV  105 (325)
T ss_pred             cCCceecCCCHHHHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHc-CCCEEEECccccHHHH--H--HHHcCC
Confidence            345679999999999974   9999999999999999999999999999885 9999999999987742  1  222233


Q ss_pred             CccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccC-C-CC-C
Q 009230          353 PFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQ-R-PV-S  429 (539)
Q Consensus       353 ~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~-~-~~-~  429 (539)
                      +..                         +++++     ...+.++....++.+++...+++|||||+..+... . .+ .
T Consensus       106 d~~-------------------------~l~v~-----~p~~~eq~l~i~~~li~s~~~~lIVIDSvaal~~~~E~~~~~  155 (325)
T cd00983         106 DLD-------------------------NLLIS-----QPDTGEQALEIADSLVRSGAVDLIVVDSVAALVPKAEIEGEM  155 (325)
T ss_pred             CHH-------------------------Hheec-----CCCCHHHHHHHHHHHHhccCCCEEEEcchHhhcccccccccc
Confidence            221                         11222     22346777777888888888999999999988742 1 11 1


Q ss_pred             -CC----HHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC---CCCC
Q 009230          430 -QT----ETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD---PEAG  501 (539)
Q Consensus       430 -~~----~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~---~~~~  501 (539)
                       ..    ....+.+.++.|..+++++||++|++.|.+..-....  ....--.|+..+.+.+...+-+.+.+.   .+..
T Consensus       156 ~~~~~~~qaR~l~~~Lr~L~~~~~k~~~~vI~tNQvr~~ig~~~--g~~e~~~GG~~L~~~ss~rl~lrk~~~~k~~~~~  233 (325)
T cd00983         156 GDSHVGLQARLMSQALRKLTGSINKSNTTVIFINQLREKIGVMF--GNPETTTGGNALKFYSSVRLDIRRIETIKDGDEV  233 (325)
T ss_pred             cccchHHHHHHHHHHHHHHHHHHHhCCCEEEEEEcccccccccc--CCCccCCCchHHhhhcceEEEEEeecccccCCcc
Confidence             11    1123567888899999999999999999443321100  111223456679999999999988652   1111


Q ss_pred             CCCcEEEEEEEeeCCCcceeeeEEEEEeCC
Q 009230          502 PIDRVQVCVRKVRNKVVGTIGEAFLSYNRV  531 (539)
Q Consensus       502 ~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~  531 (539)
                      ..+.+.+.+.|||-.+.+..-.+.+.|+.-
T Consensus       234 ~G~~~~~~v~Knk~~~p~~~~~~~i~~~~G  263 (325)
T cd00983         234 IGNRTKVKVVKNKVAPPFKTAEFDILFGEG  263 (325)
T ss_pred             cccEEEEEEEecccCCCCCceEEEEEcCcc
Confidence            234578999999999888765566777643

RecA couples ATP hydrolysis to DNA strand exchange.

>TIGR02012 tigrfam_recA protein RecA

Probab=99.81  E-value=9.9e-19  Score=171.19  Aligned_cols=218  Identities=17%  Similarity=0.106  Sum_probs=154.1

Q ss_pred             CccccccCchhhhhhh--c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          277 DEFGISTGWRALNELY--N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~--~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      ....+|||++.||.++  | |++|.++.|+|+||+|||+|+++++.+++.+ |.+|+||++|.+....    .+...|++
T Consensus        32 ~~~~i~TGi~~LD~~Lg~GGlp~G~iteI~G~~GsGKTtLaL~~~~~~~~~-g~~v~yId~E~~~~~~----~a~~lGvd  106 (321)
T TIGR02012        32 DVETISTGSLSLDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKA-GGTAAFIDAEHALDPV----YARKLGVD  106 (321)
T ss_pred             cCceecCCCHHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHc-CCcEEEEcccchhHHH----HHHHcCCC
Confidence            4568999999999998  5 9999999999999999999999999999885 9999999999887753    12223443


Q ss_pred             ccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCC--CC--C
Q 009230          354 FFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQR--PV--S  429 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~--~~--~  429 (539)
                      ..                         ..++.     ...+.++....+..+++..++++|||||+..+....  .+  +
T Consensus       107 ~~-------------------------~l~v~-----~p~~~eq~l~~~~~li~~~~~~lIVIDSv~al~~~~E~e~~~g  156 (321)
T TIGR02012       107 ID-------------------------NLLVS-----QPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMG  156 (321)
T ss_pred             HH-------------------------HeEEe-----cCCCHHHHHHHHHHHhhccCCcEEEEcchhhhccchhhccccc
Confidence            21                         11222     223467777777777878889999999999886421  00  0


Q ss_pred             C----CHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC---CCCCC
Q 009230          430 Q----TETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD---PEAGP  502 (539)
Q Consensus       430 ~----~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~---~~~~~  502 (539)
                      .    .....+.++++.|..+++++||++|++.|.+...+.....|  ..-.|..++.+.+...+-+.|...   .+...
T Consensus       157 ~~~~~~~aR~m~~~lr~L~~~l~~~~~tvi~tNQvr~~~g~~~~~~--e~~~GG~aL~~~ss~r~~lrr~~~iK~~~~~~  234 (321)
T TIGR02012       157 DSHVGLQARLMSQALRKLTGALSKSNTTAIFINQIREKIGVMFGNP--ETTTGGRALKFYASVRLDIRRIGQVKQGEEVV  234 (321)
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHhCCCEEEEEecceeccCcccCCC--ccCcCccHHHHHHhHhHhhhhhhccccCCcee
Confidence            1    11123457888899999999999999999544321100111  123455668889998888877542   11122


Q ss_pred             CCcEEEEEEEeeCCCcceeeeEEEEEeCC
Q 009230          503 IDRVQVCVRKVRNKVVGTIGEAFLSYNRV  531 (539)
Q Consensus       503 ~~~~~l~i~K~R~g~~G~~~~~~l~fd~~  531 (539)
                      .+.+.+.+.|||-.+.+..-.+.+.|+.-
T Consensus       235 g~~~~~~v~Knk~~~p~~~~~~~i~~~~G  263 (321)
T TIGR02012       235 GNRTKVKVVKNKVAPPFKEAEFDILYGEG  263 (321)
T ss_pred             ccEEEEEEEECCCCCCCCceEEEEEcCCc
Confidence            35689999999999888754556666543

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=99.80  E-value=2.4e-18  Score=181.15  Aligned_cols=203  Identities=15%  Similarity=0.203  Sum_probs=148.8

Q ss_pred             CccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCc
Q 009230          277 DEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPF  354 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~  354 (539)
                      ....++||+++||++++  +++|.+++|.|+||+|||+|++|++.+.|.+ |.+|+|+|+|++++++..|+.+  .|+++
T Consensus       241 ~~~~~~tGi~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~-ge~~~y~s~eEs~~~i~~~~~~--lg~~~  317 (484)
T TIGR02655       241 SNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLENACAN-KERAILFAYEESRAQLLRNAYS--WGIDF  317 (484)
T ss_pred             cccccCCChHhHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHHHHHC-CCeEEEEEeeCCHHHHHHHHHH--cCCCh
Confidence            45579999999999996  9999999999999999999999999999986 9999999999999999999754  34443


Q ss_pred             cccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHH
Q 009230          355 FEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETE  434 (539)
Q Consensus       355 ~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~  434 (539)
                      ....                   ....+.++ ........+++....+...+.+.++++|||||+..+....    .. .
T Consensus       318 ~~~~-------------------~~g~l~~~-~~~p~~~~~~~~~~~i~~~i~~~~~~~vvIDsi~~~~~~~----~~-~  372 (484)
T TIGR02655       318 EEME-------------------QQGLLKII-CAYPESAGLEDHLQIIKSEIADFKPARIAIDSLSALARGV----SN-N  372 (484)
T ss_pred             HHHh-------------------hCCcEEEE-EcccccCChHHHHHHHHHHHHHcCCCEEEEcCHHHHHHhc----CH-H
Confidence            2211                   01222333 2123345678888888888888999999999999875421    11 2


Q ss_pred             HHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEee
Q 009230          435 YVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVR  514 (539)
Q Consensus       435 ~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R  514 (539)
                      ...+++..|..++++.|++++++.........  ...      ....+++.||+||.|...+....   -...+.|.|.|
T Consensus       373 ~~r~~~~~l~~~lk~~~it~~~t~~~~~~~~~--~~~------~~~~~s~l~D~ii~l~~~e~~g~---~~r~i~V~K~R  441 (484)
T TIGR02655       373 AFRQFVIGVTGYAKQEEITGFFTNTSDQFMGS--HSI------TDSHISTITDTILMLQYVEIRGE---MSRAINVFKMR  441 (484)
T ss_pred             HHHHHHHHHHHHHhhCCCeEEEeecccccccC--Ccc------CCCCeeEeeeEEEEEEEEecCCE---EEEEEEEEEcc
Confidence            33567778888999999999999773322110  000      01347889999999987664321   14558899999


Q ss_pred             CCCc
Q 009230          515 NKVV  518 (539)
Q Consensus       515 ~g~~  518 (539)
                      .+..
T Consensus       442 ~~~~  445 (484)
T TIGR02655       442 GSWH  445 (484)
T ss_pred             CCCC
Confidence            8754

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.

>PRK09354 recA recombinase A; Provisional

Probab=99.80  E-value=4.3e-18  Score=167.89  Aligned_cols=221  Identities=18%  Similarity=0.113  Sum_probs=156.0

Q ss_pred             CccccccCchhhhhhhc---cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          277 DEFGISTGWRALNELYN---VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~---l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      ....+|||++.||.+++   +++|.++.|+|++|+|||+|+++++.+++.. |.+++||++|.+...-   . +...|++
T Consensus        37 ~~~~isTGi~~LD~~LG~GGip~G~IteI~G~~GsGKTtLal~~~~~~~~~-G~~~~yId~E~s~~~~---~-a~~lGvd  111 (349)
T PRK09354         37 DVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKA-GGTAAFIDAEHALDPV---Y-AKKLGVD  111 (349)
T ss_pred             CCceecCCcHHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHc-CCcEEEECCccchHHH---H-HHHcCCC
Confidence            45679999999999985   9999999999999999999999999999885 9999999999988752   2 2223443


Q ss_pred             ccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCC---CC-C
Q 009230          354 FFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQR---PV-S  429 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~---~~-~  429 (539)
                      ..+                         +++.     ...+.++....++.+++..++++|||||+..+....   +. +
T Consensus       112 ld~-------------------------lli~-----qp~~~Eq~l~i~~~li~s~~~~lIVIDSvaaL~~~~E~eg~~g  161 (349)
T PRK09354        112 IDN-------------------------LLVS-----QPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMG  161 (349)
T ss_pred             HHH-------------------------eEEe-----cCCCHHHHHHHHHHHhhcCCCCEEEEeChhhhcchhhhcCCcc
Confidence            211                         1222     223467777778888888889999999999887411   10 1


Q ss_pred             CC----HHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC---CCCCC
Q 009230          430 QT----ETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD---PEAGP  502 (539)
Q Consensus       430 ~~----~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~---~~~~~  502 (539)
                      +.    ....+.+.++.|..+++++||++|++.|.+..-+.....|  ..-.|..++.+.+...+-+.|...   .+...
T Consensus       162 d~~~~~qar~ms~~Lr~L~~~l~k~~itvI~tNQvr~~ig~~~g~p--e~~~GG~aL~~~ss~rl~lrr~~~iK~~~~~~  239 (349)
T PRK09354        162 DSHVGLQARLMSQALRKLTGNISKSNTTVIFINQIREKIGVMFGNP--ETTTGGNALKFYASVRLDIRRIGTIKDGDEVI  239 (349)
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHcCcEEEEEEeeeeccccccCCC--CcCCCchhhHhhheeeeEEecccccccCCcee
Confidence            11    1124456788899999999999999999544211000111  122456678899999999988642   11112


Q ss_pred             CCcEEEEEEEeeCCCcceeeeEEEEEeCCCce
Q 009230          503 IDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGE  534 (539)
Q Consensus       503 ~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~r  534 (539)
                      .+.+.+.+.|||-.+.+..-.+.+.|+.--.+
T Consensus       240 G~~~r~~vvKnk~~~p~~~a~~~i~~~~Gi~~  271 (349)
T PRK09354        240 GNRTKVKVVKNKVAPPFKQAEFDIMYGEGISR  271 (349)
T ss_pred             cceEEEEEEecccCCCCCceEEEEEcCCccch
Confidence            34678999999999888765566777653333

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=99.80  E-value=2.3e-18  Score=183.40  Aligned_cols=206  Identities=12%  Similarity=0.095  Sum_probs=147.0

Q ss_pred             CCccccccCchhhhhhh-c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          276 GDEFGISTGWRALNELY-N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~-~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      ....++|||+++||+++ | +++|++++|+|+||+|||+|++|++.+.+.+.|.+|+|||+|++++++.+++.+.  |++
T Consensus         8 ~~~~ri~TGI~~LD~~l~GG~p~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis~ee~~~~i~~~~~~~--g~d   85 (509)
T PRK09302          8 PGIEKLPTGIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVTFEESPEDIIRNVASF--GWD   85 (509)
T ss_pred             CCCccccCCchhHHHhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEEccCCHHHHHHHHHHc--CCC
Confidence            35568999999999999 4 9999999999999999999999999999886589999999999999999998763  555


Q ss_pred             ccccccCCCCCCCCHHHHHHHHHHhhccceeEeec-------CCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCC
Q 009230          354 FFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCE-------NDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQR  426 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~-------~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~  426 (539)
                      +.++...                   ..+.++...       ..+..+++.+...+..++.+.+++.|||||+..+....
T Consensus        86 ~~~~~~~-------------------g~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~i~~~~~~~vVIDSls~l~~~~  146 (509)
T PRK09302         86 LQKLIDE-------------------GKLFILDASPDPSEQEEAGEYDLEALFIRIEYAIDKIGAKRVVLDSIEALFSGF  146 (509)
T ss_pred             HHHHhhC-------------------CeEEEEecCcccccccccccccHHHHHHHHHHHHHhhCCCEEEECCHHHHHhhc
Confidence            4332110                   111111100       01233567788888888888999999999998875421


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcE
Q 009230          427 PVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRV  506 (539)
Q Consensus       427 ~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~  506 (539)
                         .+. ..+...+..|...+++.++++++++|......         ++...+..++.||.|+.|.......   ....
T Consensus       147 ---d~~-~~~r~~l~~L~~~Lk~~g~TvLlt~~~~~~~~---------~~~~~~~~~~laDgVI~L~~~~~~~---~~~R  210 (509)
T PRK09302        147 ---SNE-AVVRRELRRLFAWLKQKGVTAVITGERGDEYG---------PLTRYGVEEFVSDCVIILRNRLEGE---KRTR  210 (509)
T ss_pred             ---cCH-HHHHHHHHHHHHHHHhCCCEEEEEECCccCcC---------CccccCceEEEeeEEEEEeEEccCC---eEEE
Confidence               122 22345556666677889999999999322111         1222234567999999998655322   2257


Q ss_pred             EEEEEEeeCCCc
Q 009230          507 QVCVRKVRNKVV  518 (539)
Q Consensus       507 ~l~i~K~R~g~~  518 (539)
                      .+.|.|.|....
T Consensus       211 ~l~I~K~Rg~~~  222 (509)
T PRK09302        211 TLRILKYRGTTH  222 (509)
T ss_pred             EEEEEECCCCCc
Confidence            899999997543

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=99.80  E-value=9.4e-19  Score=162.73  Aligned_cols=167  Identities=23%  Similarity=0.270  Sum_probs=99.4

Q ss_pred             ccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh---------cCCeEEEEeCCCCHHHHHHHHH
Q 009230          278 EFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEH---------AGWKFVLCSMENKVREHARKLL  346 (539)
Q Consensus       278 ~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~---------~g~~vl~~s~E~~~~~~~~r~~  346 (539)
                      ...++++++.+|.+++  +++|++++|+|+||+|||+|+++++.+++..         .+.+|+|+++|++..++..|+.
T Consensus        11 ~~~~~~~~~~~~~li~g~~~~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~~~~~~~rl~   90 (193)
T PF13481_consen   11 FEDLDTGFPPLDWLIDGLLPRGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDSESQIARRLR   90 (193)
T ss_dssp             --HHHS------EEETTEE-TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-HHHHHHHHH
T ss_pred             hhhccCCCCCcceeECCcccCCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCCHHHHHHHHH
Confidence            3468899999999997  7899999999999999999999999999962         2679999999999999999987


Q ss_pred             HHhhCCCccccccCCCCCCCCHHHHHHHHHHhh-ccceeEeecCCCCCCHHHHHHHHHHHHHH-cCCcEEEEcccccccc
Q 009230          347 EKHIKKPFFEANYGGSAERMTVEEFEQGKAWLS-NTFSLIRCENDSLPSIKWVLDLAKAAVLR-HGVRGLVIDPYNELDH  424 (539)
Q Consensus       347 ~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~-~~~~~i~~~~~~~~~~~~i~~~i~~~~~~-~~~~~vvID~~~~l~~  424 (539)
                      ....+              ++..+...+..... ....++. .......++...+.+.+.+.+ +++++||||++..+..
T Consensus        91 ~~~~~--------------~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~lvviD~l~~~~~  155 (193)
T PF13481_consen   91 ALLQD--------------YDDDANLFFVDLSNWGCIRLFE-PDSGGPLLDEDLEELEAALKELYGPDLVVIDPLQSLHD  155 (193)
T ss_dssp             HHHTT--------------S-HHHHHHHHHH--E-EE---T-TS---TTSHHHHHHHHHHHTT----SEEEEE-GGGG--
T ss_pred             HHhcc--------------cCCccceEEeeccccccceeee-cccccccchHHHHHHHHHHhhcCCCcEEEEcCHHHHhc
Confidence            65422              22222222211111 1111111 112222245566666666666 7899999999998886


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCC
Q 009230          425 QRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQ  462 (539)
Q Consensus       425 ~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~  462 (539)
                      .   ..+....+.+++..|+++|+++|++|++++|.++
T Consensus       156 ~---~~~~~~~~~~~~~~l~~la~~~~~~vi~v~H~~K  190 (193)
T PF13481_consen  156 G---DENSNSAVAQLMQELKRLAKEYGVAVILVHHTNK  190 (193)
T ss_dssp             S----TT-HHHHHHHHHHHHHHHHHH--EEEEEEEE--
T ss_pred             C---CCCCHHHHHHHHHHHHHHHHHcCCEEEEEECCCC
Confidence            5   2344444589999999999999999999999444

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=99.80  E-value=7.6e-18  Score=167.39  Aligned_cols=210  Identities=13%  Similarity=0.126  Sum_probs=143.1

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-----cCCeEEEEeCCC--CHHHHHHHHH
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEH-----AGWKFVLCSMEN--KVREHARKLL  346 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-----~g~~vl~~s~E~--~~~~~~~r~~  346 (539)
                      .....++||++.||++++  +++|+++.|+|+||+|||+|+++++.+++..     .+.+|+|+++|.  +++++.+..-
T Consensus       100 ~~~~~i~tG~~~LD~lL~GG~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~qia~  179 (342)
T PLN03186        100 QEIIQITTGSRELDKILEGGIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLIQIAE  179 (342)
T ss_pred             cCcceeCCCCHHHHHhhcCCCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHHHHHH
Confidence            456789999999999875  9999999999999999999999999887631     134899999998  5666543321


Q ss_pred             HHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHH---HHHHHcCCcEEEEccccccc
Q 009230          347 EKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAK---AAVLRHGVRGLVIDPYNELD  423 (539)
Q Consensus       347 ~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~---~~~~~~~~~~vvID~~~~l~  423 (539)
                      .  .+++              .++      .+ +..++.     ...+.+.+...+.   .+....++++|||||+..+.
T Consensus       180 ~--~~~~--------------~~~------~l-~~i~~~-----~~~~~e~~~~ll~~~~~~~~~~~~~LIVIDSI~alf  231 (342)
T PLN03186        180 R--FGLN--------------GAD------VL-ENVAYA-----RAYNTDHQSELLLEAASMMAETRFALMIVDSATALY  231 (342)
T ss_pred             H--cCCC--------------hhh------hc-cceEEE-----ecCCHHHHHHHHHHHHHHhhccCCCEEEEeCcHHHH
Confidence            1  1221              111      11 223333     2234555444333   33456789999999999886


Q ss_pred             cCC--CCCC--CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCC-CCCCCCcccccccccchhccceEEEEEeCCC
Q 009230          424 HQR--PVSQ--TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNW-VGEPPNLYDISGSAHFINKCDNGIVIHRNRD  497 (539)
Q Consensus       424 ~~~--~~~~--~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~-~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~  497 (539)
                      ...  +.+.  .+...+.+++..|+.+|+++||+|+++.| ....++. .-..|.+. -.|+..++..+++.|.|.+.+.
T Consensus       232 r~~~~~~g~l~~r~~~L~~~l~~L~~lA~~~~vaVviTNqv~~~~~~~~~~~~~~~~-P~gG~~~~h~~~tRl~L~k~~~  310 (342)
T PLN03186        232 RTEFSGRGELSARQMHLGKFLRSLQRLADEFGVAVVITNQVVAQVDGSAFFAGPQLK-PIGGNIMAHASTTRLALRKGRG  310 (342)
T ss_pred             HHHhcCCccHHHHHHHHHHHHHHHHHHHHHcCCEEEEEcCEEEccCCccccCCCccc-cchhHHHHhhccEEEEEEecCC
Confidence            532  1111  12234678999999999999999999999 3333221 00011111 1255689999999999997532


Q ss_pred             CCCCCCCcEEEEEEEeeCCCcce
Q 009230          498 PEAGPIDRVQVCVRKVRNKVVGT  520 (539)
Q Consensus       498 ~~~~~~~~~~l~i~K~R~g~~G~  520 (539)
                            ..+.+.+.|+++.+.++
T Consensus       311 ------~~R~~~v~ksp~~p~~e  327 (342)
T PLN03186        311 ------ENRICKVISSPCLPEAE  327 (342)
T ss_pred             ------CeEEEEEEECCCCCCeE
Confidence                  25678999999999887

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=99.79  E-value=8.9e-18  Score=166.26  Aligned_cols=206  Identities=14%  Similarity=0.164  Sum_probs=142.0

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh--cC---CeEEEEeCCC--CHHHHHHHHH
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEH--AG---WKFVLCSMEN--KVREHARKLL  346 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~--~g---~~vl~~s~E~--~~~~~~~r~~  346 (539)
                      .....++||++.||.+++  +++|+++.|+|+||+|||+|+++++.+++..  .|   .+|+|++.|.  +++++.... 
T Consensus        73 ~~~~~~~tg~~~lD~ll~gGi~~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl~~ia-  151 (316)
T TIGR02239        73 QEVIQLTTGSKELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERLLAIA-  151 (316)
T ss_pred             cccceeCCCCHHHHHHhcCCCCCCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHHHHHH-
Confidence            566789999999999875  9999999999999999999999999876542  12   5899999998  466543332 


Q ss_pred             HHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHH---HHHHHcCCcEEEEccccccc
Q 009230          347 EKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAK---AAVLRHGVRGLVIDPYNELD  423 (539)
Q Consensus       347 ~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~---~~~~~~~~~~vvID~~~~l~  423 (539)
                       ...+.              +.+.       +.+...+.     ...+.+++...+.   .+....++++|||||+..+.
T Consensus       152 -~~~~~--------------~~~~-------~l~~i~~~-----~~~~~~~~~~~l~~~~~~~~~~~~~LvVIDSI~al~  204 (316)
T TIGR02239       152 -ERYGL--------------NPED-------VLDNVAYA-----RAYNTDHQLQLLQQAAAMMSESRFALLIVDSATALY  204 (316)
T ss_pred             -HHcCC--------------ChHH-------hhccEEEE-----ecCChHHHHHHHHHHHHhhccCCccEEEEECcHHHh
Confidence             11222              1111       11223333     2233444443333   33445689999999999985


Q ss_pred             cCCCCC--C--CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCC------CCCCCCcccccccccchhccceEEEE
Q 009230          424 HQRPVS--Q--TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNW------VGEPPNLYDISGSAHFINKCDNGIVI  492 (539)
Q Consensus       424 ~~~~~~--~--~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~------~~~~~~~~~l~gs~~i~~~aD~vl~l  492 (539)
                      ...-.+  .  .+...+.+++..|+.+|+++|++|+++.| ..+.+..      ....|     .|...++..+++.|.|
T Consensus       205 r~~~~~~~~~~~rq~~l~~~~~~L~~la~~~~vavv~tNqv~~~~~~~~~~~~g~~~~p-----~gG~~~~h~~~~ri~l  279 (316)
T TIGR02239       205 RTDFSGRGELSARQMHLARFLRSLQRLADEFGVAVVITNQVVAQVDGAGSMFAGDPKKP-----IGGNIMAHASTTRLSL  279 (316)
T ss_pred             hhhcCCcchHHHHHHHHHHHHHHHHHHHHHhCCEEEEECceEEecCCccccccCCCCcC-----CchHHHHhhccEEEEE
Confidence            432111  1  12234678999999999999999999999 4333221      01122     3567889999999999


Q ss_pred             EeCCCCCCCCCCcEEEEEEEeeCCCcce
Q 009230          493 HRNRDPEAGPIDRVQVCVRKVRNKVVGT  520 (539)
Q Consensus       493 ~r~~~~~~~~~~~~~l~i~K~R~g~~G~  520 (539)
                      .+.+.      +.+.+.+.|+|+.+.++
T Consensus       280 ~k~~~------~~R~~~v~ksp~~p~~~  301 (316)
T TIGR02239       280 RKGRG------EQRICKIYDSPCLPESE  301 (316)
T ss_pred             EecCC------CeEEEEEEECCCCCCeE
Confidence            98643      24678999999999887

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=99.79  E-value=6.8e-18  Score=160.63  Aligned_cols=197  Identities=15%  Similarity=0.191  Sum_probs=130.6

Q ss_pred             Cchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCC
Q 009230          284 GWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGG  361 (539)
Q Consensus       284 g~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~  361 (539)
                      |+++||++++  +++|++++|+|+||+|||+|++|++.+.+.+ |.+|+|+++|++++++.+++.+.  +.+..      
T Consensus         1 Gi~~LD~~l~gGi~~g~~~li~G~~G~GKt~~~~~~~~~~~~~-g~~~~y~s~e~~~~~l~~~~~~~--~~~~~------   71 (224)
T TIGR03880         1 GIPGLDEMLGGGFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKN-GEKAMYISLEEREERILGYAKSK--GWDLE------   71 (224)
T ss_pred             CchhhHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHhC-CCeEEEEECCCCHHHHHHHHHHc--CCChH------
Confidence            6889999984  9999999999999999999999999998886 99999999999999999987543  22211      


Q ss_pred             CCCCCCHHHHHHHHHHhhccceeEeecCC-CCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHH
Q 009230          362 SAERMTVEEFEQGKAWLSNTFSLIRCEND-SLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQML  440 (539)
Q Consensus       362 ~~~~l~~~~~~~~~~~l~~~~~~i~~~~~-~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~  440 (539)
                                 +   .+...+.++...+. -...++.+...++.++.+.++++|||||+..+....   .+.......+.
T Consensus        72 -----------~---~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~i~~~~~~~vVIDsls~l~~~~---~~~~~~r~~l~  134 (224)
T TIGR03880        72 -----------D---YIDKSLYIVRLDPSDFKTSLNRIKNELPILIKELGASRVVIDPISLLETLF---DDDAERRTELF  134 (224)
T ss_pred             -----------H---HHhCCeEEEecCHHHHHhhHHHHHHHHHHHHHHhCCCEEEEcChHHHhhhc---CCHHHHHHHHH
Confidence                       1   11122233321100 012356677777888888999999999887762211   11222222333


Q ss_pred             HHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCCCc
Q 009230          441 TMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVV  518 (539)
Q Consensus       441 ~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~  518 (539)
                      .-++.+ ++.|+++++++| +. ..      +...   ..+.+++.||.|+.|...+..... .....+.|.|.|....
T Consensus       135 ~l~~~l-k~~~~tvll~s~~~~-~~------~~~~---~~~~~~~l~D~vI~L~~~~~~~~~-~~~r~l~v~K~Rg~~~  201 (224)
T TIGR03880       135 RFYSSL-RETGVTTILTSEADK-TN------VFAS---KYGLIEYLADGVIILKYVRNSDLR-DVRLAVEVVKMRRSKH  201 (224)
T ss_pred             HHHHHH-HhCCCEEEEEEcccC-CC------CCcc---CCCceEEEEeEEEEEeeeecccCc-ceEEEEEEEEccCCCC
Confidence            333333 578999999999 43 21      1111   123478999999999654432111 1234688999998744

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.

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=99.79  E-value=6.4e-18  Score=162.25  Aligned_cols=208  Identities=14%  Similarity=0.152  Sum_probs=137.0

Q ss_pred             cccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc-----CCeEEEEeCCCC--HHHHHHHHHHHhhC
Q 009230          281 ISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHA-----GWKFVLCSMENK--VREHARKLLEKHIK  351 (539)
Q Consensus       281 i~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~-----g~~vl~~s~E~~--~~~~~~r~~~~~~~  351 (539)
                      +|||++.||++++  +++|+++.|.|+||+|||+|+++++.+.+...     +.+|+|+++|.+  ++++.+.+..  .+
T Consensus         1 ~~tG~~~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~~~~~~--~~   78 (235)
T cd01123           1 LTTGSKALDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLVQIAER--FG   78 (235)
T ss_pred             CCCCchhhHhhccCCCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHHHHHHH--hc
Confidence            5899999999996  99999999999999999999999998866542     379999999985  3333222211  11


Q ss_pred             CCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHc-CCcEEEEccccccccCC-CCC
Q 009230          352 KPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRH-GVRGLVIDPYNELDHQR-PVS  429 (539)
Q Consensus       352 ~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~-~~~~vvID~~~~l~~~~-~~~  429 (539)
                      .              ..+       .+.++.+++.+  .+...+..++..+.....+. ++++|||||+..+.... ...
T Consensus        79 ~--------------~~~-------~~~~~i~~~~~--~~~~~l~~~l~~l~~~l~~~~~~~liVIDSis~~~~~~~~~~  135 (235)
T cd01123          79 L--------------DPE-------EVLDNIYVARA--YNSDHQLQLLEELEAILIESSRIKLVIVDSVTALFRAEFDGR  135 (235)
T ss_pred             c--------------ChH-------hHhcCEEEEec--CCHHHHHHHHHHHHHHHhhcCCeeEEEEeCcHHHHHHHhcCC
Confidence            1              111       12233444422  11112333445555556667 89999999999875321 111


Q ss_pred             ---CCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCc
Q 009230          430 ---QTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDR  505 (539)
Q Consensus       430 ---~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~  505 (539)
                         .++...+.+++..|+.+|++++++|++++| ...............--.+...+.+.+++.+.+.+...      ..
T Consensus       136 ~~~~~r~~~l~~~~~~L~~la~~~~~avl~tn~~~~~~~~~~~~~~~~~~p~lG~~w~~~v~~Rl~l~~~~~------~~  209 (235)
T cd01123         136 GELAERQQHLAKLLRTLKRLADEFNVAVVITNQVTARPDGAAMFGGDPKKPAGGNIWAHASTTRLYLRKGRG------EE  209 (235)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhCCEEEEeccEeecCCcccccCCCCeeccCccHhhCCceEEEEEEECCC------Cc
Confidence               234456788999999999999999999999 54433210000000011234578888899999987652      24


Q ss_pred             EEEEEEEeeCCCcc
Q 009230          506 VQVCVRKVRNKVVG  519 (539)
Q Consensus       506 ~~l~i~K~R~g~~G  519 (539)
                      ..+.+.|++..+.+
T Consensus       210 r~~~i~k~~~~~~~  223 (235)
T cd01123         210 RIAKIVDSPHLPEG  223 (235)
T ss_pred             eEEEEeeCCCCCCc
Confidence            67999998877643

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 .

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=99.78  E-value=2e-17  Score=155.73  Aligned_cols=192  Identities=17%  Similarity=0.184  Sum_probs=129.6

Q ss_pred             hhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC-CHHHHHHHHHHHhhCCCccccccCCCCC
Q 009230          288 LNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN-KVREHARKLLEKHIKKPFFEANYGGSAE  364 (539)
Q Consensus       288 LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~-~~~~~~~r~~~~~~~~~~~~i~~~~~~~  364 (539)
                      ||++++  +++|.++.|+|+||+|||+|++|++.+.+.+ |.+|+|+++|. +++++.+.....                
T Consensus         1 lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~-g~~v~yi~~e~~~~~rl~~~~~~~----------------   63 (209)
T TIGR02237         1 IDELLGGGVERGTITQIYGPPGSGKTNICMILAVNAARQ-GKKVVYIDTEGLSPERFKQIAEDR----------------   63 (209)
T ss_pred             ChhhhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHhC-CCeEEEEECCCCCHHHHHHHHHhC----------------
Confidence            688885  9999999999999999999999999999885 99999999995 776655433210                


Q ss_pred             CCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCC--CHHHHHHHHHHH
Q 009230          365 RMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQ--TETEYVSQMLTM  442 (539)
Q Consensus       365 ~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~--~~~~~~~~~~~~  442 (539)
                                .+.+.++++++.+  .+......+...+..++...++++|||||+..+........  .....+.+++..
T Consensus        64 ----------~~~~~~~i~~~~~--~~~~~~~~~~~~l~~~~~~~~~~lvVIDSis~l~~~~~~~~~~~~~~~l~~~~~~  131 (209)
T TIGR02237        64 ----------PERALSNFIVFEV--FDFDEQGVAIQKTSKFIDRDSASLVVVDSFTALYRLELSDDRISRNRELARQLTL  131 (209)
T ss_pred             ----------hHHHhcCEEEEEC--CCHHHHHHHHHHHHHHHhhcCccEEEEeCcHHHhHHHhCCccHHHHHHHHHHHHH
Confidence                      0112233444421  11112223345555555666899999999998754221111  123356677888


Q ss_pred             HHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCCCccee
Q 009230          443 VKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       443 Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~G~~  521 (539)
                      |+++|+++|+++++++| .....+. ...     -.|+..+++.+|.++.|.+.+       +...+.+.|++..+.|..
T Consensus       132 L~~~~~~~~v~vl~t~~~~~~~~~~-~~~-----~~gg~~~~~~~d~vi~l~~~~-------~~r~~~i~k~~~~~~~~~  198 (209)
T TIGR02237       132 LLSLARKKNLAVVITNQVYTDVNNG-TLR-----PLGGHLLEHWSKVILRLEKFR-------GRRLATLEKHRSRPEGES  198 (209)
T ss_pred             HHHHHHHcCCEEEEEcccEEecCCC-CCc-----CCCcchhheeeeEEEEEEecC-------CEEEEEEEECCCCCCCCe
Confidence            99999999999999999 4433211 111     124556899999999998762       135566788777766553

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PTZ00035 Rad51 protein; Provisional

Probab=99.78  E-value=2.8e-17  Score=163.97  Aligned_cols=238  Identities=13%  Similarity=0.171  Sum_probs=156.8

Q ss_pred             chHHHHHHhccccCccccccccchHHHHHHHhhccCCCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHH
Q 009230          240 GALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDAL  317 (539)
Q Consensus       240 ~~~~~~~~~A~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~l  317 (539)
                      +.+.+++..|......+..+..++++.        ......++||++.||++++  +++|+++.|.|+||+|||+|++++
T Consensus        67 ~~~~~i~~~~~~~~~~~~~ta~~~~~~--------~~~~~~isTG~~~LD~lLgGGi~~G~iteI~G~~GsGKT~l~~~l  138 (337)
T PTZ00035         67 AKVEKIKEAASKLVPMGFISATEYLEA--------RKNIIRITTGSTQLDKLLGGGIETGSITELFGEFRTGKTQLCHTL  138 (337)
T ss_pred             HHHHHHHHHHHHhcccCCCCHHHHHHh--------hccCccccCCcHHHHHHhCCCCCCCeEEEEECCCCCchhHHHHHH
Confidence            556667777665444455555555432        1345679999999999996  999999999999999999999999


Q ss_pred             HHHHHHh-----cCCeEEEEeCCCC--HHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCC
Q 009230          318 ICNINEH-----AGWKFVLCSMENK--VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCEND  390 (539)
Q Consensus       318 a~~~a~~-----~g~~vl~~s~E~~--~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~  390 (539)
                      +......     .+.+|+|+++|.+  ++++....  ...+.              ..+.      .+ +...+.     
T Consensus       139 ~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri~~ia--~~~g~--------------~~~~------~l-~nI~~~-----  190 (337)
T PTZ00035        139 CVTCQLPIEQGGGEGKVLYIDTEGTFRPERIVQIA--ERFGL--------------DPED------VL-DNIAYA-----  190 (337)
T ss_pred             HHHhccccccCCCCceEEEEEccCCCCHHHHHHHH--HHhCC--------------ChHh------Hh-hceEEE-----
Confidence            9876521     3679999999975  66543332  11121              1111      12 223333     


Q ss_pred             CCCCHHHHHHHHH---HHHHHcCCcEEEEccccccccCCCC--CC--CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCC
Q 009230          391 SLPSIKWVLDLAK---AAVLRHGVRGLVIDPYNELDHQRPV--SQ--TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQ  462 (539)
Q Consensus       391 ~~~~~~~i~~~i~---~~~~~~~~~~vvID~~~~l~~~~~~--~~--~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~  462 (539)
                      ...+.++....+.   ....+.++++|||||+..+....-.  +.  .+.+.+.+++..|+.+|+++||+|+++.| ..+
T Consensus       191 ~~~~~e~~~~~l~~~~~~l~~~~~~lvVIDSital~r~~~~~~~~~~~r~~~l~~~~~~L~~la~~~~vavvvtNqv~~~  270 (337)
T PTZ00035        191 RAYNHEHQMQLLSQAAAKMAEERFALLIVDSATALFRVDYSGRGELAERQQHLGKFLRALQKLADEFNVAVVITNQVMAD  270 (337)
T ss_pred             ccCCHHHHHHHHHHHHHHhhccCccEEEEECcHHhhhhhccCcccHHHHHHHHHHHHHHHHHHHHHcCcEEEEecceEEe
Confidence            2334444444333   3334568999999999997653211  11  12345788999999999999999999999 444


Q ss_pred             CCCC--CCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCCCccee
Q 009230          463 LHNW--VGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       463 ~~~~--~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~G~~  521 (539)
                      ....  ....+  .--.|...+...+++.|.|.+.+.      +.+.+.|.|+++.+.+..
T Consensus       271 ~~~~~~~~~~~--~~p~gG~~~~h~~~~Rl~l~k~~~------~~R~~~i~ksp~~p~~~~  323 (337)
T PTZ00035        271 VDGASMFVADP--KKPIGGHIIAHASTTRLSLRKGRG------EQRICKIYDSPNLPESEA  323 (337)
T ss_pred             cCCccccCCCC--ccCCchHHHHhheeEEEEEEecCC------CeeEEEEEECCCCCCeeE
Confidence            3211  00001  112356778889999999997643      246788899999988863

>PRK08624 hypothetical protein; Provisional

Probab=99.77  E-value=2.7e-18  Score=167.38  Aligned_cols=125  Identities=22%  Similarity=0.234  Sum_probs=97.2

Q ss_pred             hcCCCHHHHHHcCcccccCCceeEEEEeEe-eCCEEEEEEeecCC------Cccccc----C----CCCCcccccccc--
Q 009230           58 ERLISAETLRRNRVMQKRHGHEVVIAFPYW-RNGKLVNCKYRDFN------KKFWQE----K----DTEKVFYGLDDI--  120 (539)
Q Consensus        58 ~Rgi~~~~~~~~~~~~~~~~~~~~i~fP~~-~~G~~~~~~~R~~~------~~~~~~----~----~~~~~l~g~~~~--  120 (539)
                      +|||+++|+++|++++.++..+++|+||+. ..|++|+|.+|.++      ++|.+.    +    .+...|||++..  
T Consensus       160 ~RGIs~etik~F~lGy~~D~Fr~RImFPI~d~~GrvIGFgGR~l~~~~~~~~KY~p~y~Nst~~~F~Kg~~LYGl~~Ak~  239 (373)
T PRK08624        160 DEGISEKTQKYWEIKFYLDVISQRIIIPHRDESGELIGIRGRLLDKELVDKNKYFPIYVNDTGYNHPKGKILYGLWQNKK  239 (373)
T ss_pred             HcCCCHHHHHHhCCCccccccCCeeEEEEECCCCCEEEEeCeEcCCCccccccccccCCCCcccccccchhhcCHHHHHH
Confidence            799999999999998777777789999998 88999999999983      235432    1    256789999764  


Q ss_pred             --CCCCcEEEEechhhHH---HHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccC--CEEEEEecC
Q 009230          121 --EGESDIIIVEGEMDKL---SMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQA--SRIILATDG  193 (539)
Q Consensus       121 --~~~~~v~i~EG~~Dal---sl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~--~~ivl~~Dn  193 (539)
                        .+.+.++||||++|++   +++|+| .++|++ +|++-       .           ..++..|.+.  ++|+||+|+
T Consensus       240 ~irk~~~vIivEGymDVI~~~a~~~~G-~naVA~-lGTal-------T-----------~~q~~lL~r~~~~~Vil~~Dg  299 (373)
T PRK08624        240 YIKEKKKVIIVESEKSVLFSDKFYGEG-NFVVAI-CGSNI-------S-----------EVQAEKLLRLGVEEVTIALDK  299 (373)
T ss_pred             HhccCCeEEEEeccHHHHHHHHHhcCC-CcEEEC-ChhhC-------C-----------HHHHHHHHhcCCCcEEEEecC
Confidence              3468999999999999   788999 888885 46543       2           1235677765  599999999


Q ss_pred             ---CccchHHHH
Q 009230          194 ---DPPGQALAE  202 (539)
Q Consensus       194 ---D~~G~~~~~  202 (539)
                         |.+|.++.+
T Consensus       300 d~~d~~~~~~~~  311 (373)
T PRK08624        300 EYMDVTEEEVYE  311 (373)
T ss_pred             CccccchHHHHH
Confidence               677754443

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=99.77  E-value=6.4e-17  Score=161.66  Aligned_cols=211  Identities=14%  Similarity=0.125  Sum_probs=144.6

Q ss_pred             CccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-----cCCeEEEEeCCC--CHHHHHHHHHH
Q 009230          277 DEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEH-----AGWKFVLCSMEN--KVREHARKLLE  347 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-----~g~~vl~~s~E~--~~~~~~~r~~~  347 (539)
                      ....++|+.+.||++++  +++|.++.|+|+||+|||+|++|++.+++..     .+.+|+|+++|.  +++++.+.+..
T Consensus        80 s~~~~~Tg~~~lD~~l~GGi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~~~~~  159 (317)
T PRK04301         80 NVGKITTGSKELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQMAEA  159 (317)
T ss_pred             cCCccCCCCHHHHHHhcCCccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHHHHHH
Confidence            44568999999999985  9999999999999999999999999988753     135999999998  57766555422


Q ss_pred             HhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHH-cCCcEEEEccccccccCC
Q 009230          348 KHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLR-HGVRGLVIDPYNELDHQR  426 (539)
Q Consensus       348 ~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~-~~~~~vvID~~~~l~~~~  426 (539)
                        .+.              +.++      .+ ++.+++..  ........+...+..+..+ .++++|||||+..+....
T Consensus       160 --~g~--------------~~~~------~l-~~i~~~~~--~~~~~~~~~~~~l~~~i~~~~~~~lvVIDSisa~~~~~  214 (317)
T PRK04301        160 --LGL--------------DPDE------VL-DNIHVARA--YNSDHQMLLAEKAEELIKEGENIKLVIVDSLTAHFRAE  214 (317)
T ss_pred             --cCC--------------ChHh------hh-ccEEEEeC--CCHHHHHHHHHHHHHHHhccCceeEEEEECchHHhhhh
Confidence              121              1111      12 23344422  1111223445555555555 689999999999886532


Q ss_pred             -CCCCC---HHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCC
Q 009230          427 -PVSQT---ETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAG  501 (539)
Q Consensus       427 -~~~~~---~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~  501 (539)
                       ....+   +...+.+++..|+.+|+++||+||++.| ..+.....+.   .....|...+.+.+++.|.|.+...    
T Consensus       215 ~~~~~~~~~r~~~l~~~~~~L~~la~~~~vavl~tnqv~~~~~~~~~~---~~~~~~G~~~~~~~~~rl~l~k~~~----  287 (317)
T PRK04301        215 YVGRGNLAERQQKLNKHLHDLLRLADLYNAAVVVTNQVMARPDAFFGD---PTQPIGGHILGHTATFRIYLRKSKG----  287 (317)
T ss_pred             ccCCccHHHHHHHHHHHHHHHHHHHHHhCCEEEEeceEEeccccccCc---cccCCcchHhHhheeEEEEEEecCC----
Confidence             11111   2334667889999999999999999999 5443221111   1122345568899999999997532    


Q ss_pred             CCCcEEEEEEEeeCCCccee
Q 009230          502 PIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       502 ~~~~~~l~i~K~R~g~~G~~  521 (539)
                        +.+.+.+.|++.++.|..
T Consensus       288 --~~R~~~v~k~~~~~~~~~  305 (317)
T PRK04301        288 --NKRIARLVDSPHLPEGEA  305 (317)
T ss_pred             --CceEEEEEeCCCCCCceE
Confidence              256899999999988875

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=99.77  E-value=1.6e-17  Score=159.95  Aligned_cols=211  Identities=18%  Similarity=0.232  Sum_probs=140.9

Q ss_pred             CccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-----cCCeEEEEeCCCC--HHHHHHHHHH
Q 009230          277 DEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEH-----AGWKFVLCSMENK--VREHARKLLE  347 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-----~g~~vl~~s~E~~--~~~~~~r~~~  347 (539)
                      ....|+||.+.||.+++  ++.|.+|-|+|+||+|||.|++|++.++...     .+.+|+||+.|.+  ++++.+ +..
T Consensus        16 ~~~~i~Tg~~~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~~-i~~   94 (256)
T PF08423_consen   16 RWSRISTGCKSLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQQ-IAE   94 (256)
T ss_dssp             TS-EE--SSHHHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHHH-HHH
T ss_pred             cCCeeCCCCHHHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHHH-Hhh
Confidence            34679999999999995  9999999999999999999999999987653     2578999999964  444432 211


Q ss_pred             HhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHH---HHHHHcCCcEEEEcccccccc
Q 009230          348 KHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAK---AAVLRHGVRGLVIDPYNELDH  424 (539)
Q Consensus       348 ~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~---~~~~~~~~~~vvID~~~~l~~  424 (539)
                      .          +     .++.++       +-++.++++     ..+.+++.+.+.   ....+.++++|||||+..++.
T Consensus        95 ~----------~-----~~~~~~-------~l~~I~v~~-----~~~~~~l~~~L~~l~~~l~~~~ikLIVIDSIaalfr  147 (256)
T PF08423_consen   95 R----------F-----GLDPEE-------ILDNIFVIR-----VFDLEELLELLEQLPKLLSESKIKLIVIDSIAALFR  147 (256)
T ss_dssp             H----------T-----TS-HHH-------HHHTEEEEE------SSHHHHHHHHHHHHHHHHHSCEEEEEEETSSHHHH
T ss_pred             c----------c-----ccccch-------hhhceeeee-----cCCHHHHHHHHHHHHhhccccceEEEEecchHHHHH
Confidence            0          0     132222       223445543     234555544443   334567899999999999875


Q ss_pred             CC--CCC--CCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCC
Q 009230          425 QR--PVS--QTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPE  499 (539)
Q Consensus       425 ~~--~~~--~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~  499 (539)
                      ..  +.+  ..+...+..++..|+.+|++++++|+++.| ..+.+....-......=.++..+.+.+++.|.|.+.+.  
T Consensus       148 ~e~~~~~~~~~R~~~L~~~~~~L~~lA~~~~iaVvvTNqv~~~~~~~~~~~~~~~~PalG~~w~h~~~~Rl~l~k~~~--  225 (256)
T PF08423_consen  148 SEFSGRGDLAERQRMLARLARILKRLARKYNIAVVVTNQVTTKIDSNSLFDGDRLKPALGHSWSHAVTTRLFLSKGRG--  225 (256)
T ss_dssp             HHSGSTTTHHHHHHHHHHHHHHHHHHHHHTT-EEEEEEEECSSTT----SSTTSEEETTHHHHHHHSSEEEEEEECST--
T ss_pred             HHHccchhhHHHHHHHHHHHHHHHHHHHhCCceEEeeceeeecCCcccccccccceecCcchhhhhccEEEEEEeCCC--
Confidence            32  111  124567889999999999999999999999 55443310000000111356779999999999998542  


Q ss_pred             CCCCCcEEEEEEEeeCCCccee
Q 009230          500 AGPIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       500 ~~~~~~~~l~i~K~R~g~~G~~  521 (539)
                          ..+.+.|.|..+-+.+..
T Consensus       226 ----~~R~~~i~ksp~~p~~~~  243 (256)
T PF08423_consen  226 ----SERVATIVKSPSLPEGSA  243 (256)
T ss_dssp             ----TEEEEEEEECSSSSSEEE
T ss_pred             ----CeEEEEEeECCCCCCceE
Confidence                257889999998877653

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=99.77  E-value=1e-16  Score=160.04  Aligned_cols=212  Identities=16%  Similarity=0.144  Sum_probs=142.6

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-----cCCeEEEEeCCC--CHHHHHHHHH
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEH-----AGWKFVLCSMEN--KVREHARKLL  346 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-----~g~~vl~~s~E~--~~~~~~~r~~  346 (539)
                      .....++|+.+.+|.+++  ++.|.++.|+|+||+|||+|++|++.+++..     .+.+|+|+++|.  +++++.+.+.
T Consensus        72 ~s~~~~~Tg~~~lD~~l~GGi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~~~~~  151 (310)
T TIGR02236        72 KTIGKITTGSKELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIMQMAE  151 (310)
T ss_pred             ccCCeecCCCHHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHHHHHH
Confidence            344568899999999996  9999999999999999999999999987641     134999999998  5766544332


Q ss_pred             HHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHc--CCcEEEEcccccccc
Q 009230          347 EKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRH--GVRGLVIDPYNELDH  424 (539)
Q Consensus       347 ~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~--~~~~vvID~~~~l~~  424 (539)
                      .  .+              ++.++       +.++..++...  .....-.+.+.+..+..+.  .+++|||||+..+..
T Consensus       152 ~--~g--------------l~~~~-------~~~~i~i~~~~--~~~~~~~lld~l~~~i~~~~~~~~lVVIDSisa~~r  206 (310)
T TIGR02236       152 A--RG--------------LDPDE-------VLKNIYVARAY--NSNHQMLLVEKAEDLIKELNNPVKLLIVDSLTSHFR  206 (310)
T ss_pred             H--cC--------------CCHHH-------HhhceEEEecC--CHHHHHHHHHHHHHHHHhcCCCceEEEEecchHhhh
Confidence            1  12              22211       11233443211  1111112334444555554  389999999998754


Q ss_pred             CCCCCC----CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCC
Q 009230          425 QRPVSQ----TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPE  499 (539)
Q Consensus       425 ~~~~~~----~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~  499 (539)
                      ..-.+.    .+.+.+.+++..|+.+|+++||+|+++.| ..+.....+.   .....|...++..+++.|.|.+...  
T Consensus       207 ~e~~~~~~~~~r~~~l~~~~~~L~~~a~~~~~~v~~tnqv~~~~~~~~~~---~~~~~~G~~~~h~~~~rl~l~~~~~--  281 (310)
T TIGR02236       207 AEYVGRGALAERQQKLNKHLHDLLRLADLYNAAVVVTNQVMARPDAFFGD---PTRPIGGHILGHAATFRVYLRKGKG--  281 (310)
T ss_pred             HhhcCchhHHHHHHHHHHHHHHHHHHHHHhCcEEEEeceeeecCccccCc---cccCCcchhhhhheeEEEEEEecCC--
Confidence            321111    12234677889999999999999999999 5443211111   1123467789999999999998432  


Q ss_pred             CCCCCcEEEEEEEeeCCCccee
Q 009230          500 AGPIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       500 ~~~~~~~~l~i~K~R~g~~G~~  521 (539)
                          +.+.+.+.|+|.++.|..
T Consensus       282 ----~~R~~~~~k~~~~~~~~~  299 (310)
T TIGR02236       282 ----DKRIARLVDSPHLPEGEA  299 (310)
T ss_pred             ----CeEEEEEEECCCCCCeeE
Confidence                246799999999999875

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=99.75  E-value=8.1e-17  Score=169.62  Aligned_cols=201  Identities=12%  Similarity=0.087  Sum_probs=136.0

Q ss_pred             ccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCcccc
Q 009230          280 GISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEA  357 (539)
Q Consensus       280 gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i  357 (539)
                      .++||+++||++++  |++|.+++|.|+||+|||+|++|++.+.+.+.|.+++|+|+|++++++.+++.+  .|+++.+.
T Consensus         2 r~~TGI~gLD~il~GGlp~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~eE~~~~l~~~~~~--~G~~~~~~   79 (484)
T TIGR02655         2 KIRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFEESPQDIIKNARS--FGWDLQKL   79 (484)
T ss_pred             cCCCCchhHHHhcCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEecCHHHHHHHHHH--cCCCHHHH
Confidence            48999999999985  999999999999999999999999999887558999999999999999888754  35544332


Q ss_pred             ccCCCCCCCCHHHHHHHHHHhhccceeEeecC-------CCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCC
Q 009230          358 NYGGSAERMTVEEFEQGKAWLSNTFSLIRCEN-------DSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQ  430 (539)
Q Consensus       358 ~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~-------~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~  430 (539)
                      ..                   .+.+.++...+       .....++.+...+.......+++.||||++..+.....   
T Consensus        80 ~~-------------------~g~l~~~~~~~~~~~~~~~~~~~l~~~l~~i~~~ls~g~~qRVvIDSl~aL~~~~~---  137 (484)
T TIGR02655        80 VD-------------------EGKLFILDASPDPEGQDVVGGFDLSALIERINYAIRKYKAKRVSIDSVTAVFQQYD---  137 (484)
T ss_pred             hh-------------------cCceEEEecCchhccccccccCCHHHHHHHHHHHHHHhCCcEEEEeehhHhhhhcC---
Confidence            11                   01111111000       12345677777777777778899999998887754321   


Q ss_pred             CHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEE
Q 009230          431 TETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCV  510 (539)
Q Consensus       431 ~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i  510 (539)
                      ........+.+-++ ..++.++++++++|......         +....+..++.||.||.|.......   .....+.|
T Consensus       138 ~~~~~r~~l~~Li~-~L~~~g~TvLLtsh~~~~~~---------~~~~~~~~e~laDgVI~L~~~~~~~---~~~R~l~I  204 (484)
T TIGR02655       138 AVSVVRREIFRLVA-RLKQIGVTTVMTTERIEEYG---------PIARYGVEEFVSDNVVILRNVLEGE---RRRRTLEI  204 (484)
T ss_pred             chHHHHHHHHHHHH-HHHHCCCEEEEEecCccccc---------ccccCCceeEeeeeEEEEEEEecCC---EEEEEEEE
Confidence            11112223333333 33467999999999332211         0111222378999999998654321   12467999


Q ss_pred             EEeeCCC
Q 009230          511 RKVRNKV  517 (539)
Q Consensus       511 ~K~R~g~  517 (539)
                      .|.|...
T Consensus       205 ~K~Rgs~  211 (484)
T TIGR02655       205 LKLRGTS  211 (484)
T ss_pred             EECCCCC
Confidence            9999653

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.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=99.75  E-value=7.3e-17  Score=171.90  Aligned_cols=202  Identities=14%  Similarity=0.163  Sum_probs=146.1

Q ss_pred             CccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCc
Q 009230          277 DEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPF  354 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~  354 (539)
                      ....++||+++||++++  +++|.+++|.|+||+|||+|+++++.+.+.+ |.+|+|+|+|++++++..++.+  .|+++
T Consensus       251 ~~~~~~tGi~~lD~~l~GG~~~g~~~li~G~~G~GKT~l~~~~~~~~~~~-g~~~~yis~e~~~~~i~~~~~~--~g~~~  327 (509)
T PRK09302        251 SNERISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLASKFAEAACRR-GERCLLFAFEESRAQLIRNARS--WGIDL  327 (509)
T ss_pred             ccccccCCcHHHHHhhcCCCCCCcEEEEEcCCCCCHHHHHHHHHHHHHhC-CCcEEEEEecCCHHHHHHHHHH--cCCCh
Confidence            45679999999999995  9999999999999999999999999999885 9999999999999999887743  34443


Q ss_pred             cccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHH
Q 009230          355 FEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETE  434 (539)
Q Consensus       355 ~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~  434 (539)
                      .+...                   .+...++. .......++++...+...+.++++++|||||++.+....    . ..
T Consensus       328 ~~~~~-------------------~g~l~i~~-~~~~~~~~~~~~~~i~~~i~~~~~~~vVIDslt~l~~~~----~-~~  382 (509)
T PRK09302        328 EKMEE-------------------KGLLKIIC-ARPESYGLEDHLIIIKREIEEFKPSRVAIDPLSALARGG----S-LN  382 (509)
T ss_pred             HHHhh-------------------cCCceeec-CCcccCCHHHHHHHHHHHHHHcCCCEEEEcCHHHHHHhC----C-HH
Confidence            22110                   11111221 112233567777788887888899999999999886422    1 23


Q ss_pred             HHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEee
Q 009230          435 YVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVR  514 (539)
Q Consensus       435 ~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R  514 (539)
                      .+.+.+..|..+++++|++++++.|......  .....      ...+++.||.+|.|...+....   -...+.|.|.|
T Consensus       383 ~~~~~l~~l~~~~k~~~~t~l~t~~~~~~~g--~~~~~------~~~~~~l~D~vI~L~~~~~~~~---~~R~l~I~K~R  451 (509)
T PRK09302        383 EFRQFVIRLTDYLKSEEITGLFTNLTPDFMG--SHSIT------ESHISSLTDTWILLQYVEINGE---MNRALYVLKMR  451 (509)
T ss_pred             HHHHHHHHHHHHHHhCCCeEEEEeccccccC--CCCCC------cCceEEeeeEEEEEEEeecCCe---eEEEEEEEEcC
Confidence            4567788899999999999999998332110  00011      1236789999999987654221   14678999999


Q ss_pred             CCC
Q 009230          515 NKV  517 (539)
Q Consensus       515 ~g~  517 (539)
                      ...
T Consensus       452 g~~  454 (509)
T PRK09302        452 GSW  454 (509)
T ss_pred             CCC
Confidence            754

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=99.74  E-value=1.2e-16  Score=153.14  Aligned_cols=200  Identities=15%  Similarity=0.120  Sum_probs=138.5

Q ss_pred             CccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCc
Q 009230          277 DEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPF  354 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~  354 (539)
                      ....++||++.||++++  +++|++++|.|+||+|||+|+.|++...+.+ |.+|+|+++|.+++++.+++.+  .|++.
T Consensus         3 ~~~~~~tGi~~LD~~l~gG~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~-g~~~~y~~~e~~~~~~~~~~~~--~g~~~   79 (234)
T PRK06067          3 KKEIISTGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQ-GKKVYVITTENTSKSYLKQMES--VKIDI   79 (234)
T ss_pred             CceEEecCCHHHHHhhCCCCcCCcEEEEECCCCCChHHHHHHHHHHHHhC-CCEEEEEEcCCCHHHHHHHHHH--CCCCh
Confidence            34569999999999985  9999999999999999999999999998885 9999999999999999888754  34433


Q ss_pred             cccccCCCCCCCCHHHHHHHHHHhhccceeEeec----CCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCC
Q 009230          355 FEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCE----NDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQ  430 (539)
Q Consensus       355 ~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~----~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~  430 (539)
                      .+...                   .....++...    .......+.+...+...+.+.++++||||++..+....    
T Consensus        80 ~~~~~-------------------~g~l~i~~~~~~~~~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t~~~~~~----  136 (234)
T PRK06067         80 SDFFL-------------------WGYLRIFPLNTEGFEWNSTLANKLLELIIEFIKSKREDVIIIDSLTIFATYA----  136 (234)
T ss_pred             hHHHh-------------------CCCceEEeccccccccCcchHHHHHHHHHHHHHhcCCCEEEEecHHHHHhcC----
Confidence            22100                   0111111000    01123456777777777777899999999988764321    


Q ss_pred             CHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEE
Q 009230          431 TETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCV  510 (539)
Q Consensus       431 ~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i  510 (539)
                      + ...+..++..|+.+++ .++++++++|......+           ....+...+|.++.|...+...   .-...|.|
T Consensus       137 ~-~~~~~~~l~~l~~l~~-~g~tvllt~~~~~~~~~-----------~~~~~~~l~DgvI~L~~~~~~~---~~~r~l~i  200 (234)
T PRK06067        137 E-EDDILNFLTEAKNLVD-LGKTILITLHPYAFSEE-----------LLSRIRSICDVYLKLRAEQIGG---RYVKVLEV  200 (234)
T ss_pred             C-HHHHHHHHHHHHHHHh-CCCEEEEEecCCcCCHH-----------HHHHHHhheEEEEEEEeeccCC---EEeEEEEE
Confidence            1 2335666677766665 58889998883221110           0134678999999998654321   22467999


Q ss_pred             EEeeCCCc
Q 009230          511 RKVRNKVV  518 (539)
Q Consensus       511 ~K~R~g~~  518 (539)
                      .|.|....
T Consensus       201 ~K~Rg~~~  208 (234)
T PRK06067        201 VKLRGARK  208 (234)
T ss_pred             EhhcCCCC
Confidence            99997644

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=99.71  E-value=3.9e-16  Score=149.95  Aligned_cols=182  Identities=15%  Similarity=0.139  Sum_probs=123.6

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHh-----------cCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEH-----------AGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAER  365 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~-----------~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~  365 (539)
                      |.+.+|+|+||+|||+|++++|.++|..           .+.+|+|+++|++..++.+|+.+.........+..     .
T Consensus         1 g~~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~Ed~~~~i~~Rl~~i~~~~~~~~~~~-----r   75 (239)
T cd01125           1 GYVSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAEDPREEIHRRLEAILQHLEPDDAGD-----R   75 (239)
T ss_pred             CceeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEECCCCHHHHHHHHHHHHhhcCCcCccc-----c
Confidence            6899999999999999999999998842           25789999999999999999987665543221110     0


Q ss_pred             CCHHHHHHHHHHhhccceeEeecCCC-CCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHH
Q 009230          366 MTVEEFEQGKAWLSNTFSLIRCENDS-LPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVK  444 (539)
Q Consensus       366 l~~~~~~~~~~~l~~~~~~i~~~~~~-~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk  444 (539)
                      +-.       ......++.+.  ... ......+...++. +...++++||||++..+ ...  ..++......++..|+
T Consensus        76 l~~-------~~g~~~~l~~~--~~~~~~~~~~~~~l~~~-~~~~~~~lvviDpl~~~-~~~--~~~d~~~~~~~~~~L~  142 (239)
T cd01125          76 LFI-------DSGRIQPISIA--REGRIIVVPEFERIIEQ-LLIRRIDLVVIDPLVSF-HGV--SENDNGAMDAVIKALR  142 (239)
T ss_pred             eEE-------eccCCCceecc--cCCcccccHHHHHHHHH-HHhcCCCEEEECChHHh-CCC--CcCCHHHHHHHHHHHH
Confidence            000       00000111110  001 1122333333332 33578999999988777 221  2344556778999999


Q ss_pred             HHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCC
Q 009230          445 RFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDP  498 (539)
Q Consensus       445 ~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~  498 (539)
                      .+++++|++|++++|..|....  .....++.+||.++...++.++.|.+..+.
T Consensus       143 ~~a~~~g~avl~v~H~~K~~~~--~~~~~~~~rGssal~~~~r~~~~l~~~~~~  194 (239)
T cd01125         143 RIAAQTGAAILLVHHVRKGSAK--DGDTQEAARGASALVDGARWVRALTRMTSE  194 (239)
T ss_pred             HHHHHhCCEEEEEeccCccccc--CcccccccCcHHHHhcccceEEEEeeCCHH
Confidence            9999999999999994443321  114667899999999999999999997754

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.

>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=99.69  E-value=1.5e-15  Score=140.38  Aligned_cols=179  Identities=12%  Similarity=0.076  Sum_probs=117.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHh
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWL  378 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l  378 (539)
                      .++|.|+||+|||+|+++++...+.+ |.+|+|+|+|++++++..++.+.  |++...+...                  
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~~~-g~~v~~~s~e~~~~~~~~~~~~~--g~~~~~l~~~------------------   59 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLAR-GEPGLYVTLEESPEELIENAESL--GWDLERLEDE------------------   59 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHC-CCcEEEEECCCCHHHHHHHHHHc--CCChHHHHhc------------------
Confidence            37899999999999999999999985 99999999999999999887654  5543322110                  


Q ss_pred             hccceeEeecC----CC-CCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcE
Q 009230          379 SNTFSLIRCEN----DS-LPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACH  453 (539)
Q Consensus       379 ~~~~~~i~~~~----~~-~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~  453 (539)
                       ....++...+    .+ ....+++...+...+...++++||||++..+...     +.......+.+.++.+. +.|++
T Consensus        60 -g~l~~~d~~~~~~s~~~~~~~~~~~~~i~~~~~~~~~~~lviD~~~~~~~~-----~~~~~~~~i~~l~~~l~-~~g~t  132 (187)
T cd01124          60 -GLLAIVDADPDEIGPAESSLRLELIQRLKDAIEEFKAKRVVIDSVSGLLLM-----EQSTARLEIRRLLFALK-RFGVT  132 (187)
T ss_pred             -CCeEEEecCccccchhhhhhhHHHHHHHHHHHHHhCCCEEEEeCcHHHhhc-----ChHHHHHHHHHHHHHHH-HCCCE
Confidence             0111110000    00 0011245566667777789999999988876542     12222233444444443 45999


Q ss_pred             EEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCCCc
Q 009230          454 VWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVV  518 (539)
Q Consensus       454 vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~  518 (539)
                      +++++| .....          ...++..+++.||.++.|++.....   .....+.|.|+|..+.
T Consensus       133 vi~v~~~~~~~~----------~~~~~~~~~~~aD~ii~l~~~~~~~---~~~r~l~i~K~R~~~~  185 (187)
T cd01124         133 TLLTSEQSGLEG----------TGFGGGDVEYLVDGVIRLRLDEEGG---RLRRSLSVVKMRGGPH  185 (187)
T ss_pred             EEEEeccccCCC----------cccCcCceeEeeeEEEEEEEEccCC---EEEEEEEEEEccCCCC
Confidence            999999 43321          1235567899999999999875321   1245699999997643

A related protein is found in archaea.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=99.69  E-value=3.1e-15  Score=142.06  Aligned_cols=213  Identities=13%  Similarity=0.095  Sum_probs=135.5

Q ss_pred             ccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCcccc
Q 009230          280 GISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEA  357 (539)
Q Consensus       280 gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i  357 (539)
                      .+.++++.||++++  +++|++++|.|+||+|||+|+++++...+.+ |.+++|+++|.++.++.+.+.+  .|.+....
T Consensus         5 ~~~~~~~~ld~~l~ggi~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~-g~~~~yi~~e~~~~~~~~~~~~--~g~~~~~~   81 (230)
T PRK08533          5 KIELSRDELHKRLGGGIPAGSLILIEGDESTGKSILSQRLAYGFLQN-GYSVSYVSTQLTTTEFIKQMMS--LGYDINKK   81 (230)
T ss_pred             EEEEEEeeeehhhCCCCCCCcEEEEECCCCCCHHHHHHHHHHHHHhC-CCcEEEEeCCCCHHHHHHHHHH--hCCchHHH
Confidence            46778999999996  9999999999999999999999999998875 9999999999999988877732  33332211


Q ss_pred             ccCCCCCCCCHHHHHHHHHHhhccceeEeecCC--CCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHH
Q 009230          358 NYGGSAERMTVEEFEQGKAWLSNTFSLIRCEND--SLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEY  435 (539)
Q Consensus       358 ~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~--~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~  435 (539)
                      .                   ..+.+.++...+.  +....+.....+.......+++++|||++..+....    .+...
T Consensus        82 ~-------------------~~~~l~~~~~~~~~~~~~~~~~~l~~il~~~~~~~~~~lVIDe~t~~l~~~----~d~~~  138 (230)
T PRK08533         82 L-------------------ISGKLLYIPVYPLLSGNSEKRKFLKKLMNTRRFYEKDVIIIDSLSSLISND----ASEVA  138 (230)
T ss_pred             h-------------------hcCcEEEEEecccccChHHHHHHHHHHHHHHHhcCCCEEEEECccHHhcCC----cchHH
Confidence            0                   0112222211111  111123344444444445689999999998876321    11223


Q ss_pred             HHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeC
Q 009230          436 VSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRN  515 (539)
Q Consensus       436 ~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~  515 (539)
                      ...+++.|+.+++. +++++++++......           .....+++.||.||.|...+....   -...+.|.|.|-
T Consensus       139 ~~~l~~~l~~l~~~-g~tvi~t~~~~~~~~-----------~~~~~~~~~~DgvI~L~~~~~~~~---~~R~i~V~KmR~  203 (230)
T PRK08533        139 VNDLMAFFKRISSL-NKVIILTANPKELDE-----------SVLTILRTAATMLIRLEVKVFGGD---LKNSAKIVKYNM  203 (230)
T ss_pred             HHHHHHHHHHHHhC-CCEEEEEeccccccc-----------ccceeEEEeeeEEEEEEEeecCCE---EEEEEEEEEecC
Confidence            45566677767654 776666655322111           011357899999999997664321   146688999997


Q ss_pred             CCcceeeeEEEEEeCCCc
Q 009230          516 KVVGTIGEAFLSYNRVTG  533 (539)
Q Consensus       516 g~~G~~~~~~l~fd~~~~  533 (539)
                      -+...-+.+++.+.+-.|
T Consensus       204 ~~~~~~~~~~f~i~~~~g  221 (230)
T PRK08533        204 AKGSFQKSIPFRVEPKIG  221 (230)
T ss_pred             CccccCCEEEEEEcCCcc
Confidence            322211245666665544

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=99.67  E-value=6e-15  Score=143.58  Aligned_cols=208  Identities=18%  Similarity=0.192  Sum_probs=143.3

Q ss_pred             cccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccc
Q 009230          279 FGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFE  356 (539)
Q Consensus       279 ~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~  356 (539)
                      ..+|||+++||++++  +++|.+++|.|+||+|||+|++|++.+.+.. |.+|+|+|+|++++++...+.+  .|.++..
T Consensus         3 ~~~~TGI~glD~~l~GG~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~-ge~vlyvs~~e~~~~l~~~~~~--~g~d~~~   79 (260)
T COG0467           3 ERIPTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGARE-GEPVLYVSTEESPEELLENARS--FGWDLEV   79 (260)
T ss_pred             ccccCCCcchHHHhcCCCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhc-CCcEEEEEecCCHHHHHHHHHH--cCCCHHH
Confidence            468999999999996  9999999999999999999999999999996 9999999999999999877755  4555432


Q ss_pred             cccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHH
Q 009230          357 ANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYV  436 (539)
Q Consensus       357 i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~  436 (539)
                      ....+   .+...+   +..........+   .....+++.+...+..++...+...+||||+..+....    +.....
T Consensus        80 ~~~~g---~l~i~d---~~~~~~~~~~~~---~~~~~~~~~l~~~I~~~~~~~~~~~~ViDsi~~~~~~~----~~~~~~  146 (260)
T COG0467          80 YIEKG---KLAILD---AFLSEKGLVSIV---VGDPLDLEELLDRIREIVEKEGADRVVIDSITELTLYL----NDPALV  146 (260)
T ss_pred             HhhcC---CEEEEE---cccccccccccc---ccCCccHHHHHHHHHHHHHHhCCCEEEEeCCchHhhhc----CchHHH
Confidence            21110   000000   000000000001   01234677888999999999999999999998654321    222233


Q ss_pred             HHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcE-EEEEEEeeC
Q 009230          437 SQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRV-QVCVRKVRN  515 (539)
Q Consensus       437 ~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~-~l~i~K~R~  515 (539)
                      ..++..++.+.++++++.+++++.......    .       ++..+..+|.+|-|.........   .. .+.+.|.|.
T Consensus       147 r~~~~~l~~~~~~~~~t~~~~~~~~~~~~~----~-------~~~~~~~vdgvI~l~~~~~~~~~---~r~~~~i~k~r~  212 (260)
T COG0467         147 RRILLLLKRFLKKLGVTSLLTTEAPVEERG----E-------SGVEEYIVDGVIRLDLKEIEGGG---DRRYLRILKMRG  212 (260)
T ss_pred             HHHHHHHHHHHHhCCCEEEEEecccccCCC----c-------cceEEEEEEEEEEEeeecccCce---EEEEEEEEeccc
Confidence            678889999999999999998883222110    0       03445699999999876543221   23 788888887


Q ss_pred             C
Q 009230          516 K  516 (539)
Q Consensus       516 g  516 (539)
                      -
T Consensus       213 ~  213 (260)
T COG0467         213 T  213 (260)
T ss_pred             c
Confidence            3

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=99.67  E-value=6.6e-15  Score=158.55  Aligned_cols=217  Identities=17%  Similarity=0.107  Sum_probs=149.9

Q ss_pred             CCccccccCchhhhhhh--c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCC
Q 009230          276 GDEFGISTGWRALNELY--N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKK  352 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~--~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~  352 (539)
                      .....++||++.||.++  | +++|.++.|+|+||+|||+|+++++.+.+.+ |.+|+|+++|.+...-  +  +...|+
T Consensus        36 ~~v~~isTGi~~LD~lLg~GGip~GsiteI~G~~GsGKTtLal~~~~~a~~~-G~~v~yId~E~t~~~~--~--A~~lGv  110 (790)
T PRK09519         36 QPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAA-GGVAAFIDAEHALDPD--Y--AKKLGV  110 (790)
T ss_pred             cCCceecCCcHHHHHhhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHc-CCcEEEECCccchhHH--H--HHHcCC
Confidence            34568999999999998  4 9999999999999999999999999988875 9999999999887732  2  222344


Q ss_pred             CccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcccccccc-CC--CC-
Q 009230          353 PFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDH-QR--PV-  428 (539)
Q Consensus       353 ~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~-~~--~~-  428 (539)
                      +...                         .++.     ...+.+.+...+..++.+.++++|||||++.+.. ..  +. 
T Consensus       111 Dl~~-------------------------llv~-----~~~~~E~~l~~i~~lv~~~~~~LVVIDSI~aL~~r~E~~g~~  160 (790)
T PRK09519        111 DTDS-------------------------LLVS-----QPDTGEQALEIADMLIRSGALDIVVIDSVAALVPRAELEGEM  160 (790)
T ss_pred             ChhH-------------------------eEEe-----cCCCHHHHHHHHHHHhhcCCCeEEEEcchhhhcchhhccCCC
Confidence            3221                         1222     2334566777777777778899999999998884 11  11 


Q ss_pred             CCC---H-HHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC---CCCC
Q 009230          429 SQT---E-TEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD---PEAG  501 (539)
Q Consensus       429 ~~~---~-~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~---~~~~  501 (539)
                      +..   . ...+.+++..|..+++++||+||++.|.+..-+...  ++...--|...+...|.+-|.|.+.+.   .+..
T Consensus       161 g~~~~~~q~rl~~q~L~~L~~~l~~~nvtvi~TNQv~~~~g~~f--g~p~~~~GG~~l~h~ss~Ri~lrk~~~ik~~~~~  238 (790)
T PRK09519        161 GDSHVGLQARLMSQALRKMTGALNNSGTTAIFINQLRDKIGVMF--GSPETTTGGKALKFYASVRMDVRRVETLKDGTNA  238 (790)
T ss_pred             CcccHHHHHHHHHHHHHHHHHHHHhCCCEEEEEecceecCCCcC--CCCCcCCCCcccceeccEEEEeeeccccccCccc
Confidence            111   1 122356888899999999999999999444321111  111223467778999999999987532   1112


Q ss_pred             CCCcEEEEEEEeeCCCcceeeeEEEEEeCCCce
Q 009230          502 PIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGE  534 (539)
Q Consensus       502 ~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~r  534 (539)
                      ..+.+.+.|.|++.=+.++     ..|+..||+
T Consensus       239 ~G~~~~~kv~ks~cLpe~e-----~v~~i~tG~  266 (790)
T PRK09519        239 VGNRTRVKVVKNKCLAEGT-----RIFDPVTGT  266 (790)
T ss_pred             cceEEEEEEEECCCCCCce-----EEEEecCCC
Confidence            2456788899888655443     446666653

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=99.64  E-value=4.2e-14  Score=135.58  Aligned_cols=217  Identities=19%  Similarity=0.175  Sum_probs=149.6

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC--HHHHHHHHHHHhhC
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK--VREHARKLLEKHIK  351 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~--~~~~~~r~~~~~~~  351 (539)
                      .....++||...||.++|  +++|.++-|+|++|+|||++++|++.++... |..++|++.|-+  ++++.  -++.  +
T Consensus        37 ~~~~~i~TGs~~LD~~LGGGl~~g~ItEiyG~~gsGKT~lal~~~~~aq~~-g~~a~fIDtE~~l~p~r~~--~l~~--~  111 (279)
T COG0468          37 EDIEAISTGSLALDEALGGGLPRGRITEIYGPESSGKTTLALQLVANAQKP-GGKAAFIDTEHALDPERAK--QLGV--D  111 (279)
T ss_pred             hccccccccchhHHHHhcCCcccceEEEEecCCCcchhhHHHHHHHHhhcC-CCeEEEEeCCCCCCHHHHH--HHHH--h
Confidence            346789999999999997  9999999999999999999999999998885 889999999964  44321  1111  0


Q ss_pred             CCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcC--CcEEEEccccccccCCCCC
Q 009230          352 KPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHG--VRGLVIDPYNELDHQRPVS  429 (539)
Q Consensus       352 ~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~--~~~vvID~~~~l~~~~~~~  429 (539)
                                               .+ +.+++.     ...+.++-...+..+.....  +++|||||++.+.......
T Consensus       112 -------------------------~~-d~l~v~-----~~~~~e~q~~i~~~~~~~~~~~i~LvVVDSvaa~~r~~~~~  160 (279)
T COG0468         112 -------------------------LL-DNLLVS-----QPDTGEQQLEIAEKLARSGAEKIDLLVVDSVAALVRAEEIE  160 (279)
T ss_pred             -------------------------hh-cceeEe-----cCCCHHHHHHHHHHHHHhccCCCCEEEEecCcccchhhhcC
Confidence                                     01 122332     23334444444444444444  9999999999987643111


Q ss_pred             ----CCHHHHHHHHHHHHHHHHHHhCcEEEEEecCC-CCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCC
Q 009230          430 ----QTETEYVSQMLTMVKRFAQHHACHVWFVAHPR-QLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPID  504 (539)
Q Consensus       430 ----~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r-~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~  504 (539)
                          ....+.+...++.|..+|+++|++|+++.|.+ +.....+   +...=-|...+...|.+.+.+.+....-....+
T Consensus       161 d~~~~~~~r~ls~~l~~L~~~a~~~~~~vi~~NQv~~k~~~~f~---~~~~~~GG~~L~~~as~rl~l~k~~~~~~~~g~  237 (279)
T COG0468         161 DGHLGLRARLLSKALRKLTRLANKYNTAVIFTNQVRAKIGVMFG---DPETTTGGNALKFYASVRLDLRRIESLKEDVGN  237 (279)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHcCcEEEEECceeeecCcccC---CcccCCCchHHHhhhheEEEEeeccccccccCC
Confidence                12334677899999999999999999999943 3322111   222334677888999999999886320000234


Q ss_pred             cEEEEEEEeeCCCcceeeeEEEEEeCC
Q 009230          505 RVQVCVRKVRNKVVGTIGEAFLSYNRV  531 (539)
Q Consensus       505 ~~~l~i~K~R~g~~G~~~~~~l~fd~~  531 (539)
                      .+.+.+.|+|.-+.+..-.+.+.|+.-
T Consensus       238 ~r~~~vvk~~~~p~~~~a~f~I~~~~~  264 (279)
T COG0468         238 KRRVKVVKNKVAPPFKEAEFDITYGGG  264 (279)
T ss_pred             eEEEEEEeCCCCCCCceeEEEeecCcc
Confidence            688999999999888544556666643

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=99.63  E-value=2.3e-14  Score=140.02  Aligned_cols=218  Identities=16%  Similarity=0.118  Sum_probs=144.1

Q ss_pred             CCccccccCchhhhhhhc---cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCC
Q 009230          276 GDEFGISTGWRALNELYN---VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKK  352 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~---l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~  352 (539)
                      .....+|||++.||..++   +++|.++.|+|++++|||+|+++++.++... |..++|+..|-+...-   + +...|+
T Consensus        29 ~~~~~i~TG~~~LD~aLg~GG~p~G~ivEi~G~~ssGKttLaL~~ia~~q~~-g~~~a~ID~e~~ld~~---~-a~~lGv  103 (322)
T PF00154_consen   29 QNIEVISTGSPALDYALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKQ-GGICAFIDAEHALDPE---Y-AESLGV  103 (322)
T ss_dssp             CSS-EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT-T-EEEEEESSS---HH---H-HHHTT-
T ss_pred             cccceEecCCcccchhhccCccccCceEEEeCCCCCchhhhHHHHHHhhhcc-cceeEEecCcccchhh---H-HHhcCc
Confidence            345679999999999884   9999999999999999999999999887765 9999999999765432   2 223466


Q ss_pred             CccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCC---C--
Q 009230          353 PFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQR---P--  427 (539)
Q Consensus       353 ~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~---~--  427 (539)
                      ++.                         +.+++.+     .+.++..+.++.+++...+++|||||+..+....   +  
T Consensus       104 dl~-------------------------rllv~~P-----~~~E~al~~~e~lirsg~~~lVVvDSv~al~p~~E~e~~~  153 (322)
T PF00154_consen  104 DLD-------------------------RLLVVQP-----DTGEQALWIAEQLIRSGAVDLVVVDSVAALVPKAELEGEI  153 (322)
T ss_dssp             -GG-------------------------GEEEEE------SSHHHHHHHHHHHHHTTSESEEEEE-CTT-B-HHHHTTST
T ss_pred             ccc-------------------------ceEEecC-----CcHHHHHHHHHHHhhcccccEEEEecCcccCCHHHHhhcc
Confidence            543                         2344421     2346666777777777778999999999885421   1  


Q ss_pred             ---CCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC---CCCC
Q 009230          428 ---VSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD---PEAG  501 (539)
Q Consensus       428 ---~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~---~~~~  501 (539)
                         ........+.++++.|..+..+.|+++|++.|.|..-+.....|  .-..|+.++.+.|++.|-+.+.+.   .+..
T Consensus       154 ~~~~~g~~Ar~ms~~lr~lt~~l~~~~~~~i~INQ~R~~ig~~~g~~--~~t~GG~alkfyas~rl~i~k~~~ik~~~~~  231 (322)
T PF00154_consen  154 GDQQVGLQARLMSQALRKLTPLLSKSNTTLIFINQVRDKIGVMFGNP--ETTPGGRALKFYASVRLEIRKKEQIKEGDEV  231 (322)
T ss_dssp             SSTSSSHHHHHHHHHHHHHHHHHHTTT-EEEEEEEESSSSSSSSSSS--SCCTSHHHHHHHCSEEEEEEEEEEEEETTCE
T ss_pred             ccccCcchHHHHHHHHHHHHHHHHhhceEEEEeehHHHHHhhccCCC--cCCCCCchhhhhhhhHHhhhcccccccCCcc
Confidence               01123346788899999999999999999999665432111122  234688999999999999987542   1111


Q ss_pred             CCCcEEEEEEEeeCCCcceeeeEEEEEeC
Q 009230          502 PIDRVQVCVRKVRNKVVGTIGEAFLSYNR  530 (539)
Q Consensus       502 ~~~~~~l~i~K~R~g~~G~~~~~~l~fd~  530 (539)
                      ....+.+.|.|||-.+.-..-.+.+.|+.
T Consensus       232 iG~~~~vkv~KnKva~P~k~a~~~i~y~~  260 (322)
T PF00154_consen  232 IGNKIKVKVVKNKVAPPFKKAEFDIYYGR  260 (322)
T ss_dssp             CEEEEEEEEEEESSS-TTEEEEEEEETTT
T ss_pred             cccEEEEEEEEcccCCCcceeEEEEecCC
Confidence            23467899999999766554445666543

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>PF13155 Toprim_2: Toprim-like

Probab=99.53  E-value=1.5e-14  Score=118.08  Aligned_cols=85  Identities=31%  Similarity=0.368  Sum_probs=60.5

Q ss_pred             EEEechhhHHHHHHhCCCce----EEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHh--ccCCEEEEEecCCccchHH
Q 009230          127 IIVEGEMDKLSMEEAGFLNC----VSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYL--KQASRIILATDGDPPGQAL  200 (539)
Q Consensus       127 ~i~EG~~Dalsl~~~g~~~~----v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l--~~~~~ivl~~DnD~~G~~~  200 (539)
                      |||||++|+||++|++..+.    +++++++....                 .....+|  .+.++|++|+|||+||+++
T Consensus         1 ~v~Eg~iDaLS~~~~~~~~~~~~~~~l~~~~~~~~-----------------~~~~~~l~~~~~~~i~l~~DnD~aG~~~   63 (96)
T PF13155_consen    1 VVFEGPIDALSYYQLGKENIKDNSLSLAGGGTLSE-----------------KQQIKFLKENPYKKIVLAFDNDEAGRKA   63 (96)
T ss_pred             cEEeCHHHHHHHHHhCchhcCCceEEEECCchHHH-----------------HHHHHHHHhCCCCcEEEEeCCCHHHHHH
Confidence            68999999999999987642    45554443210                 1123455  3347899999999999999


Q ss_pred             HHHHHHHhcCCc-----eEEEecCCCCCCCCCCChHHHH
Q 009230          201 AEELARRVGRER-----CWRVRWPKKNDVDHFKDANEVL  234 (539)
Q Consensus       201 ~~~~~~~l~~~~-----~~~~~~p~~~~~~~~kD~nd~l  234 (539)
                      ++++.+.+....     +.+..+|      .+|||||+|
T Consensus        64 ~~~~~~~l~~~~~~~~~~~~~~~~------~~KD~Nd~L   96 (96)
T PF13155_consen   64 AEKLQKELKEEGFPNIKVRIEDPP------DGKDWNDYL   96 (96)
T ss_pred             HHHHHHHHHhhCCCcceeeecCCC------CCcCchhhC
Confidence            999999885432     3334444      459999986

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=99.49  E-value=6.3e-13  Score=119.68  Aligned_cols=163  Identities=21%  Similarity=0.238  Sum_probs=110.7

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHh
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWL  378 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l  378 (539)
                      +++|.|+||+|||+|+.+++...+.+ +.+|+|++.|.....+..++......                        ...
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~~~-~~~v~~~~~e~~~~~~~~~~~~~~~~------------------------~~~   55 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIATK-GGKVVYVDIEEEIEELTERLIGESLK------------------------GAL   55 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHHhc-CCEEEEEECCcchHHHHHHHhhhhhc------------------------ccc
Confidence            37899999999999999999998884 99999999999988776665211000                        001


Q ss_pred             hccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCC-CCCHHHHHHHHHHHHHHHHHHhCcEEEEE
Q 009230          379 SNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPV-SQTETEYVSQMLTMVKRFAQHHACHVWFV  457 (539)
Q Consensus       379 ~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~-~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~  457 (539)
                       ....++. ..............+.......+++++|||++..+...... .......+.+.+..|..++++.+++|+++
T Consensus        56 -~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~vv~~  133 (165)
T cd01120          56 -DNLIIVF-ATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDEELRELLERARKGGVTVIFT  133 (165)
T ss_pred             -ccEEEEE-cCCCCCcHHHHHHHHHHHHhCCCCEEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhcCCceEEEE
Confidence             1122221 11233334444445556667788999999988877542110 00112345678888899999999999999


Q ss_pred             ec-CCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          458 AH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       458 ~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      +| ++......+      +.+|+..+++.||.++.|.|
T Consensus       134 ~~~~~~~~~~~~------~~~~~~~~~~~~d~~~~l~~  165 (165)
T cd01120         134 LQVPSGDKGDPR------LTRGAQNLEDIADTVIVLSR  165 (165)
T ss_pred             EecCCccccCcc------cccCccceeeecceEEEEeC
Confidence            99 544432111      17788999999999999875

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.

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=99.47  E-value=2.5e-12  Score=115.36  Aligned_cols=212  Identities=17%  Similarity=0.167  Sum_probs=145.9

Q ss_pred             ccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCcccc
Q 009230          280 GISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEA  357 (539)
Q Consensus       280 gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i  357 (539)
                      -+++|=++||+-+|  ++-|+|++|-|..|+|||.|+.+++.-++.+ |++|.|+|.|++..+....|.+.-.++..   
T Consensus         9 ii~~gndelDkrLGGGiP~GsL~lIEGd~~tGKSvLsqr~~YG~L~~-g~~v~yvsTe~T~refi~qm~sl~ydv~~---   84 (235)
T COG2874           9 IIKSGNDELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGFLMN-GYRVTYVSTELTVREFIKQMESLSYDVSD---   84 (235)
T ss_pred             hccCCcHHHHhhccCCCccCeEEEEECCCCccHHHHHHHHHHHHHhC-CceEEEEEechhHHHHHHHHHhcCCCchH---
Confidence            37889999999997  9999999999999999999999999998886 99999999999999999888764322211   


Q ss_pred             ccCCCCCCCCHHHHHHHHHHhhccceeEeec----CCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHH
Q 009230          358 NYGGSAERMTVEEFEQGKAWLSNTFSLIRCE----NDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTET  433 (539)
Q Consensus       358 ~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~----~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~  433 (539)
                                        ..+..++.++..+    ..+....+.+++.+....+...-++|+|||+..++.-     ++.
T Consensus        85 ------------------~~l~G~l~~~~~~~~~~~~~~~~~~~~L~~l~~~~k~~~~dViIIDSls~~~~~-----~~~  141 (235)
T COG2874          85 ------------------FLLSGRLLFFPVNLEPVNWGRRSARKLLDLLLEFIKRWEKDVIIIDSLSAFATY-----DSE  141 (235)
T ss_pred             ------------------HHhcceeEEEEecccccccChHHHHHHHHHHHhhHHhhcCCEEEEecccHHhhc-----ccH
Confidence                              1133444444321    1122233455555555556677899999999887642     245


Q ss_pred             HHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEe
Q 009230          434 EYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKV  513 (539)
Q Consensus       434 ~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~  513 (539)
                      .++.+++..+|.|+. .|-.|+++.|+..-...     .      -..+.+.||+.+.|+-.+--.+   -.-.+.+.|-
T Consensus       142 ~~vl~fm~~~r~l~d-~gKvIilTvhp~~l~e~-----~------~~rirs~~d~~l~L~~~~~Gg~---~~~~~~i~K~  206 (235)
T COG2874         142 DAVLNFMTFLRKLSD-LGKVIILTVHPSALDED-----V------LTRIRSACDVYLRLRLEELGGD---LIKVLEIVKY  206 (235)
T ss_pred             HHHHHHHHHHHHHHh-CCCEEEEEeChhhcCHH-----H------HHHHHHhhheeEEEEhhhhCCe---eeEEEEEeee
Confidence            578889999999996 45556666664333210     0      1247789999999987664222   2456778888


Q ss_pred             eCCCcceeeeEEEEEeCCCc
Q 009230          514 RNKVVGTIGEAFLSYNRVTG  533 (539)
Q Consensus       514 R~g~~G~~~~~~l~fd~~~~  533 (539)
                      |....+.-..+.+.-+|..|
T Consensus       207 ~ga~~s~~~~I~F~V~P~~G  226 (235)
T COG2874         207 RGARKSFQNIISFRVEPGFG  226 (235)
T ss_pred             cCchhhcCCceeEEecCCCc
Confidence            87544322234555555544

>PRK07078 hypothetical protein; Validated

Probab=99.43  E-value=8.9e-13  Score=143.44  Aligned_cols=138  Identities=24%  Similarity=0.371  Sum_probs=100.5

Q ss_pred             eEEEEeEe-eCCEEEEEEeecC----CCcccc--cC------CCCCccccccccCCCCcEEEEechhhHHHHHHhCCCce
Q 009230           80 VVIAFPYW-RNGKLVNCKYRDF----NKKFWQ--EK------DTEKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNC  146 (539)
Q Consensus        80 ~~i~fP~~-~~G~~~~~~~R~~----~~~~~~--~~------~~~~~l~g~~~~~~~~~v~i~EG~~Dalsl~~~g~~~~  146 (539)
                      ....+||. .+|+++...+|..    .|.|++  +.      .....|||++.+.....|+|||||.||.++++.|+. +
T Consensus       134 ~~~~~~Y~D~~G~~~~~v~R~~~~~~~K~fr~~~g~~~~~~~~~~~pLy~lp~l~~a~~V~lvEGEk~adal~~~g~~-a  212 (759)
T PRK07078        134 ATAKWDYLDAAGKLIAVVYRYDPPGRRKEFRPWDAKRRKMAPPEPRPLYNQPGLLSAEQVVLVEGEKCAQALIDAGVV-A  212 (759)
T ss_pred             ceeEEEEECCCCCEEEEEEeecCCCCCceeecccCCcceecCCCCcCCcCchhhhcCCeEEEEeChHHHHHHHhcCCe-E
Confidence            45678887 8899998888876    255654  21      234678999988777899999999999999999987 4


Q ss_pred             EEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCccchHHHHHHHHHh---cCCceEEEecCCCCC
Q 009230          147 VSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELARRV---GRERCWRVRWPKKND  223 (539)
Q Consensus       147 v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~~G~~~~~~~~~~l---~~~~~~~~~~p~~~~  223 (539)
                      ++.+.|+.....           +.+     +..|.. ++||||+|||++|+++++++++.|   +...|.++ +|.. +
T Consensus       213 tt~~~Ga~~~~~-----------~~d-----~~~L~g-~~VvI~pD~D~~G~~~a~~va~~l~~~g~~~~~v~-~p~~-~  273 (759)
T PRK07078        213 TTAMHGANAPVD-----------KTD-----WSPLAG-KAVLIWPDRDKPGWEYADRAAQAILSAGASSCAVL-LPPE-D  273 (759)
T ss_pred             EecCCCCCCCcc-----------ccc-----ccccCC-CEEEEEcCCChHHHHHHHHHHHHHHhcCCeEEEEE-ecCc-c
Confidence            555667754211           011     223554 799999999999999999999999   33344444 4532 1


Q ss_pred             CCCCCChHHHHHhc
Q 009230          224 VDHFKDANEVLMYL  237 (539)
Q Consensus       224 ~~~~kD~nd~l~~~  237 (539)
                      .+.++|++|++..+
T Consensus       274 ~~~~~D~aD~~~~G  287 (759)
T PRK07078        274 LPEGWDAADAIAEG  287 (759)
T ss_pred             cCcCCCHHHHHHcC
Confidence            24689999999885

>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]

Probab=99.39  E-value=1.5e-11  Score=116.33  Aligned_cols=149  Identities=13%  Similarity=0.183  Sum_probs=106.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc---------CCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHA---------GWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAE  364 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~---------g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~  364 (539)
                      |+.|-..+|+|.+|+|||+++++++.+++...         -.+|+|+|+|...+++++|+-....++            
T Consensus        86 fr~g~~~~~~gdsg~GKttllL~l~IalaaG~~lfG~~v~epGkvlyvslEl~re~~L~Rl~~v~a~m------------  153 (402)
T COG3598          86 FRKGYVSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELYREDILERLEPVRARM------------  153 (402)
T ss_pred             hhcCeeEEEecCCcccHhHHHHHHHHHHHhhHHHhcccccCCCeEEEEEeccChHHHHHHHHHHHHHc------------
Confidence            88888889999999999999999999998741         268999999999999999986554433            


Q ss_pred             CCCHHHHHHHHHH-hhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHH
Q 009230          365 RMTVEEFEQGKAW-LSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMV  443 (539)
Q Consensus       365 ~l~~~~~~~~~~~-l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~L  443 (539)
                      .+++.+++.+..+ ++..-     ...+...+ .+..+......+..+++||||++..+..+.   +.....+.++++.+
T Consensus       154 gLsPadvrn~dltd~~Gaa-----~~~d~l~p-kl~rRfek~~~Q~rp~~vViDp~v~f~~G~---s~s~vqv~~fi~~~  224 (402)
T COG3598         154 GLSPADVRNMDLTDVSGAA-----DESDVLSP-KLYRRFEKILEQKRPDFVVIDPFVAFYEGK---SISDVQVKEFIKKT  224 (402)
T ss_pred             CCChHhhhheeccccccCC-----CccccccH-HHHHHHHHHHHHhCCCeEEEcchhhhcCCc---cchhHHHHHHHHHH
Confidence            2444444332110 00000     00111122 455555555667789999999998887653   23346788999999


Q ss_pred             HHHHHHhCcEEEEEecCCCC
Q 009230          444 KRFAQHHACHVWFVAHPRQL  463 (539)
Q Consensus       444 k~lA~~~~i~vi~~~q~r~~  463 (539)
                      +++|..++|+||.+||+.+.
T Consensus       225 rkla~~l~caIiy~hHtsks  244 (402)
T COG3598         225 RKLARNLECAIIYIHHTSKS  244 (402)
T ss_pred             HHHHHhcCCeEEEEeccccc
Confidence            99999999999999994433

>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG

Probab=99.38  E-value=2.3e-12  Score=100.72  Aligned_cols=74  Identities=30%  Similarity=0.377  Sum_probs=57.1

Q ss_pred             CcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccC-CEEEEEecCCccchHHHH
Q 009230          124 SDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQA-SRIILATDGDPPGQALAE  202 (539)
Q Consensus       124 ~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~-~~ivl~~DnD~~G~~~~~  202 (539)
                      ++|+||||++|+||+++.|..++++++ |+...                  ..+...|.++ ++|++|+|||++|+++++
T Consensus         1 ~~v~i~EG~~D~ls~~~~g~~~~va~~-G~~~~------------------~~~~~~L~~~~~~vii~~D~D~aG~~a~~   61 (79)
T cd03364           1 KKVILVEGYMDVIALHQAGIKNVVASL-GTALT------------------EEQAELLKRLAKEVILAFDGDEAGQKAAL   61 (79)
T ss_pred             CeEEEEeCHHHHHHHHHcCCCCEEECC-CccCc------------------HHHHHHHHhcCCeEEEEECCCHHHHHHHH
Confidence            468999999999999999988888865 43321                  0124566664 899999999999999999


Q ss_pred             HHHHHhcC--CceEEE
Q 009230          203 ELARRVGR--ERCWRV  216 (539)
Q Consensus       203 ~~~~~l~~--~~~~~~  216 (539)
                      ++.++|..  ..++++
T Consensus        62 ~~~~~l~~~g~~~~~~   77 (79)
T cd03364          62 RALELLLKLGLNVRVL   77 (79)
T ss_pred             HHHHHHHHCCCeEEEE
Confidence            99999943  334444

Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.

>KOG1564 consensus DNA repair protein RHP57 [Replication, recombination and repair]

Probab=99.30  E-value=8.5e-12  Score=115.72  Aligned_cols=166  Identities=14%  Similarity=0.155  Sum_probs=108.0

Q ss_pred             cccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHH--h---cCCeEEEEeCCCCHH-HHHHHHHHHhh
Q 009230          279 FGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINE--H---AGWKFVLCSMENKVR-EHARKLLEKHI  350 (539)
Q Consensus       279 ~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~--~---~g~~vl~~s~E~~~~-~~~~r~~~~~~  350 (539)
                      ..++||-..||+.++  +..+.+|-|+|.+|+|||.|++|+++..-.  .   .|..++|++.|.+-. +-...+.+...
T Consensus        82 ~~lttgc~~LD~~L~GGi~~~giTEi~GeSg~GKtQL~lQL~L~VQLp~~~GGL~~~~vYI~TE~~fP~rRL~qL~~~~~  161 (351)
T KOG1564|consen   82 SKLTTGCVALDECLRGGIPTDGITEICGESGCGKTQLLLQLSLCVQLPRSHGGLGGGAVYICTESPFPTRRLHQLSHTLP  161 (351)
T ss_pred             hhcccccHHHHHHhcCCcccccHHHHhhccCCcHHHHHHHHHHHhhCchhhCCCCCceEEEEcCCCCcHHHHHHHHHhcc
Confidence            458999999999996  999999999999999999999999887643  2   257899999997632 21122222221


Q ss_pred             CCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHH----HHHHHcCCcEEEEccccccccCC
Q 009230          351 KKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAK----AAVLRHGVRGLVIDPYNELDHQR  426 (539)
Q Consensus       351 ~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~----~~~~~~~~~~vvID~~~~l~~~~  426 (539)
                      ..+             ..+..........++.+..     .-.+++.++..+.    .+..+.++++|||||...+....
T Consensus       162 ~rp-------------~~~~~~~~~~Npgd~IFv~-----~~~d~d~l~~iv~~qlPiL~~r~~i~LVIiDSVAa~fR~E  223 (351)
T KOG1564|consen  162 QRP-------------NPEKELNYNDNPGDHIFVE-----NVHDVDHLLHIVNRQLPILLNRKKIKLVIIDSVAALFRSE  223 (351)
T ss_pred             cCC-------------CcchhhhhccCCCceEEEE-----eccchhhHHHHHhhhccceeccCcceEEEEehhhHHHHHH
Confidence            111             0010011111112233333     2234444444443    23455679999999999876532


Q ss_pred             C----C-CCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCC
Q 009230          427 P----V-SQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQ  462 (539)
Q Consensus       427 ~----~-~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~  462 (539)
                      -    + ...+...+..+...|+.+|.+++++|+++.| ...
T Consensus       224 ~d~~~Sdl~~r~~~l~rla~~Lr~LA~~~~~aVV~~NQVtd~  265 (351)
T KOG1564|consen  224 FDYNPSDLKKRARHLFRLAGKLRQLASKFDLAVVCANQVTDR  265 (351)
T ss_pred             hccChhhhhhHHHHHHHHHHHHHHHHHhcCccEEEeeccccc
Confidence            1    1 1123456788999999999999999999999 444

>PF13362 Toprim_3: Toprim domain

Probab=99.25  E-value=3.7e-11  Score=97.82  Aligned_cols=91  Identities=31%  Similarity=0.330  Sum_probs=65.6

Q ss_pred             cEEEEechhhHHHH-HHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCcc--chHHH
Q 009230          125 DIIIVEGEMDKLSM-EEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPP--GQALA  201 (539)
Q Consensus       125 ~v~i~EG~~Dalsl-~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~~--G~~~~  201 (539)
                      +++||||+.|+||+ .+.....++++. |+.+...                   +......++|+||.|||.+  |++++
T Consensus         1 tl~i~EG~etals~~~~~~~~~~~a~~-~~~nl~~-------------------~~~~~~~~~vii~~D~D~~~~G~~~a   60 (96)
T PF13362_consen    1 TLIIAEGIETALSIAQQATGVPVVAAL-GAGNLKN-------------------VAIPEPGRRVIIAADNDKANEGQKAA   60 (96)
T ss_pred             CEEEEEhHHHHHHHHHhcCCCeEEEEE-Chhhhhh-------------------hcCCCCCCeEEEEECCCCchhhHHHH
Confidence            48999999999999 566555566653 4444211                   1112357899999999999  99999


Q ss_pred             HHHHHHhcCCc--eEEEecCCCCCCCCCCChHHHHHhcCcc
Q 009230          202 EELARRVGRER--CWRVRWPKKNDVDHFKDANEVLMYLGPG  240 (539)
Q Consensus       202 ~~~~~~l~~~~--~~~~~~p~~~~~~~~kD~nd~l~~~g~~  240 (539)
                      .++++++....  +.++. |    ...++||||+|+..|.+
T Consensus        61 ~~~~~~~~~~g~~~~~~~-p----~~~g~D~ND~l~~~G~e   96 (96)
T PF13362_consen   61 EKAAERLEAAGIAVSIVE-P----GPEGKDWNDLLQARGKE   96 (96)
T ss_pred             HHHHHHHHhCCCeEEEEC-C----CCCCchHHHHHHhhCCC
Confidence            99999996433  34444 3    13578999999998754

>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A

Probab=99.22  E-value=2.8e-11  Score=95.10  Aligned_cols=71  Identities=34%  Similarity=0.606  Sum_probs=49.6

Q ss_pred             CcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhcc-CCEEEEEecCCccchHHHH
Q 009230          124 SDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQ-ASRIILATDGDPPGQALAE  202 (539)
Q Consensus       124 ~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~-~~~ivl~~DnD~~G~~~~~  202 (539)
                      +.++||||++|+++++++|+++++++.+++..       +..+      .   ....+.. .++|+||+|+|.+|+++++
T Consensus         1 k~viIvEG~~D~~~l~~~g~~~~v~~~g~~~~-------~~~~------~---~~~~~~~~~~~Vii~~D~D~~G~~~a~   64 (81)
T PF13662_consen    1 KEVIIVEGEFDAIALEQAGYKNVVAVLGGNLS-------PLDQ------I---LREKLEKKVKEVIIAFDNDKAGEKAAQ   64 (81)
T ss_dssp             --EEEESSHHHHHHHHHTT-TTEEEESSSS----------HHH------H---HHHHHH---SEEEEEEESSHHHHHHHH
T ss_pred             CEEEEECCHHHHHHHHHhCCCeEEEECCCCCC-------hHHH------h---ChHhhhccCceEEEEeCcCHHHHHHHH
Confidence            46999999999999999999998887654431       1110      0   0122322 5899999999999999999


Q ss_pred             HHHHHhcC
Q 009230          203 ELARRVGR  210 (539)
Q Consensus       203 ~~~~~l~~  210 (539)
                      ++.+.|..
T Consensus        65 ~i~~~l~~   72 (81)
T PF13662_consen   65 KIAKKLLP   72 (81)
T ss_dssp             HHHHHHG-
T ss_pred             HHHHHHHh
Confidence            99998854

>KOG1434 consensus Meiotic recombination protein Dmc1 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.22  E-value=4.5e-11  Score=109.34  Aligned_cols=193  Identities=15%  Similarity=0.198  Sum_probs=125.5

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-----cCCeEEEEeCCCCHHHHHHHHHHH
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEH-----AGWKFVLCSMENKVREHARKLLEK  348 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-----~g~~vl~~s~E~~~~~~~~r~~~~  348 (539)
                      .....|.||-..||.++|  +..=.+|-|+|.+|+|||.+..+++...-..     .+.++.|+..|.+-.-  .|+...
T Consensus        92 ~~v~~ItTgs~~lD~ILGGGI~~m~iTEifGefr~GKTQlshtLcVt~QlPr~~Gg~~Gk~ifIDTEgtFrp--dRi~~I  169 (335)
T KOG1434|consen   92 KTVGSITTGSSALDDILGGGIPSMSITEIFGEFRCGKTQLSHTLCVTVQLPREMGGVGGKAIFIDTEGTFRP--DRIKDI  169 (335)
T ss_pred             hccceeecchHHHhhhhcCCccchhhHHHcCCCCcCccceeeEEEEEeecchhhCCCCceEEEEecCCccch--HHHHHH
Confidence            455679999999999997  8888999999999999999999988765432     2579999999976321  122221


Q ss_pred             hhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHc-CCcEEEEccccccccCCC
Q 009230          349 HIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRH-GVRGLVIDPYNELDHQRP  427 (539)
Q Consensus       349 ~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~-~~~~vvID~~~~l~~~~~  427 (539)
                      .-+.            .+.++..      | +..+|+++-  .....-+++..+.....++ ..++||||+++.++..+-
T Consensus       170 Ae~~------------~~d~d~~------L-dNI~y~Ra~--~se~qmelv~~L~~~~se~g~~rlvIVDsIma~FRvDy  228 (335)
T KOG1434|consen  170 AERF------------KVDPDFT------L-DNILYFRAY--NSEEQMELVYLLGDFLSEHGKYRLVIVDSIMALFRVDY  228 (335)
T ss_pred             HHHh------------CCCHHHH------H-HHHHHHHHc--ChHHHHHHHHHHHHHHhhcCcEEEEEEeceehheeecc
Confidence            1110            2333321      1 122333221  1111112223333334444 589999999999876542


Q ss_pred             C--C--CCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCC-----CCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          428 V--S--QTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHN-----WVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       428 ~--~--~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~-----~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      +  +  ..+.+.+.+++.+|..+|+++|++|+++.| ..+...     ..+..|     .|+..+...+.+-++|++..
T Consensus       229 ~grgeLseRqqkLn~ml~kl~~laeefnvAVfltNQvttdpga~~~f~s~~~kp-----~gGh~~aHAsttRlilrkgr  302 (335)
T KOG1434|consen  229 DGRGELSERQQKLNQMLQKLNKLAEEFNVAVFLTNQVTTDPGAGMTFASQDLKP-----AGGHSWAHASTTRLILRKGR  302 (335)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHHHhccEEEEEecceecCCcccccccccccCc-----cccchhhhhhheeEEEEcCC
Confidence            1  1  234567889999999999999999999999 555432     112223     35566777778888888766

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=99.21  E-value=1.3e-10  Score=139.32  Aligned_cols=178  Identities=17%  Similarity=0.216  Sum_probs=116.5

Q ss_pred             hhhcccccCCCCCCcHHHHHHH-HhcCCCHHHHHHcCccccc---C----CceeEEEEeEe-eCCEEEEEEeecCCC---
Q 009230           35 IREITEDSLELEPLGNELRAYF-AERLISAETLRRNRVMQKR---H----GHEVVIAFPYW-RNGKLVNCKYRDFNK---  102 (539)
Q Consensus        35 ~~~~~~~~~~~~p~~~~~~~Yl-~~Rgi~~~~~~~~~~~~~~---~----~~~~~i~fP~~-~~G~~~~~~~R~~~~---  102 (539)
                      ++.+|....+.  ....+..|| ..|||+.  +..+.++.+.   +    ...++++||+. .+|+++++..+.+++   
T Consensus      1672 A~rl~~~a~pi--~gt~A~~YL~~~RGI~~--~~~~~LrfhP~~y~~~~~~~~Paliapv~D~~G~i~gv~rt~L~p~~g 1747 (1960)
T TIGR02760      1672 AKSLFQGSQEL--KGTLAEKYLKQHRGLAS--IDNDDIRFHPTVYSSDKKNKHPALIAAARNEKGEITGIQITYLDKDDA 1747 (1960)
T ss_pred             HHHHHHhcCCC--CCHHHHHHHHhcCCCCC--CCccceEECcccccCCCCCcCCeEEEEEECCCCCEEEEEEEEccCCCC
Confidence            55677766432  135688999 8999976  2444444332   1    24689999987 899999999998742   


Q ss_pred             ---cccccC-----CCCCccccccccCCCCcEEEEechhhHHHHHHhCC--CceEEcCCCCCCCCCCCCCCChhhhhhhH
Q 009230          103 ---KFWQEK-----DTEKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGF--LNCVSVPDGAPSSVSKKNVPSEEQDTKYQ  172 (539)
Q Consensus       103 ---~~~~~~-----~~~~~l~g~~~~~~~~~v~i~EG~~Dalsl~~~g~--~~~v~l~~g~~~~~~~~~l~~~~~~~~~~  172 (539)
                         ++...+     .....+++++....++.++|+||..|+||+++++.  .+++++ .|+.+....             
T Consensus      1748 ~~~k~l~~~kr~~G~k~g~~v~l~~~~~~~~liiaEGiEtaLS~~~a~~~~~~vvA~-lg~~~l~~i------------- 1813 (1960)
T TIGR02760      1748 NKDKDMDNNKRVKGSISGQFVVINKGMQGDRSYIAEGIETGLSIALANPKATVVIAV-GGKNNLSPI------------- 1813 (1960)
T ss_pred             CCCccCCCcccccccccCcEEEecCCCCCCeEEEEcCHHHHHHHHHhCCCCccEEEE-CCccccccc-------------
Confidence               232221     22333445544444578999999999999999975  445554 344332110             


Q ss_pred             HHHhHHHHhc-cCCEEEEEecCCc--c-chHHHHHHHHHhcC--CceEEEecCCCCCCCCCCChHHHHHhcCcchHHHHH
Q 009230          173 YLWNCKMYLK-QASRIILATDGDP--P-GQALAEELARRVGR--ERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVV  246 (539)
Q Consensus       173 ~l~~~~~~l~-~~~~ivl~~DnD~--~-G~~~~~~~~~~l~~--~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~~~~~  246 (539)
                             .+. ..++||||.|||.  + |+.++.++++++..  ..+.++ +|      +  ||||.    |.+++.+.+
T Consensus      1814 -------~~~~~~~~viI~~D~D~~~a~G~~Aa~k~~~~l~~~G~~v~i~-~P------~--Dfnd~----g~~~~~~~l 1873 (1960)
T TIGR02760      1814 -------IPKFIPKNVVIVLDNDGEEAKSQRAIEKIINKFKQDNISARIV-FP------D--DWNDI----GEEELQKQL 1873 (1960)
T ss_pred             -------cCCCCCceEEEEeCCCCcccchHHHHHHHHHHHHhCCCeeEEe-CC------c--hhhhh----hHHHHHHHH
Confidence                   011 1379999999994  5 99999999999843  345545 56      2  88888    456677776


Q ss_pred             Hhcc
Q 009230          247 ENAE  250 (539)
Q Consensus       247 ~~A~  250 (539)
                      ..+.
T Consensus      1874 ~~~~ 1877 (1960)
T TIGR02760      1874 MRAI 1877 (1960)
T ss_pred             HHhh
Confidence            6554

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.

>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs

Probab=99.14  E-value=2.1e-10  Score=89.81  Aligned_cols=68  Identities=32%  Similarity=0.439  Sum_probs=52.7

Q ss_pred             CcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccC-CEEEEEecCCccchHHHH
Q 009230          124 SDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQA-SRIILATDGDPPGQALAE  202 (539)
Q Consensus       124 ~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~-~~ivl~~DnD~~G~~~~~  202 (539)
                      ++++||||++|++|+++.|..+++++. |+.+.      +            ..+..+.+. ++|++|+|||.+|+++++
T Consensus         1 ~~v~i~EG~~Dals~~~~~~~~~~~~~-g~~~~------~------------~~~~~l~~~~~~vii~~D~D~~G~~~~~   61 (79)
T cd01029           1 DEVIIVEGYMDVLALHQAGIKNVVAAL-GTANT------E------------EQLRLLKRFARTVILAFDNDEAGKKAAA   61 (79)
T ss_pred             CEEEEEeCHHHHHHHHHcCCCCEEECC-CccCc------H------------HHHHHHHhcCCEEEEEECCCHHHHHHHH
Confidence            468999999999999999987677753 55431      0            113445554 999999999999999999


Q ss_pred             HHHHHhcC
Q 009230          203 ELARRVGR  210 (539)
Q Consensus       203 ~~~~~l~~  210 (539)
                      ++.+.+..
T Consensus        62 ~~~~~~~~   69 (79)
T cd01029          62 RALELLLA   69 (79)
T ss_pred             HHHHHHHH
Confidence            99888854

Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.

>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins

Probab=99.12  E-value=9.8e-10  Score=107.22  Aligned_cols=204  Identities=11%  Similarity=0.087  Sum_probs=129.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQ  373 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~  373 (539)
                      -..|...+|-|.||+|||+|++.++..+..  ..+|+|+|.-.++..+..........++              ...+-.
T Consensus         7 ~~~G~TLLIKG~PGTGKTtfaLelL~~l~~--~~~v~YISTRVd~d~vy~~y~~~~~~i~--------------~~~vlD   70 (484)
T PF07088_consen    7 QEPGQTLLIKGEPGTGKTTFALELLNSLKD--HGNVMYISTRVDQDTVYEMYPWIEESID--------------PTNVLD   70 (484)
T ss_pred             CCCCcEEEEecCCCCCceeeehhhHHHHhc--cCCeEEEEeccCHHHHHHhhhhhccccC--------------hhhhhh
Confidence            467899999999999999999999977765  5799999999888876554422222221              111111


Q ss_pred             H-HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCc
Q 009230          374 G-KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHAC  452 (539)
Q Consensus       374 ~-~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i  452 (539)
                      + .+.+.- .... ..+.....++.+.+.+++........+|++||+-.++..-....+..+.+..+...|-.||+..++
T Consensus        71 atQd~~~~-~~~~-~vp~~~l~~ds~~~f~~~i~~~~k~~iI~~DSWdaiieyla~~~~~~ed~e~l~~dLv~lard~g~  148 (484)
T PF07088_consen   71 ATQDPFEL-PLDK-DVPFERLDIDSFRDFVDKINEAGKKPIIAFDSWDAIIEYLAEEHDEPEDIETLTNDLVELARDMGI  148 (484)
T ss_pred             hccchhhc-cccc-cCcccccCHHHHHHHHHHhhhcccCcEEEEecHHHHHHHhhhhhcCcHHHHHHHHHHHHHHhhcCc
Confidence            1 000000 0000 001223457777777775433345678999997776652211123334467788888899999999


Q ss_pred             EEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCC
Q 009230          453 HVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVT  532 (539)
Q Consensus       453 ~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~  532 (539)
                      ++|+++...+..                .+++.+|-|+.|+-..+ +++ ...+.|.+.|.|-=..+..   .+.|--..
T Consensus       149 ~LIlVsEsa~~~----------------~LdYivDGVVTL~v~~d-erG-R~~R~L~LeKLRGV~I~q~---~Y~fTL~n  207 (484)
T PF07088_consen  149 NLILVSESAENE----------------PLDYIVDGVVTLQVKND-ERG-RTRRYLRLEKLRGVRIKQR---LYPFTLAN  207 (484)
T ss_pred             eEEEEEecCCCC----------------cchheeeeEEEEEeccc-cCC-ceEEEEEehhhcCcccCCc---cceEEeeC
Confidence            999998854432                38899999999953333 322 3357899999986555542   23366666


Q ss_pred             ceec
Q 009230          533 GEYM  536 (539)
Q Consensus       533 ~rf~  536 (539)
                      |||.
T Consensus       208 GrF~  211 (484)
T PF07088_consen  208 GRFR  211 (484)
T ss_pred             CEEE
Confidence            6664

GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding

>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins

Probab=98.79  E-value=1.8e-08  Score=78.05  Aligned_cols=68  Identities=38%  Similarity=0.498  Sum_probs=48.3

Q ss_pred             CcEEEEechhhHHHHHHhCCC--ceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhcc-C--CEEEEEecCCccch
Q 009230          124 SDIIIVEGEMDKLSMEEAGFL--NCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQ-A--SRIILATDGDPPGQ  198 (539)
Q Consensus       124 ~~v~i~EG~~Dalsl~~~g~~--~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~-~--~~ivl~~DnD~~G~  198 (539)
                      ++++||||++|++++++++..  .++++ .|...       +.       .    .+..+++ .  .+|+||+|+|.+|+
T Consensus         1 ~~l~ivEg~~da~~~~~~~~~~~~~~~~-~G~~~-------~~-------~----~~~~l~~~~~~~~Iii~~D~D~~G~   61 (76)
T smart00493        1 KVLIIVEGPADAIALEKAGGFGGNVVAL-GGHLL-------KK-------E----IIKLLKRLAKKKEVILATDPDREGE   61 (76)
T ss_pred             CEEEEEcCHHHHHHHHHhcCCCEEEEEE-eeeec-------HH-------H----HHHHHHHHhcCCEEEEEcCCChhHH
Confidence            468999999999999999984  33443 23321       00       0    1122322 1  68999999999999


Q ss_pred             HHHHHHHHHhcC
Q 009230          199 ALAEELARRVGR  210 (539)
Q Consensus       199 ~~~~~~~~~l~~  210 (539)
                      ++++++.+.+..
T Consensus        62 ~~~~~i~~~l~~   73 (76)
T smart00493       62 AIAWKLAELLKP   73 (76)
T ss_pred             HHHHHHHHHhhh
Confidence            999999998854

>PF12965 DUF3854: Domain of unknown function (DUF3854); InterPro: IPR024385 This is a family of uncharacterised proteins, found by clustering human gut metagenomic sequences []

Probab=98.78  E-value=5.9e-08  Score=82.67  Aligned_cols=112  Identities=17%  Similarity=0.244  Sum_probs=73.8

Q ss_pred             CCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhc-cCCEEEEEecCCcc-----
Q 009230          123 ESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLK-QASRIILATDGDPP-----  196 (539)
Q Consensus       123 ~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~-~~~~ivl~~DnD~~-----  196 (539)
                      .-+|+||||++-|.|+.++|+. +++||+ -.+......... . ......|...+..+. +.++|++|||.|..     
T Consensus        10 ~~pi~ItEG~kKA~al~s~G~~-aIalpG-V~~~~~~~~~~~-~-~~~~~~L~p~L~~~~~~gr~v~iaFD~D~~~~Tn~   85 (130)
T PF12965_consen   10 NIPIWITEGAKKAGALLSQGYP-AIALPG-VNNGYRWPKDEG-D-KIGKRRLIPELAKLAKPGREVYIAFDADTKPKTNK   85 (130)
T ss_pred             CccEEEEechHHHHHHHcCCce-EEEeCc-eecccccccccc-c-cccchhcchhHHHhccCCceEEEEecCCCccchhH
Confidence            5689999999999999999987 799884 333221100000 0 001113344454553 57899999999932     


Q ss_pred             -chHHHHHHHHHhcC--CceEEEecCCCCCCCCCCChHHHHHhcCcchH
Q 009230          197 -GQALAEELARRVGR--ERCWRVRWPKKNDVDHFKDANEVLMYLGPGAL  242 (539)
Q Consensus       197 -G~~~~~~~~~~l~~--~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~  242 (539)
                       =.++.+++.+.|..  ..++++.||.    ...|-++|+|.++|+++|
T Consensus        86 ~V~~a~~~l~~~L~~~G~~v~~~~w~~----~~~KGiDD~l~~~G~~~f  130 (130)
T PF12965_consen   86 NVRRAIKRLGKLLKEAGCKVKIITWPP----GEGKGIDDLLAAKGPDAF  130 (130)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEEEeCC----CCCCCHhHHHHhcCcccC
Confidence             23556677777743  3467888884    468999999999987753

>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea

Probab=98.60  E-value=2e-07  Score=72.52  Aligned_cols=68  Identities=24%  Similarity=0.415  Sum_probs=52.7

Q ss_pred             CcEEEEechhhHHHHHHhCC-CceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhcc-CCEEEEEecCCccchHHH
Q 009230          124 SDIIIVEGEMDKLSMEEAGF-LNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQ-ASRIILATDGDPPGQALA  201 (539)
Q Consensus       124 ~~v~i~EG~~Dalsl~~~g~-~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~-~~~ivl~~DnD~~G~~~~  201 (539)
                      +.++||||..|+.+++++|+ .++++. +|+..       +.           .+.+.+.+ .++|++++|+|.+|++++
T Consensus         2 ~~vIiVEG~~D~~~l~~~g~~~~~i~t-~Gt~~-------~~-----------~~~~~l~~~~~~VIiltD~D~aG~~i~   62 (81)
T cd01027           2 GEVIIVEGKNDTESLKKLGIEAEIIET-NGSII-------NK-----------ETIELIKKAYRGVIILTDPDRKGEKIR   62 (81)
T ss_pred             CeEEEEEchHHHHHHHHhCCCccEEEE-CCCcC-------CH-----------HHHHHHHHhCCEEEEEECCCHHHHHHH
Confidence            46899999999999999998 777775 35432       11           11233443 689999999999999999


Q ss_pred             HHHHHHhcC
Q 009230          202 EELARRVGR  210 (539)
Q Consensus       202 ~~~~~~l~~  210 (539)
                      .++.+.|..
T Consensus        63 ~~~~~~l~~   71 (81)
T cd01027          63 KKLSEYLSG   71 (81)
T ss_pred             HHHHHHhcc
Confidence            999999854

RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.

>PRK04031 DNA primase; Provisional

Probab=98.58  E-value=2.3e-07  Score=91.79  Aligned_cols=98  Identities=27%  Similarity=0.396  Sum_probs=74.4

Q ss_pred             CCCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCccchHHH
Q 009230          122 GESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALA  201 (539)
Q Consensus       122 ~~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~~G~~~~  201 (539)
                      ..+.++||||.+|+++|+++|+.|+|++. |+.       ++..            ...|.+-++|++|+|+|.+|+.+.
T Consensus       168 k~~~iIVVEG~~DVi~L~~aGi~nvVAt~-GT~-------l~~~------------i~~l~k~~~Vil~~DgD~aGe~I~  227 (408)
T PRK04031        168 DSDAIIVVEGRADVLNLLRYGIKNAIAVE-GTN-------VPET------------IIELSKKKTVTAFLDGDRGGELIL  227 (408)
T ss_pred             cCCeEEEEeCHHHHHHHHhcccceEEEeC-Ccc-------cHHH------------HHHHhcCCCEEEEECCCHHHHHHH
Confidence            45789999999999999999999999963 553       2211            223334689999999999999988


Q ss_pred             HHHHHHhcCCceEEEecCCCCCCCCCCChHHHHHhcCcchHHHHHHhccc
Q 009230          202 EELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAEL  251 (539)
Q Consensus       202 ~~~~~~l~~~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~~~~~~~A~~  251 (539)
                      +.+.+ . ....++.+.|      .++|+.++    ..+++.+++.++.+
T Consensus       228 k~l~~-v-~~~d~VaraP------~G~dVE~l----s~eeI~kAL~~~~p  265 (408)
T PRK04031        228 KELLQ-V-ADIDYVARAP------PGKEVEEL----TKKEIAKALRNKVP  265 (408)
T ss_pred             HHHHh-h-cceeEEecCC------CCCChhhC----CHHHHHHHHHhcCC
Confidence            88876 3 2345777777      34888888    46788888887765

>PRK04296 thymidine kinase; Provisional

Probab=98.58  E-value=3.9e-07  Score=84.11  Aligned_cols=140  Identities=16%  Similarity=0.154  Sum_probs=86.1

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC--CCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM--ENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG  374 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~--E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~  374 (539)
                      |.+++++|++|+||||++++++..++.. |.+|+++..  +....  ..++ ....|++...                  
T Consensus         2 g~i~litG~~GsGKTT~~l~~~~~~~~~-g~~v~i~k~~~d~~~~--~~~i-~~~lg~~~~~------------------   59 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQRAYNYEER-GMKVLVFKPAIDDRYG--EGKV-VSRIGLSREA------------------   59 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHHHHHc-CCeEEEEecccccccc--CCcE-ecCCCCcccc------------------
Confidence            7899999999999999999999998875 999999943  33211  1111 1111221100                  


Q ss_pred             HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEE
Q 009230          375 KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHV  454 (539)
Q Consensus       375 ~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~v  454 (539)
                              +.+       ...+++...+..  ...++++||||... ++.       + +   ++ ..|-+.++..+++|
T Consensus        60 --------~~~-------~~~~~~~~~~~~--~~~~~dvviIDEaq-~l~-------~-~---~v-~~l~~~l~~~g~~v  109 (190)
T PRK04296         60 --------IPV-------SSDTDIFELIEE--EGEKIDCVLIDEAQ-FLD-------K-E---QV-VQLAEVLDDLGIPV  109 (190)
T ss_pred             --------eEe-------CChHHHHHHHHh--hCCCCCEEEEEccc-cCC-------H-H---HH-HHHHHHHHHcCCeE
Confidence                    001       123445544443  34568999999663 221       1 1   12 33445556899999


Q ss_pred             EEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          455 WFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       455 i~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      +++.....-.+        .-+.++..+...||.|+.|...-
T Consensus       110 i~tgl~~~~~~--------~~f~~~~~L~~~aD~V~~l~~vC  143 (190)
T PRK04296        110 ICYGLDTDFRG--------EPFEGSPYLLALADKVTELKAIC  143 (190)
T ss_pred             EEEecCccccc--------CcCchHHHHHHhcCeEEEeeEEc
Confidence            99877433221        11335567888999999998754

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=98.54  E-value=8.5e-07  Score=84.21  Aligned_cols=174  Identities=19%  Similarity=0.158  Sum_probs=99.6

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHH--HHhhCCCc-------
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---ENKVREHARKLL--EKHIKKPF-------  354 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---E~~~~~~~~r~~--~~~~~~~~-------  354 (539)
                      |+.+.- +++|+++.|.||.|+||||++..++.-..-. ...|.+-.-   +++..++++++.  .+....++       
T Consensus        18 l~~ls~~i~~G~i~~iiGpNG~GKSTLLk~l~g~l~p~-~G~V~l~g~~i~~~~~kelAk~ia~vpQ~~~~~~~~tV~d~   96 (258)
T COG1120          18 LDDLSFSIPKGEITGILGPNGSGKSTLLKCLAGLLKPK-SGEVLLDGKDIASLSPKELAKKLAYVPQSPSAPFGLTVYEL   96 (258)
T ss_pred             EecceEEecCCcEEEEECCCCCCHHHHHHHHhccCCCC-CCEEEECCCchhhcCHHHHhhhEEEeccCCCCCCCcEEeeh
Confidence            444444 8999999999999999999998877554432 334443321   255666666541  11111110       


Q ss_pred             ---cccccCCCCCCCCHHHHHHHHHHh--------hccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccc
Q 009230          355 ---FEANYGGSAERMTVEEFEQGKAWL--------SNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELD  423 (539)
Q Consensus       355 ---~~i~~~~~~~~l~~~~~~~~~~~l--------~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~  423 (539)
                         .+..+-+.....+.++.+.+.+.+        .++.+-     +-+..-.+....++.++  .+++++++|.=+.- 
T Consensus        97 V~~GR~p~~~~~~~~~~~D~~~v~~aL~~~~~~~la~r~~~-----~LSGGerQrv~iArALa--Q~~~iLLLDEPTs~-  168 (258)
T COG1120          97 VLLGRYPHLGLFGRPSKEDEEIVEEALELLGLEHLADRPVD-----ELSGGERQRVLIARALA--QETPILLLDEPTSH-  168 (258)
T ss_pred             HhhcCCcccccccCCCHhHHHHHHHHHHHhCcHHHhcCccc-----ccChhHHHHHHHHHHHh--cCCCEEEeCCCccc-
Confidence               111111122345666554443322        222211     11112222333333333  47899999933322 


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          424 HQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                            .+ -..+-++++-+++++++.|.+||++.| ..-                   -...||.+++|...+
T Consensus       169 ------LD-i~~Q~evl~ll~~l~~~~~~tvv~vlHDlN~-------------------A~ryad~~i~lk~G~  216 (258)
T COG1120         169 ------LD-IAHQIEVLELLRDLNREKGLTVVMVLHDLNL-------------------AARYADHLILLKDGK  216 (258)
T ss_pred             ------cC-HHHHHHHHHHHHHHHHhcCCEEEEEecCHHH-------------------HHHhCCEEEEEECCe
Confidence                  22 234568999999999999999999999 321                   236899999998654

>PF08275 Toprim_N: DNA primase catalytic core, N-terminal domain; InterPro: IPR013264 This is the N-terminal, catalytic core domain of DNA primases

Probab=98.44  E-value=1.5e-07  Score=80.51  Aligned_cols=71  Identities=24%  Similarity=0.416  Sum_probs=49.3

Q ss_pred             HHHHHHHHhcCCCHHHHHHcCcccccCC-----------------------------------ceeEEEEeEe-eCCEEE
Q 009230           50 NELRAYFAERLISAETLRRNRVMQKRHG-----------------------------------HEVVIAFPYW-RNGKLV   93 (539)
Q Consensus        50 ~~~~~Yl~~Rgi~~~~~~~~~~~~~~~~-----------------------------------~~~~i~fP~~-~~G~~~   93 (539)
                      .++++||.+|||++++++.|++++...+                                   -.++|+||+. ..|+||
T Consensus        12 ~~a~~YL~~Rgl~~e~i~~F~lGyap~~~~~l~~~l~~~~~~~~~l~~~GL~~~~~~~~~~d~F~~RiifPI~d~~G~vv   91 (128)
T PF08275_consen   12 KEALEYLKKRGLSDETIKKFQLGYAPGNWDSLLEYLKKKGFSLEELLEAGLIRKNENGGYYDFFRGRIIFPIRDERGRVV   91 (128)
T ss_dssp             HHHHHHHHHTT--HHHHHHTT-EEE-SCSCHHHHHHCCCCHHHHHHCCTTCEECCTTTEEEETTTTEEEEEEE-TTS-EE
T ss_pred             HHHHHHHHHcCCCHHHHHHhCCCcccCcHHHHHHHHHhccccHHHHHHCCCcEEcCCCCcccccCCeEEEEEEcCCCCEE
Confidence            4589999999999999999988543321                                   1479999988 889999


Q ss_pred             EEEeecC----CCcccccC-----CCCCcccccccc
Q 009230           94 NCKYRDF----NKKFWQEK-----DTEKVFYGLDDI  120 (539)
Q Consensus        94 ~~~~R~~----~~~~~~~~-----~~~~~l~g~~~~  120 (539)
                      ++.+|.+    .+||.+++     .++..|||++.+
T Consensus        92 gF~gR~l~~~~~pKYlNs~et~if~K~~~Lyg~~~A  127 (128)
T PF08275_consen   92 GFGGRRLDDENPPKYLNSPETPIFKKSRILYGLDQA  127 (128)
T ss_dssp             EEEEEESSSSSS-SEEE---BTTB-GGG-EETHHHH
T ss_pred             EEecccCCCCCCCceECCCCCccccCCceecCcccc
Confidence            9999999    36888865     456778887653

DNA primase (2.7.7 from EC) is a nucleotidyltransferase which synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division []. ; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A 2AU3_A.

>KOG1433 consensus DNA repair protein RAD51/RHP55 [Replication, recombination and repair]

Probab=98.42  E-value=3.5e-06  Score=82.65  Aligned_cols=165  Identities=19%  Similarity=0.221  Sum_probs=97.7

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      ...--++||...||++++  +..|+++.|.|+||+|||.|++.++... ..-...++|+..|.. .++ .|+.......-
T Consensus        88 ~~~~~l~Tg~~~lD~lL~gGi~~g~~TEi~G~p~~GKtQlc~~~~v~~-~gge~~~l~IDs~s~-~~~-~~~~~ia~~~~  164 (326)
T KOG1433|consen   88 SELGFLSTGSKALDKLLGGGIETGSLTELVGPPGSGKTQLCHTLAVTC-GGGEGKVLYIDTEST-FRL-ERLTEIAGRSG  164 (326)
T ss_pred             ccceeeccchhhhhHhhccCcccCceeEEecCCCccHHHHHHHHHHhc-cCCcceEEEEecchh-ccc-chhhhhhhhhh
Confidence            444568999999999996  9999999999999999999998777654 222578999999974 211 12211110000


Q ss_pred             ccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCC---
Q 009230          354 FFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQ---  430 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~---  430 (539)
                                  +...+   ..+.+.-.-. +.+  +.  .+. ....+.....+....++++|+...+....-.+.   
T Consensus       165 ------------~~~~~---~~~~l~~~~~-~~~--~~--~l~-~~~~a~~~~~~~~~~l~~vds~ta~~~~~~~g~~~~  223 (326)
T KOG1433|consen  165 ------------LRGRD---TLSNLMLARA-YNL--DH--QLQ-LIQEAEIMINQSRVKLLIVDSATALYRTTFKGRGEL  223 (326)
T ss_pred             ------------hhhHH---HHHHHHHHHH-Hhh--HH--HHH-HHHHHHHHhhccceeEEEecccccccccccccccch
Confidence                        00000   0001100000 000  00  011 111122223334578999999988875432221   


Q ss_pred             -CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCC
Q 009230          431 -TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLH  464 (539)
Q Consensus       431 -~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~  464 (539)
                       ....-+...++.|++++++++++||+..| .+..+
T Consensus       224 ~a~~~~~~~~~~~l~~la~~~g~~vvitn~v~~~~d  259 (326)
T KOG1433|consen  224 SARQMLLAKFLRSLKKLADEFGVAVVITNQVTAQVD  259 (326)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCceEEEecccccccc
Confidence             11223456889999999999999999988 54443

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=98.32  E-value=3.5e-06  Score=75.83  Aligned_cols=43  Identities=26%  Similarity=0.390  Sum_probs=33.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH-HHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV-REHARKL  345 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~-~~~~~r~  345 (539)
                      +++|.|++|+|||+|+.+++..    .+.+++|++.+.+. .++..|+
T Consensus         1 ~~li~G~~~sGKS~~a~~~~~~----~~~~~~y~at~~~~d~em~~rI   44 (169)
T cd00544           1 IILVTGGARSGKSRFAERLAAE----LGGPVTYIATAEAFDDEMAERI   44 (169)
T ss_pred             CEEEECCCCCCHHHHHHHHHHh----cCCCeEEEEccCcCCHHHHHHH
Confidence            4789999999999999999865    37899999888663 3344444

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.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.30  E-value=4.2e-06  Score=72.15  Aligned_cols=117  Identities=24%  Similarity=0.339  Sum_probs=77.5

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhc----CCeEEEEeCC--CCHHHHHHHHHHHhhCCCccccccCCCCCCCCHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHA----GWKFVLCSME--NKVREHARKLLEKHIKKPFFEANYGGSAERMTVE  369 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~----g~~vl~~s~E--~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~  369 (539)
                      .+.+++|.|+||+|||+++.+++.......    ..+++++.+.  .+...+...+... .+.+.               
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~-l~~~~---------------   66 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEA-LGLPL---------------   66 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHH-HT-SS---------------
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHH-hCccc---------------
Confidence            457899999999999999999998876521    5677777654  2234444444322 11110               


Q ss_pred             HHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009230          370 EFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQH  449 (539)
Q Consensus       370 ~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~  449 (539)
                                          ....+.+++.+.+.....+.+..+||||.+..+.  .          ..++..|+.++.+
T Consensus        67 --------------------~~~~~~~~l~~~~~~~l~~~~~~~lviDe~~~l~--~----------~~~l~~l~~l~~~  114 (131)
T PF13401_consen   67 --------------------KSRQTSDELRSLLIDALDRRRVVLLVIDEADHLF--S----------DEFLEFLRSLLNE  114 (131)
T ss_dssp             --------------------SSTS-HHHHHHHHHHHHHHCTEEEEEEETTHHHH--T----------HHHHHHHHHHTCS
T ss_pred             --------------------cccCCHHHHHHHHHHHHHhcCCeEEEEeChHhcC--C----------HHHHHHHHHHHhC
Confidence                                1123566777777777777777899999777653  0          4677888888889


Q ss_pred             hCcEEEEEecC
Q 009230          450 HACHVWFVAHP  460 (539)
Q Consensus       450 ~~i~vi~~~q~  460 (539)
                      .++++|++.++
T Consensus       115 ~~~~vvl~G~~  125 (131)
T PF13401_consen  115 SNIKVVLVGTP  125 (131)
T ss_dssp             CBEEEEEEESS
T ss_pred             CCCeEEEEECh
Confidence            99999999884

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=98.29  E-value=2.8e-05  Score=67.72  Aligned_cols=176  Identities=16%  Similarity=0.179  Sum_probs=97.9

Q ss_pred             cCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC----CCHHHHHHHHHHHhhCCCc---
Q 009230          283 TGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME----NKVREHARKLLEKHIKKPF---  354 (539)
Q Consensus       283 tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E----~~~~~~~~r~~~~~~~~~~---  354 (539)
                      ++-+-||.+.- +++||.+.|+||+|+|||||+.++|.-+.-  .-.+++|-.|    ..++....+.... ...+-   
T Consensus        14 ~~a~il~~isl~v~~Ge~iaitGPSG~GKStllk~va~Lisp--~~G~l~f~Ge~vs~~~pea~Rq~VsY~-~Q~paLfg   90 (223)
T COG4619          14 GDAKILNNISLSVRAGEFIAITGPSGCGKSTLLKIVASLISP--TSGTLLFEGEDVSTLKPEAYRQQVSYC-AQTPALFG   90 (223)
T ss_pred             CCCeeecceeeeecCCceEEEeCCCCccHHHHHHHHHhccCC--CCceEEEcCccccccChHHHHHHHHHH-HcCccccc
Confidence            34455665554 999999999999999999999998865554  4556777776    4466666665322 22210   


Q ss_pred             ----------cccccCCCCCCCCHHHHHHHHHHhhccceeE-eec-CCCCCCHHHHHHHHHHHHHHcCCcEEEEcccccc
Q 009230          355 ----------FEANYGGSAERMTVEEFEQGKAWLSNTFSLI-RCE-NDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNEL  422 (539)
Q Consensus       355 ----------~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i-~~~-~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l  422 (539)
                                ..++.    .+.+..........+. .+.++ ... .+-+..-.+.++.++.+  ++.++++.+|..+..
T Consensus        91 ~tVeDNlifP~~~r~----rr~dr~aa~~llar~~-l~~~~L~k~it~lSGGE~QriAliR~L--q~~P~ILLLDE~TsA  163 (223)
T COG4619          91 DTVEDNLIFPWQIRN----RRPDRAAALDLLARFA-LPDSILTKNITELSGGEKQRIALIRNL--QFMPKILLLDEITSA  163 (223)
T ss_pred             cchhhccccchHHhc----cCCChHHHHHHHHHcC-CchhhhcchhhhccchHHHHHHHHHHh--hcCCceEEecCchhh
Confidence                      01111    1222222222111111 11111 000 01111223455555554  478999999977665


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          423 DHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       423 ~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      +..     +....++++   +..+.++-++.|+-++|....                  -.++||.+|.+..
T Consensus       164 LD~-----~nkr~ie~m---i~~~v~~q~vAv~WiTHd~dq------------------a~rha~k~itl~~  209 (223)
T COG4619         164 LDE-----SNKRNIEEM---IHRYVREQNVAVLWITHDKDQ------------------AIRHADKVITLQP  209 (223)
T ss_pred             cCh-----hhHHHHHHH---HHHHhhhhceEEEEEecChHH------------------HhhhhheEEEecc
Confidence            532     222344444   344455889999999994322                  1357788887764

>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=98.27  E-value=9.9e-06  Score=72.38  Aligned_cols=155  Identities=18%  Similarity=0.197  Sum_probs=88.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC---HHHHHHHHHHHhhC---C--------
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK---VREHARKLLEKHIK---K--------  352 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~---~~~~~~r~~~~~~~---~--------  352 (539)
                      +|++.- +++|.+|-|.||.|+||||++.-++.-+... ...|.+=..|++   ..++++++ +.+-.   +        
T Consensus        17 l~~isl~i~~g~iTs~IGPNGAGKSTLLS~~sRL~~~d-~G~i~i~g~~~~~~~s~~LAk~l-SILkQ~N~i~~rlTV~d   94 (252)
T COG4604          17 LDDVSLDIPKGGITSIIGPNGAGKSTLLSMMSRLLKKD-SGEITIDGLELTSTPSKELAKKL-SILKQENHINSRLTVRD   94 (252)
T ss_pred             eccceeeecCCceeEEECCCCccHHHHHHHHHHhcccc-CceEEEeeeecccCChHHHHHHH-HHHHhhchhhheeEHHH
Confidence            444444 9999999999999999999988776555443 456666666654   34555554 22111   1        


Q ss_pred             --CccccccCCCCCCCCHHHHHHHHHHhhc---c---ceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcccccccc
Q 009230          353 --PFFEANYGGSAERMTVEEFEQGKAWLSN---T---FSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDH  424 (539)
Q Consensus       353 --~~~~i~~~~~~~~l~~~~~~~~~~~l~~---~---~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~  424 (539)
                        .+.++.+  +.++++.+++..+.+.+.-   .   --|+. +-.+.......+    .++...+.+.|++|.=+.   
T Consensus        95 Lv~FGRfPY--SqGRlt~eD~~~I~~aieyl~L~~l~dryLd-~LSGGQrQRAfI----AMVlaQdTdyvlLDEPLN---  164 (252)
T COG4604          95 LVGFGRFPY--SQGRLTKEDRRIINEAIEYLHLEDLSDRYLD-ELSGGQRQRAFI----AMVLAQDTDYVLLDEPLN---  164 (252)
T ss_pred             HhhcCCCcc--cCCCCchHHHHHHHHHHHHhcccchHHHhHH-hcccchhhhhhh----heeeeccCcEEEecCccc---
Confidence              1222222  2457888876654433321   0   01110 001111111111    122335678999982211   


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          425 QRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       425 ~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                          ..+ -..--++|+.|+++|.++|-+|++|-|
T Consensus       165 ----NLD-mkHsv~iMk~Lrrla~el~KtiviVlH  194 (252)
T COG4604         165 ----NLD-MKHSVQIMKILRRLADELGKTIVVVLH  194 (252)
T ss_pred             ----ccc-hHHHHHHHHHHHHHHHHhCCeEEEEEe
Confidence                111 122347999999999999999999999

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=98.25  E-value=5.6e-06  Score=78.30  Aligned_cols=167  Identities=17%  Similarity=0.181  Sum_probs=92.0

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC---------------CeEEEEeC----C----CCHHHH
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAG---------------WKFVLCSM----E----NKVREH  341 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g---------------~~vl~~s~----E----~~~~~~  341 (539)
                      +.|+++.- +.+|+++.|.||.|+|||||+.-++--+--..|               .++.|+.=    +    .+.+++
T Consensus        18 ~vl~~i~l~v~~G~~~~iiGPNGaGKSTLlK~iLGll~p~~G~i~~~g~~~~~~~~~~~IgYVPQ~~~~d~~fP~tV~d~   97 (254)
T COG1121          18 PVLEDISLSVEKGEITALIGPNGAGKSTLLKAILGLLKPSSGEIKIFGKPVRKRRKRLRIGYVPQKSSVDRSFPITVKDV   97 (254)
T ss_pred             eeeeccEEEEcCCcEEEEECCCCCCHHHHHHHHhCCCcCCcceEEEccccccccccCCeEEEcCcccccCCCCCcCHHHH
Confidence            35666655 999999999999999999998776532211111               24555421    1    122222


Q ss_pred             HHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhc--------cceeEeecCCCCCCHHHHHHHHHHHHHHcCCcE
Q 009230          342 ARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSN--------TFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRG  413 (539)
Q Consensus       342 ~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~--------~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~  413 (539)
                          +.+  |.    ....+....++.++.+++.+.|..        +.+--   =.+......+++  +.  -..++++
T Consensus        98 ----V~~--g~----~~~~g~~~~~~~~d~~~v~~aL~~Vgm~~~~~r~i~~---LSGGQ~QRV~lA--RA--L~~~p~l  160 (254)
T COG1121          98 ----VLL--GR----YGKKGWFRRLNKKDKEKVDEALERVGMEDLRDRQIGE---LSGGQKQRVLLA--RA--LAQNPDL  160 (254)
T ss_pred             ----HHc--cC----cccccccccccHHHHHHHHHHHHHcCchhhhCCcccc---cCcHHHHHHHHH--HH--hccCCCE
Confidence                211  11    011112234565665555444432        21110   011111112222  22  2357999


Q ss_pred             EEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEE
Q 009230          414 LVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIH  493 (539)
Q Consensus       414 vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~  493 (539)
                      +++|-=.+       +-+ ......+++-|+.+.++ |++|++++|.=.                  ...+.+|.|+.|.
T Consensus       161 llLDEP~~-------gvD-~~~~~~i~~lL~~l~~e-g~tIl~vtHDL~------------------~v~~~~D~vi~Ln  213 (254)
T COG1121         161 LLLDEPFT-------GVD-VAGQKEIYDLLKELRQE-GKTVLMVTHDLG------------------LVMAYFDRVICLN  213 (254)
T ss_pred             EEecCCcc-------cCC-HHHHHHHHHHHHHHHHC-CCEEEEEeCCcH------------------HhHhhCCEEEEEc
Confidence            99992221       112 23346788899999999 999999999311                  2456899999998


Q ss_pred             eCC
Q 009230          494 RNR  496 (539)
Q Consensus       494 r~~  496 (539)
                      +.-
T Consensus       214 ~~~  216 (254)
T COG1121         214 RHL  216 (254)
T ss_pred             Cee
Confidence            743

>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=98.22  E-value=3.9e-06  Score=80.17  Aligned_cols=144  Identities=20%  Similarity=0.184  Sum_probs=91.7

Q ss_pred             eEEEEeEeeCCEEEEEEeecC--CCcccccCCCCCcccccccc-CCCCcEEEEechhhHHHHHHhCCCceEEcCCCCCCC
Q 009230           80 VVIAFPYWRNGKLVNCKYRDF--NKKFWQEKDTEKVFYGLDDI-EGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSS  156 (539)
Q Consensus        80 ~~i~fP~~~~G~~~~~~~R~~--~~~~~~~~~~~~~l~g~~~~-~~~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~  156 (539)
                      ..++.+.+.+|++.+.++-..  .|+|..++..+...+.+... ....++||+||...++++.|+-...++ ....+.| 
T Consensus       160 ~slip~~d~~Gel~~lq~I~~dG~Krf~~Ggr~kg~f~p~~g~~~~aa~lvi~EGyATal~i~~~~ga~v~-aAi~agN-  237 (366)
T COG4643         160 GSLIPLRDADGELTGLQLIQPDGTKRFLKGGRVKGCFIPLGGLAGPAARLVIAEGYATALSISQATGAPVA-AAIDAGN-  237 (366)
T ss_pred             cceEEEEcCCCCEeeeEEEcCCccceeccCCcccceeeecCCCcccccceEEeechhHHHHHHHHhhhhHH-hhhhccc-
Confidence            356644669999999887655  68888766555444444322 235679999999999999998643222 2233333 


Q ss_pred             CCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCc-----cchHHHHHHHHHhcCCceEEEecCCCCCCCCCCChH
Q 009230          157 VSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDP-----PGQALAEELARRVGRERCWRVRWPKKNDVDHFKDAN  231 (539)
Q Consensus       157 ~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~-----~G~~~~~~~~~~l~~~~~~~~~~p~~~~~~~~kD~n  231 (539)
                           |.....+.+        ..+ +..+||||.|+|.     +|...+++.+......    +.+|..    ..-||+
T Consensus       238 -----ll~VA~al~--------~~~-Pda~iIIaAD~D~~~~nnpG~t~A~eaA~Avng~----~~lP~~----~~adwp  295 (366)
T COG4643         238 -----LLAVASALR--------KKF-PDAQIIIAADDDINTANNPGLTKAEEAAQAVNGT----VALPPF----GPADWP  295 (366)
T ss_pred             -----HHHHHHHHH--------HhC-CCcceEEEeccccccCCCcchHHHHHHHHhhCce----eecCCC----CCCcCc
Confidence                 111211111        112 3468999999997     7999999998877542    444521    226899


Q ss_pred             HHHHhcCcchHHHHHH
Q 009230          232 EVLMYLGPGALKEVVE  247 (539)
Q Consensus       232 d~l~~~g~~~~~~~~~  247 (539)
                      |+....+..+.+..+.
T Consensus       296 D~~tq~n~la~r~~~~  311 (366)
T COG4643         296 DGFTQFNDLATRCAFG  311 (366)
T ss_pred             chhhhcchhhhhhhhc
Confidence            9988876655555444

>PF13479 AAA_24: AAA domain

Probab=98.15  E-value=2.8e-05  Score=73.16  Aligned_cols=146  Identities=16%  Similarity=0.102  Sum_probs=81.6

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHh
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWL  378 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l  378 (539)
                      -++|.|+||+|||+|+..+         .+++|+++|-....+...-     +.+.-.                      
T Consensus         5 ~~lIyG~~G~GKTt~a~~~---------~k~l~id~E~g~~~~~~~~-----~~~~i~----------------------   48 (213)
T PF13479_consen    5 KILIYGPPGSGKTTLAASL---------PKPLFIDTENGSDSLKFLD-----DGDVIP----------------------   48 (213)
T ss_pred             EEEEECCCCCCHHHHHHhC---------CCeEEEEeCCCccchhhhc-----CCCeeC----------------------
Confidence            5789999999999998765         5889999998744321000     111100                      


Q ss_pred             hccceeEeecCCCCCCHHHHHHHHHHHHH-HcCCcEEEEcccccccc-------------CC--C--CCCCHHHHHH-HH
Q 009230          379 SNTFSLIRCENDSLPSIKWVLDLAKAAVL-RHGVRGLVIDPYNELDH-------------QR--P--VSQTETEYVS-QM  439 (539)
Q Consensus       379 ~~~~~~i~~~~~~~~~~~~i~~~i~~~~~-~~~~~~vvID~~~~l~~-------------~~--~--~~~~~~~~~~-~~  439 (539)
                            +       .+.+++.+.+..+.. ..+.+.||||++..+..             ..  +  .....+..+. .+
T Consensus        49 ------i-------~s~~~~~~~~~~l~~~~~~y~tiVIDsis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~  115 (213)
T PF13479_consen   49 ------I-------TSWEDFLEALDELEEDEADYDTIVIDSISWLEDMCLEYICRQNKKKIKRSGDPDYGKGYGELQQEF  115 (213)
T ss_pred             ------c-------CCHHHHHHHHHHHHhccCCCCEEEEECHHHHHHHHHHHHhhhhcccccccCCCcccchHHHHHHHH
Confidence                  0       034444444433322 34677777777766511             00  0  0123344443 34


Q ss_pred             HHHHHHHHHHhCcEEEEEec-CCCCCCCCC----CCCCcccccccccchhccceEEEEEe
Q 009230          440 LTMVKRFAQHHACHVWFVAH-PRQLHNWVG----EPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       440 ~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~----~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      .+.++.+....+++||+++| -.......+    -.|.+.. +-...+...+|.|.-+..
T Consensus       116 ~~~i~~l~~~~~~~VI~tah~~~~~~~~~~~~~~~~~~l~~-k~~~~l~~~~D~V~~l~~  174 (213)
T PF13479_consen  116 MRFIDKLLNALGKNVIFTAHAKEEEDEDGGKYTRYKPKLGK-KVRNELPGWFDVVGRLRV  174 (213)
T ss_pred             HHHHHHHHHHCCCcEEEEEEEEEEEcCCCCceeEEeeccCh-hHHhhhhecccEEEEEEE
Confidence            55555566679999999999 322221111    1233322 334668889999976664

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=98.11  E-value=3.5e-05  Score=76.07  Aligned_cols=176  Identities=18%  Similarity=0.181  Sum_probs=95.2

Q ss_pred             chhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH--HHHHHHHHHHhhCCCccccccCC
Q 009230          285 WRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV--REHARKLLEKHIKKPFFEANYGG  361 (539)
Q Consensus       285 ~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~--~~~~~r~~~~~~~~~~~~i~~~~  361 (539)
                      ...|+.+-- +.+|+++.|.|++|+||||++.-++--.-- ....+.++..+...  .++..++ +....-+.       
T Consensus        18 ~~~l~~vs~~i~~Gei~gllG~NGAGKTTllk~l~gl~~p-~~G~i~i~G~~~~~~~~~~~~~i-gy~~~~~~-------   88 (293)
T COG1131          18 KTALDGVSFEVEPGEIFGLLGPNGAGKTTLLKILAGLLKP-TSGEILVLGYDVVKEPAKVRRRI-GYVPQEPS-------   88 (293)
T ss_pred             CEEEeceeEEEcCCeEEEEECCCCCCHHHHHHHHhCCcCC-CceEEEEcCEeCccCHHHHHhhe-EEEccCCC-------
Confidence            345666666 999999999999999999997766644322 34566655544433  2233232 11111110       


Q ss_pred             CCCCCCHHHHHHHHHHhh---------------ccceeEe--ecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcccccccc
Q 009230          362 SAERMTVEEFEQGKAWLS---------------NTFSLIR--CENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDH  424 (539)
Q Consensus       362 ~~~~l~~~~~~~~~~~l~---------------~~~~~i~--~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~  424 (539)
                      ..+.++..|.-+....+.               +.+-+-.  .......+...-....-..+--++|+++|+|.=     
T Consensus        89 ~~~~lT~~e~l~~~~~l~~~~~~~~~~~~~~~l~~~~L~~~~~~~~~~lS~G~kqrl~ia~aL~~~P~lliLDEP-----  163 (293)
T COG1131          89 LYPELTVRENLEFFARLYGLSKEEAEERIEELLELFGLEDKANKKVRTLSGGMKQRLSIALALLHDPELLILDEP-----  163 (293)
T ss_pred             CCccccHHHHHHHHHHHhCCChhHHHHHHHHHHHHcCCchhhCcchhhcCHHHHHHHHHHHHHhcCCCEEEECCC-----
Confidence            112344443222211111               1000000  000011122111111112233467999999922     


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          425 QRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       425 ~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                        ..+.+. ....++.+.|+.++++.+.+|++.+| ..                   .+++.||.|++|++-+
T Consensus       164 --t~GLDp-~~~~~~~~~l~~l~~~g~~tvlissH~l~-------------------e~~~~~d~v~il~~G~  214 (293)
T COG1131         164 --TSGLDP-ESRREIWELLRELAKEGGVTILLSTHILE-------------------EAEELCDRVIILNDGK  214 (293)
T ss_pred             --CcCCCH-HHHHHHHHHHHHHHhCCCcEEEEeCCcHH-------------------HHHHhCCEEEEEeCCE
Confidence              123333 34567899999999999999999999 42                   2567799999998754

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.11  E-value=3.7e-05  Score=74.40  Aligned_cols=119  Identities=16%  Similarity=0.122  Sum_probs=76.7

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHh-----cCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEH-----AGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG  374 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~-----~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~  374 (539)
                      .+|.|+||.|||+++..+...-...     ...||+++  +|++.--..++...                         +
T Consensus        64 lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~v--q~P~~p~~~~~Y~~-------------------------I  116 (302)
T PF05621_consen   64 LLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYV--QMPPEPDERRFYSA-------------------------I  116 (302)
T ss_pred             eEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEE--ecCCCCChHHHHHH-------------------------H
Confidence            6799999999999987766432111     01356555  33333222222211                         1


Q ss_pred             HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEE
Q 009230          375 KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHV  454 (539)
Q Consensus       375 ~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~v  454 (539)
                      .+.+. .+  +    ....+...+...+..+.+..+++++|||.+..++.+.      ...+.+++..||.|+.++++|+
T Consensus       117 L~~lg-aP--~----~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs------~~~qr~~Ln~LK~L~NeL~ipi  183 (302)
T PF05621_consen  117 LEALG-AP--Y----RPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGS------YRKQREFLNALKFLGNELQIPI  183 (302)
T ss_pred             HHHhC-cc--c----CCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhccc------HHHHHHHHHHHHHHhhccCCCe
Confidence            11111 01  1    1333556667777778888999999999999887653      2346789999999999999999


Q ss_pred             EEEe
Q 009230          455 WFVA  458 (539)
Q Consensus       455 i~~~  458 (539)
                      |++-
T Consensus       184 V~vG  187 (302)
T PF05621_consen  184 VGVG  187 (302)
T ss_pred             EEec
Confidence            9874

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=98.11  E-value=5e-05  Score=69.15  Aligned_cols=176  Identities=16%  Similarity=0.155  Sum_probs=92.0

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCcccc---ccC-
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEA---NYG-  360 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i---~~~-  360 (539)
                      .-|+.+.- +.+|++++|.||||||||||+.-+  +.........+++..+......-.+.+....|+=++.+   .+- 
T Consensus        16 ~VLkgi~l~v~~Gevv~iiGpSGSGKSTlLRcl--N~LE~~~~G~I~i~g~~~~~~~~~~~~R~~vGmVFQ~fnLFPHlT   93 (240)
T COG1126          16 EVLKGISLSVEKGEVVVIIGPSGSGKSTLLRCL--NGLEEPDSGSITVDGEDVGDKKDILKLRRKVGMVFQQFNLFPHLT   93 (240)
T ss_pred             EEecCcceeEcCCCEEEEECCCCCCHHHHHHHH--HCCcCCCCceEEECCEeccchhhHHHHHHhcCeecccccccccch
Confidence            33444443 999999999999999999998743  43333233445555532211101111222233322211   000 


Q ss_pred             ---------CCCCCCCHHHHH-HHHHHhhc-----cceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccC
Q 009230          361 ---------GSAERMTVEEFE-QGKAWLSN-----TFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQ  425 (539)
Q Consensus       361 ---------~~~~~l~~~~~~-~~~~~l~~-----~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~  425 (539)
                               .....++.++.+ .+.+.|..     +...+  ...-+....+=.+.++.++  .+|+++..|--++.+  
T Consensus        94 vleNv~lap~~v~~~~k~eA~~~A~~lL~~VGL~~ka~~y--P~qLSGGQqQRVAIARALa--M~P~vmLFDEPTSAL--  167 (240)
T COG1126          94 VLENVTLAPVKVKKLSKAEAREKALELLEKVGLADKADAY--PAQLSGGQQQRVAIARALA--MDPKVMLFDEPTSAL--  167 (240)
T ss_pred             HHHHHHhhhHHHcCCCHHHHHHHHHHHHHHcCchhhhhhC--ccccCcHHHHHHHHHHHHc--CCCCEEeecCCcccC--
Confidence                     000123433332 23333322     11111  0001111223333444433  478999999444322  


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          426 RPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       426 ~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                            +.+.+.+++.-++.||+ .|.+.++++| -+=                   ....||.|+++..-
T Consensus       168 ------DPElv~EVL~vm~~LA~-eGmTMivVTHEM~F-------------------Ar~VadrviFmd~G  212 (240)
T COG1126         168 ------DPELVGEVLDVMKDLAE-EGMTMIIVTHEMGF-------------------AREVADRVIFMDQG  212 (240)
T ss_pred             ------CHHHHHHHHHHHHHHHH-cCCeEEEEechhHH-------------------HHHhhheEEEeeCC
Confidence                  23567889999999997 5699999999 321                   23588999999754

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=98.09  E-value=8.1e-05  Score=69.41  Aligned_cols=176  Identities=18%  Similarity=0.221  Sum_probs=89.4

Q ss_pred             chhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHHHHhhCCCccccccC
Q 009230          285 WRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLLEKHIKKPFFEANYG  360 (539)
Q Consensus       285 ~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~~~~i~~~  360 (539)
                      ...|+.+.- +.+||++.|.||||||||||+.-+. .+....+..|.+...+   ++..+. ..+-....|.=++...  
T Consensus        18 ~~~L~~v~l~i~~Ge~vaI~GpSGSGKSTLLniig-~ld~pt~G~v~i~g~d~~~l~~~~~-~~~R~~~iGfvFQ~~n--   93 (226)
T COG1136          18 VEALKDVNLEIEAGEFVAIVGPSGSGKSTLLNLLG-GLDKPTSGEVLINGKDLTKLSEKEL-AKLRRKKIGFVFQNFN--   93 (226)
T ss_pred             eEecccceEEEcCCCEEEEECCCCCCHHHHHHHHh-cccCCCCceEEECCEEcCcCCHHHH-HHHHHHhEEEECccCC--
Confidence            345555544 9999999999999999999966544 3333234455554423   333222 1111112222111100  


Q ss_pred             CCCCCCCHHH---------------HHHHHHHhhccc-e--eEeecCCCCCC--HHHHHHHHHHHHHHcCCcEEEEcccc
Q 009230          361 GSAERMTVEE---------------FEQGKAWLSNTF-S--LIRCENDSLPS--IKWVLDLAKAAVLRHGVRGLVIDPYN  420 (539)
Q Consensus       361 ~~~~~l~~~~---------------~~~~~~~l~~~~-~--~i~~~~~~~~~--~~~i~~~i~~~~~~~~~~~vvID~~~  420 (539)
                       -.+.++..|               ..+....+.+.+ +  ..........+  -.+=.+.++.++  .+|++|+-|-=+
T Consensus        94 -Ll~~ltv~ENv~lpl~~~~~~~~~~~~~~~~l~~~lgl~~~~~~~~p~eLSGGqqQRVAIARAL~--~~P~iilADEPT  170 (226)
T COG1136          94 -LLPDLTVLENVELPLLIAGKSAGRRKRAAEELLEVLGLEDRLLKKKPSELSGGQQQRVAIARALI--NNPKIILADEPT  170 (226)
T ss_pred             -CCCCCCHHHHHHhHHHHcCCChhHHHHHHHHHHHhcCChhhhccCCchhcCHHHHHHHHHHHHHh--cCCCeEEeeCcc
Confidence             011233222               111111111110 0  00000011111  122233333333  578999999222


Q ss_pred             ccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          421 ELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       421 ~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                              +.-+.+.-.+++.-|+.++++.|.+||+++|...                   +...||.+|.+..
T Consensus       171 --------gnLD~~t~~~V~~ll~~~~~~~g~tii~VTHd~~-------------------lA~~~dr~i~l~d  217 (226)
T COG1136         171 --------GNLDSKTAKEVLELLRELNKERGKTIIMVTHDPE-------------------LAKYADRVIELKD  217 (226)
T ss_pred             --------ccCChHHHHHHHHHHHHHHHhcCCEEEEEcCCHH-------------------HHHhCCEEEEEeC
Confidence                    2222344567999999999999999999999322                   3457888887763

>KOG2859 consensus DNA repair protein, member of the recA/RAD51 family [Replication, recombination and repair]

Probab=98.07  E-value=9.8e-05  Score=66.77  Aligned_cols=161  Identities=14%  Similarity=0.146  Sum_probs=94.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-----cCCeEEEEeCCCCH--HHHHHHHHHHhhCCCccccccCCCCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEH-----AGWKFVLCSMENKV--REHARKLLEKHIKKPFFEANYGGSAERM  366 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-----~g~~vl~~s~E~~~--~~~~~r~~~~~~~~~~~~i~~~~~~~~l  366 (539)
                      ...|+++-|.||.|+|||.++.|++.+....     .++.|+|+.++-.-  .++.+-+-..+...+..+..-.   .--
T Consensus        35 ~daG~~vEi~Gp~~sgKt~vL~ql~a~CilPk~~GGl~~~VLfidld~~fd~lrL~~~l~hrL~q~~~~e~~~~---~c~  111 (293)
T KOG2859|consen   35 ADAGTLVEISGPGNSGKTLVLQQLVAHCILPKKFGGLQWSVLFIDLDHKFDRLRLAKSLRHRLKQYSVGEVIAA---KCP  111 (293)
T ss_pred             cccCcEEEEeCCCCccHHHHHHHHHHHeecccccCCceeEEEEEeccccccHHHHHHHHHHHHHHhhhhhhhhh---cCC
Confidence            5579999999999999999999999988763     25789999988543  2332222111111112111100   122


Q ss_pred             CHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHH-cCCcEEEEccccccccCCC-CC----CCHHHHHHHHH
Q 009230          367 TVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLR-HGVRGLVIDPYNELDHQRP-VS----QTETEYVSQML  440 (539)
Q Consensus       367 ~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~-~~~~~vvID~~~~l~~~~~-~~----~~~~~~~~~~~  440 (539)
                      +++..+++...-..++.+++|.  .+..+-.-.-.++.++.. .++-++++|++...---+. +.    ......+..+.
T Consensus       112 te~~~eEi~~~Cm~Rf~~v~C~--~s~~ll~sL~~l~y~i~~~p~~cll~~DslsaFyW~Dr~~~le~~n~~~~~lr~~~  189 (293)
T KOG2859|consen  112 TEEQLEEIAGECMSRFRFVNCF--ASDDLLTSLIDLRYAIINDPGICLLAMDSLSAFYWLDRPKILEKRNSMYRHLRLLQ  189 (293)
T ss_pred             cHhHHHHHHHHHHhhEEEEEee--ccHHHHHHHHHHHHHHhcCCceeEEeecchhhheeecccchHhhhhhHHHHHHHHH
Confidence            3444456655555678888774  222221111223333333 3578999998876532211 11    11223456788


Q ss_pred             HHHHHHHHHhCcEEEEEec
Q 009230          441 TMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       441 ~~Lk~lA~~~~i~vi~~~q  459 (539)
                      +.|+++.+.+-+.++.+.+
T Consensus       190 q~LeKL~~d~~lv~~aT~~  208 (293)
T KOG2859|consen  190 QRLEKLCKDAILVGMATVE  208 (293)
T ss_pred             HHHHHHHhhheeeeeeehh
Confidence            9999999988887777776

>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=98.06  E-value=1.9e-05  Score=74.81  Aligned_cols=175  Identities=19%  Similarity=0.224  Sum_probs=92.4

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC----CHHHHHHHHHHHhhCCC-------
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN----KVREHARKLLEKHIKKP-------  353 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~----~~~~~~~r~~~~~~~~~-------  353 (539)
                      +.|+.+.- +.+|+.++|.|++|+||||++..++-=+-- ....|.+.....    +..++.++. .....-+       
T Consensus        18 ~~l~~v~~~i~~Ge~~~i~G~nGsGKSTL~~~l~GLl~p-~~G~v~~~g~~~~~~~~~~~~~~~v-G~VfQnpd~q~~~~   95 (235)
T COG1122          18 AALKDVSLEIEKGERVLLIGPNGSGKSTLLKLLNGLLKP-TSGEVLVDGLDTSSEKSLLELRQKV-GLVFQNPDDQLFGP   95 (235)
T ss_pred             eeeeeeEEEECCCCEEEEECCCCCCHHHHHHHHcCcCcC-CCCEEEECCeeccchhhHHHhhcce-EEEEECcccccccC
Confidence            34444444 999999999999999999998876533222 233443222222    223332222 1000000       


Q ss_pred             --ccccccCCCCCCCCHHHHHHHHH-Hhh--------c-cceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccc
Q 009230          354 --FFEANYGGSAERMTVEEFEQGKA-WLS--------N-TFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNE  421 (539)
Q Consensus       354 --~~~i~~~~~~~~l~~~~~~~~~~-~l~--------~-~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~  421 (539)
                        ..++.++-....++.+++.+..+ .+.        + .++..    .+..  .+..+.+-  +-..+|+++++|-=+.
T Consensus        96 tV~~evafg~~n~g~~~~e~~~rv~~~l~~vgl~~~~~r~p~~L----SGGq--kqRvaIA~--vLa~~P~iliLDEPta  167 (235)
T COG1122          96 TVEDEVAFGLENLGLPREEIEERVAEALELVGLEELLDRPPFNL----SGGQ--KQRVAIAG--VLAMGPEILLLDEPTA  167 (235)
T ss_pred             cHHHHHhhchhhcCCCHHHHHHHHHHHHHHcCchhhccCCcccc----CCcc--eeeHHhhH--HHHcCCCEEEEcCCCC
Confidence              01122221122345555443221 111        1 11111    1111  11122221  2235799999993332


Q ss_pred             cccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          422 LDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       422 l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      .       . +.....++++.|+++..+.+.+||+++|.-.                  .+...||.++.+...+
T Consensus       168 ~-------L-D~~~~~~l~~~l~~L~~~~~~tii~~tHd~~------------------~~~~~ad~v~vl~~G~  216 (235)
T COG1122         168 G-------L-DPKGRRELLELLKKLKEEGGKTIIIVTHDLE------------------LVLEYADRVVVLDDGK  216 (235)
T ss_pred             C-------C-CHHHHHHHHHHHHHHHhcCCCeEEEEeCcHH------------------HHHhhCCEEEEEECCE
Confidence            2       2 2345678999999999999999999999322                  1456899999997543

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=98.01  E-value=7.7e-05  Score=67.28  Aligned_cols=122  Identities=16%  Similarity=0.226  Sum_probs=67.7

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKA  376 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~  376 (539)
                      .+++|.|+||+|||+|+.+++..    .+.+++|++...+ .+++..|+.......                        
T Consensus         2 ~~ili~G~~~sGKS~~a~~l~~~----~~~~~~~iat~~~~~~e~~~ri~~h~~~R------------------------   53 (170)
T PRK05800          2 MLILVTGGARSGKSRFAERLAAQ----SGLQVLYIATAQPFDDEMAARIAHHRQRR------------------------   53 (170)
T ss_pred             CEEEEECCCCccHHHHHHHHHHH----cCCCcEeCcCCCCChHHHHHHHHHHHhcC------------------------
Confidence            46899999999999999988754    3667888877543 445555653322111                        


Q ss_pred             HhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEE
Q 009230          377 WLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWF  456 (539)
Q Consensus       377 ~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~  456 (539)
                        ...+..+    +...++..++   ...  ..+.++|+||++..+....-...+ .......+..|...-++.++++|+
T Consensus        54 --~~~w~t~----E~~~~l~~~i---~~~--~~~~~~VlID~Lt~~~~n~l~~~~-~~~~~~~l~~li~~L~~~~~tvVl  121 (170)
T PRK05800         54 --PAHWQTV----EEPLDLAELL---RAD--AAPGRCVLVDCLTTWVTNLLFEEG-EEAIAAEIDALLAALQQLPAKIIL  121 (170)
T ss_pred             --CCCCeEe----cccccHHHHH---Hhh--cCCCCEEEehhHHHHHHHHhcccc-hHHHHHHHHHHHHHHHcCCCCEEE
Confidence              0112222    2222333332   211  134679999998887542211011 012222333333333458899999


Q ss_pred             Eec
Q 009230          457 VAH  459 (539)
Q Consensus       457 ~~q  459 (539)
                      ++.
T Consensus       122 Vs~  124 (170)
T PRK05800        122 VTN  124 (170)
T ss_pred             EEc
Confidence            987

>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=98.00  E-value=0.00024  Score=64.43  Aligned_cols=38  Identities=18%  Similarity=0.344  Sum_probs=34.4

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      ++++.|+||+|||+++..++..++.. |.+|++++++.-
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~-g~~v~~i~~D~~   39 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKK-GKKVLLVAADTY   39 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-CCcEEEEEcCCC
Confidence            67899999999999999999998875 899999998864

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.

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=97.99  E-value=0.00027  Score=65.38  Aligned_cols=57  Identities=23%  Similarity=0.332  Sum_probs=41.6

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC---HHHHHHHHHHHhhCCCccc
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK---VREHARKLLEKHIKKPFFE  356 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~---~~~~~~r~~~~~~~~~~~~  356 (539)
                      .++++.|++|+||||.+..+|.....+ +.+|.++|++--   +.+-+ +.++...++++..
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~~~~~-~~~v~lis~D~~R~ga~eQL-~~~a~~l~vp~~~   61 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAARLKLK-GKKVALISADTYRIGAVEQL-KTYAEILGVPFYV   61 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEESTSSTHHHHHH-HHHHHHHTEEEEE
T ss_pred             EEEEEECCCCCchHhHHHHHHHHHhhc-cccceeecCCCCCccHHHHH-HHHHHHhccccch
Confidence            378999999999999999999999987 999999999844   22222 3345556666543

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 ....

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.98  E-value=7.9e-05  Score=74.56  Aligned_cols=42  Identities=10%  Similarity=0.108  Sum_probs=37.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      +.+|.+++|.|++|+||||++..++..+..+ |.+|.+++.+-
T Consensus       203 ~~~~~ii~lvGptGvGKTTt~akLA~~l~~~-g~~V~lItaDt  244 (407)
T PRK12726        203 LSNHRIISLIGQTGVGKTTTLVKLGWQLLKQ-NRTVGFITTDT  244 (407)
T ss_pred             ecCCeEEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEEeCCc
Confidence            5678999999999999999999999887665 99999999873

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.98  E-value=0.00015  Score=67.88  Aligned_cols=153  Identities=18%  Similarity=0.171  Sum_probs=82.7

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAW  377 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~  377 (539)
                      .+++|+|+||+||||++.+++        .++++++.+.+...+        .|.+...+                    
T Consensus        13 ~~~liyG~~G~GKtt~a~~~~--------~~~~~~~~d~~~~~l--------~g~~~~~v--------------------   56 (220)
T TIGR01618        13 NMYLIYGKPGTGKTSTIKYLP--------GKTLVLSFDMSSKVL--------IGDENVDI--------------------   56 (220)
T ss_pred             cEEEEECCCCCCHHHHHHhcC--------CCCEEEeccccchhc--------cCCCCCce--------------------
Confidence            579999999999999987652        367788888865533        11110000                    


Q ss_pred             hhccceeEeecCCCCCCHHHHHHHHHHHH-HHcCCcEEEEcccccccc------CC--CC---CCCHHHHH-HHHHHHHH
Q 009230          378 LSNTFSLIRCENDSLPSIKWVLDLAKAAV-LRHGVRGLVIDPYNELDH------QR--PV---SQTETEYV-SQMLTMVK  444 (539)
Q Consensus       378 l~~~~~~i~~~~~~~~~~~~i~~~i~~~~-~~~~~~~vvID~~~~l~~------~~--~~---~~~~~~~~-~~~~~~Lk  444 (539)
                             +..  +.....+.+.+.+..+. ...+++.||||++..+..      ..  ..   ....+..+ ..+++.|+
T Consensus        57 -------~~~--d~~~~~~~~~d~l~~~~~~~~~ydtVVIDsI~~l~~~~~~~~~r~~k~~~~~~~~yg~~~~~fl~~l~  127 (220)
T TIGR01618        57 -------ADH--DDMPPIQAMVEFYVMQNIQAVKYDNIVIDNISALQNLWLENIGRAAKNGQPELQHYQKLDLWFLDLLT  127 (220)
T ss_pred             -------eec--CCCCCHHHHHHHHHHHHhccccCCEEEEecHHHHHHHHHHHHhhhcCCCCcccccHHHHHHHHHHHHH
Confidence                   000  11222333333333221 124578888888877643      11  11   11123333 34666666


Q ss_pred             HHHHHhCcEEEEEec-C-CCCCCCCCCCCC--cccccc--cccchhccceEEEEEeCC
Q 009230          445 RFAQHHACHVWFVAH-P-RQLHNWVGEPPN--LYDISG--SAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       445 ~lA~~~~i~vi~~~q-~-r~~~~~~~~~~~--~~~l~g--s~~i~~~aD~vl~l~r~~  496 (539)
                      .|. .++++||+++| . +......+...+  ..+|++  ...+.-.+|.|.-+....
T Consensus       128 ~L~-~~g~nII~tAhe~~~~~~de~G~~~~r~~P~i~~K~~n~l~G~~DvV~rl~i~~  184 (220)
T TIGR01618       128 VLK-ESNKNIYATAWELTNQSSGESGQIYNRYQPDIREKVLNAFLGLTDVVGRIVLNG  184 (220)
T ss_pred             HHH-hCCCcEEEEEeeccccccCCCCCCcceechhhhhhHHHhhcccccEEEEEEEcc
Confidence            664 49999999999 3 322221122111  123443  123666889999887444

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.98  E-value=4.5e-05  Score=65.92  Aligned_cols=44  Identities=27%  Similarity=0.423  Sum_probs=36.0

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREH  341 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~  341 (539)
                      +..++|.|+||+|||+++..++..+... +..+++++.+......
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~-~~~~~~~~~~~~~~~~   45 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPP-GGGVIYIDGEDILEEV   45 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCC-CCCEEEECCEEccccC
Confidence            5689999999999999999998877653 4479999998766543

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.

>cd00188 TOPRIM Topoisomerase-primase domain

Probab=97.96  E-value=2.9e-05  Score=60.42  Aligned_cols=69  Identities=32%  Similarity=0.394  Sum_probs=47.0

Q ss_pred             CcEEEEechhhHHHHHHhCCC--ceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhcc-CCEEEEEecCCccchHH
Q 009230          124 SDIIIVEGEMDKLSMEEAGFL--NCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQ-ASRIILATDGDPPGQAL  200 (539)
Q Consensus       124 ~~v~i~EG~~Dalsl~~~g~~--~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~-~~~ivl~~DnD~~G~~~  200 (539)
                      +.++||||+.|++++.+.+..  .++++. |.....               + ...+..+.+ ..+|++++|+|.+|+..
T Consensus         1 ~~viivEg~~d~~~l~~~~~~~~~~~~~~-G~~~~~---------------~-~~~~~~~~~~~~~v~i~~D~D~~g~~~   63 (83)
T cd00188           1 KKLIIVEGPSDALALAQAGGYGGAVVALG-GHALNK---------------T-RELLKRLLGEAKEVIIATDADREGEAI   63 (83)
T ss_pred             CEEEEEecHHHHHHHHHHcCCCEEEEEEc-cEEcHH---------------H-HHHHHHHhcCCCEEEEEcCCChhHHHH
Confidence            368999999999999999874  455542 332200               0 011223333 48999999999999977


Q ss_pred             HHHHHHHhc
Q 009230          201 AEELARRVG  209 (539)
Q Consensus       201 ~~~~~~~l~  209 (539)
                      +..+.+.+.
T Consensus        64 ~~~~~~~~~   72 (83)
T cd00188          64 ALRLLELLK   72 (83)
T ss_pred             HHHHHHHHH
Confidence            777776664

This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=97.95  E-value=8.9e-06  Score=75.40  Aligned_cols=62  Identities=16%  Similarity=0.259  Sum_probs=48.5

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      ..+++++.|--+..+        +...+.+++.-|..+.+++|.+.++++|+-                  +.+++.||.
T Consensus       158 ~~PklLIlDEptSaL--------D~siQa~IlnlL~~l~~~~~lt~l~IsHdl------------------~~v~~~cdR  211 (252)
T COG1124         158 PEPKLLILDEPTSAL--------DVSVQAQILNLLLELKKERGLTYLFISHDL------------------ALVEHMCDR  211 (252)
T ss_pred             cCCCEEEecCchhhh--------cHHHHHHHHHHHHHHHHhcCceEEEEeCcH------------------HHHHHHhhh
Confidence            468999999444333        223467899999999999999999999942                  236789999


Q ss_pred             EEEEEeCC
Q 009230          489 GIVIHRNR  496 (539)
Q Consensus       489 vl~l~r~~  496 (539)
                      ++++.+..
T Consensus       212 i~Vm~~G~  219 (252)
T COG1124         212 IAVMDNGQ  219 (252)
T ss_pred             eeeeeCCe
Confidence            99998755

>PRK09544 znuC high-affinity zinc transporter ATPase; Reviewed

Probab=97.93  E-value=0.00014  Score=70.28  Aligned_cols=143  Identities=15%  Similarity=0.184  Sum_probs=71.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-------CeEEEEeCCCCHHH----HHHHHHHHhhCCCccccccCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAG-------WKFVLCSMENKVRE----HARKLLEKHIKKPFFEANYGGS  362 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-------~~vl~~s~E~~~~~----~~~r~~~~~~~~~~~~i~~~~~  362 (539)
                      +.+|+.+.|.|++|+|||||+.-++-...-..|       ..+.|+.-+.....    .....+.         +.    
T Consensus        27 i~~Ge~~~I~G~NGsGKSTLl~~i~Gl~~p~~G~i~~~~~~~i~~v~q~~~~~~~l~~~~~~~~~---------~~----   93 (251)
T PRK09544         27 LKPGKILTLLGPNGAGKSTLVRVVLGLVAPDEGVIKRNGKLRIGYVPQKLYLDTTLPLTVNRFLR---------LR----   93 (251)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCCCCCceEEEECCccCEEEeccccccccccChhHHHHHh---------cc----
Confidence            899999999999999999998877643221112       13444432211000    0001110         00    


Q ss_pred             CCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHH
Q 009230          363 AERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTM  442 (539)
Q Consensus       363 ~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~  442 (539)
                       .....+++..+.+.+.-. .+.. ......+-.+....+-..+...+++++++|.-+.       +.+ ......+.+.
T Consensus        94 -~~~~~~~~~~~l~~~gl~-~~~~-~~~~~LSgGq~qrv~laral~~~p~lllLDEPt~-------~LD-~~~~~~l~~~  162 (251)
T PRK09544         94 -PGTKKEDILPALKRVQAG-HLID-APMQKLSGGETQRVLLARALLNRPQLLVLDEPTQ-------GVD-VNGQVALYDL  162 (251)
T ss_pred             -ccccHHHHHHHHHHcCCh-HHHh-CChhhCCHHHHHHHHHHHHHhcCCCEEEEeCCCc-------CCC-HHHHHHHHHH
Confidence             012223333332222100 0000 0011222232222111222335789999993332       222 2345567788


Q ss_pred             HHHHHHHhCcEEEEEecC
Q 009230          443 VKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       443 Lk~lA~~~~i~vi~~~q~  460 (539)
                      |+.++++.+.+||+++|.
T Consensus       163 L~~~~~~~g~tiiivsH~  180 (251)
T PRK09544        163 IDQLRRELDCAVLMVSHD  180 (251)
T ss_pred             HHHHHHhcCCEEEEEecC
Confidence            888888889999999994

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.92  E-value=0.00028  Score=71.32  Aligned_cols=64  Identities=17%  Similarity=0.211  Sum_probs=48.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-CeEEEEeCCCC---HHHHHHHHHHHhhCCCccccc
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAG-WKFVLCSMENK---VREHARKLLEKHIKKPFFEAN  358 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-~~vl~~s~E~~---~~~~~~r~~~~~~~~~~~~i~  358 (539)
                      +..|.+++|.|++|+||||++..++...+..+| .+|.+++.+.-   ..+.+ +.++...|++...+.
T Consensus       134 ~~~g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL-~~~a~~~gv~~~~~~  201 (374)
T PRK14722        134 MERGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQL-RIFGKILGVPVHAVK  201 (374)
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHH-HHHHHHcCCceEecC
Confidence            778999999999999999999999998776556 68999998863   22222 334556677766543

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=97.92  E-value=0.00032  Score=66.04  Aligned_cols=60  Identities=17%  Similarity=0.199  Sum_probs=42.3

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+++.|++++++.+.+||+++|...                  .+.+.+|.
T Consensus       147 ~~p~llllDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tvi~~sH~~~------------------~~~~~~d~  200 (213)
T cd03301         147 REPKVFLMDEPLS-------NLD-AKLRVQMRAELKRLQQRLGTTTIYVTHDQV------------------EAMTMADR  200 (213)
T ss_pred             cCCCEEEEcCCcc-------cCC-HHHHHHHHHHHHHHHHHcCCEEEEEeCCHH------------------HHHHhcCe
Confidence            5789999993322       222 344567888888898888999999999322                  13457888


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|.+
T Consensus       201 i~~l~~  206 (213)
T cd03301         201 IAVMND  206 (213)
T ss_pred             EEEEEC
Confidence            888863

ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=97.91  E-value=7.4e-05  Score=71.83  Aligned_cols=60  Identities=13%  Similarity=0.108  Sum_probs=42.7

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|...                  .+...||.
T Consensus       161 ~~p~llllDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tii~~tH~~~------------------~~~~~~d~  214 (241)
T cd03256         161 QQPKLILADEPVA-------SLD-PASSRQVMDLLKRINREEGITVIVSLHQVD------------------LAREYADR  214 (241)
T ss_pred             cCCCEEEEeCccc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHhCCE
Confidence            5789999993222       222 334567888888888888999999999422                  14467899


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|..
T Consensus       215 v~~l~~  220 (241)
T cd03256         215 IVGLKD  220 (241)
T ss_pred             EEEEEC
Confidence            998864

Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03293 ABC_NrtD_SsuB_transporters NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively

Probab=97.90  E-value=0.00039  Score=65.82  Aligned_cols=60  Identities=13%  Similarity=0.057  Sum_probs=41.8

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|++++++.+.+||+++|...                  .+...||.
T Consensus       148 ~~p~lllLDEPt~-------~LD-~~~~~~~~~~l~~~~~~~~~tiii~sH~~~------------------~~~~~~d~  201 (220)
T cd03293         148 VDPDVLLLDEPFS-------ALD-ALTREQLQEELLDIWRETGKTVLLVTHDID------------------EAVFLADR  201 (220)
T ss_pred             cCCCEEEECCCCC-------CCC-HHHHHHHHHHHHHHHHHcCCEEEEEecCHH------------------HHHHhCCE
Confidence            5789999993222       222 334567788888888888999999999322                  14467899


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|.+
T Consensus       202 i~~l~~  207 (220)
T cd03293         202 VVVLSA  207 (220)
T ss_pred             EEEEEC
Confidence            888863

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK13634 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.89  E-value=0.00016  Score=71.58  Aligned_cols=61  Identities=16%  Similarity=0.221  Sum_probs=43.4

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|.-.                  .+...||.
T Consensus       162 ~~P~llllDEPt~-------~LD-~~~~~~l~~~L~~l~~~~g~tviiitHd~~------------------~~~~~~dr  215 (290)
T PRK13634        162 MEPEVLVLDEPTA-------GLD-PKGRKEMMEMFYKLHKEKGLTTVLVTHSME------------------DAARYADQ  215 (290)
T ss_pred             cCCCEEEEECCcc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHhCCE
Confidence            5799999993332       222 344567888899998888999999999321                  13467888


Q ss_pred             EEEEEeC
Q 009230          489 GIVIHRN  495 (539)
Q Consensus       489 vl~l~r~  495 (539)
                      |+.|..-
T Consensus       216 v~~l~~G  222 (290)
T PRK13634        216 IVVMHKG  222 (290)
T ss_pred             EEEEECC
Confidence            8888643

>COG1127 Ttg2A ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]

Probab=97.89  E-value=0.0002  Score=66.40  Aligned_cols=178  Identities=13%  Similarity=0.140  Sum_probs=92.6

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHH---HHHHHHH------HHhhCCCc
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVR---EHARKLL------EKHIKKPF  354 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~---~~~~r~~------~~~~~~~~  354 (539)
                      +|.+-- +++|+++.|.|++|+|||+++..++--..-. ...|.++.-+   ++.+   ++..|+-      +.++..+.
T Consensus        24 ld~v~l~V~~Gei~~iiGgSGsGKStlLr~I~Gll~P~-~GeI~i~G~~i~~ls~~~~~~ir~r~GvlFQ~gALFssltV  102 (263)
T COG1127          24 LDGVDLDVPRGEILAILGGSGSGKSTLLRLILGLLRPD-KGEILIDGEDIPQLSEEELYEIRKRMGVLFQQGALFSSLTV  102 (263)
T ss_pred             ecCceeeecCCcEEEEECCCCcCHHHHHHHHhccCCCC-CCeEEEcCcchhccCHHHHHHHHhheeEEeeccccccccch
Confidence            344433 9999999999999999999998887554433 4566666544   2332   2233320      01111110


Q ss_pred             cc-cccC-CCCCCCCHHHHHHHH-HHhhc---cce---eEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccC
Q 009230          355 FE-ANYG-GSAERMTVEEFEQGK-AWLSN---TFS---LIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQ  425 (539)
Q Consensus       355 ~~-i~~~-~~~~~l~~~~~~~~~-~~l~~---~~~---~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~  425 (539)
                      .+ +... .....+++..++++. .+|.-   +..   .+  -.+=+..+..=.+.++.  ...+|++++.|-       
T Consensus       103 ~eNVafplre~~~lp~~~i~~lv~~KL~~VGL~~~~~~~~--PsELSGGM~KRvaLARA--ialdPell~~DE-------  171 (263)
T COG1127         103 FENVAFPLREHTKLPESLIRELVLMKLELVGLRGAAADLY--PSELSGGMRKRVALARA--IALDPELLFLDE-------  171 (263)
T ss_pred             hHhhheehHhhccCCHHHHHHHHHHHHHhcCCChhhhhhC--chhhcchHHHHHHHHHH--HhcCCCEEEecC-------
Confidence            00 0000 001256666666542 33321   000   00  00111122222222332  235789999992       


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          426 RPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       426 ~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      +.++.++ -....+.+-++++-+.++.++++|+|.-.                  .+...||.+++|..-+
T Consensus       172 PtsGLDP-I~a~~~~~LI~~L~~~lg~T~i~VTHDl~------------------s~~~i~Drv~~L~~gk  223 (263)
T COG1127         172 PTSGLDP-ISAGVIDELIRELNDALGLTVIMVTHDLD------------------SLLTIADRVAVLADGK  223 (263)
T ss_pred             CCCCCCc-chHHHHHHHHHHHHHhhCCEEEEEECChH------------------HHHhhhceEEEEeCCE
Confidence            2122332 22344555566677789999999999221                  1345789999887644

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=97.89  E-value=0.00032  Score=67.56  Aligned_cols=61  Identities=16%  Similarity=0.149  Sum_probs=43.0

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.-       .+ ......+.+.|+.++++.+.+||+++|...                  .+.+.||
T Consensus       131 ~~~p~llllDEPt~~-------LD-~~~~~~l~~~l~~~~~~~~~tiiivsHd~~------------------~~~~~~d  184 (246)
T cd03237         131 SKDADIYLLDEPSAY-------LD-VEQRLMASKVIRRFAENNEKTAFVVEHDII------------------MIDYLAD  184 (246)
T ss_pred             hcCCCEEEEeCCccc-------CC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHhCC
Confidence            357899999933322       22 234567888888888888999999999422                  1456789


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       185 ~i~~l~~  191 (246)
T cd03237         185 RLIVFEG  191 (246)
T ss_pred             EEEEEcC
Confidence            8888854

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>TIGR01184 ntrCD nitrate transport ATP-binding subunits C and D

Probab=97.89  E-value=0.00043  Score=65.98  Aligned_cols=63  Identities=11%  Similarity=0.093  Sum_probs=44.1

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|++++++.+.+||+++|...                  .+.+.||
T Consensus       130 ~~~p~lllLDEPt~-------gLD-~~~~~~l~~~l~~~~~~~~~tii~~sH~~~------------------~~~~~~d  183 (230)
T TIGR01184       130 SIRPKVLLLDEPFG-------ALD-ALTRGNLQEELMQIWEEHRVTVLMVTHDVD------------------EALLLSD  183 (230)
T ss_pred             HcCCCEEEEcCCCc-------CCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHhcC
Confidence            35789999993322       222 334567888888888888999999999321                  2456789


Q ss_pred             eEEEEEeCC
Q 009230          488 NGIVIHRNR  496 (539)
Q Consensus       488 ~vl~l~r~~  496 (539)
                      .++.|.+.+
T Consensus       184 ~v~~l~~G~  192 (230)
T TIGR01184       184 RVVMLTNGP  192 (230)
T ss_pred             EEEEEeCCc
Confidence            998887543

This model describes the ATP binding subunits of nitrate transport in bacteria and archaea. This protein belongs to the ATP-binding cassette (ABC) superfamily. It is thought that the two subunits encoded by ntrC and ntrD form the binding surface for interaction with ATP. This model is restricted in identifying ATP binding subunit associated with the nitrate transport. Nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA - a regulatory protein; ntrB - a hydropbobic transmembrane permease and narB - a reductase.

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=97.88  E-value=0.00032  Score=64.17  Aligned_cols=153  Identities=20%  Similarity=0.186  Sum_probs=80.4

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHHHHhhCCCccccccCCCC
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLLEKHIKKPFFEANYGGSA  363 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~~~~i~~~~~~  363 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-..-. ....|.+-.-.   .++..+..++ +....    -+.     
T Consensus        15 l~~~~~~i~~G~~~~l~G~nGsGKStLl~~i~G~~~~-~~G~v~~~g~~~~~~~~~~~~~~i-~~~~q----~l~-----   83 (180)
T cd03214          15 LDDLSLSIEAGEIVGILGPNGAGKSTLLKTLAGLLKP-SSGEILLDGKDLASLSPKELARKI-AYVPQ----ALE-----   83 (180)
T ss_pred             EeeeEEEECCCCEEEEECCCCCCHHHHHHHHhCCCCC-CCcEEEECCEECCcCCHHHHHHHH-hHHHH----HHH-----
Confidence            444433 999999999999999999998877644322 23344432111   2233222221 11000    000     


Q ss_pred             CCCCHHHHHHHHHHhhccceeEeecCCCCCCHHH--HHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHH
Q 009230          364 ERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKW--VLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLT  441 (539)
Q Consensus       364 ~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~--i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~  441 (539)
                       .+.      +.+.+...+        ...+-.+  -...++.+  ..+++++++|.-+.       +.+ ......+.+
T Consensus        84 -~~g------l~~~~~~~~--------~~LS~G~~qrl~laral--~~~p~llllDEP~~-------~LD-~~~~~~~~~  138 (180)
T cd03214          84 -LLG------LAHLADRPF--------NELSGGERQRVLLARAL--AQEPPILLLDEPTS-------HLD-IAHQIELLE  138 (180)
T ss_pred             -HcC------CHhHhcCCc--------ccCCHHHHHHHHHHHHH--hcCCCEEEEeCCcc-------CCC-HHHHHHHHH
Confidence             000      001111111        1122222  22233332  35789999993332       122 234556777


Q ss_pred             HHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          442 MVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       442 ~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      .|++++++.+.++|+++|....                  +...+|.++.+..
T Consensus       139 ~l~~~~~~~~~tiii~sh~~~~------------------~~~~~d~~~~l~~  173 (180)
T cd03214         139 LLRRLARERGKTVVMVLHDLNL------------------AARYADRVILLKD  173 (180)
T ss_pred             HHHHHHHhcCCEEEEEeCCHHH------------------HHHhCCEEEEEEC
Confidence            7888877778999999994221                  3457888888864

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=97.88  E-value=0.00044  Score=65.06  Aligned_cols=60  Identities=12%  Similarity=0.159  Sum_probs=42.3

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+++.|++++++.+.+||+++|...                  .+...||.
T Consensus       147 ~~p~~lllDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tii~~sH~~~------------------~~~~~~d~  200 (213)
T cd03259         147 REPSLLLLDEPLS-------ALD-AKLREELREELKELQRELGITTIYVTHDQE------------------EALALADR  200 (213)
T ss_pred             cCCCEEEEcCCcc-------cCC-HHHHHHHHHHHHHHHHHcCCEEEEEecCHH------------------HHHHhcCE
Confidence            5789999992221       222 344567888888888878999999999422                  14467899


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|.+
T Consensus       201 v~~l~~  206 (213)
T cd03259         201 IAVMNE  206 (213)
T ss_pred             EEEEEC
Confidence            888864

This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR01277 thiQ thiamine ABC transporter, ATP-binding protein

Probab=97.88  E-value=0.00029  Score=66.33  Aligned_cols=60  Identities=15%  Similarity=0.107  Sum_probs=42.2

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.-       . +......+.+.|+.+.++.+.+||+++|....                  +...+|.
T Consensus       145 ~~p~llllDEPt~~-------L-D~~~~~~~~~~l~~~~~~~~~tii~vsh~~~~------------------~~~~~d~  198 (213)
T TIGR01277       145 RPNPILLLDEPFSA-------L-DPLLREEMLALVKQLCSERQRTLLMVTHHLSD------------------ARAIASQ  198 (213)
T ss_pred             cCCCEEEEcCCCcc-------C-CHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHH------------------HHhhcCe
Confidence            57899999933322       2 23345678888888888789999999994221                  3457899


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|+.
T Consensus       199 v~~l~~  204 (213)
T TIGR01277       199 IAVVSQ  204 (213)
T ss_pred             EEEEEC
Confidence            888864

This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found.

>PRK11308 dppF dipeptide transporter ATP-binding subunit; Provisional

Probab=97.87  E-value=0.00036  Score=70.12  Aligned_cols=45  Identities=16%  Similarity=0.107  Sum_probs=33.7

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      ..+++++|+|.-+.-+       + .....++++.|+++.++.+.+||+++|.
T Consensus       170 ~~~P~lLilDEPts~L-------D-~~~~~~i~~lL~~l~~~~g~til~iTHd  214 (327)
T PRK11308        170 MLDPDVVVADEPVSAL-------D-VSVQAQVLNLMMDLQQELGLSYVFISHD  214 (327)
T ss_pred             HcCCCEEEEECCCccC-------C-HHHHHHHHHHHHHHHHHcCCEEEEEeCC
Confidence            3578999999333222       2 3345678888999999999999999993

>cd03261 ABC_Org_Solvent_Resistant ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=97.87  E-value=0.00027  Score=67.68  Aligned_cols=60  Identities=10%  Similarity=0.030  Sum_probs=42.1

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+++.|++++++.+.+||+++|...                  .+...||.
T Consensus       153 ~~p~llllDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tvi~vsH~~~------------------~~~~~~d~  206 (235)
T cd03261         153 LDPELLLYDEPTA-------GLD-PIASGVIDDLIRSLKKELGLTSIMVTHDLD------------------TAFAIADR  206 (235)
T ss_pred             cCCCEEEecCCcc-------cCC-HHHHHHHHHHHHHHHHhcCcEEEEEecCHH------------------HHHHhcCE
Confidence            5799999993222       222 234567788888888778999999999322                  13467899


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|..
T Consensus       207 v~~l~~  212 (235)
T cd03261         207 IAVLYD  212 (235)
T ss_pred             EEEEEC
Confidence            998864

The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR02770 nickel_nikD nickel import ATP-binding protein NikD

Probab=97.87  E-value=0.00014  Score=69.41  Aligned_cols=61  Identities=11%  Similarity=0.109  Sum_probs=42.2

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|++++++.+.+||+++|.-.                  .+...+|
T Consensus       141 ~~~p~vllLDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tiii~sH~~~------------------~~~~~~d  194 (230)
T TIGR02770       141 LLEPPFLIADEPTT-------DLD-VVNQARVLKLLRELRQLFGTGILLITHDLG------------------VVARIAD  194 (230)
T ss_pred             hcCCCEEEEcCCcc-------ccC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHhCC
Confidence            35789999993322       222 234456788888888878999999999321                  1446789


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       195 ~i~~l~~  201 (230)
T TIGR02770       195 EVAVMDD  201 (230)
T ss_pred             EEEEEEC
Confidence            9888865

This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are homologous.

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.84  E-value=8.1e-05  Score=66.89  Aligned_cols=33  Identities=27%  Similarity=0.304  Sum_probs=26.8

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        16 l~~i~~~i~~Ge~~~l~G~nGsGKSTLl~~i~G~   49 (163)
T cd03216          16 LDGVSLSVRRGEVHALLGENGAGKSTLMKILSGL   49 (163)
T ss_pred             EeeeEEEEeCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            444433 999999999999999999998876643

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>KOG0061 consensus Transporter, ABC superfamily (Breast cancer resistance protein) [Secondary metabolites biosynthesis, transport and catabolism]

Probab=97.83  E-value=0.00014  Score=78.99  Aligned_cols=162  Identities=19%  Similarity=0.156  Sum_probs=82.5

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-cCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCC----
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEH-AGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGG----  361 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~----  361 (539)
                      |+.+.| +.+|+++.|.|++|+||||++.-++-..... .-.-.+.+..+....+..+++.+....   .+.-.+.    
T Consensus        46 L~~vsg~~~~Gel~AimG~SGsGKtTLL~~Lagr~~~~~~~~G~ilvNG~~~~~~~~~~~s~yV~Q---dD~l~~~LTV~  122 (613)
T KOG0061|consen   46 LKGVSGTAKPGELLAIMGPSGSGKTTLLNALAGRLNGGLKLSGEILLNGRPRDSRSFRKISGYVQQ---DDVLLPTLTVR  122 (613)
T ss_pred             eeCcEEEEecCeEEEEECCCCCCHHHHHHHHhccccCCCcceEEEEECCccCchhhhhheeEEEcc---cccccccccHH
Confidence            556677 9999999999999999999999888776532 011223344433333333333221111   1110000    


Q ss_pred             ----------CCCCCCHHHHHHHHHHhhccceeEeecC--CC-----CCCHHHHHHHHHHHHHHcCCcEEEEcccccccc
Q 009230          362 ----------SAERMTVEEFEQGKAWLSNTFSLIRCEN--DS-----LPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDH  424 (539)
Q Consensus       362 ----------~~~~l~~~~~~~~~~~l~~~~~~i~~~~--~~-----~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~  424 (539)
                                -...++.++.++.++.+-..+-...+.+  -+     ..+-.+-....-..-.-.+|.++++|       
T Consensus       123 EtL~f~A~lrlp~~~~~~~k~~~V~~vi~~LgL~~~~~t~ig~~~~rgiSGGErkRvsia~Ell~~P~iLflD-------  195 (613)
T KOG0061|consen  123 ETLRFSALLRLPSSLSKEEKRERVEEVISELGLEKCADTLIGNPGIRGLSGGERKRVSIALELLTDPSILFLD-------  195 (613)
T ss_pred             HHHHHHHHhcCCCCCCHHHHHHHHHHHHHHcCChhhccceecCCCCCccccchhhHHHHHHHHHcCCCEEEec-------
Confidence                      0012344444333322211110000100  01     11112222111111223578999999       


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CC
Q 009230          425 QRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PR  461 (539)
Q Consensus       425 ~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r  461 (539)
                      .+.++.+... ..++++.|+++|++ |.+||++-| ++
T Consensus       196 EPTSGLDS~s-A~~vv~~Lk~lA~~-grtVi~tIHQPs  231 (613)
T KOG0061|consen  196 EPTSGLDSFS-ALQVVQLLKRLARS-GRTVICTIHQPS  231 (613)
T ss_pred             CCCCCcchhh-HHHHHHHHHHHHhC-CCEEEEEEeCCc
Confidence            2223334332 35799999999999 998888877 64

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=97.83  E-value=0.00013  Score=66.52  Aligned_cols=61  Identities=13%  Similarity=0.127  Sum_probs=41.4

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +. +......+.+.|+.++++.+.++++++|....                  +...+|
T Consensus       116 ~~~p~llilDEP~~-------~L-D~~~~~~l~~~l~~~~~~~~~tiii~sH~~~~------------------~~~~~d  169 (178)
T cd03229         116 AMDPDVLLLDEPTS-------AL-DPITRREVRALLKSLQAQLGITVVLVTHDLDE------------------AARLAD  169 (178)
T ss_pred             HCCCCEEEEeCCcc-------cC-CHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHH------------------HHHhcC
Confidence            35789999993221       22 23345677888888888778999999994321                  345678


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       170 ~i~~l~~  176 (178)
T cd03229         170 RVVVLRD  176 (178)
T ss_pred             EEEEEeC
Confidence            8887753

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK10867 signal recognition particle protein; Provisional

Probab=97.83  E-value=0.00052  Score=70.94  Aligned_cols=58  Identities=19%  Similarity=0.299  Sum_probs=42.5

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHH--HHHhhCCCcc
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKL--LEKHIKKPFF  355 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~--~~~~~~~~~~  355 (539)
                      .+++++|++|+||||++..+|..+..+.|.+|++++++.-.-....++  ++...++++.
T Consensus       101 ~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D~~R~aa~eQL~~~a~~~gv~v~  160 (433)
T PRK10867        101 TVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVYRPAAIEQLKTLGEQIGVPVF  160 (433)
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEccccchHHHHHHHHHHhhcCCeEE
Confidence            689999999999999999999988774489999999995432222222  2344555543

>cd03298 ABC_ThiQ_thiamine_transporter ABC-type thiamine tranport system; part of the binding-protein-dependent transport system tbpA-thiPQ for thiamine and TPP

Probab=97.83  E-value=0.00029  Score=66.23  Aligned_cols=60  Identities=13%  Similarity=0.155  Sum_probs=42.2

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|++++++.+.+||+++|...                  .+.+.||.
T Consensus       145 ~~p~llllDEP~~-------~LD-~~~~~~l~~~l~~~~~~~~~tii~~sH~~~------------------~~~~~~d~  198 (211)
T cd03298         145 RDKPVLLLDEPFA-------ALD-PALRAEMLDLVLDLHAETKMTVLMVTHQPE------------------DAKRLAQR  198 (211)
T ss_pred             cCCCEEEEcCCcc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEecCHH------------------HHHhhhCE
Confidence            5789999993332       222 234456888888888888999999999422                  14467898


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|..
T Consensus       199 i~~l~~  204 (211)
T cd03298         199 VVFLDN  204 (211)
T ss_pred             EEEEEC
Confidence            888864

Probably responsible for the translocation of thiamine across the membrane. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03267 ABC_NatA_like Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake

Probab=97.83  E-value=0.00045  Score=66.15  Aligned_cols=61  Identities=13%  Similarity=0.141  Sum_probs=42.7

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +. +......+.+.|++++++.+.+||+++|....                  +...||
T Consensus       169 ~~~p~llllDEPt~-------~L-D~~~~~~l~~~l~~~~~~~~~tiiivsH~~~~------------------~~~~~d  222 (236)
T cd03267         169 LHEPEILFLDEPTI-------GL-DVVAQENIRNFLKEYNRERGTTVLLTSHYMKD------------------IEALAR  222 (236)
T ss_pred             hcCCCEEEEcCCCC-------CC-CHHHHHHHHHHHHHHHhcCCCEEEEEecCHHH------------------HHHhCC
Confidence            35789999993322       22 23445678888888888889999999994321                  346788


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       223 ~i~~l~~  229 (236)
T cd03267         223 RVLVIDK  229 (236)
T ss_pred             EEEEEeC
Confidence            8888863

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single intergral membrane protein.

>PRK13646 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.83  E-value=0.00019  Score=70.84  Aligned_cols=34  Identities=24%  Similarity=0.358  Sum_probs=29.0

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        22 ~l~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~L~Gl   56 (286)
T PRK13646         22 AIHDVNTEFEQGKYYAIVGQTGSGKSTLIQNINAL   56 (286)
T ss_pred             ceeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            5666655 999999999999999999998887754

>cd03265 ABC_DrrA DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin

Probab=97.82  E-value=0.00039  Score=65.80  Aligned_cols=61  Identities=11%  Similarity=0.199  Sum_probs=42.5

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|...                  .+.+.+|
T Consensus       147 ~~~p~llllDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tvi~~tH~~~------------------~~~~~~d  200 (220)
T cd03265         147 VHRPEVLFLDEPTI-------GLD-PQTRAHVWEYIEKLKEEFGMTILLTTHYME------------------EAEQLCD  200 (220)
T ss_pred             hcCCCEEEEcCCcc-------CCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHhCC
Confidence            45899999993332       222 234567788888888888999999999422                  1446788


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       201 ~i~~l~~  207 (220)
T cd03265         201 RVAIIDH  207 (220)
T ss_pred             EEEEEeC
Confidence            8888864

In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG4107 PhnK ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.82  E-value=0.00037  Score=61.13  Aligned_cols=155  Identities=17%  Similarity=0.275  Sum_probs=85.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH-------HHHHHHhhCCCccc----cc----
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA-------RKLLEKHIKKPFFE----AN----  358 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~-------~r~~~~~~~~~~~~----i~----  358 (539)
                      +.|||+..|.|.+|+||||++.-++.+++-. ...|.|-+-.-.+.++.       ++++....|+--..    ++    
T Consensus        29 l~PGeVLgiVGESGSGKtTLL~~is~rl~p~-~G~v~Y~~r~~~~~dl~~msEaeRR~L~RTeWG~VhQnP~DGLRm~VS  107 (258)
T COG4107          29 LYPGEVLGIVGESGSGKTTLLKCISGRLTPD-AGTVTYRMRDGQPRDLYTMSEAERRRLLRTEWGFVHQNPRDGLRMQVS  107 (258)
T ss_pred             ecCCcEEEEEecCCCcHHhHHHHHhcccCCC-CCeEEEEcCCCCchhHhhhchHHHHHHhhhccceeecCccccceeeec
Confidence            9999999999999999999999988887765 55777776433322221       22332222221111    11    


Q ss_pred             cCCCCCC--CCH-----HHH-HHHHHHhhccceeE-eecCCC---CCCHHHHHHHHHHHHHHcCCcEEEEccccccccCC
Q 009230          359 YGGSAER--MTV-----EEF-EQGKAWLSNTFSLI-RCENDS---LPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQR  426 (539)
Q Consensus       359 ~~~~~~~--l~~-----~~~-~~~~~~l~~~~~~i-~~~~~~---~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~  426 (539)
                      .|++.+.  |..     ..+ +.+.+|+.+--+-. +.++.+   +..+.+-+..++.++  ..+++||.|.-+      
T Consensus       108 AG~NiGERlma~G~RHYG~iR~~a~~WL~~VEI~~~RiDD~PrtFSGGMqQRLQiARnLV--t~PrLvfMDEPT------  179 (258)
T COG4107         108 AGGNIGERLMAIGARHYGNIRAEAQDWLEEVEIDLDRIDDLPRTFSGGMQQRLQIARNLV--TRPRLVFMDEPT------  179 (258)
T ss_pred             cCCccchhHHhhhhhhhhhHHHHHHHHHHhcccCcccccCcccccchHHHHHHHHHHHhc--cCCceEEecCCC------
Confidence            0111000  000     011 33467776521100 011000   111222233333332  368999999221      


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          427 PVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       427 ~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                        +.-+-..+..++.-|+.+..+++.++++++|
T Consensus       180 --GGLDVSVQARLLDllrgLv~~l~la~viVTH  210 (258)
T COG4107         180 --GGLDVSVQARLLDLLRGLVRELGLAVVIVTH  210 (258)
T ss_pred             --CCcchhhHHHHHHHHHHHHHhcCceEEEEec
Confidence              2223345678999999999999999999999

>PRK15079 oligopeptide ABC transporter ATP-binding protein OppF; Provisional

Probab=97.82  E-value=0.00059  Score=68.62  Aligned_cols=34  Identities=29%  Similarity=0.340  Sum_probs=28.1

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++.+.- +.+|+++.|.|++|+|||||+.-|+--
T Consensus        36 ~l~~vsl~i~~Ge~~~lvG~sGsGKSTLlk~i~Gl   70 (331)
T PRK15079         36 AVDGVTLRLYEGETLGVVGESGCGKSTFARAIIGL   70 (331)
T ss_pred             EEeeEEEEEcCCCEEEEECCCCCCHHHHHHHHHCC
Confidence            4555544 999999999999999999998887643

>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein

Probab=97.81  E-value=0.00015  Score=69.74  Aligned_cols=60  Identities=15%  Similarity=0.110  Sum_probs=41.7

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|....                  +.+.||.
T Consensus       162 ~~p~llllDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tiii~tH~~~~------------------~~~~~d~  215 (243)
T TIGR02315       162 QQPDLILADEPIA-------SLD-PKTSKQVMDYLKRINKEDGITVIINLHQVDL------------------AKKYADR  215 (243)
T ss_pred             cCCCEEEEeCCcc-------cCC-HHHHHHHHHHHHHHHHHcCCEEEEEeCCHHH------------------HHHhcCe
Confidence            5789999993322       222 2344567788888887778999999994221                  3467899


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|.+
T Consensus       216 v~~l~~  221 (243)
T TIGR02315       216 IVGLKA  221 (243)
T ss_pred             EEEEEC
Confidence            888864

Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.

>PRK15112 antimicrobial peptide ABC system ATP-binding protein SapF; Provisional

Probab=97.81  E-value=0.00038  Score=68.00  Aligned_cols=61  Identities=13%  Similarity=0.174  Sum_probs=42.4

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|++++++.+.+||+++|...                  .+...+|
T Consensus       165 ~~~p~lllLDEPt~-------~LD-~~~~~~l~~~l~~~~~~~g~tviivsH~~~------------------~~~~~~d  218 (267)
T PRK15112        165 ILRPKVIIADEALA-------SLD-MSMRSQLINLMLELQEKQGISYIYVTQHLG------------------MMKHISD  218 (267)
T ss_pred             HhCCCEEEEcCCcc-------cCC-HHHHHHHHHHHHHHHHHcCcEEEEEeCCHH------------------HHHHhcC
Confidence            35799999993332       222 234567788888888888999999999422                  1445788


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       219 ~i~~l~~  225 (267)
T PRK15112        219 QVLVMHQ  225 (267)
T ss_pred             EEEEEEC
Confidence            8888864

>PRK11153 metN DL-methionine transporter ATP-binding subunit; Provisional

Probab=97.80  E-value=0.00059  Score=69.10  Aligned_cols=45  Identities=11%  Similarity=0.204  Sum_probs=33.0

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|.
T Consensus       156 ~~~p~iLlLDEPts-------~LD-~~~~~~l~~~L~~l~~~~g~tiilvtH~  200 (343)
T PRK11153        156 ASNPKVLLCDEATS-------ALD-PATTRSILELLKDINRELGLTIVLITHE  200 (343)
T ss_pred             HcCCCEEEEeCCcc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            35799999993322       222 2345678888888888889999999993

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.80  E-value=0.00033  Score=70.47  Aligned_cols=38  Identities=8%  Similarity=0.143  Sum_probs=34.2

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      ..++|.|++|+||||++..+|..+..+ |.+|++++.+-
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~-GkkVglI~aDt  279 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGK-KKTVGFITTDH  279 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHc-CCcEEEEecCC
Confidence            588999999999999999999988764 99999999874

>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport

Probab=97.80  E-value=0.00074  Score=64.50  Aligned_cols=61  Identities=13%  Similarity=0.267  Sum_probs=42.6

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|...                  .+...||
T Consensus       156 ~~~p~lllLDEP~~-------~LD-~~~~~~l~~~l~~~~~~~~~tvii~sH~~~------------------~~~~~~d  209 (233)
T cd03258         156 ANNPKVLLCDEATS-------ALD-PETTQSILALLRDINRELGLTIVLITHEME------------------VVKRICD  209 (233)
T ss_pred             hcCCCEEEecCCCC-------cCC-HHHHHHHHHHHHHHHHHcCCEEEEEeCCHH------------------HHHHhCC
Confidence            35789999993221       222 234567888888888888999999999321                  1456789


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|.+
T Consensus       210 ~i~~l~~  216 (233)
T cd03258         210 RVAVMEK  216 (233)
T ss_pred             EEEEEEC
Confidence            9888864

Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export

Probab=97.79  E-value=0.00043  Score=65.72  Aligned_cols=33  Identities=27%  Similarity=0.251  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        38 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~l~G~   71 (224)
T cd03220          38 LKDVSFEVPRGERIGLIGRNGAGKSTLLRLLAGI   71 (224)
T ss_pred             EeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            444433 999999999999999999998877753

Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.

>TIGR03864 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system

Probab=97.79  E-value=0.00072  Score=64.76  Aligned_cols=60  Identities=17%  Similarity=0.201  Sum_probs=41.1

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|....                  +. .||
T Consensus       148 ~~~p~llllDEP~~-------~LD-~~~~~~l~~~l~~~~~~~~~tiii~sH~~~~------------------~~-~~d  200 (236)
T TIGR03864       148 LHRPALLLLDEPTV-------GLD-PASRAAIVAHVRALCRDQGLSVLWATHLVDE------------------IE-ADD  200 (236)
T ss_pred             hcCCCEEEEcCCcc-------CCC-HHHHHHHHHHHHHHHHhCCCEEEEEecChhh------------------Hh-hCC
Confidence            35789999993322       222 3345678888888887778999999994321                  23 378


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       201 ~i~~l~~  207 (236)
T TIGR03864       201 RLVVLHR  207 (236)
T ss_pred             EEEEEeC
Confidence            8888864

Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.78  E-value=0.00038  Score=70.87  Aligned_cols=42  Identities=24%  Similarity=0.279  Sum_probs=36.2

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      .++.+++|.|++|+||||++.++|.......|.+|++++++.
T Consensus       221 ~~~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~Dt  262 (432)
T PRK12724        221 NQRKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDN  262 (432)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecccc
Confidence            356789999999999999999999877544589999999885

>TIGR00959 ffh signal recognition particle protein

Probab=97.78  E-value=0.00069  Score=69.99  Aligned_cols=40  Identities=20%  Similarity=0.327  Sum_probs=35.5

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .+++++|++|+||||++..+|..+..+.|.+|++++++.-
T Consensus       100 ~vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D~~  139 (428)
T TIGR00959       100 TVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLY  139 (428)
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEecccc
Confidence            5899999999999999999999976435899999999954

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.

>PRK11247 ssuB aliphatic sulfonates transport ATP-binding subunit; Provisional

Probab=97.78  E-value=0.00047  Score=66.87  Aligned_cols=33  Identities=30%  Similarity=0.384  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        28 l~~isl~i~~Ge~~~I~G~NGsGKSTLlk~l~Gl   61 (257)
T PRK11247         28 LNQLDLHIPAGQFVAVVGRSGCGKSTLLRLLAGL   61 (257)
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            444433 999999999999999999998877643

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.78  E-value=0.0003  Score=64.49  Aligned_cols=34  Identities=26%  Similarity=0.417  Sum_probs=27.7

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        15 ~l~~vs~~i~~G~~~~i~G~nGsGKSTLl~~l~G~   49 (182)
T cd03215          15 AVRDVSFEVRAGEIVGIAGLVGNGQTELAEALFGL   49 (182)
T ss_pred             eecceEEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            4455544 999999999999999999998876644

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=97.77  E-value=0.00026  Score=64.22  Aligned_cols=33  Identities=24%  Similarity=0.346  Sum_probs=26.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        16 l~~~~~~i~~Ge~~~i~G~nGsGKStLl~~l~G~   49 (173)
T cd03230          16 LDDISLTVEKGEIYGLLGPNGAGKTTLIKIILGL   49 (173)
T ss_pred             eeeeEEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            444433 999999999999999999998876643

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=97.77  E-value=0.00064  Score=63.56  Aligned_cols=33  Identities=27%  Similarity=0.396  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        16 l~~v~~~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   49 (205)
T cd03226          16 LDDLSLDLYAGEIIALTGKNGAGKTTLAKILAGL   49 (205)
T ss_pred             eeeeeEEEcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            444433 999999999999999999998877643

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=97.77  E-value=0.00031  Score=63.80  Aligned_cols=132  Identities=16%  Similarity=0.051  Sum_probs=74.5

Q ss_pred             hhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCC
Q 009230          288 LNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMT  367 (539)
Q Consensus       288 LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~  367 (539)
                      ++..+.+.+|+++.|.|++|+|||||+.-++-...- ....+.+-...                  ...+.+.   ..++
T Consensus        16 l~~~~~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~p-~~G~i~~~g~~------------------i~~~~q~---~~LS   73 (177)
T cd03222          16 LVELGVVKEGEVIGIVGPNGTGKTTAVKILAGQLIP-NGDNDEWDGIT------------------PVYKPQY---IDLS   73 (177)
T ss_pred             EccCcEECCCCEEEEECCCCChHHHHHHHHHcCCCC-CCcEEEECCEE------------------EEEEccc---CCCC
Confidence            343334899999999999999999998866643322 23344332100                  0000000   0011


Q ss_pred             HHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHH
Q 009230          368 VEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFA  447 (539)
Q Consensus       368 ~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA  447 (539)
                      ..+                         ..-...++.+  ..+++++++|.-+.       +.+ ......+.+.|++++
T Consensus        74 gGq-------------------------~qrv~laral--~~~p~lllLDEPts-------~LD-~~~~~~l~~~l~~~~  118 (177)
T cd03222          74 GGE-------------------------LQRVAIAAAL--LRNATFYLFDEPSA-------YLD-IEQRLNAARAIRRLS  118 (177)
T ss_pred             HHH-------------------------HHHHHHHHHH--hcCCCEEEEECCcc-------cCC-HHHHHHHHHHHHHHH
Confidence            111                         1112222222  24789999993322       222 234456777787777


Q ss_pred             HHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          448 QHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       448 ~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      ++.+.+|++++|....                  +...||.++.+..
T Consensus       119 ~~~~~tiiivsH~~~~------------------~~~~~d~i~~l~~  147 (177)
T cd03222         119 EEGKKTALVVEHDLAV------------------LDYLSDRIHVFEG  147 (177)
T ss_pred             HcCCCEEEEEECCHHH------------------HHHhCCEEEEEcC
Confidence            7656899999994321                  3467888888864

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=97.77  E-value=0.00067  Score=61.51  Aligned_cols=31  Identities=35%  Similarity=0.458  Sum_probs=25.5

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      |+.+-- +.+|+++.|.|++|+|||||+.-++
T Consensus        11 l~~isl~i~~G~~~~l~G~nG~GKSTLl~~il   42 (176)
T cd03238          11 LQNLDVSIPLNVLVVVTGVSGSGKSTLVNEGL   42 (176)
T ss_pred             ecceEEEEcCCCEEEEECCCCCCHHHHHHHHh
Confidence            444433 9999999999999999999997653

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>PRK09536 btuD corrinoid ABC transporter ATPase; Reviewed

Probab=97.76  E-value=0.00028  Score=72.56  Aligned_cols=33  Identities=24%  Similarity=0.300  Sum_probs=27.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+-- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        19 L~~vs~~i~~Geiv~liGpNGaGKSTLLk~LaGl   52 (402)
T PRK09536         19 LDGVDLSVREGSLVGLVGPNGAGKTTLLRAINGT   52 (402)
T ss_pred             EEeeEEEECCCCEEEEECCCCchHHHHHHHHhcC
Confidence            444433 999999999999999999998877643

>COG3638 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.76  E-value=0.00035  Score=64.59  Aligned_cols=183  Identities=20%  Similarity=0.172  Sum_probs=96.5

Q ss_pred             cccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC----CCHHHHHHHHHHHhhCCCcc
Q 009230          281 ISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME----NKVREHARKLLEKHIKKPFF  355 (539)
Q Consensus       281 i~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E----~~~~~~~~r~~~~~~~~~~~  355 (539)
                      +|-+-..|+++-- +.+||++.|.|++|+|||||+..+.-- ... ....+++..+    +...++ +++. ...|+=+.
T Consensus        13 yp~~~~aL~~Vnl~I~~GE~VaiIG~SGaGKSTLLR~lngl-~d~-t~G~i~~~g~~i~~~~~k~l-r~~r-~~iGmIfQ   88 (258)
T COG3638          13 YPGGHQALKDVNLEINQGEMVAIIGPSGAGKSTLLRSLNGL-VDP-TSGEILFNGVQITKLKGKEL-RKLR-RDIGMIFQ   88 (258)
T ss_pred             cCCCceeeeeEeEEeCCCcEEEEECCCCCcHHHHHHHHhcc-cCC-CcceEEecccchhccchHHH-HHHH-HhceeEec
Confidence            4445566666654 999999999999999999999877652 211 2223334433    222222 1111 11111110


Q ss_pred             c-----------------cccC----CCCCCCCHHHHHHHHHHhhccc----eeEeecCCCCCCHHHHHHHHHHHHHHcC
Q 009230          356 E-----------------ANYG----GSAERMTVEEFEQGKAWLSNTF----SLIRCENDSLPSIKWVLDLAKAAVLRHG  410 (539)
Q Consensus       356 ~-----------------i~~~----~~~~~l~~~~~~~~~~~l~~~~----~~i~~~~~~~~~~~~i~~~i~~~~~~~~  410 (539)
                      .                 +-+.    ...+-++.++...+.+.|..--    -+-+.+ .-+...-+=.+.++.++  .+
T Consensus        89 ~~nLv~r~sv~~NVl~grl~~~s~~~slfglfsk~dk~~Al~aLervgi~~~A~qra~-~LSGGQQQRVaIARaL~--Q~  165 (258)
T COG3638          89 QFNLVPRLSVLENVLLGRLGYTSTWRSLFGLFSKEDKAQALDALERVGILDKAYQRAS-TLSGGQQQRVAIARALV--QQ  165 (258)
T ss_pred             cCCcccccHHHHHHHhhhcccchHHHHHhCCCCHHHHHHHHHHHHHcCcHHHHHHHhc-cCCcchhHHHHHHHHHh--cC
Confidence            0                 0000    0012456666666655443210    011111 01111122233333333  46


Q ss_pred             CcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEE
Q 009230          411 VRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGI  490 (539)
Q Consensus       411 ~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl  490 (539)
                      +++|.=|.=..       +.+ ......+|+.|++++++.|++||+..|.-..                  ..++||.++
T Consensus       166 pkiILADEPva-------sLD-p~~a~~Vm~~l~~in~~~g~Tvi~nLH~vdl------------------A~~Y~~Rii  219 (258)
T COG3638         166 PKIILADEPVA-------SLD-PESAKKVMDILKDINQEDGITVIVNLHQVDL------------------AKKYADRII  219 (258)
T ss_pred             CCEEecCCccc-------ccC-hhhHHHHHHHHHHHHHHcCCEEEEEechHHH------------------HHHHHhhhe
Confidence            88988882221       222 2345689999999999999999999993221                  125778888


Q ss_pred             EEEeCC
Q 009230          491 VIHRNR  496 (539)
Q Consensus       491 ~l~r~~  496 (539)
                      .|...+
T Consensus       220 gl~~G~  225 (258)
T COG3638         220 GLKAGR  225 (258)
T ss_pred             EecCCc
Confidence            876543

>PRK11022 dppD dipeptide transporter ATP-binding subunit; Provisional

Probab=97.76  E-value=0.0011  Score=66.71  Aligned_cols=35  Identities=31%  Similarity=0.326  Sum_probs=29.1

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ..|+.+.- +.+|+++.|.|++|+|||||+.-++--
T Consensus        21 ~~l~~vsl~i~~Ge~~~lvG~sGsGKSTL~~~l~Gl   56 (326)
T PRK11022         21 RAVDRISYSVKQGEVVGIVGESGSGKSVSSLAIMGL   56 (326)
T ss_pred             EEEeeeEEEECCCCEEEEECCCCChHHHHHHHHHcC
Confidence            34666554 999999999999999999998887754

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=97.75  E-value=0.00036  Score=65.59  Aligned_cols=33  Identities=27%  Similarity=0.410  Sum_probs=26.9

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        17 l~~vs~~i~~G~~~~l~G~nGsGKSTLl~~l~G~   50 (211)
T cd03225          17 LDDISLTIKKGEFVLIVGPNGSGKSTLLRLLNGL   50 (211)
T ss_pred             ecceEEEEcCCcEEEEECCCCCCHHHHHHHHhcC
Confidence            444433 899999999999999999998877643

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>cd03219 ABC_Mj1267_LivG_branched The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine

Probab=97.75  E-value=0.00087  Score=64.16  Aligned_cols=33  Identities=24%  Similarity=0.382  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        16 l~~vsl~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl   49 (236)
T cd03219          16 LDDVSFSVRPGEIHGLIGPNGAGKTTLFNLISGF   49 (236)
T ss_pred             ecCceEEecCCcEEEEECCCCCCHHHHHHHHcCC
Confidence            444433 999999999999999999998877643

MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs. The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=97.74  E-value=0.0011  Score=63.05  Aligned_cols=62  Identities=13%  Similarity=0.251  Sum_probs=42.7

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|....                  +. .||
T Consensus       153 ~~~p~llllDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tvii~sh~~~~------------------~~-~~d  205 (225)
T PRK10247        153 QFMPKVLLLDEITS-------ALD-ESNKHNVNEIIHRYVREQNIAVLWVTHDKDE------------------IN-HAD  205 (225)
T ss_pred             hcCCCEEEEeCCcc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEECChHH------------------HH-hCC
Confidence            35789999993322       222 2345677888888888889999999994321                  33 489


Q ss_pred             eEEEEEeCC
Q 009230          488 NGIVIHRNR  496 (539)
Q Consensus       488 ~vl~l~r~~  496 (539)
                      .++.|.+..
T Consensus       206 ~i~~l~~~~  214 (225)
T PRK10247        206 KVITLQPHA  214 (225)
T ss_pred             EEEEEeccc
Confidence            999986543

>PRK13636 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.74  E-value=0.00061  Score=67.15  Aligned_cols=62  Identities=16%  Similarity=0.171  Sum_probs=42.8

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.-       .+ ......+++.|++++++.+.+|++++|.-.                  .+.+.||
T Consensus       157 ~~~p~lLilDEPt~g-------LD-~~~~~~l~~~l~~l~~~~g~tillvsH~~~------------------~~~~~~d  210 (283)
T PRK13636        157 VMEPKVLVLDEPTAG-------LD-PMGVSEIMKLLVEMQKELGLTIIIATHDID------------------IVPLYCD  210 (283)
T ss_pred             HcCCCEEEEeCCccC-------CC-HHHHHHHHHHHHHHHHhCCCEEEEEecCHH------------------HHHHhCC
Confidence            457999999933322       22 234557888888888888999999999321                  1345788


Q ss_pred             eEEEEEeC
Q 009230          488 NGIVIHRN  495 (539)
Q Consensus       488 ~vl~l~r~  495 (539)
                      .++.|...
T Consensus       211 ri~~l~~G  218 (283)
T PRK13636        211 NVFVMKEG  218 (283)
T ss_pred             EEEEEECC
Confidence            88888653

>TIGR00968 3a0106s01 sulfate ABC transporter, ATP-binding protein

Probab=97.74  E-value=0.00024  Score=68.05  Aligned_cols=61  Identities=11%  Similarity=0.166  Sum_probs=42.0

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++.+.+.+||+++|....                  +...||
T Consensus       146 ~~~p~llllDEP~~-------~LD-~~~~~~~~~~l~~~~~~~~~tvli~sH~~~~------------------~~~~~d  199 (237)
T TIGR00968       146 AVEPQVLLLDEPFG-------ALD-AKVRKELRSWLRKLHDEVHVTTVFVTHDQEE------------------AMEVAD  199 (237)
T ss_pred             hcCCCEEEEcCCcc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHHH------------------HHhhcC
Confidence            35789999993332       222 2345677888888887779999999994321                  345778


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       200 ~i~~l~~  206 (237)
T TIGR00968       200 RIVVMSN  206 (237)
T ss_pred             EEEEEEC
Confidence            8888864

>PRK14974 cell division protein FtsY; Provisional

Probab=97.74  E-value=0.001  Score=66.59  Aligned_cols=39  Identities=21%  Similarity=0.400  Sum_probs=34.0

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      ..++++.|++|+||||.+..++..+.. .|.+|++++.+.
T Consensus       140 ~~vi~~~G~~GvGKTTtiakLA~~l~~-~g~~V~li~~Dt  178 (336)
T PRK14974        140 PVVIVFVGVNGTGKTTTIAKLAYYLKK-NGFSVVIAAGDT  178 (336)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHH-cCCeEEEecCCc
Confidence            469999999999999999999987765 489999998874

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=97.74  E-value=0.00052  Score=64.46  Aligned_cols=33  Identities=24%  Similarity=0.309  Sum_probs=26.9

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        16 l~~v~~~i~~G~~~~i~G~nGsGKSTLl~~l~G~   49 (210)
T cd03269          16 LDDISFSVEKGEIFGLLGPNGAGKTTTIRMILGI   49 (210)
T ss_pred             EeeeEEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            344433 999999999999999999998887743

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK11248 tauB taurine transporter ATP-binding subunit; Provisional

Probab=97.74  E-value=0.001  Score=64.48  Aligned_cols=61  Identities=13%  Similarity=0.107  Sum_probs=42.1

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|...                  .+...||
T Consensus       144 ~~~p~lllLDEPt~-------~LD-~~~~~~l~~~L~~~~~~~g~tviivsH~~~------------------~~~~~~d  197 (255)
T PRK11248        144 AANPQLLLLDEPFG-------ALD-AFTREQMQTLLLKLWQETGKQVLLITHDIE------------------EAVFMAT  197 (255)
T ss_pred             hcCCCEEEEeCCCc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHhCC
Confidence            35799999993222       222 234566778888887777999999999422                  1456789


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       198 ~i~~l~~  204 (255)
T PRK11248        198 ELVLLSP  204 (255)
T ss_pred             EEEEEeC
Confidence            9888863

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=97.73  E-value=0.00078  Score=63.53  Aligned_cols=34  Identities=26%  Similarity=0.500  Sum_probs=27.6

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++--
T Consensus        18 il~~isl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   52 (216)
T TIGR00960        18 ALDNLNFHITKGEMVFLVGHSGAGKSTFLKLILGI   52 (216)
T ss_pred             EEEeeEEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3454444 999999999999999999998877643

>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE)

Probab=97.73  E-value=0.001  Score=63.34  Aligned_cols=60  Identities=15%  Similarity=0.202  Sum_probs=42.3

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|++++++.+.+||+++|...                  .+.+.||.
T Consensus       162 ~~p~lllLDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tii~~sH~~~------------------~~~~~~d~  215 (228)
T cd03257         162 LNPKLLIADEPTS-------ALD-VSVQAQILDLLKKLQEELGLTLLFITHDLG------------------VVAKIADR  215 (228)
T ss_pred             cCCCEEEecCCCC-------CCC-HHHHHHHHHHHHHHHHHcCCEEEEEeCCHH------------------HHHHhcCe
Confidence            5789999993322       222 234567888888888877999999999422                  14567899


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|+.
T Consensus       216 i~~l~~  221 (228)
T cd03257         216 VAVMYA  221 (228)
T ss_pred             EEEEeC
Confidence            988864

The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=97.73  E-value=0.00087  Score=63.29  Aligned_cols=34  Identities=29%  Similarity=0.346  Sum_probs=27.7

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        19 il~~~s~~i~~G~~~~l~G~nGsGKSTLl~~i~Gl   53 (218)
T cd03255          19 ALKGVSLSIEKGEFVAIVGPSGSGKSTLLNILGGL   53 (218)
T ss_pred             EEeeeEEEEcCCCEEEEEcCCCCCHHHHHHHHhCC
Confidence            3444444 999999999999999999998877644

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=97.72  E-value=0.00044  Score=64.04  Aligned_cols=34  Identities=35%  Similarity=0.546  Sum_probs=27.8

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        24 ~l~~~~~~i~~Ge~~~l~G~nGsGKStLl~~i~Gl   58 (194)
T cd03213          24 LLKNVSGKAKPGELTAIMGPSGAGKSTLLNALAGR   58 (194)
T ss_pred             ceecceEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3444444 999999999999999999998877654

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>PRK13537 nodulation ABC transporter NodI; Provisional

Probab=97.72  E-value=0.00071  Score=67.41  Aligned_cols=34  Identities=24%  Similarity=0.221  Sum_probs=28.3

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+||||++.-++--
T Consensus        22 ~l~~vsl~i~~Gei~gllGpNGaGKSTLl~~l~Gl   56 (306)
T PRK13537         22 VVDGLSFHVQRGECFGLLGPNGAGKTTTLRMLLGL   56 (306)
T ss_pred             EEecceEEEeCCcEEEEECCCCCCHHHHHHHHhcC
Confidence            4555544 999999999999999999998887643

>PF13173 AAA_14: AAA domain

Probab=97.72  E-value=0.00033  Score=60.14  Aligned_cols=41  Identities=15%  Similarity=0.257  Sum_probs=35.0

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR  339 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~  339 (539)
                      +.+++|.|+.|+||||++.|++....  ...+++|++++....
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~--~~~~~~yi~~~~~~~   42 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL--PPENILYINFDDPRD   42 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc--ccccceeeccCCHHH
Confidence            46899999999999999999998776  367899999987555

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=97.72  E-value=0.001  Score=62.68  Aligned_cols=33  Identities=21%  Similarity=0.410  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        17 l~~~sl~i~~G~~~~i~G~nGsGKSTLl~~l~G~   50 (214)
T cd03292          17 LDGINISISAGEFVFLVGPSGAGKSTLLKLIYKE   50 (214)
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            444433 999999999999999999998877654

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>cd03300 ABC_PotA_N PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D

Probab=97.72  E-value=0.00075  Score=64.42  Aligned_cols=61  Identities=16%  Similarity=0.186  Sum_probs=42.0

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-..       +.+ ......+.+.|+.++++.+.+||+++|....                  +...+|
T Consensus       146 ~~~p~llllDEP~~-------gLD-~~~~~~l~~~l~~~~~~~~~tiii~sh~~~~------------------~~~~~d  199 (232)
T cd03300         146 VNEPKVLLLDEPLG-------ALD-LKLRKDMQLELKRLQKELGITFVFVTHDQEE------------------ALTMSD  199 (232)
T ss_pred             hcCCCEEEEcCCcc-------cCC-HHHHHHHHHHHHHHHHHcCCEEEEEeCCHHH------------------HHHhcC
Confidence            35789999993221       222 2344567788888888789999999993221                  346788


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       200 ~i~~l~~  206 (232)
T cd03300         200 RIAVMNK  206 (232)
T ss_pred             EEEEEEC
Confidence            8888864

PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required for homodimerization with PotA and heterdimerization with PotB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=97.71  E-value=0.00042  Score=65.84  Aligned_cols=139  Identities=17%  Similarity=0.166  Sum_probs=80.0

Q ss_pred             chhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHHHHhhCCCccccccC
Q 009230          285 WRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLLEKHIKKPFFEANYG  360 (539)
Q Consensus       285 ~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~~~~i~~~  360 (539)
                      ...+|.+-- +.+|+...|.|.+|+||||++.-++.= ..-....+.|=.-+   ++.++...++...+..+.+      
T Consensus        26 v~avd~Vsf~i~~ge~~glVGESG~GKSTlgr~i~~L-~~pt~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl------   98 (268)
T COG4608          26 VKAVDGVSFSIKEGETLGLVGESGCGKSTLGRLILGL-EEPTSGEILFEGKDITKLSKEERRERVLELLEKVGL------   98 (268)
T ss_pred             eEEecceeEEEcCCCEEEEEecCCCCHHHHHHHHHcC-cCCCCceEEEcCcchhhcchhHHHHHHHHHHHHhCC------
Confidence            355666655 999999999999999999998876532 22223444433222   2223333333322222211      


Q ss_pred             CCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHH
Q 009230          361 GSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQML  440 (539)
Q Consensus       361 ~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~  440 (539)
                            .++       .+...++-+    .+.....  +..++.+  ..+++++|-|-....+.        .....+++
T Consensus        99 ------~~~-------~~~ryPhel----SGGQrQR--i~IARAL--al~P~liV~DEpvSaLD--------vSiqaqIl  149 (268)
T COG4608          99 ------PEE-------FLYRYPHEL----SGGQRQR--IGIARAL--ALNPKLIVADEPVSALD--------VSVQAQIL  149 (268)
T ss_pred             ------CHH-------HhhcCCccc----Cchhhhh--HHHHHHH--hhCCcEEEecCchhhcc--------hhHHHHHH
Confidence                  111       111222322    2333222  2222322  24799999995444332        23456888


Q ss_pred             HHHHHHHHHhCcEEEEEec
Q 009230          441 TMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       441 ~~Lk~lA~~~~i~vi~~~q  459 (539)
                      .-|+.+-++++++.+.++|
T Consensus       150 nLL~dlq~~~~lt~lFIsH  168 (268)
T COG4608         150 NLLKDLQEELGLTYLFISH  168 (268)
T ss_pred             HHHHHHHHHhCCeEEEEEE
Confidence            9999999999999999999

>PRK13637 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.71  E-value=0.00033  Score=69.21  Aligned_cols=62  Identities=15%  Similarity=0.222  Sum_probs=42.6

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|.-.                  .+...||
T Consensus       160 ~~~P~llllDEPt~-------gLD-~~~~~~l~~~l~~l~~~~g~tvi~vtHd~~------------------~~~~~~d  213 (287)
T PRK13637        160 AMEPKILILDEPTA-------GLD-PKGRDEILNKIKELHKEYNMTIILVSHSME------------------DVAKLAD  213 (287)
T ss_pred             HcCCCEEEEECCcc-------CCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHhCC
Confidence            35789999993332       222 244567888888888888999999999311                  1335788


Q ss_pred             eEEEEEeC
Q 009230          488 NGIVIHRN  495 (539)
Q Consensus       488 ~vl~l~r~  495 (539)
                      .++.|...
T Consensus       214 rv~~l~~G  221 (287)
T PRK13637        214 RIIVMNKG  221 (287)
T ss_pred             EEEEEECC
Confidence            88888653

>TIGR03740 galliderm_ABC gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit

Probab=97.71  E-value=0.0009  Score=63.48  Aligned_cols=27  Identities=19%  Similarity=0.170  Sum_probs=24.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+++.|.|++|+|||||+.-++-.
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~G~   49 (223)
T TIGR03740        23 VPKNSVYGLLGPNGAGKSTLLKMITGI   49 (223)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999999998876643

Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family describes the ATP-binding subunit of a gallidermin/epidermin class lantibiotic protection transporter. It is largely restricted to gallidermin-family lantibiotic biosynthesis and export cassettes, but also occurs in orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes.

>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional

Probab=97.71  E-value=0.00043  Score=67.55  Aligned_cols=61  Identities=20%  Similarity=0.275  Sum_probs=41.7

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|....                  +...||
T Consensus       163 ~~~p~lllLDEPt~-------~LD-~~~~~~~~~~l~~l~~~~~~tiii~sH~~~~------------------i~~~~d  216 (265)
T PRK10575        163 AQDSRCLLLDEPTS-------ALD-IAHQVDVLALVHRLSQERGLTVIAVLHDINM------------------AARYCD  216 (265)
T ss_pred             hcCCCEEEEcCCcc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHHH------------------HHHhCC
Confidence            35899999993322       222 2345577888888888789999999994221                  345677


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|.+
T Consensus       217 ~i~~l~~  223 (265)
T PRK10575        217 YLVALRG  223 (265)
T ss_pred             EEEEEEC
Confidence            7777764

>TIGR02769 nickel_nikE nickel import ATP-binding protein NikE

Probab=97.70  E-value=0.00076  Score=65.80  Aligned_cols=60  Identities=13%  Similarity=0.232  Sum_probs=42.0

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|...                  .+...||.
T Consensus       167 ~~p~illLDEPt~-------~LD-~~~~~~l~~~l~~~~~~~g~tiiivsH~~~------------------~~~~~~d~  220 (265)
T TIGR02769       167 VKPKLIVLDEAVS-------NLD-MVLQAVILELLRKLQQAFGTAYLFITHDLR------------------LVQSFCQR  220 (265)
T ss_pred             cCCCEEEEeCCcc-------cCC-HHHHHHHHHHHHHHHHhcCcEEEEEeCCHH------------------HHHHHhcE
Confidence            5789999993332       222 234457888888888888999999999322                  13457888


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|.+
T Consensus       221 i~~l~~  226 (265)
T TIGR02769       221 VAVMDK  226 (265)
T ss_pred             EEEEeC
Confidence            888864

This family represents the NikE subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase.

>PRK11432 fbpC ferric transporter ATP-binding subunit; Provisional

Probab=97.70  E-value=0.00033  Score=71.01  Aligned_cols=33  Identities=15%  Similarity=0.307  Sum_probs=27.0

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        21 ~l~~isl~i~~Ge~~~llGpsGsGKSTLLr~IaG   54 (351)
T PRK11432         21 VIDNLNLTIKQGTMVTLLGPSGCGKTTVLRLVAG   54 (351)
T ss_pred             EEeeeEEEEcCCCEEEEECCCCCcHHHHHHHHHC
Confidence            3555543 99999999999999999999877653

>PRK10771 thiQ thiamine transporter ATP-binding subunit; Provisional

Probab=97.70  E-value=0.00066  Score=64.80  Aligned_cols=61  Identities=16%  Similarity=0.171  Sum_probs=42.2

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|....                  +.+.+|
T Consensus       145 ~~~p~lllLDEP~~-------gLD-~~~~~~~~~~l~~~~~~~~~tiii~sH~~~~------------------~~~~~d  198 (232)
T PRK10771        145 VREQPILLLDEPFS-------ALD-PALRQEMLTLVSQVCQERQLTLLMVSHSLED------------------AARIAP  198 (232)
T ss_pred             hcCCCEEEEeCCcc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEECCHHH------------------HHHhCC
Confidence            35789999993322       222 2344567788888888889999999994322                  346788


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       199 ~i~~l~~  205 (232)
T PRK10771        199 RSLVVAD  205 (232)
T ss_pred             EEEEEEC
Confidence            8888864

>cd03295 ABC_OpuCA_Osmoprotection OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment

Probab=97.70  E-value=0.0012  Score=63.58  Aligned_cols=60  Identities=17%  Similarity=0.117  Sum_probs=41.6

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|...                  .+...||.
T Consensus       152 ~~p~llllDEPt~-------~LD-~~~~~~l~~~L~~~~~~~g~tvii~sH~~~------------------~~~~~~d~  205 (242)
T cd03295         152 ADPPLLLMDEPFG-------ALD-PITRDQLQEEFKRLQQELGKTIVFVTHDID------------------EAFRLADR  205 (242)
T ss_pred             cCCCEEEecCCcc-------cCC-HHHHHHHHHHHHHHHHHcCCEEEEEecCHH------------------HHHHhCCE
Confidence            5789999993322       222 234557788888888877899999999321                  13467888


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|.+
T Consensus       206 i~~l~~  211 (242)
T cd03295         206 IAIMKN  211 (242)
T ss_pred             EEEEEC
Confidence            888864

ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition, to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03262 ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively

Probab=97.69  E-value=0.0011  Score=62.33  Aligned_cols=27  Identities=30%  Similarity=0.443  Sum_probs=24.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        23 i~~G~~~~l~G~nGsGKSTLl~~l~G~   49 (213)
T cd03262          23 VKKGEVVVIIGPSGSGKSTLLRCINLL   49 (213)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999999998877644

Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM. The two HisP subunits form a homodimer within the complex. The domain structure of the amino acid uptake systems is typical for prokaryote extracellular solute binding protein-dependent uptake systems. All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria. The best-studied member of the PAAT (polar amino acid transport) family is the HisJQM

>PRK13645 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.69  E-value=0.0011  Score=65.43  Aligned_cols=34  Identities=32%  Similarity=0.244  Sum_probs=27.8

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        26 il~~is~~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl   60 (289)
T PRK13645         26 ALNNTSLTFKKNKVTCVIGTTGSGKSTMIQLTNGL   60 (289)
T ss_pred             eeeeeEEEEeCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3455444 999999999999999999998877644

>PRK10418 nikD nickel transporter ATP-binding protein NikD; Provisional

Probab=97.69  E-value=0.00099  Score=64.55  Aligned_cols=61  Identities=13%  Similarity=0.130  Sum_probs=41.8

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|...                  .+...+|
T Consensus       156 ~~~p~lLlLDEPt~-------~LD-~~~~~~l~~~L~~~~~~~g~til~~sH~~~------------------~~~~~~d  209 (254)
T PRK10418        156 LCEAPFIIADEPTT-------DLD-VVAQARILDLLESIVQKRALGMLLVTHDMG------------------VVARLAD  209 (254)
T ss_pred             hcCCCEEEEeCCCc-------ccC-HHHHHHHHHHHHHHHHhcCcEEEEEecCHH------------------HHHHhCC
Confidence            35789999993332       222 234457788888888888999999999321                  1345678


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       210 ~v~~l~~  216 (254)
T PRK10418        210 DVAVMSH  216 (254)
T ss_pred             EEEEEEC
Confidence            8887764

>PRK13633 cobalt transporter ATP-binding subunit; Provisional

Probab=97.69  E-value=0.00056  Score=67.32  Aligned_cols=34  Identities=29%  Similarity=0.374  Sum_probs=27.9

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        25 vl~~vs~~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl   59 (280)
T PRK13633         25 ALDDVNLEVKKGEFLVILGRNGSGKSTIAKHMNAL   59 (280)
T ss_pred             eeeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4555544 999999999999999999998877644

>PRK10419 nikE nickel transporter ATP-binding protein NikE; Provisional

Probab=97.69  E-value=0.0013  Score=64.27  Aligned_cols=61  Identities=15%  Similarity=0.268  Sum_probs=42.5

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|....                  +...||
T Consensus       167 ~~~p~lllLDEPt~-------~LD-~~~~~~~~~~l~~~~~~~~~tiiivsH~~~~------------------i~~~~d  220 (268)
T PRK10419        167 AVEPKLLILDEAVS-------NLD-LVLQAGVIRLLKKLQQQFGTACLFITHDLRL------------------VERFCQ  220 (268)
T ss_pred             hcCCCEEEEeCCCc-------ccC-HHHHHHHHHHHHHHHHHcCcEEEEEECCHHH------------------HHHhCC
Confidence            35789999993322       222 2345568888888888889999999994321                  445788


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       221 ~i~~l~~  227 (268)
T PRK10419        221 RVMVMDN  227 (268)
T ss_pred             EEEEEEC
Confidence            8888864

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=97.69  E-value=0.0014  Score=63.97  Aligned_cols=41  Identities=20%  Similarity=0.310  Sum_probs=35.9

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      .++.++++.|++|+||||.+..+|..++.. |.+|++++.+.
T Consensus        70 ~~~~vi~l~G~~G~GKTTt~akLA~~l~~~-g~~V~li~~D~  110 (272)
T TIGR00064        70 NKPNVILFVGVNGVGKTTTIAKLANKLKKQ-GKSVLLAAGDT  110 (272)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHhc-CCEEEEEeCCC
Confidence            345688899999999999999999988764 89999999885

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.

>PRK09473 oppD oligopeptide transporter ATP-binding component; Provisional

Probab=97.69  E-value=0.0011  Score=66.84  Aligned_cols=44  Identities=11%  Similarity=0.220  Sum_probs=33.2

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                      -.++++++.|.-+.-       . +......+++.|+.+.++++.++|+++|
T Consensus       177 ~~~P~llilDEPts~-------L-D~~~~~~i~~lL~~l~~~~g~til~iTH  220 (330)
T PRK09473        177 LCRPKLLIADEPTTA-------L-DVTVQAQIMTLLNELKREFNTAIIMITH  220 (330)
T ss_pred             HcCCCEEEEeCCCcc-------C-CHHHHHHHHHHHHHHHHHcCCEEEEEEC
Confidence            357999999933322       2 2344567888899999889999999999

>PRK11650 ugpC glycerol-3-phosphate transporter ATP-binding subunit; Provisional

Probab=97.68  E-value=0.00084  Score=68.24  Aligned_cols=34  Identities=21%  Similarity=0.321  Sum_probs=27.7

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+||||++.-++--
T Consensus        19 ~l~~vsl~i~~Ge~~~llG~sGsGKSTLLr~iaGl   53 (356)
T PRK11650         19 VIKGIDLDVADGEFIVLVGPSGCGKSTLLRMVAGL   53 (356)
T ss_pred             EEeeeeEEEcCCCEEEEECCCCCcHHHHHHHHHCC
Confidence            4555544 999999999999999999998877643

>PRK13652 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.68  E-value=0.00075  Score=66.28  Aligned_cols=62  Identities=15%  Similarity=0.181  Sum_probs=41.9

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|++++++.+.+||+++|.-.                  .+...||
T Consensus       153 ~~~p~llilDEPt~-------gLD-~~~~~~l~~~l~~l~~~~g~tvli~tH~~~------------------~~~~~~d  206 (277)
T PRK13652        153 AMEPQVLVLDEPTA-------GLD-PQGVKELIDFLNDLPETYGMTVIFSTHQLD------------------LVPEMAD  206 (277)
T ss_pred             HcCCCEEEEeCCcc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEecCHH------------------HHHHhCC
Confidence            35789999993332       222 234557788888888888999999999322                  1345777


Q ss_pred             eEEEEEeC
Q 009230          488 NGIVIHRN  495 (539)
Q Consensus       488 ~vl~l~r~  495 (539)
                      .++.|+..
T Consensus       207 rv~~l~~G  214 (277)
T PRK13652        207 YIYVMDKG  214 (277)
T ss_pred             EEEEEECC
Confidence            87777653

>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake

Probab=97.68  E-value=0.00093  Score=63.10  Aligned_cols=33  Identities=27%  Similarity=0.330  Sum_probs=27.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+.+.|.|++|+|||||+.-++--
T Consensus        21 l~~~sl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   54 (218)
T cd03266          21 VDGVSFTVKPGEVTGLLGPNGAGKTTTLRMLAGL   54 (218)
T ss_pred             ecceEEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            444443 999999999999999999998877643

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.

>COG3840 ThiQ ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]

Probab=97.68  E-value=0.00026  Score=62.75  Aligned_cols=163  Identities=15%  Similarity=0.187  Sum_probs=85.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhh-------------CCCccccccC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHI-------------KKPFFEANYG  360 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~-------------~~~~~~i~~~  360 (539)
                      ++.|+.+.|.|++|+|||||+.=+|--..-+ ...+..-.-+++...-.+|=.++..             ++.+..-   
T Consensus        22 v~~ge~vAi~GpSGaGKSTLLnLIAGF~~P~-~G~i~i~g~d~t~~~P~~RPVSmlFQEnNLFaHLtV~qNigLGl~---   97 (231)
T COG3840          22 VPAGEIVAILGPSGAGKSTLLNLIAGFETPA-SGEILINGVDHTASPPAERPVSMLFQENNLFAHLTVAQNIGLGLS---   97 (231)
T ss_pred             ecCCcEEEEECCCCccHHHHHHHHHhccCCC-CceEEEcCeecCcCCcccCChhhhhhccccchhhhhhhhhcccCC---
Confidence            8999999999999999999976655433322 2333333333332222222211111             1111100   


Q ss_pred             CCCCCCCHHHHHHHHHHh---------hccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCC
Q 009230          361 GSAERMTVEEFEQGKAWL---------SNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQT  431 (539)
Q Consensus       361 ~~~~~l~~~~~~~~~~~l---------~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~  431 (539)
                       +.-+++.++.+++...+         +..+--.    .+  .-.+-.+.++-+++..  .+..+|.-..-+       +
T Consensus        98 -P~LkL~a~~r~~v~~aa~~vGl~~~~~RLP~~L----SG--GqRQRvALARclvR~~--PilLLDEPFsAL-------d  161 (231)
T COG3840          98 -PGLKLNAEQREKVEAAAAQVGLAGFLKRLPGEL----SG--GQRQRVALARCLVREQ--PILLLDEPFSAL-------D  161 (231)
T ss_pred             -cccccCHHHHHHHHHHHHHhChhhHhhhCcccc----Cc--hHHHHHHHHHHHhccC--CeEEecCchhhc-------C
Confidence             11256666655443222         1111111    12  2233344445555543  367777222211       1


Q ss_pred             HHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          432 ETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       432 ~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      . .--.++..-+..++.+.+.++++|+| +..                   ..+.+|.++++.+-+
T Consensus       162 P-~LR~eMl~Lv~~l~~E~~~TllmVTH~~~D-------------------a~~ia~~~~fl~~Gr  207 (231)
T COG3840         162 P-ALRAEMLALVSQLCDERKMTLLMVTHHPED-------------------AARIADRVVFLDNGR  207 (231)
T ss_pred             H-HHHHHHHHHHHHHHHhhCCEEEEEeCCHHH-------------------HHHhhhceEEEeCCE
Confidence            1 11245677778899999999999999 432                   235788888887543

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=97.68  E-value=0.00068  Score=69.68  Aligned_cols=38  Identities=21%  Similarity=0.354  Sum_probs=34.3

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      .+++++|++|+||||.+..+|..+..+ |.+|+.++.+-
T Consensus       101 ~vi~lvG~~GvGKTTtaaKLA~~l~~~-G~kV~lV~~D~  138 (429)
T TIGR01425       101 NVIMFVGLQGSGKTTTCTKLAYYYQRK-GFKPCLVCADT  138 (429)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHC-CCCEEEEcCcc
Confidence            589999999999999999999987764 99999999884

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.

>PRK14250 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.67  E-value=0.0011  Score=63.76  Aligned_cols=61  Identities=8%  Similarity=0.117  Sum_probs=42.5

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|....                  +...||
T Consensus       147 ~~~p~llllDEPt~-------~LD-~~~~~~l~~~l~~~~~~~g~tii~~sH~~~~------------------~~~~~d  200 (241)
T PRK14250        147 ANNPEVLLLDEPTS-------ALD-PTSTEIIEELIVKLKNKMNLTVIWITHNMEQ------------------AKRIGD  200 (241)
T ss_pred             hcCCCEEEEeCCcc-------cCC-HHHHHHHHHHHHHHHHhCCCEEEEEeccHHH------------------HHHhCC
Confidence            35889999993332       222 2345567788888888789999999994221                  346789


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       201 ~i~~l~~  207 (241)
T PRK14250        201 YTAFLNK  207 (241)
T ss_pred             EEEEEeC
Confidence            9888874

>cd03296 ABC_CysA_sulfate_importer Part of the ABC transporter complex cysAWTP involved in sulfate import

Probab=97.67  E-value=0.0011  Score=63.64  Aligned_cols=60  Identities=13%  Similarity=0.228  Sum_probs=41.5

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|...                  .+...||.
T Consensus       153 ~~p~llllDEP~~-------~LD-~~~~~~l~~~l~~~~~~~~~tvii~sH~~~------------------~~~~~~d~  206 (239)
T cd03296         153 VEPKVLLLDEPFG-------ALD-AKVRKELRRWLRRLHDELHVTTVFVTHDQE------------------EALEVADR  206 (239)
T ss_pred             cCCCEEEEcCCcc-------cCC-HHHHHHHHHHHHHHHHHcCCEEEEEeCCHH------------------HHHHhCCE
Confidence            5789999993322       222 234456778888888878999999999322                  13457888


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|..
T Consensus       207 i~~l~~  212 (239)
T cd03296         207 VVVMNK  212 (239)
T ss_pred             EEEEEC
Confidence            888864

Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK09452 potA putrescine/spermidine ABC transporter ATPase protein; Reviewed

Probab=97.67  E-value=0.00014  Score=74.29  Aligned_cols=44  Identities=18%  Similarity=0.198  Sum_probs=32.2

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      .+++++++|.=+.       +.+ ......+...|+++.++.++++|+++|.
T Consensus       161 ~~P~llLLDEP~s-------~LD-~~~r~~l~~~L~~l~~~~g~tiI~vTHd  204 (375)
T PRK09452        161 NKPKVLLLDESLS-------ALD-YKLRKQMQNELKALQRKLGITFVFVTHD  204 (375)
T ss_pred             cCCCEEEEeCCCC-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            4789999992221       222 2334568888899999999999999993

>TIGR03265 PhnT2 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein

Probab=97.67  E-value=0.0012  Score=67.12  Aligned_cols=33  Identities=21%  Similarity=0.331  Sum_probs=27.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-|+--
T Consensus        20 l~~vs~~i~~Ge~~~l~GpsGsGKSTLLr~iaGl   53 (353)
T TIGR03265        20 LKDISLSVKKGEFVCLLGPSGCGKTTLLRIIAGL   53 (353)
T ss_pred             EEeeEEEEcCCCEEEEECCCCCCHHHHHHHHHCC
Confidence            444443 899999999999999999998877643

This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.

>TIGR03258 PhnT 2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT

Probab=97.66  E-value=0.0011  Score=67.34  Aligned_cols=33  Identities=27%  Similarity=0.437  Sum_probs=27.3

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        20 ~l~~vsl~i~~Ge~~~llGpsGsGKSTLLr~iaG   53 (362)
T TIGR03258        20 VLDDLSLEIEAGELLALIGKSGCGKTTLLRAIAG   53 (362)
T ss_pred             EEeeeEEEECCCCEEEEECCCCCCHHHHHHHHhC
Confidence            3555544 99999999999999999999887764

This ATP-binding component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate.

>TIGR01188 drrA daunorubicin resistance ABC transporter ATP-binding subunit

Probab=97.66  E-value=0.00071  Score=67.35  Aligned_cols=33  Identities=27%  Similarity=0.271  Sum_probs=27.0

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus         8 ~l~~vs~~i~~Ge~~~l~G~NGaGKSTLl~~l~G   41 (302)
T TIGR01188         8 AVDGVNFKVREGEVFGFLGPNGAGKTTTIRMLTT   41 (302)
T ss_pred             EEeeeeEEEcCCcEEEEECCCCCCHHHHHHHHhC
Confidence            3555544 99999999999999999999877664

This model describes daunorubicin resistance ABC transporter, ATP binding subunit in bacteria and archaea. This model is restricted in its scope to preferentially recognize the ATP binding subunit associated with effux of the drug, daunorubicin. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. In eukaryotes proteins of similar function include p-gyco proteins, multidrug resistance protein etc.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.66  E-value=0.00036  Score=68.56  Aligned_cols=43  Identities=19%  Similarity=0.265  Sum_probs=37.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-CeEEEEeCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAG-WKFVLCSMEN  336 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-~~vl~~s~E~  336 (539)
                      +..+.+++|.|++|+||||++..++..++..+| .+|.+++++.
T Consensus       191 ~~~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~  234 (282)
T TIGR03499       191 LEQGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDT  234 (282)
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCc
Confidence            346789999999999999999999999887534 8999999885

>cd03294 ABC_Pro_Gly_Bertaine This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea

Probab=97.65  E-value=0.0014  Score=64.15  Aligned_cols=61  Identities=11%  Similarity=0.077  Sum_probs=42.3

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|...                  .+...+|
T Consensus       176 ~~~p~illLDEPt~-------~LD-~~~~~~l~~~l~~~~~~~g~tiii~tH~~~------------------~~~~~~d  229 (269)
T cd03294         176 AVDPDILLMDEAFS-------ALD-PLIRREMQDELLRLQAELQKTIVFITHDLD------------------EALRLGD  229 (269)
T ss_pred             hcCCCEEEEcCCCc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHhcC
Confidence            35789999993221       222 344567788888888777899999999421                  1446789


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       230 ~v~~l~~  236 (269)
T cd03294         230 RIAIMKD  236 (269)
T ss_pred             EEEEEEC
Confidence            8888864

This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK13648 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.65  E-value=0.00049  Score=67.34  Aligned_cols=33  Identities=27%  Similarity=0.333  Sum_probs=27.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        25 l~~isl~i~~Ge~~~I~G~nGsGKSTLl~~i~Gl   58 (269)
T PRK13648         25 LKDVSFNIPKGQWTSIVGHNGSGKSTIAKLMIGI   58 (269)
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            444444 999999999999999999998777644

>PRK11701 phnK phosphonate C-P lyase system protein PhnK; Provisional

Probab=97.65  E-value=0.00094  Score=64.88  Aligned_cols=61  Identities=11%  Similarity=0.115  Sum_probs=42.8

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|....                  +.+.||
T Consensus       167 ~~~p~llllDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tii~isH~~~~------------------~~~~~d  220 (258)
T PRK11701        167 VTHPRLVFMDEPTG-------GLD-VSVQARLLDLLRGLVRELGLAVVIVTHDLAV------------------ARLLAH  220 (258)
T ss_pred             hcCCCEEEEcCCcc-------cCC-HHHHHHHHHHHHHHHHhcCcEEEEEeCCHHH------------------HHHhcC
Confidence            35799999993322       222 2345677888888888889999999994322                  345788


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       221 ~i~~l~~  227 (258)
T PRK11701        221 RLLVMKQ  227 (258)
T ss_pred             EEEEEEC
Confidence            8888875

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=97.65  E-value=0.0012  Score=61.85  Aligned_cols=34  Identities=21%  Similarity=0.285  Sum_probs=27.4

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        15 ~l~~~~~~i~~G~~~~i~G~nGsGKSTLl~~l~Gl   49 (208)
T cd03268          15 VLDDISLHVKKGEIYGFLGPNGAGKTTTMKIILGL   49 (208)
T ss_pred             eEeeeEEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3444433 899999999999999999998877643

Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.

>PRK10908 cell division protein FtsE; Provisional

Probab=97.65  E-value=0.0014  Score=62.04  Aligned_cols=33  Identities=27%  Similarity=0.439  Sum_probs=27.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        18 l~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~l~G~   51 (222)
T PRK10908         18 LQGVTFHMRPGEMAFLTGHSGAGKSTLLKLICGI   51 (222)
T ss_pred             EeeeeEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            444433 999999999999999999998887643

>TIGR01288 nodI ATP-binding ABC transporter family nodulation protein NodI

Probab=97.65  E-value=0.0011  Score=66.13  Aligned_cols=34  Identities=26%  Similarity=0.268  Sum_probs=27.6

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        19 ~l~~vsl~i~~Ge~~~l~G~NGaGKSTLl~~l~Gl   53 (303)
T TIGR01288        19 VVNDLSFTIARGECFGLLGPNGAGKSTIARMLLGM   53 (303)
T ss_pred             EEcceeEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3455544 999999999999999999998877643

This model does not recognize the highly divergent NodI from Azorhizobium caulinodans.

>PRK13651 cobalt transporter ATP-binding subunit; Provisional

Probab=97.64  E-value=0.00055  Score=68.07  Aligned_cols=35  Identities=29%  Similarity=0.480  Sum_probs=28.7

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.|+.+.- +.+|+++.|.|++|+|||||+.-++--
T Consensus        21 ~~l~~vsl~i~~Ge~v~iiG~nGsGKSTLl~~L~Gl   56 (305)
T PRK13651         21 KALDNVSVEINQGEFIAIIGQTGSGKTTFIEHLNAL   56 (305)
T ss_pred             cceeeeEEEEeCCCEEEEECCCCCcHHHHHHHHhCC
Confidence            35666554 999999999999999999998877643

>COG4559 ABC-type hemin transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.64  E-value=0.0017  Score=59.11  Aligned_cols=173  Identities=20%  Similarity=0.159  Sum_probs=95.5

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHH--HHhhCC--Cc-----
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLL--EKHIKK--PF-----  354 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~--~~~~~~--~~-----  354 (539)
                      ||.+-- +++||+..|.||.|+|||||+..+.-.+.-. +..|.|+...   .+++++.++..  -+.+.+  +|     
T Consensus        17 l~~vsl~~~pGev~ailGPNGAGKSTlLk~LsGel~p~-~G~v~~~g~~l~~~~~~~lA~~raVlpQ~s~laFpFtv~eV   95 (259)
T COG4559          17 LDGVSLDLRPGEVLAILGPNGAGKSTLLKALSGELSPD-SGEVTLNGVPLNSWPPEELARHRAVLPQNSSLAFPFTVQEV   95 (259)
T ss_pred             ccCcceeccCCcEEEEECCCCccHHHHHHHhhCccCCC-CCeEeeCCcChhhCCHHHHHHHhhhcccCcccccceEHHHH
Confidence            444433 9999999999999999999999988777643 5677777654   55666654431  111111  11     


Q ss_pred             ---cccccCCCCCCCCHHHH---HHHHH-----HhhccceeEeecCCCCCCHHHHHHHHHHHHHHcC----CcEEEEccc
Q 009230          355 ---FEANYGGSAERMTVEEF---EQGKA-----WLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHG----VRGLVIDPY  419 (539)
Q Consensus       355 ---~~i~~~~~~~~l~~~~~---~~~~~-----~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~----~~~vvID~~  419 (539)
                         ..+..+  .+.-..++-   +++..     .+..+.+-- .  .+..  .+=...++-++....    .+.+++|.=
T Consensus        96 V~mGr~p~~--~g~~~~e~~~i~~~ala~~d~~~la~R~y~~-L--SGGE--qQRVqlARvLaQl~~~v~~~r~L~LDEP  168 (259)
T COG4559          96 VQMGRIPHR--SGREPEEDERIAAQALAATDLSGLAGRDYRT-L--SGGE--QQRVQLARVLAQLWPPVPSGRWLFLDEP  168 (259)
T ss_pred             HHhcccccc--cCCCchhhHHHHHHHHHHcChhhhhccchhh-c--CchH--HHHHHHHHHHHHccCCCCCCceEEecCC
Confidence               111111  112211221   22221     222222211 0  1111  222333444444443    358899922


Q ss_pred             cccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          420 NELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       420 ~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      +       +..+- .-+..+++..+.||++- +.|+++-| -.-                   -.++||.++.|++-+
T Consensus       169 t-------saLDi-~HQ~~tl~laR~la~~g-~~V~~VLHDLNL-------------------AA~YaDrivll~~Gr  218 (259)
T COG4559         169 T-------SALDI-AHQHHTLRLARQLAREG-GAVLAVLHDLNL-------------------AAQYADRIVLLHQGR  218 (259)
T ss_pred             c-------cccch-HHHHHHHHHHHHHHhcC-CcEEEEEccchH-------------------HHHhhheeeeeeCCe
Confidence            2       22222 23456889999999876 77888777 221                   236899999998755

>PRK13635 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.64  E-value=0.00052  Score=67.47  Aligned_cols=45  Identities=11%  Similarity=0.149  Sum_probs=32.9

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      ...++++++|.-+.       +.+ ......+++.|+.++++.+.+||+++|.
T Consensus       156 ~~~p~lllLDEPt~-------gLD-~~~~~~l~~~l~~l~~~~~~tilivsH~  200 (279)
T PRK13635        156 ALQPDIIILDEATS-------MLD-PRGRREVLETVRQLKEQKGITVLSITHD  200 (279)
T ss_pred             HcCCCEEEEeCCcc-------cCC-HHHHHHHHHHHHHHHHcCCCEEEEEecC
Confidence            35789999993322       222 2345678888888988889999999993

>PRK10619 histidine/lysine/arginine/ornithine transporter subunit; Provisional

Probab=97.64  E-value=0.0014  Score=63.72  Aligned_cols=33  Identities=21%  Similarity=0.333  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        21 l~~is~~i~~Ge~~~l~G~nGsGKSTLl~~i~G~   54 (257)
T PRK10619         21 LKGVSLQANAGDVISIIGSSGSGKSTFLRCINFL   54 (257)
T ss_pred             EeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            444433 999999999999999999998877654

>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters

Probab=97.64  E-value=0.00079  Score=63.35  Aligned_cols=33  Identities=30%  Similarity=0.500  Sum_probs=27.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        15 l~~isl~i~~Ge~~~l~G~nGsGKSTLl~~l~G~   48 (213)
T cd03235          15 LEDVSFEVKPGEFLAIVGPNGAGKSTLLKAILGL   48 (213)
T ss_pred             eecceeEEcCCCEEEEECCCCCCHHHHHHHHcCC
Confidence            444443 999999999999999999998876643

This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.

>cd03299 ABC_ModC_like Archeal protein closely related to ModC

Probab=97.63  E-value=0.0013  Score=62.82  Aligned_cols=62  Identities=13%  Similarity=0.095  Sum_probs=42.1

Q ss_pred             HHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhcc
Q 009230          407 LRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKC  486 (539)
Q Consensus       407 ~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~a  486 (539)
                      -..+++++++|.-+.       +.+ ......+.+.|+.++.+.+.+||+++|....                  +...+
T Consensus       144 l~~~p~llllDEPt~-------gLD-~~~~~~l~~~l~~~~~~~~~tili~tH~~~~------------------~~~~~  197 (235)
T cd03299         144 LVVNPKILLLDEPFS-------ALD-VRTKEKLREELKKIRKEFGVTVLHVTHDFEE------------------AWALA  197 (235)
T ss_pred             HHcCCCEEEECCCcc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEecCHHH------------------HHHhC
Confidence            345889999993332       122 2345577788888888789999999993211                  34567


Q ss_pred             ceEEEEEe
Q 009230          487 DNGIVIHR  494 (539)
Q Consensus       487 D~vl~l~r  494 (539)
                      |.++.+..
T Consensus       198 d~i~~l~~  205 (235)
T cd03299         198 DKVAIMLN  205 (235)
T ss_pred             CEEEEEEC
Confidence            88888864

ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK13536 nodulation factor exporter subunit NodI; Provisional

Probab=97.63  E-value=0.0012  Score=66.77  Aligned_cols=34  Identities=26%  Similarity=0.238  Sum_probs=28.3

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+||||++.-++-.
T Consensus        56 ~l~~is~~i~~Gei~gLlGpNGaGKSTLl~~L~Gl   90 (340)
T PRK13536         56 VVNGLSFTVASGECFGLLGPNGAGKSTIARMILGM   90 (340)
T ss_pred             EEeeeEEEEcCCCEEEEECCCCCCHHHHHHHHHcC
Confidence            4555544 999999999999999999998877653

>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]

Probab=97.63  E-value=0.00035  Score=65.08  Aligned_cols=170  Identities=16%  Similarity=0.183  Sum_probs=92.4

Q ss_pred             Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc-C-----CeEE-E------EeCCCCHHHHHHHHHHHh
Q 009230          284 GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHA-G-----WKFV-L------CSMENKVREHARKLLEKH  349 (539)
Q Consensus       284 g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~-g-----~~vl-~------~s~E~~~~~~~~r~~~~~  349 (539)
                      .+..|+++.- +.+|+-+.|.|++|+||||++.=++- +.... |     .+|. .      |..|++..+-+ ++.+..
T Consensus        39 ~~~aL~disf~i~~Ge~vGiiG~NGaGKSTLlkliaG-i~~Pt~G~v~v~G~v~~li~lg~Gf~pelTGreNi-~l~~~~  116 (249)
T COG1134          39 EFWALKDISFEIYKGERVGIIGHNGAGKSTLLKLIAG-IYKPTSGKVKVTGKVAPLIELGAGFDPELTGRENI-YLRGLI  116 (249)
T ss_pred             eEEEecCceEEEeCCCEEEEECCCCCcHHHHHHHHhC-ccCCCCceEEEcceEehhhhcccCCCcccchHHHH-HHHHHH
Confidence            3455666655 99999999999999999999765543 22211 1     1222 1      22334433221 233444


Q ss_pred             hCCCccccccCCCCCCCC-HHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHH-HHHHHcCCcEEEEccccccccCCC
Q 009230          350 IKKPFFEANYGGSAERMT-VEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAK-AAVLRHGVRGLVIDPYNELDHQRP  427 (539)
Q Consensus       350 ~~~~~~~i~~~~~~~~l~-~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~-~~~~~~~~~~vvID~~~~l~~~~~  427 (539)
                      .|....++...     ++ -.++.++-+.+. .|+       ...+ .-...++. ..+....+++++||..+..-    
T Consensus       117 ~G~~~~ei~~~-----~~eIieFaELG~fi~-~Pv-------ktYS-SGM~aRLaFsia~~~~pdILllDEvlavG----  178 (249)
T COG1134         117 LGLTRKEIDEK-----VDEIIEFAELGDFID-QPV-------KTYS-SGMYARLAFSVATHVEPDILLLDEVLAVG----  178 (249)
T ss_pred             hCccHHHHHHH-----HHHHHHHHHHHHHhh-Cch-------hhcc-HHHHHHHHHhhhhhcCCCEEEEehhhhcC----
Confidence            45443333210     00 001112222221 111       0111 11222222 23344679999999665442    


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          428 VSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       428 ~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                          +...+......+..+.++. .+||+++|+-                  +.|.+.||.++.|+.-+
T Consensus       179 ----D~~F~~K~~~rl~e~~~~~-~tiv~VSHd~------------------~~I~~~Cd~~i~l~~G~  224 (249)
T COG1134         179 ----DAAFQEKCLERLNELVEKN-KTIVLVSHDL------------------GAIKQYCDRAIWLEHGQ  224 (249)
T ss_pred             ----CHHHHHHHHHHHHHHHHcC-CEEEEEECCH------------------HHHHHhcCeeEEEeCCE
Confidence                2345667778888887655 8899999942                  23678999999998643

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=97.63  E-value=0.0017  Score=61.13  Aligned_cols=33  Identities=24%  Similarity=0.421  Sum_probs=26.6

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+-- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        18 l~~is~~i~~G~~~~l~G~nGsGKSTLl~~i~Gl   51 (214)
T TIGR02673        18 LHDVSLHIRKGEFLFLTGPSGAGKTTLLKLLYGA   51 (214)
T ss_pred             ecceeEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            444433 999999999999999999998766543

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>PRK11000 maltose/maltodextrin transporter ATP-binding protein; Provisional

Probab=97.63  E-value=0.0013  Score=67.31  Aligned_cols=32  Identities=19%  Similarity=0.362  Sum_probs=26.6

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        19 l~~vsl~i~~Ge~~~l~G~nGsGKSTLL~~iaG   51 (369)
T PRK11000         19 SKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAG   51 (369)
T ss_pred             EeeeEEEEcCCCEEEEECCCCCcHHHHHHHHhC
Confidence            444433 99999999999999999999887764

>COG4555 NatA ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]

Probab=97.63  E-value=0.0012  Score=59.54  Aligned_cols=50  Identities=16%  Similarity=0.210  Sum_probs=36.5

Q ss_pred             chhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          285 WRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       285 ~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ...++++.- ...|+++.|-|+.|+||||++.-++.-+.-. ...|..-++.
T Consensus        15 v~AvrdVSF~ae~Gei~GlLG~NGAGKTT~LRmiatlL~P~-~G~v~idg~d   65 (245)
T COG4555          15 VQAVRDVSFEAEEGEITGLLGENGAGKTTLLRMIATLLIPD-SGKVTIDGVD   65 (245)
T ss_pred             HhhhhheeEEeccceEEEEEcCCCCCchhHHHHHHHhccCC-CceEEEeecc
Confidence            345666665 8999999999999999999998887655432 3455555544

>PRK13643 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.62  E-value=0.00051  Score=67.84  Aligned_cols=34  Identities=32%  Similarity=0.305  Sum_probs=28.0

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        21 ~l~~vsl~i~~Ge~v~i~G~nGsGKSTLl~~l~Gl   55 (288)
T PRK13643         21 ALFDIDLEVKKGSYTALIGHTGSGKSTLLQHLNGL   55 (288)
T ss_pred             ceeeeEEEEcCCCEEEEECCCCChHHHHHHHHhcC
Confidence            4555544 999999999999999999998877643

>TIGR03005 ectoine_ehuA ectoine/hydroxyectoine ABC transporter, ATP-binding protein

Probab=97.61  E-value=0.0014  Score=63.32  Aligned_cols=61  Identities=16%  Similarity=0.274  Sum_probs=42.2

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|++++++.+.+||+++|....                  +...+|
T Consensus       162 ~~~p~llllDEP~~-------~LD-~~~~~~l~~~l~~~~~~~~~tiiivsH~~~~------------------~~~~~d  215 (252)
T TIGR03005       162 AMRPKVMLFDEVTS-------ALD-PELVGEVLNVIRRLASEHDLTMLLVTHEMGF------------------AREFAD  215 (252)
T ss_pred             HcCCCEEEEeCCcc-------cCC-HHHHHHHHHHHHHHHHhcCcEEEEEeCCHHH------------------HHHhcC
Confidence            35789999993332       222 2334577888888888889999999994221                  345788


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       216 ~i~~l~~  222 (252)
T TIGR03005       216 RVCFFDK  222 (252)
T ss_pred             EEEEEEC
Confidence            8888864

Members of this family are the ATP-binding protein of a conserved four gene ABC transporter operon found next to ectoine unilization operons and ectoine biosynthesis operons. Ectoine is a compatible solute that protects enzymes from high osmolarity. It is released by some species in response to hypoosmotic shock, and it is taken up by a number of bacteria as a compatible solute or for consumption. This family shows strong sequence similiarity to a number of amino acid ABC transporter ATP-binding proteins.

>COG1123 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]

Probab=97.61  E-value=0.00088  Score=70.08  Aligned_cols=178  Identities=19%  Similarity=0.161  Sum_probs=96.5

Q ss_pred             chhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC--CCHHHHH--HHHHHHhhCCCcccccc
Q 009230          285 WRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME--NKVREHA--RKLLEKHIKKPFFEANY  359 (539)
Q Consensus       285 ~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E--~~~~~~~--~r~~~~~~~~~~~~i~~  359 (539)
                      ...+|++.- +++||...|.|.|||||||++.-++--. ...+..+.|..-+  ++..+..  +|-+.+...-++..+  
T Consensus       304 ~~Av~~VSf~l~~GE~lglVGeSGsGKSTlar~i~gL~-~P~~G~i~~~g~~~~~~~~~~~~~r~~~QmvFQdp~~SL--  380 (539)
T COG1123         304 VKAVDDVSFDLREGETLGLVGESGSGKSTLARILAGLL-PPSSGSIIFDGQDLDLTGGELRRLRRRIQMVFQDPYSSL--  380 (539)
T ss_pred             eeeeeeeeeEecCCCEEEEECCCCCCHHHHHHHHhCCC-CCCCceEEEeCcccccccchhhhhhhheEEEEeCccccc--
Confidence            455666655 9999999999999999999988776433 2235566665533  3321111  111111111111111  


Q ss_pred             CCCCCCCCH----------------HHHHHHHHHhhcc----c-eeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcc
Q 009230          360 GGSAERMTV----------------EEFEQGKAWLSNT----F-SLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDP  418 (539)
Q Consensus       360 ~~~~~~l~~----------------~~~~~~~~~l~~~----~-~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~  418 (539)
                         +++++-                .+.++...++-+.    . +.-++-++-+....+=...++.+  ...|+++|.|.
T Consensus       381 ---nPr~tV~~~i~epL~~~~~~~~~~~~~rv~~ll~~VgL~~~~l~ryP~elSGGQrQRvaIARAL--a~~P~lli~DE  455 (539)
T COG1123         381 ---NPRMTVGDILAEPLRIHGGGSGAERRARVAELLELVGLPPEFLDRYPHELSGGQRQRVAIARAL--ALEPKLLILDE  455 (539)
T ss_pred             ---CccccHHHHHHhHHhhhcccchHHHHHHHHHHHHHcCCCHHHHhcCchhcCcchhHHHHHHHHH--hcCCCEEEecC
Confidence               111211                1111111111110    0 01000001111122222233333  35799999994


Q ss_pred             ccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          419 YNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       419 ~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      -...+        +..-..+++.-|+.+-+++|++.++++|.-.                  .+.+.||.|.++++-+
T Consensus       456 p~SaL--------Dvsvqa~VlnLl~~lq~e~g~t~lfISHDl~------------------vV~~i~drv~vm~~G~  507 (539)
T COG1123         456 PVSAL--------DVSVQAQVLNLLKDLQEELGLTYLFISHDLA------------------VVRYIADRVAVMYDGR  507 (539)
T ss_pred             Ccccc--------CHHHHHHHHHHHHHHHHHhCCEEEEEeCCHH------------------HHHhhCceEEEEECCe
Confidence            44333        2234578999999999999999999999322                  3678999999999755

>PRK13546 teichoic acids export protein ATP-binding subunit; Provisional

Probab=97.61  E-value=0.00086  Score=65.26  Aligned_cols=35  Identities=23%  Similarity=0.314  Sum_probs=28.3

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.|+.+.- +.+|+.+.|.|++|+|||||+.-++--
T Consensus        38 ~il~~is~~i~~Ge~~~liG~NGsGKSTLlk~L~Gl   73 (264)
T PRK13546         38 FALDDISLKAYEGDVIGLVGINGSGKSTLSNIIGGS   73 (264)
T ss_pred             EEEeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34554444 999999999999999999998877654

>PRK11831 putative ABC transporter ATP-binding protein YrbF; Provisional

Probab=97.61  E-value=0.0013  Score=64.29  Aligned_cols=33  Identities=18%  Similarity=0.311  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        23 l~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   56 (269)
T PRK11831         23 FDNISLTVPRGKITAIMGPSGIGKTTLLRLIGGQ   56 (269)
T ss_pred             EeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            444433 999999999999999999998877644

>cd03297 ABC_ModC_molybdenum_transporter ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB

Probab=97.60  E-value=0.0018  Score=60.89  Aligned_cols=61  Identities=18%  Similarity=0.137  Sum_probs=42.7

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|...                  .+...+|
T Consensus       147 ~~~p~llllDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tiii~sH~~~------------------~~~~~~d  200 (214)
T cd03297         147 AAQPELLLLDEPFS-------ALD-RALRLQLLPELKQIKKNLNIPVIFVTHDLS------------------EAEYLAD  200 (214)
T ss_pred             hcCCCEEEEcCCcc-------cCC-HHHHHHHHHHHHHHHHHcCcEEEEEecCHH------------------HHHHhcC
Confidence            35789999993222       222 334567888888888888999999999422                  1446788


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|.+
T Consensus       201 ~i~~l~~  207 (214)
T cd03297         201 RIVVMED  207 (214)
T ss_pred             EEEEEEC
Confidence            8888864

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG1123 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]

Probab=97.60  E-value=0.0017  Score=67.95  Aligned_cols=65  Identities=17%  Similarity=0.234  Sum_probs=49.9

Q ss_pred             HHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhc
Q 009230          406 VLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINK  485 (539)
Q Consensus       406 ~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~  485 (539)
                      +...+|+++|.|-=++.       . +-..+.++++.|+.+.+++|+++++++|.-                  +-+++.
T Consensus       168 ALa~~P~LLIaDEPTTa-------L-Dvt~q~qIL~llk~l~~e~g~a~l~ITHDl------------------~Vva~~  221 (539)
T COG1123         168 ALALKPKLLIADEPTTA-------L-DVTTQAQILDLLKDLQRELGMAVLFITHDL------------------GVVAEL  221 (539)
T ss_pred             HHhCCCCEEEECCCccc-------c-CHHHHHHHHHHHHHHHHHcCcEEEEEcCCH------------------HHHHHh
Confidence            34568999999933322       2 234567899999999999999999999932                  246789


Q ss_pred             cceEEEEEeCC
Q 009230          486 CDNGIVIHRNR  496 (539)
Q Consensus       486 aD~vl~l~r~~  496 (539)
                      ||.|++|++-+
T Consensus       222 aDrv~Vm~~G~  232 (539)
T COG1123         222 ADRVVVMYKGE  232 (539)
T ss_pred             cCeEEEEECCE
Confidence            99999999855

>COG0410 LivF ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]

Probab=97.60  E-value=0.00057  Score=63.14  Aligned_cols=163  Identities=18%  Similarity=0.250  Sum_probs=89.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLLEKHIKKPFFEANYGGSAERMTVEE  370 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~  370 (539)
                      +.+|+++.|-|+.|+||||++..++-..-. ....|.|-.-+   .++.+.+++=+   +-++..+-.    .+.|+.+|
T Consensus        26 v~~Geiv~llG~NGaGKTTlLkti~Gl~~~-~~G~I~~~G~dit~~p~~~r~r~Gi---~~VPegR~i----F~~LTVeE   97 (237)
T COG0410          26 VERGEIVALLGRNGAGKTTLLKTIMGLVRP-RSGRIIFDGEDITGLPPHERARLGI---AYVPEGRRI----FPRLTVEE   97 (237)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCCC-CCeeEEECCeecCCCCHHHHHhCCe---EeCcccccc----hhhCcHHH
Confidence            899999999999999999999887644322 23455554444   33444433321   122221111    12344333


Q ss_pred             -H-----------------HHHH---HHhhccceeEeecCCCCC--CHHHHHHHHHHHHHHcCCcEEEEccccccccCCC
Q 009230          371 -F-----------------EQGK---AWLSNTFSLIRCENDSLP--SIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRP  427 (539)
Q Consensus       371 -~-----------------~~~~---~~l~~~~~~i~~~~~~~~--~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~  427 (539)
                       +                 ++++   -.|.++..    ..-+..  .-.+..+..+.+.  ..|+++++|       .+.
T Consensus        98 NL~~g~~~~~~~~~~~~~~e~v~~lFP~Lker~~----~~aG~LSGGEQQMLAiaRALm--~~PklLLLD-------EPs  164 (237)
T COG0410          98 NLLLGAYARRDKEAQERDLEEVYELFPRLKERRN----QRAGTLSGGEQQMLAIARALM--SRPKLLLLD-------EPS  164 (237)
T ss_pred             HHhhhhhcccccccccccHHHHHHHChhHHHHhc----CcccCCChHHHHHHHHHHHHh--cCCCEEEec-------CCc
Confidence             1                 1111   11111100    000111  1223444444433  479999999       111


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          428 VSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       428 ~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      -+. ....+.++.+.++.+.++.+++|+++-||-..                  .-..||...+|.+-+
T Consensus       165 ~GL-aP~iv~~I~~~i~~l~~~~g~tIlLVEQn~~~------------------Al~iaDr~yvle~Gr  214 (237)
T COG0410         165 EGL-APKIVEEIFEAIKELRKEGGMTILLVEQNARF------------------ALEIADRGYVLENGR  214 (237)
T ss_pred             cCc-CHHHHHHHHHHHHHHHHcCCcEEEEEeccHHH------------------HHHhhCEEEEEeCCE
Confidence            122 23567889999999999999999999995332                  124778888887543

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.60  E-value=0.0027  Score=65.99  Aligned_cols=42  Identities=17%  Similarity=0.225  Sum_probs=36.7

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHH-HhcCCeEEEEeCCC
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNIN-EHAGWKFVLCSMEN  336 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a-~~~g~~vl~~s~E~  336 (539)
                      ..|..+++.|++|+||||++..+|..++ ...|.+|++++++.
T Consensus       219 ~~~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~  261 (424)
T PRK05703        219 KQGGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDT  261 (424)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCc
Confidence            4578999999999999999999999887 44478999999875

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

Probab=97.59  E-value=0.0005  Score=75.41  Aligned_cols=123  Identities=11%  Similarity=0.106  Sum_probs=80.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFE  372 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~  372 (539)
                      +.+|+-..|.||||+|||||.+-+++..|.+ |.+++|+-.-.+ ..+...|+....-+.....+... ....|+..+.+
T Consensus        94 ~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~k-gkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~-yh~~l~~~eke  171 (1187)
T COG1110          94 LVRGKSFAIIAPTGVGKTTFGLLMSLYLAKK-GKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVV-YHSALPTKEKE  171 (1187)
T ss_pred             HHcCCceEEEcCCCCchhHHHHHHHHHHHhc-CCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeee-eccccchHHHH
Confidence            8889999999999999999999999999997 888887754433 56777777554422221111111 12367778888


Q ss_pred             HHHHHhhcc-c-eeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCC
Q 009230          373 QGKAWLSNT-F-SLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQR  426 (539)
Q Consensus       373 ~~~~~l~~~-~-~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~  426 (539)
                      ++.+.+.+. + ++|.       |..-+....+.+. .++.++||||+...++...
T Consensus       172 e~le~i~~gdfdIlit-------Ts~FL~k~~e~L~-~~kFdfifVDDVDA~Lkas  219 (1187)
T COG1110         172 EALERIESGDFDILIT-------TSQFLSKRFEELS-KLKFDFIFVDDVDAILKAS  219 (1187)
T ss_pred             HHHHHHhcCCccEEEE-------eHHHHHhhHHHhc-ccCCCEEEEccHHHHHhcc
Confidence            888888753 2 2331       1111222333333 3689999999988877543

>COG4586 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.59  E-value=0.0014  Score=61.85  Aligned_cols=174  Identities=15%  Similarity=0.159  Sum_probs=90.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHHHHhhCCCccc---cc--c----CCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLLEKHIKKPFFE---AN--Y----GGSA  363 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~~~~~~~~~~~---i~--~----~~~~  363 (539)
                      +++|+.+.+.|+.|+||||.+--+.--+.- .+..|-.-..+-- ..+-..|-+...+|.-..-   +.  .    ....
T Consensus        47 IP~G~ivgflGaNGAGKSTtLKmLTGll~p-~~G~v~V~G~~Pf~~~~~~~~~~~~v~gqk~ql~Wdlp~~ds~~v~~~I  125 (325)
T COG4586          47 IPKGEIVGFLGANGAGKSTTLKMLTGLLLP-TSGKVRVNGKDPFRRREEYLRSIGLVMGQKLQLWWDLPALDSLEVLKLI  125 (325)
T ss_pred             cCCCcEEEEEcCCCCcchhhHHHHhCcccc-CCCeEEecCcCcchhHHHHHHHHHHHhhhhheeeeechhhhhHHHHHHH
Confidence            999999999999999999986655432222 2455555554421 2222233333333322110   00  0    0000


Q ss_pred             CCCCHHHHHHHHHHhhccce---eEeecCCCCCCHHH-HHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHH
Q 009230          364 ERMTVEEFEQGKAWLSNTFS---LIRCENDSLPSIKW-VLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQM  439 (539)
Q Consensus       364 ~~l~~~~~~~~~~~l~~~~~---~i~~~~~~~~~~~~-i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~  439 (539)
                      ..+.++++++-.+.+.+..-   +++ .+....++.+ ....+ .+.--|+++++++|--+ +      + -+-.....+
T Consensus       126 y~Ipd~~F~~r~~~l~eiLdl~~~lk-~~vr~LSlGqRmraeL-aaaLLh~p~VLfLDEpT-v------g-LDV~aq~~i  195 (325)
T COG4586         126 YEIPDDEFAERLDFLTEILDLEGFLK-WPVRKLSLGQRMRAEL-AAALLHPPKVLFLDEPT-V------G-LDVNAQANI  195 (325)
T ss_pred             HhCCHHHHHHHHHHHHHHhcchhhhh-hhhhhccchHHHHHHH-HHHhcCCCcEEEecCCc-c------C-cchhHHHHH
Confidence            01233333332222221100   000 0111222222 11111 12334789999999221 1      1 122344567


Q ss_pred             HHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          440 LTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       440 ~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      -+.|+....+++++|++++|.-                  +.|++.||.|+.++.-+
T Consensus       196 r~Flke~n~~~~aTVllTTH~~------------------~di~~lc~rv~~I~~Gq  234 (325)
T COG4586         196 REFLKEYNEERQATVLLTTHIF------------------DDIATLCDRVLLIDQGQ  234 (325)
T ss_pred             HHHHHHHHHhhCceEEEEecch------------------hhHHHhhhheEEeeCCc
Confidence            7888899999999999999932                  13788999999998866

>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional

Probab=97.59  E-value=0.0021  Score=61.10  Aligned_cols=33  Identities=30%  Similarity=0.281  Sum_probs=27.3

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        26 l~~~s~~i~~Ge~~~i~G~nGsGKSTLl~~i~Gl   59 (228)
T PRK10584         26 LTGVELVVKRGETIALIGESGSGKSTLLAILAGL   59 (228)
T ss_pred             EeccEEEEcCCCEEEEECCCCCCHHHHHHHHHcC
Confidence            444443 999999999999999999998877644

>TIGR03771 anch_rpt_ABC anchored repeat-type ABC transporter, ATP-binding subunit

Probab=97.59  E-value=0.0017  Score=61.55  Aligned_cols=27  Identities=26%  Similarity=0.320  Sum_probs=24.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+++.|.|++|+|||||+.-++-.
T Consensus         3 i~~Ge~~~l~G~nGsGKSTLl~~l~G~   29 (223)
T TIGR03771         3 ADKGELLGLLGPNGAGKTTLLRAILGL   29 (223)
T ss_pred             cCCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            678999999999999999998877754

This protein family is the ATP-binding cassette subunit of binding protein-dependent ABC transporter complex that strictly co-occurs with TIGR03769. TIGRFAMs model TIGR03769 describes a protein domain that occurs singly or as one of up to three repeats in proteins of a number of Actinobacteria, including Propionibacterium acnes KPA171202. The TIGR03769 domain occurs both in an adjacent gene for the substrate-binding protein and in additional (often nearby) proteins, often with LPXTG-like sortase recognition signals. Homologous ATP-binding subunits outside the scope of this family include manganese transporter MntA in Synechocystis sp. PCC 6803 and chelated iron transporter subunits. The function of this transporter complex is unknown.

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=97.59  E-value=0.00065  Score=59.06  Aligned_cols=40  Identities=20%  Similarity=0.369  Sum_probs=33.2

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      .+..++|.|+||+|||+++..++..+... +.++.+++...
T Consensus        18 ~~~~v~i~G~~G~GKT~l~~~i~~~~~~~-~~~v~~~~~~~   57 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTLARAIANELFRP-GAPFLYLNASD   57 (151)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHhhcC-CCCeEEEehhh
Confidence            36789999999999999999999887753 78888887643

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.

>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional

Probab=97.59  E-value=0.001  Score=69.83  Aligned_cols=33  Identities=30%  Similarity=0.369  Sum_probs=27.4

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        40 L~nVSfsI~~GEivgIiGpNGSGKSTLLkiLaGL   73 (549)
T PRK13545         40 LNNISFEVPEGEIVGIIGLNGSGKSTLSNLIAGV   73 (549)
T ss_pred             EeeeEEEEeCCCEEEEEcCCCCCHHHHHHHHhCC
Confidence            455544 999999999999999999998877644

>TIGR02142 modC_ABC molybdenum ABC transporter, ATP-binding protein

Probab=97.59  E-value=0.0016  Score=66.23  Aligned_cols=44  Identities=16%  Similarity=0.248  Sum_probs=32.4

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      .+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|.
T Consensus       148 ~~p~lllLDEPts-------~LD-~~~~~~l~~~L~~l~~~~g~tiiivtH~  191 (354)
T TIGR02142       148 SSPRLLLMDEPLA-------ALD-DPRKYEILPYLERLHAEFGIPILYVSHS  191 (354)
T ss_pred             cCCCEEEEcCCCc-------CCC-HHHHHHHHHHHHHHHHhcCCEEEEEecC
Confidence            5789999993332       222 2345678888888988889999999993

This model represents the ATP-binding cassette (ABC) protein of the three subunit molybdate ABC transporter. The three proteins of this complex are homologous to proteins of the sulfate ABC transporter. Molybdenum may be used in nitrogenases of nitrogen-fixing bacteria and in molybdopterin cofactors. In some cases, molybdate may be transported by a sulfate transporter rather than by a specific molybdate transporter.

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=97.59  E-value=0.00081  Score=62.72  Aligned_cols=35  Identities=37%  Similarity=0.580  Sum_probs=28.1

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++--.
T Consensus        22 il~~~s~~i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   57 (202)
T cd03233          22 ILKDFSGVVKPGEMVLVLGRPGSGCSTLLKALANRT   57 (202)
T ss_pred             eeeeEEEEECCCcEEEEECCCCCCHHHHHHHhcccC
Confidence            3444444 9999999999999999999988776543

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK13641 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.58  E-value=0.0015  Score=64.59  Aligned_cols=33  Identities=21%  Similarity=0.350  Sum_probs=27.8

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        22 ~l~~vsl~i~~Ge~~~iiG~NGaGKSTLl~~l~G   55 (287)
T PRK13641         22 GLDNISFELEEGSFVALVGHTGSGKSTLMQHFNA   55 (287)
T ss_pred             ceeeeEEEEeCCCEEEEECCCCCCHHHHHHHHhc
Confidence            4555554 99999999999999999999887764

>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional

Probab=97.58  E-value=0.0021  Score=61.39  Aligned_cols=34  Identities=26%  Similarity=0.317  Sum_probs=27.6

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++--
T Consensus        24 il~~isl~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl   58 (233)
T PRK11629         24 VLHNVSFSIGEGEMMAIVGSSGSGKSTLLHLLGGL   58 (233)
T ss_pred             eEEeeEEEEcCCcEEEEECCCCCCHHHHHHHHhcC
Confidence            3444443 999999999999999999998877643

>TIGR02314 ABC_MetN D-methionine ABC transporter, ATP-binding protein

Probab=97.58  E-value=0.0017  Score=65.54  Aligned_cols=44  Identities=11%  Similarity=0.220  Sum_probs=33.0

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      .+++++++|--+.-       .+ ......+++.|+++.++.+++||+++|.
T Consensus       157 ~~P~iLLlDEPts~-------LD-~~t~~~i~~lL~~l~~~~g~tiiliTH~  200 (343)
T TIGR02314       157 SNPKVLLCDEATSA-------LD-PATTQSILELLKEINRRLGLTILLITHE  200 (343)
T ss_pred             hCCCEEEEeCCccc-------CC-HHHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            57899999933322       22 2345678888999999999999999993

Members of this family are the ATP-binding protein of the D-methionine ABC transporter complex. Known members belong to the Proteobacteria.

>PRK11300 livG leucine/isoleucine/valine transporter ATP-binding subunit; Provisional

Probab=97.58  E-value=0.00076  Score=65.39  Aligned_cols=62  Identities=11%  Similarity=0.183  Sum_probs=42.7

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+++||+++|...                  .+...+|
T Consensus       169 ~~~p~llllDEPt~-------~LD-~~~~~~l~~~L~~~~~~~~~tii~~sH~~~------------------~~~~~~d  222 (255)
T PRK11300        169 VTQPEILMLDEPAA-------GLN-PKETKELDELIAELRNEHNVTVLLIEHDMK------------------LVMGISD  222 (255)
T ss_pred             hcCCCEEEEcCCcc-------CCC-HHHHHHHHHHHHHHHhhcCCEEEEEeCCHH------------------HHHHhCC
Confidence            45799999993332       222 234556778888888777999999999322                  1446789


Q ss_pred             eEEEEEeC
Q 009230          488 NGIVIHRN  495 (539)
Q Consensus       488 ~vl~l~r~  495 (539)
                      .++.|...
T Consensus       223 ~i~~l~~g  230 (255)
T PRK11300        223 RIYVVNQG  230 (255)
T ss_pred             EEEEEECC
Confidence            88888753

>TIGR02323 CP_lyasePhnK phosphonate C-P lyase system protein PhnK

Probab=97.58  E-value=0.00096  Score=64.60  Aligned_cols=61  Identities=11%  Similarity=0.103  Sum_probs=41.7

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|...                  .+...+|
T Consensus       164 ~~~p~vlllDEP~~-------~LD-~~~~~~l~~~l~~~~~~~~~tii~vsH~~~------------------~~~~~~d  217 (253)
T TIGR02323       164 VTRPRLVFMDEPTG-------GLD-VSVQARLLDLLRGLVRDLGLAVIIVTHDLG------------------VARLLAQ  217 (253)
T ss_pred             hcCCCEEEEcCCCc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHhcC
Confidence            45899999993332       122 233456778888888888999999999422                  1345778


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       218 ~~~~l~~  224 (253)
T TIGR02323       218 RLLVMQQ  224 (253)
T ss_pred             EEEEEEC
Confidence            8888864

Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se.

>PRK11607 potG putrescine transporter ATP-binding subunit; Provisional

Probab=97.58  E-value=0.0019  Score=66.08  Aligned_cols=33  Identities=24%  Similarity=0.413  Sum_probs=26.6

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|+.+-- +.+|+++.|.|++|+|||||+.-|+-
T Consensus        34 ~l~~vsl~i~~Ge~~~llGpsGsGKSTLLr~IaG   67 (377)
T PRK11607         34 AVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAG   67 (377)
T ss_pred             EEeeeEEEEcCCCEEEEECCCCCcHHHHHHHHhC
Confidence            3444433 99999999999999999999877663

>PRK11264 putative amino-acid ABC transporter ATP-binding protein YecC; Provisional

Probab=97.58  E-value=0.0016  Score=62.96  Aligned_cols=33  Identities=27%  Similarity=0.413  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        19 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~l~G~   52 (250)
T PRK11264         19 LHGIDLEVKPGEVVAIIGPSGSGKTTLLRCINLL   52 (250)
T ss_pred             eccceEEEcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            444444 999999999999999999998877643

>cd03218 ABC_YhbG The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids

Probab=97.57  E-value=0.00073  Score=64.48  Aligned_cols=33  Identities=21%  Similarity=0.237  Sum_probs=27.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        16 l~~vs~~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl   49 (232)
T cd03218          16 VNGVSLSVKQGEIVGLLGPNGAGKTTTFYMIVGL   49 (232)
T ss_pred             eccceeEecCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            444444 999999999999999999998877643

The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.

>PRK11144 modC molybdate transporter ATP-binding protein; Provisional

Probab=97.57  E-value=0.0017  Score=66.12  Aligned_cols=44  Identities=18%  Similarity=0.244  Sum_probs=32.2

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      .+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|.
T Consensus       145 ~~p~llLLDEPts-------~LD-~~~~~~l~~~L~~l~~~~g~tii~vTHd  188 (352)
T PRK11144        145 TAPELLLMDEPLA-------SLD-LPRKRELLPYLERLAREINIPILYVSHS  188 (352)
T ss_pred             cCCCEEEEcCCcc-------cCC-HHHHHHHHHHHHHHHHhcCCeEEEEecC
Confidence            5789999993322       222 2334577888888988889999999994

>PRK13548 hmuV hemin importer ATP-binding subunit; Provisional

Probab=97.57  E-value=0.00058  Score=66.34  Aligned_cols=61  Identities=18%  Similarity=0.234  Sum_probs=41.3

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|....                  +...||.
T Consensus       157 ~~p~lllLDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tiii~sH~~~~------------------~~~~~d~  210 (258)
T PRK13548        157 GPPRWLLLDEPTS-------ALD-LAHQHHVLRLARQLAHERGLAVIVVLHDLNL------------------AARYADR  210 (258)
T ss_pred             CCCCEEEEeCCcc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEECCHHH------------------HHHhcCE
Confidence            4789999993332       222 2344567888888886678999999993221                  3457788


Q ss_pred             EEEEEeC
Q 009230          489 GIVIHRN  495 (539)
Q Consensus       489 vl~l~r~  495 (539)
                      ++.|.+.
T Consensus       211 i~~l~~G  217 (258)
T PRK13548        211 IVLLHQG  217 (258)
T ss_pred             EEEEECC
Confidence            8877653

>PRK10851 sulfate/thiosulfate transporter subunit; Provisional

Probab=97.56  E-value=0.00084  Score=68.15  Aligned_cols=34  Identities=21%  Similarity=0.369  Sum_probs=27.7

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-|+--
T Consensus        17 ~l~~isl~i~~Ge~~~llGpsGsGKSTLLr~IaGl   51 (353)
T PRK10851         17 VLNDISLDIPSGQMVALLGPSGSGKTTLLRIIAGL   51 (353)
T ss_pred             EEEEeEEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3444433 899999999999999999998877754

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=97.56  E-value=0.0025  Score=59.73  Aligned_cols=164  Identities=16%  Similarity=0.098  Sum_probs=82.4

Q ss_pred             Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC----CCHHHHHHHHHHHhhCCCc---c
Q 009230          284 GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME----NKVREHARKLLEKHIKKPF---F  355 (539)
Q Consensus       284 g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E----~~~~~~~~r~~~~~~~~~~---~  355 (539)
                      +...+|++.- +..|+++++.|+|||||||.+.- ...+... ...-++|..|    +++.++.+++-...-++.+   .
T Consensus        13 ~~~av~~v~l~I~~gef~vliGpSGsGKTTtLkM-INrLiep-t~G~I~i~g~~i~~~d~~~LRr~IGYviQqigLFPh~   90 (309)
T COG1125          13 NKKAVDDVNLTIEEGEFLVLIGPSGSGKTTTLKM-INRLIEP-TSGEILIDGEDISDLDPVELRRKIGYVIQQIGLFPHL   90 (309)
T ss_pred             CceeeeeeeEEecCCeEEEEECCCCCcHHHHHHH-HhcccCC-CCceEEECCeecccCCHHHHHHhhhhhhhhcccCCCc
Confidence            4455666655 99999999999999999998654 3344433 3334445444    4466676665322222221   1


Q ss_pred             ccccCC----CCCCCCHHHHHHHHHHhhcc----c-eeE-eecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccC
Q 009230          356 EANYGG----SAERMTVEEFEQGKAWLSNT----F-SLI-RCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQ  425 (539)
Q Consensus       356 ~i~~~~----~~~~l~~~~~~~~~~~l~~~----~-~~i-~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~  425 (539)
                      .+..+.    .-..++.+++++-.+.|-..    + .|. ++..+-+....+=...++.++  .++.++..|-=...+.+
T Consensus        91 Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~~~RyP~eLSGGQQQRVGv~RALA--adP~ilLMDEPFgALDp  168 (309)
T COG1125          91 TVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEYADRYPHELSGGQQQRVGVARALA--ADPPILLMDEPFGALDP  168 (309)
T ss_pred             cHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHHhhcCchhcCcchhhHHHHHHHHh--cCCCeEeecCCccccCh
Confidence            111000    00123333333222222110    1 010 000011111223334445444  36889999933222211


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          426 RPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       426 ~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                          -++    .++-..++++-++++.+||+|+|
T Consensus       169 ----I~R----~~lQ~e~~~lq~~l~kTivfVTH  194 (309)
T COG1125         169 ----ITR----KQLQEEIKELQKELGKTIVFVTH  194 (309)
T ss_pred             ----hhH----HHHHHHHHHHHHHhCCEEEEEec
Confidence                122    23456677788999999999999

>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.56  E-value=0.0016  Score=59.33  Aligned_cols=32  Identities=25%  Similarity=0.375  Sum_probs=26.1

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      .|..+.- ++++.+|.+.||+|||||||+..+=
T Consensus        22 aL~~i~l~i~~~~VTAlIGPSGcGKST~LR~lN   54 (253)
T COG1117          22 ALKDINLDIPKNKVTALIGPSGCGKSTLLRCLN   54 (253)
T ss_pred             hhccCceeccCCceEEEECCCCcCHHHHHHHHH
Confidence            3444444 9999999999999999999988654

>PRK09984 phosphonate/organophosphate ester transporter subunit; Provisional

Probab=97.56  E-value=0.0019  Score=62.82  Aligned_cols=60  Identities=12%  Similarity=0.199  Sum_probs=41.9

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|....                  +...||.
T Consensus       169 ~~p~llllDEPt~-------~LD-~~~~~~l~~~l~~~~~~~g~tvii~tH~~~~------------------~~~~~d~  222 (262)
T PRK09984        169 QQAKVILADEPIA-------SLD-PESARIVMDTLRDINQNDGITVVVTLHQVDY------------------ALRYCER  222 (262)
T ss_pred             cCCCEEEecCccc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHHH------------------HHHhCCE
Confidence            5789999993322       222 3445678888888888789999999994321                  3457788


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|.+
T Consensus       223 i~~l~~  228 (262)
T PRK09984        223 IVALRQ  228 (262)
T ss_pred             EEEEEC
Confidence            888864

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=97.55  E-value=0.0018  Score=64.50  Aligned_cols=41  Identities=24%  Similarity=0.299  Sum_probs=36.8

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      .+|+++++.|++|+||||++..+|..+... |.+|++++.+.
T Consensus       112 ~~~~vi~lvGpnGsGKTTt~~kLA~~l~~~-g~~V~Li~~D~  152 (318)
T PRK10416        112 KKPFVILVVGVNGVGKTTTIGKLAHKYKAQ-GKKVLLAAGDT  152 (318)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHhc-CCeEEEEecCc
Confidence            467899999999999999999999988764 89999999875

>PRK10070 glycine betaine transporter ATP-binding subunit; Provisional

Probab=97.55  E-value=0.0024  Score=65.67  Aligned_cols=33  Identities=24%  Similarity=0.358  Sum_probs=27.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++--
T Consensus        44 L~~isl~i~~Gei~~LvG~NGsGKSTLLr~I~Gl   77 (400)
T PRK10070         44 VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRL   77 (400)
T ss_pred             EEeEEEEEcCCCEEEEECCCCchHHHHHHHHHcC
Confidence            454444 999999999999999999998877644

>PRK13647 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.55  E-value=0.0007  Score=66.37  Aligned_cols=33  Identities=30%  Similarity=0.269  Sum_probs=27.3

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        20 ~l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~l~G   53 (274)
T PRK13647         20 ALKGLSLSIPEGSKTALLGPNGAGKSTLLLHLNG   53 (274)
T ss_pred             eeeeEEEEEcCCCEEEEECCCCCcHHHHHHHHhc
Confidence            3454444 99999999999999999999887764

>PRK12377 putative replication protein; Provisional

Probab=97.55  E-value=0.00075  Score=64.61  Aligned_cols=37  Identities=16%  Similarity=0.320  Sum_probs=33.0

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .-++|.|+||+|||.|+..++..+..+ |.+|+|++..
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l~~~-g~~v~~i~~~  138 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRLLAK-GRSVIVVTVP  138 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc-CCCeEEEEHH
Confidence            467899999999999999999998875 9999999864

>PRK10253 iron-enterobactin transporter ATP-binding protein; Provisional

Probab=97.54  E-value=0.00045  Score=67.41  Aligned_cols=33  Identities=24%  Similarity=0.300  Sum_probs=27.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        23 l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~i~G~   56 (265)
T PRK10253         23 AENLTVEIPDGHFTAIIGPNGCGKSTLLRTLSRL   56 (265)
T ss_pred             eeecceEECCCCEEEEECCCCCCHHHHHHHHcCC
Confidence            444444 999999999999999999998877644

>PRK08181 transposase; Validated

Probab=97.54  E-value=0.00091  Score=64.87  Aligned_cols=47  Identities=26%  Similarity=0.481  Sum_probs=38.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKL  345 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~  345 (539)
                      +..++-++|.|+||+|||.|+..++..++.+ |++|+|++.    .+++..+
T Consensus       103 ~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~~-g~~v~f~~~----~~L~~~l  149 (269)
T PRK08181        103 LAKGANLLLFGPPGGGKSHLAAAIGLALIEN-GWRVLFTRT----TDLVQKL  149 (269)
T ss_pred             HhcCceEEEEecCCCcHHHHHHHHHHHHHHc-CCceeeeeH----HHHHHHH
Confidence            4567789999999999999999999988875 999999984    3454444

>cd03234 ABCG_White The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors

Probab=97.53  E-value=0.00092  Score=63.54  Aligned_cols=35  Identities=29%  Similarity=0.472  Sum_probs=28.3

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        22 ~l~~vsl~i~~Ge~~~l~G~nGsGKSTLlk~l~G~~   57 (226)
T cd03234          22 ILNDVSLHVESGQVMAILGSSGSGKTTLLDAISGRV   57 (226)
T ss_pred             cccCceEEEcCCeEEEEECCCCCCHHHHHHHHhCcc
Confidence            3444444 9999999999999999999988776543

The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=97.53  E-value=0.00072  Score=62.94  Aligned_cols=33  Identities=24%  Similarity=0.369  Sum_probs=27.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        16 l~~is~~i~~Ge~~~i~G~nGsGKStLl~~l~G~   49 (200)
T cd03217          16 LKGVNLTIKKGEVHALMGPNGSGKSTLAKTIMGH   49 (200)
T ss_pred             eeccceEECCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            444443 999999999999999999998877654

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>TIGR03410 urea_trans_UrtE urea ABC transporter, ATP-binding protein UrtE

Probab=97.53  E-value=0.00086  Score=63.91  Aligned_cols=62  Identities=13%  Similarity=0.132  Sum_probs=42.1

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|.-+.-       .+ ......+.+.|++++++.+.+||+++|.-.                  .+...+|
T Consensus       147 ~~~p~illlDEPt~~-------LD-~~~~~~l~~~l~~~~~~~~~tii~~sH~~~------------------~~~~~~d  200 (230)
T TIGR03410       147 VTRPKLLLLDEPTEG-------IQ-PSIIKDIGRVIRRLRAEGGMAILLVEQYLD------------------FARELAD  200 (230)
T ss_pred             hcCCCEEEecCCccc-------CC-HHHHHHHHHHHHHHHHcCCcEEEEEeCCHH------------------HHHHhCC
Confidence            357899999933322       22 234456777788887777899999999321                  1456788


Q ss_pred             eEEEEEeC
Q 009230          488 NGIVIHRN  495 (539)
Q Consensus       488 ~vl~l~r~  495 (539)
                      .++.+...
T Consensus       201 ~v~~l~~g  208 (230)
T TIGR03410       201 RYYVMERG  208 (230)
T ss_pred             EEEEEECC
Confidence            88888643

Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=97.53  E-value=0.00064  Score=62.46  Aligned_cols=131  Identities=18%  Similarity=0.213  Sum_probs=77.8

Q ss_pred             cCCCcE-EEEEcCCCCChhHHHHHHHHHHHHh----cCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCH
Q 009230          294 VLPGEL-TIVTGVPNSGKSEWIDALICNINEH----AGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTV  368 (539)
Q Consensus       294 l~~G~l-~~i~G~~G~GKT~~~~~la~~~a~~----~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~  368 (539)
                      ...|.+ ++|.|||++||||++..+|..++..    .+.+|+.+.  .+.+ +.    +..-|++...+           
T Consensus       133 y~~g~lntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiD--ersE-Ia----g~~~gvpq~~~-----------  194 (308)
T COG3854         133 YQNGWLNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIID--ERSE-IA----GCLNGVPQHGR-----------  194 (308)
T ss_pred             HhcCceeeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEe--ccch-hh----ccccCCchhhh-----------
Confidence            567778 8999999999999999999998875    357788775  2222 22    22333332211           


Q ss_pred             HHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHH
Q 009230          369 EEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQ  448 (539)
Q Consensus       369 ~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~  448 (539)
                         .       .+.-+.    ++.+...-++    .+++.+-|.++|+|.+-.        ..+   ...+..     |-
T Consensus       195 ---g-------~R~dVl----d~cpk~~gmm----maIrsm~PEViIvDEIGt--------~~d---~~A~~t-----a~  240 (308)
T COG3854         195 ---G-------RRMDVL----DPCPKAEGMM----MAIRSMSPEVIIVDEIGT--------EED---ALAILT-----AL  240 (308)
T ss_pred             ---h-------hhhhhc----ccchHHHHHH----HHHHhcCCcEEEEecccc--------HHH---HHHHHH-----HH
Confidence               1       111111    2333333333    345567899999993321        111   112222     33


Q ss_pred             HhCcEEEEEec-CCCCCCCCCCCCCcccccc
Q 009230          449 HHACHVWFVAH-PRQLHNWVGEPPNLYDISG  478 (539)
Q Consensus       449 ~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~g  478 (539)
                      +.|+-++.++| +.-.+-  .++|++.|+-+
T Consensus       241 ~~GVkli~TaHG~~iedl--~krp~lkdlv~  269 (308)
T COG3854         241 HAGVKLITTAHGNGIEDL--IKRPTLKDLVE  269 (308)
T ss_pred             hcCcEEEEeeccccHHHh--hcChhHHHHHh
Confidence            68999999999 654432  46788877664

>cd03260 ABC_PstB_phosphate_transporter Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient

Probab=97.51  E-value=0.0018  Score=61.50  Aligned_cols=34  Identities=26%  Similarity=0.324  Sum_probs=27.9

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        16 l~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~i~G~~   50 (227)
T cd03260          16 LKDISLDIPKGEITALIGPSGCGKSTLLRLLNRLN   50 (227)
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            444433 9999999999999999999998877554

The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein is a phosphate-binding protein located in the periplasmic space. P stA and PstC are hydrophobic and they form the transmembrane portion of the Pst system. PstB is the catalytic subunit, which couples the energy of ATP hydrolysis to the import of phosphate across cellular membranes through the Pst system, often referred as ABC-protein. PstB belongs to one of the largest superfamilies of proteins characterized by a highly conserved adenosine triphosphate (ATP) binding cassette (ABC), which is also a nucleotide binding domain (NBD).

>PRK15093 antimicrobial peptide ABC transporter ATP-binding protein; Provisional

Probab=97.51  E-value=0.001  Score=67.02  Aligned_cols=45  Identities=16%  Similarity=0.302  Sum_probs=33.6

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      ..+++++++|--+.       +.+ .....++++.|+++.++.+++||+++|.
T Consensus       174 ~~~P~llilDEPts-------~LD-~~~~~~i~~lL~~l~~~~g~tii~itHd  218 (330)
T PRK15093        174 ANQPRLLIADEPTN-------AME-PTTQAQIFRLLTRLNQNNNTTILLISHD  218 (330)
T ss_pred             HCCCCEEEEeCCCC-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEECC
Confidence            45799999993332       222 3345678888899988899999999993

>PRK13638 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.51  E-value=0.0018  Score=63.47  Aligned_cols=33  Identities=24%  Similarity=0.135  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        17 l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   50 (271)
T PRK13638         17 LKGLNLDFSLSPVTGLVGANGCGKSTLFMNLSGL   50 (271)
T ss_pred             ccceEEEEcCCCEEEEECCCCCCHHHHHHHHcCC
Confidence            444444 999999999999999999998876643

>TIGR03873 F420-0_ABC_ATP proposed F420-0 ABC transporter, ATP-binding protein

Probab=97.50  E-value=0.0007  Score=65.71  Aligned_cols=33  Identities=30%  Similarity=0.351  Sum_probs=27.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        17 l~~is~~i~~Ge~~~i~G~nGsGKSTLl~~i~G~   50 (256)
T TIGR03873        17 VDGVDVTAPPGSLTGLLGPNGSGKSTLLRLLAGA   50 (256)
T ss_pred             EeeeeEEEcCCcEEEEECCCCCCHHHHHHHHcCC
Confidence            444433 899999999999999999998877643

This small clade of ABC-type transporter ATP-binding protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and a permease (TIGR03869). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with a F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this ATP-binding protein is a component of an F420-0 (that is, F420 lacking only the polyglutamate tail) transporter.

>PRK09493 glnQ glutamine ABC transporter ATP-binding protein; Reviewed

Probab=97.50  E-value=0.002  Score=61.83  Aligned_cols=33  Identities=24%  Similarity=0.363  Sum_probs=27.3

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        17 l~~~s~~i~~Ge~~~l~G~nGsGKSTLl~~l~G~   50 (240)
T PRK09493         17 LHNIDLNIDQGEVVVIIGPSGSGKSTLLRCINKL   50 (240)
T ss_pred             eeeeeEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            444444 899999999999999999998877754

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=97.50  E-value=0.0023  Score=60.56  Aligned_cols=33  Identities=24%  Similarity=0.337  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++--
T Consensus        18 l~~is~~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (220)
T cd03263          18 VDDLSLNVYKGEIFGLLGHNGAGKTTTLKMLTGE   51 (220)
T ss_pred             ecceEEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            444444 999999999999999999998877643

Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.

>PRK10261 glutathione transporter ATP-binding protein; Provisional

Probab=97.50  E-value=0.0012  Score=72.66  Aligned_cols=36  Identities=31%  Similarity=0.270  Sum_probs=29.5

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +.|+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        30 ~~l~~is~~v~~Ge~~~lvG~nGsGKSTLl~~l~Gll   66 (623)
T PRK10261         30 AAVRNLSFSLQRGETLAIVGESGSGKSVTALALMRLL   66 (623)
T ss_pred             eEEEeeEEEECCCCEEEEECCCCChHHHHHHHHHcCC
Confidence            34555554 9999999999999999999988877543

>PRK13639 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.50  E-value=0.00073  Score=66.29  Aligned_cols=33  Identities=24%  Similarity=0.245  Sum_probs=27.1

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        17 ~l~~vsl~i~~Ge~~~l~G~nGsGKSTLl~~i~G   50 (275)
T PRK13639         17 ALKGINFKAEKGEMVALLGPNGAGKSTLFLHFNG   50 (275)
T ss_pred             eeeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            3444444 99999999999999999999887764

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein

Probab=97.50  E-value=0.0031  Score=59.64  Aligned_cols=34  Identities=26%  Similarity=0.303  Sum_probs=27.6

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        20 ~l~~isl~i~~G~~~~i~G~nGsGKSTLl~~i~G~   54 (221)
T TIGR02211        20 VLKGVSLSIGKGEIVAIVGSSGSGKSTLLHLLGGL   54 (221)
T ss_pred             eEeeeEEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3444433 999999999999999999998877644

This model represents LolD, a member of the ABC transporter family (pfam00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina.

>PRK13649 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.50  E-value=0.0016  Score=64.17  Aligned_cols=34  Identities=29%  Similarity=0.264  Sum_probs=27.7

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        22 ~l~~is~~i~~Ge~~~l~G~nGsGKSTLl~~i~Gl   56 (280)
T PRK13649         22 ALFDVNLTIEDGSYTAFIGHTGSGKSTIMQLLNGL   56 (280)
T ss_pred             eeeeeEEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3555544 999999999999999999998877643

>TIGR01978 sufC FeS assembly ATPase SufC

Probab=97.49  E-value=0.0049  Score=59.23  Aligned_cols=33  Identities=27%  Similarity=0.352  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        16 l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   49 (243)
T TIGR01978        16 LKGVNLTVKKGEIHAIMGPNGSGKSTLSKTIAGH   49 (243)
T ss_pred             EeccceEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            444433 999999999999999999998887654

SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (pfam00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic (PubMed:12554644) or associated with the membrane (PubMed:11943156). The SUF system also includes a cysteine desulfurase (SufS, enhanced by SufE) and a probable iron-sulfur cluster assembly scaffold protein, SufA.

>PRK13650 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.49  E-value=0.00075  Score=66.34  Aligned_cols=45  Identities=11%  Similarity=0.117  Sum_probs=33.4

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      -.+++++++|.-+.       +.+ ......+++.|+.++++.+.+||+++|.
T Consensus       156 ~~~p~lLlLDEPt~-------~LD-~~~~~~l~~~l~~l~~~~g~tilivtH~  200 (279)
T PRK13650        156 AMRPKIIILDEATS-------MLD-PEGRLELIKTIKGIRDDYQMTVISITHD  200 (279)
T ss_pred             HcCCCEEEEECCcc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEecC
Confidence            35789999993332       222 2345678888999988889999999993

>PRK15134 microcin C ABC transporter ATP-binding protein YejF; Provisional

Probab=97.49  E-value=0.0015  Score=70.55  Aligned_cols=35  Identities=23%  Similarity=0.271  Sum_probs=28.5

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        24 ~l~~isl~i~~Ge~~~iiG~nGsGKSTLl~~i~G~~   59 (529)
T PRK15134         24 VVNDVSLQIEAGETLALVGESGSGKSVTALSILRLL   59 (529)
T ss_pred             eeeceEEEEeCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            4555544 9999999999999999999988777543

>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins

Probab=97.49  E-value=0.0008  Score=64.33  Aligned_cols=34  Identities=24%  Similarity=0.327  Sum_probs=27.4

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++--.
T Consensus        18 l~~i~~~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (234)
T cd03251          18 LRDISLDIPAGETVALVGPSGSGKSTLVNLIPRFY   52 (234)
T ss_pred             eeeeeEEEcCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            444443 9999999999999999999988776443

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03224 ABC_TM1139_LivF_branched LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids

Probab=97.49  E-value=0.0011  Score=62.84  Aligned_cols=33  Identities=21%  Similarity=0.329  Sum_probs=26.7

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        15 ~l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~l~G   48 (222)
T cd03224          15 ILFGVSLTVPEGEIVALLGRNGAGKTTLLKTIMG   48 (222)
T ss_pred             EeeeeeEEEcCCeEEEEECCCCCCHHHHHHHHhC
Confidence            3444443 99999999999999999999876653

The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=97.49  E-value=0.002  Score=59.76  Aligned_cols=36  Identities=25%  Similarity=0.283  Sum_probs=28.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHH-hcCCeE
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINE-HAGWKF  329 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~-~~g~~v  329 (539)
                      +..|++++|+|++|+|||||+..++..... +.|.+|
T Consensus        22 l~~g~~~~ltGpNg~GKSTllr~i~~~~~l~~~G~~v   58 (199)
T cd03283          22 MEKKNGILITGSNMSGKSTFLRTIGVNVILAQAGAPV   58 (199)
T ss_pred             EcCCcEEEEECCCCCChHHHHHHHHHHHHHHHcCCEE
Confidence            777899999999999999999999866532 236544

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.49  E-value=0.0054  Score=63.63  Aligned_cols=40  Identities=20%  Similarity=0.286  Sum_probs=35.3

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      ..+++++|++|+||||.+..+|..+..+ |++|++++.+.-
T Consensus        95 p~vI~lvG~~GsGKTTtaakLA~~L~~~-g~kV~lV~~D~~  134 (437)
T PRK00771         95 PQTIMLVGLQGSGKTTTAAKLARYFKKK-GLKVGLVAADTY  134 (437)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHHc-CCeEEEecCCCC
Confidence            3589999999999999999999888764 999999999853

>PRK13409 putative ATPase RIL; Provisional

Probab=97.49  E-value=0.0017  Score=70.52  Aligned_cols=61  Identities=13%  Similarity=0.102  Sum_probs=43.0

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|-=+       .+.+ ......+++.|++++++.+.+||+++|...                  .+.+.||
T Consensus       469 ~~~p~llLLDEPt-------~~LD-~~~~~~l~~~l~~l~~~~g~tviivsHD~~------------------~~~~~aD  522 (590)
T PRK13409        469 SRDADLYLLDEPS-------AHLD-VEQRLAVAKAIRRIAEEREATALVVDHDIY------------------MIDYISD  522 (590)
T ss_pred             hcCCCEEEEeCCc-------cCCC-HHHHHHHHHHHHHHHHhCCCEEEEEeCCHH------------------HHHHhCC
Confidence            3579999999222       1222 344567888999999988999999999321                  1346788


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.++.
T Consensus       523 rvivl~~  529 (590)
T PRK13409        523 RLMVFEG  529 (590)
T ss_pred             EEEEEcC
Confidence            8888853

>PRK10938 putative molybdenum transport ATP-binding protein ModF; Provisional

Probab=97.48  E-value=0.0016  Score=69.58  Aligned_cols=34  Identities=26%  Similarity=0.203  Sum_probs=27.9

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        18 il~~vsl~i~~Ge~~~liG~nGsGKSTLl~~l~G~   52 (490)
T PRK10938         18 TLQLPSLTLNAGDSWAFVGANGSGKSALARALAGE   52 (490)
T ss_pred             ecccceEEEcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            3555544 999999999999999999998877644

>PRK13631 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.48  E-value=0.0011  Score=66.34  Aligned_cols=34  Identities=24%  Similarity=0.280  Sum_probs=28.3

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++--
T Consensus        41 ~L~~vsl~i~~Ge~~~I~G~nGsGKSTLl~~L~Gl   75 (320)
T PRK13631         41 ALNNISYTFEKNKIYFIIGNSGSGKSTLVTHFNGL   75 (320)
T ss_pred             ceeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4565554 999999999999999999998877643

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=97.48  E-value=0.00092  Score=59.58  Aligned_cols=26  Identities=31%  Similarity=0.470  Sum_probs=23.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +.+|+++.|.|++|+|||||+.-++-
T Consensus        22 i~~g~~~~i~G~nGsGKStll~~l~g   47 (157)
T cd00267          22 LKAGEIVALVGPNGSGKSTLLRAIAG   47 (157)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            89999999999999999999887764

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG1118 CysA ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=97.47  E-value=0.0012  Score=63.56  Aligned_cols=35  Identities=26%  Similarity=0.470  Sum_probs=28.7

Q ss_pred             Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          284 GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       284 g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      .+..++++.- ++.|+++.+.|++|+||||++.-||
T Consensus        14 ~~~a~~di~l~i~~Ge~vaLlGpSGaGKsTlLRiIA   49 (345)
T COG1118          14 AFGALDDISLDIKSGELVALLGPSGAGKSTLLRIIA   49 (345)
T ss_pred             cccccccceeeecCCcEEEEECCCCCcHHHHHHHHh
Confidence            4555665544 9999999999999999999988665

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.47  E-value=0.0068  Score=63.58  Aligned_cols=43  Identities=16%  Similarity=0.244  Sum_probs=37.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc-CCeEEEEeCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHA-GWKFVLCSMEN  336 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~-g~~vl~~s~E~  336 (539)
                      +..|++++|.|++|+||||++..++..++..+ +.+|.+++.+.
T Consensus       347 l~~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDt  390 (559)
T PRK12727        347 LERGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDT  390 (559)
T ss_pred             ccCCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEeccc
Confidence            67799999999999999999999999887753 47899999864

>PRK11614 livF leucine/isoleucine/valine transporter ATP-binding subunit; Provisional

Probab=97.47  E-value=0.00062  Score=65.24  Aligned_cols=34  Identities=26%  Similarity=0.452  Sum_probs=27.4

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++--
T Consensus        20 ~l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~l~G~   54 (237)
T PRK11614         20 ALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGD   54 (237)
T ss_pred             eeeeeEEEEcCCcEEEEECCCCCCHHHHHHHHcCC
Confidence            3444444 999999999999999999998876643

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=97.45  E-value=0.00067  Score=58.15  Aligned_cols=32  Identities=25%  Similarity=0.470  Sum_probs=25.6

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ++|.|+||+|||+++..++..+    +.+++.++..
T Consensus         1 ill~G~~G~GKT~l~~~la~~l----~~~~~~i~~~   32 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL----GFPFIEIDGS   32 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT----TSEEEEEETT
T ss_pred             CEEECcCCCCeeHHHHHHHhhc----cccccccccc
Confidence            4799999999999988877663    6777766654

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=97.45  E-value=0.0024  Score=59.00  Aligned_cols=32  Identities=38%  Similarity=0.607  Sum_probs=26.8

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        23 l~~vs~~i~~Ge~~~l~G~nGsGKSTLl~~l~G   55 (192)
T cd03232          23 LNNISGYVKPGTLTALMGESGAGKTTLLDVLAG   55 (192)
T ss_pred             EEccEEEEeCCcEEEEECCCCCCHHHHHHHHhC
Confidence            444443 99999999999999999999887773

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1

Probab=97.45  E-value=0.0012  Score=63.39  Aligned_cols=35  Identities=26%  Similarity=0.303  Sum_probs=28.5

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        18 ~l~~i~~~i~~Ge~~~l~G~nGsGKSTLl~~i~G~~   53 (238)
T cd03249          18 ILKGLSLTIPPGKTVALVGSSGCGKSTVVSLLERFY   53 (238)
T ss_pred             ceeceEEEecCCCEEEEEeCCCCCHHHHHHHHhccC
Confidence            4555544 9999999999999999999988777543

In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.

>PRK11124 artP arginine transporter ATP-binding subunit; Provisional

Probab=97.44  E-value=0.0036  Score=60.17  Aligned_cols=27  Identities=26%  Similarity=0.325  Sum_probs=24.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~G~   51 (242)
T PRK11124         25 CPQGETLVLLGPSGAGKSSLLRVLNLL   51 (242)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999999998877643

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=97.44  E-value=0.0016  Score=57.08  Aligned_cols=26  Identities=23%  Similarity=0.386  Sum_probs=23.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +.+|+.+.|.|++|+|||||+.-++-
T Consensus        23 ~~~Ge~~~i~G~nGsGKStLl~~l~G   48 (144)
T cd03221          23 INPGDRIGLVGRNGAGKSTLLKLIAG   48 (144)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHcC
Confidence            99999999999999999999876654

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>TIGR00955 3a01204 The Eye Pigment Precursor Transporter (EPP) Family protein

Probab=97.43  E-value=0.0014  Score=71.84  Aligned_cols=34  Identities=32%  Similarity=0.521  Sum_probs=29.5

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      -|+.+.+ +.+|+++.|.|++|+|||||+.-++-.
T Consensus        40 iL~~vs~~i~~Ge~~aI~G~sGsGKSTLL~~L~g~   74 (617)
T TIGR00955        40 LLKNVSGVAKPGELLAVMGSSGAGKTTLMNALAFR   74 (617)
T ss_pred             cccCCEEEEeCCeEEEEECCCCCCHHHHHHHHhCC
Confidence            4666777 999999999999999999998877654

>COG4172 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]

Probab=97.43  E-value=0.0019  Score=64.27  Aligned_cols=181  Identities=18%  Similarity=0.224  Sum_probs=96.8

Q ss_pred             chhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC-CC---HHH--HHHHHHHHhhCCCcccc
Q 009230          285 WRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME-NK---VRE--HARKLLEKHIKKPFFEA  357 (539)
Q Consensus       285 ~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E-~~---~~~--~~~r~~~~~~~~~~~~i  357 (539)
                      +...|.+-- +++|+...|.|.+||||||+.+.+..-+..+ | . ++|..+ .+   ..+  -.+|-+.....-++..+
T Consensus       300 ~~AVd~isl~L~~gqTlGlVGESGSGKsTlG~allrL~~s~-G-~-I~F~G~~i~~~~~~~mrplR~~mQvVFQDPygSL  376 (534)
T COG4172         300 LRAVDGISLTLRRGQTLGLVGESGSGKSTLGLALLRLIPSQ-G-E-IRFDGQDIDGLSRKEMRPLRRRMQVVFQDPYGSL  376 (534)
T ss_pred             eEEeccceeEecCCCeEEEEecCCCCcchHHHHHHhhcCcC-c-e-EEECCccccccChhhhhhhhhhceEEEeCCCCCC
Confidence            344455544 9999999999999999999999887655442 2 2 333333 11   111  11121222222222211


Q ss_pred             ccC---------C---CCCCCCHHHHH-HHHHHhhcc---c-eeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcccc
Q 009230          358 NYG---------G---SAERMTVEEFE-QGKAWLSNT---F-SLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYN  420 (539)
Q Consensus       358 ~~~---------~---~~~~l~~~~~~-~~~~~l~~~---~-~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~  420 (539)
                      ...         +   ....++..|.. ++.+.+.+-   + ..-++..+-+....+=++.++.++  .++++|++|.=+
T Consensus       377 sPRmtV~qII~EGL~vh~~~ls~~eR~~rv~~aL~EVGLDp~~r~RYPhEFSGGQRQRIAIARAli--LkP~~i~LDEPT  454 (534)
T COG4172         377 SPRMTVGQIIEEGLRVHEPKLSAAERDQRVIEALEEVGLDPATRNRYPHEFSGGQRQRIAIARALI--LKPELILLDEPT  454 (534)
T ss_pred             CcccCHHHHhhhhhhhcCCCCCHHHHHHHHHHHHHHcCCChhHhhcCCcccCcchhhHHHHHHHHh--cCCcEEEecCCc
Confidence            100         0   01234443332 223333220   0 000000111222233334444333  478999999222


Q ss_pred             ccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          421 ELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       421 ~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                              +.-+...+.++++-|+.|-+++|..-++++|.-+                  .+-..||.||.+..-+
T Consensus       455 --------SALD~SVQaQvv~LLr~LQ~k~~LsYLFISHDL~------------------VvrAl~~~viVm~~Gk  504 (534)
T COG4172         455 --------SALDRSVQAQVLDLLRDLQQKHGLSYLFISHDLA------------------VVRALCHRVIVMRDGK  504 (534)
T ss_pred             --------hHhhHHHHHHHHHHHHHHHHHhCCeEEEEeccHH------------------HHHHhhceEEEEeCCE
Confidence                    2223455678999999999999999999999222                  2446889999987644

>PRK15177 Vi polysaccharide export ATP-binding protein VexC; Provisional

Probab=97.43  E-value=0.0027  Score=59.71  Aligned_cols=27  Identities=22%  Similarity=0.103  Sum_probs=24.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+++.|.|++|+|||||+.-++-.
T Consensus        10 i~~Ge~~~l~G~NGsGKSTLlk~i~Gl   36 (213)
T PRK15177         10 MGYHEHIGILAAPGSGKTTLTRLLCGL   36 (213)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999999998877644

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=97.42  E-value=0.0023  Score=59.79  Aligned_cols=33  Identities=24%  Similarity=0.360  Sum_probs=26.9

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        14 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~l~G~   47 (206)
T TIGR03608        14 LDDLNLTIEKGKMYAIIGESGSGKSTLLNIIGLL   47 (206)
T ss_pred             EeceEEEEeCCcEEEEECCCCCCHHHHHHHHhcC
Confidence            444433 899999999999999999998877643

A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=97.42  E-value=0.0017  Score=64.51  Aligned_cols=34  Identities=24%  Similarity=0.255  Sum_probs=27.5

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++--
T Consensus        17 ~l~~is~~i~~Gei~~l~G~NGaGKTTLl~~l~Gl   51 (301)
T TIGR03522        17 ALDEVSFEAQKGRIVGFLGPNGAGKSTTMKIITGY   51 (301)
T ss_pred             EEEEeEEEEeCCeEEEEECCCCCCHHHHHHHHhCC
Confidence            3454544 999999999999999999998877643

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.

>TIGR00750 lao LAO/AO transport system ATPase

Probab=97.42  E-value=0.00088  Score=66.52  Aligned_cols=49  Identities=22%  Similarity=0.381  Sum_probs=41.5

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      |+++.. ..++.++.|.|+||+|||||+..++..+... |.+|.+++++..
T Consensus        24 ~~~~~~~~~~~~~i~i~G~~G~GKttl~~~l~~~~~~~-~~~v~~i~~D~~   73 (300)
T TIGR00750        24 LDRIMPYTGNAHRVGITGTPGAGKSTLLEALGMELRRR-GLKVAVIAVDPS   73 (300)
T ss_pred             HHhCCcccCCceEEEEECCCCCCHHHHHHHHHHHHHHC-CCeEEEEecCCC
Confidence            444444 6778999999999999999999999988775 999999998854

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=97.42  E-value=0.0015  Score=60.24  Aligned_cols=32  Identities=28%  Similarity=0.273  Sum_probs=26.3

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus         8 l~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~i~G   40 (190)
T TIGR01166         8 LKGLNFAAERGEVLALLGANGAGKSTLLLHLNG   40 (190)
T ss_pred             ecceeEEEcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            444443 99999999999999999999876654

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria

Probab=97.41  E-value=0.001  Score=63.68  Aligned_cols=34  Identities=24%  Similarity=0.311  Sum_probs=27.6

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        17 l~~i~~~i~~Ge~~~l~G~nGsGKSTLl~~i~Gl~   51 (236)
T cd03253          17 LKDVSFTIPAGKKVAIVGPSGSGKSTILRLLFRFY   51 (236)
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            444433 8999999999999999999988877543

Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=97.41  E-value=0.0017  Score=58.90  Aligned_cols=27  Identities=30%  Similarity=0.417  Sum_probs=24.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+++.|.|++|+|||||+.-++-.
T Consensus        25 i~~Ge~~~i~G~nGsGKStLl~~l~G~   51 (173)
T cd03246          25 IEPGESLAIIGPSGSGKSTLARLILGL   51 (173)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHHhc
Confidence            899999999999999999998877654

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=97.41  E-value=0.0017  Score=58.77  Aligned_cols=33  Identities=30%  Similarity=0.467  Sum_probs=26.9

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        18 l~~i~~~i~~G~~~~l~G~nGsGKstLl~~i~G~   51 (171)
T cd03228          18 LKDVSLTIKPGEKVAIVGPSGSGKSTLLKLLLRL   51 (171)
T ss_pred             ccceEEEEcCCCEEEEECCCCCCHHHHHHHHHcC
Confidence            444433 999999999999999999998877644

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF13245 AAA_19: Part of AAA domain

Probab=97.41  E-value=0.00042  Score=53.30  Aligned_cols=50  Identities=22%  Similarity=0.338  Sum_probs=37.9

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHh---cCCeEEEEeCCCCH-HHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEH---AGWKFVLCSMENKV-REHARKL  345 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~---~g~~vl~~s~E~~~-~~~~~r~  345 (539)
                      .+.+.+|.|+||+|||+.+.+.+.+....   .+.+|++++.--.. +++.+|+
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            35688899999999999999998888752   16789999877443 3444554

>cd03236 ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 of RNase L inhibitor

Probab=97.41  E-value=0.0025  Score=61.63  Aligned_cols=29  Identities=21%  Similarity=0.237  Sum_probs=25.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      +.+|+++.|.|++|+|||||+.-++--..
T Consensus        23 i~~Ge~~~IvG~nGsGKSTLlk~l~Gl~~   51 (255)
T cd03236          23 PREGQVLGLVGPNGIGKSTALKILAGKLK   51 (255)
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHhCCcC
Confidence            78999999999999999999877665543

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI s are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLIs have an N-terminal Fe-S domain and two nucleotide binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=97.40  E-value=0.0027  Score=63.49  Aligned_cols=38  Identities=24%  Similarity=0.614  Sum_probs=33.4

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      |.++.|.||+||||++..++..+....|++|.+++.+.
T Consensus         1 ~~~l~Gl~GaGKST~~~~l~~~l~~~~g~~v~~~~~Dd   38 (340)
T TIGR03575         1 LCVLCGLPAAGKSTLARSLSATLRRERGWAVAVITYDD   38 (340)
T ss_pred             CeEEECCCCCCHHHHHHHHHHHHHhccCCeEEEEcccc
Confidence            46899999999999999999888754599999999884

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>COG0444 DppD ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=97.40  E-value=0.0037  Score=60.84  Aligned_cols=65  Identities=15%  Similarity=0.203  Sum_probs=48.6

Q ss_pred             HHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhc
Q 009230          406 VLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINK  485 (539)
Q Consensus       406 ~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~  485 (539)
                      +....++++|=|-=++-        -+...+.++++-|+++.+++|.++++++|.=+                  -+.+.
T Consensus       167 ala~~P~LlIADEPTTA--------LDvt~QaqIl~Ll~~l~~e~~~aiilITHDl~------------------vva~~  220 (316)
T COG0444         167 ALALNPKLLIADEPTTA--------LDVTVQAQILDLLKELQREKGTALILITHDLG------------------VVAEI  220 (316)
T ss_pred             HHhCCCCEEEeCCCcch--------hhHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHh
Confidence            44568999999932221        23345678999999999999999999999322                  35678


Q ss_pred             cceEEEEEeCC
Q 009230          486 CDNGIVIHRNR  496 (539)
Q Consensus       486 aD~vl~l~r~~  496 (539)
                      ||.|.+++.-+
T Consensus       221 aDri~VMYaG~  231 (316)
T COG0444         221 ADRVAVMYAGR  231 (316)
T ss_pred             cceEEEEECcE
Confidence            99999888744

>PRK13640 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.40  E-value=0.0017  Score=63.96  Aligned_cols=35  Identities=29%  Similarity=0.300  Sum_probs=28.2

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        22 ~l~~v~l~i~~Ge~~~I~G~nGaGKSTLl~~l~G~~   57 (282)
T PRK13640         22 ALNDISFSIPRGSWTALIGHNGSGKSTISKLINGLL   57 (282)
T ss_pred             ceeeEEEEEcCCCEEEEECCCCCcHHHHHHHHhccc
Confidence            3444444 9999999999999999999988876443

>TIGR03411 urea_trans_UrtD urea ABC transporter, ATP-binding protein UrtD

Probab=97.38  E-value=0.002  Score=61.90  Aligned_cols=34  Identities=38%  Similarity=0.613  Sum_probs=27.8

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        17 ~l~~vs~~i~~Ge~~~l~G~nGsGKSTLl~~l~G~   51 (242)
T TIGR03411        17 ALNDLSLYVDPGELRVIIGPNGAGKTTMMDVITGK   51 (242)
T ss_pred             EeeeeeEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3444444 999999999999999999998877754

Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.

>PRK10895 lipopolysaccharide ABC transporter ATP-binding protein; Provisional

Probab=97.38  E-value=0.003  Score=60.65  Aligned_cols=34  Identities=18%  Similarity=0.256  Sum_probs=27.5

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        19 l~~~sl~i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   53 (241)
T PRK10895         19 VEDVSLTVNSGEIVGLLGPNGAGKTTTFYMVVGIV   53 (241)
T ss_pred             EeeeeEEEcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            444433 9999999999999999999988777543

>PRK10261 glutathione transporter ATP-binding protein; Provisional

Probab=97.38  E-value=0.003  Score=69.47  Aligned_cols=44  Identities=9%  Similarity=0.221  Sum_probs=33.2

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      .+++++++|--+.       +. +.....++++.|+.++++++.+||+++|.
T Consensus       480 ~~p~llllDEPts-------~L-D~~~~~~i~~ll~~l~~~~g~tvi~isHd  523 (623)
T PRK10261        480 LNPKVIIADEAVS-------AL-DVSIRGQIINLLLDLQRDFGIAYLFISHD  523 (623)
T ss_pred             cCCCEEEEeCCcc-------cC-CHHHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            5899999993322       22 23445678888899988899999999993

>PRK14258 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.37  E-value=0.0071  Score=58.83  Aligned_cols=60  Identities=8%  Similarity=0.025  Sum_probs=42.2

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|+.++++.+.+||+++|...                  .+...||.
T Consensus       167 ~~p~vllLDEP~~-------~LD-~~~~~~l~~~l~~l~~~~~~tiiivsH~~~------------------~i~~~~d~  220 (261)
T PRK14258        167 VKPKVLLMDEPCF-------GLD-PIASMKVESLIQSLRLRSELTMVIVSHNLH------------------QVSRLSDF  220 (261)
T ss_pred             cCCCEEEEeCCCc-------cCC-HHHHHHHHHHHHHHHHhCCCEEEEEECCHH------------------HHHHhcCE
Confidence            5789999993332       122 334556778888887777899999999322                  24578899


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|..
T Consensus       221 i~~l~~  226 (261)
T PRK14258        221 TAFFKG  226 (261)
T ss_pred             EEEEcc
Confidence            999875

>PF05729 NACHT: NACHT domain

Probab=97.36  E-value=0.0018  Score=57.82  Aligned_cols=26  Identities=31%  Similarity=0.507  Sum_probs=24.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHh
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEH  324 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~  324 (539)
                      +.+|.|.||+|||+++..++..++.+
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~   27 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEE   27 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhc
Confidence            68899999999999999999999886

>PRK08116 hypothetical protein; Validated

Probab=97.36  E-value=0.0035  Score=61.05  Aligned_cols=35  Identities=14%  Similarity=0.238  Sum_probs=31.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      -++|.|++|+|||.|+..++..+..+ |.+|+|++.
T Consensus       116 gl~l~G~~GtGKThLa~aia~~l~~~-~~~v~~~~~  150 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANELIEK-GVPVIFVNF  150 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEEEH
Confidence            47899999999999999999998876 999999983

>TIGR01186 proV glycine betaine/L-proline transport ATP binding subunit

Probab=97.36  E-value=0.0043  Score=63.08  Aligned_cols=34  Identities=29%  Similarity=0.402  Sum_probs=27.6

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++--.
T Consensus         9 l~~vs~~i~~Gei~~l~G~sGsGKSTLLr~L~Gl~   43 (363)
T TIGR01186         9 VNDADLAIAKGEIFVIMGLSGSGKSTTVRMLNRLI   43 (363)
T ss_pred             EEeeEEEEcCCCEEEEECCCCChHHHHHHHHhCCC
Confidence            444444 9999999999999999999988776443

This model describes the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits these transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L.lact

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.36  E-value=0.013  Score=56.82  Aligned_cols=41  Identities=7%  Similarity=0.102  Sum_probs=36.5

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +|+.+++.|++|+|||+++..++..+..+ +.+|.+++.+-.
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~l~~~-~~~v~~i~~D~~  114 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQFHGK-KKTVGFITTDHS  114 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHHHc-CCeEEEEecCCC
Confidence            67899999999999999999999887764 899999998854

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.36  E-value=0.0063  Score=66.82  Aligned_cols=114  Identities=13%  Similarity=0.117  Sum_probs=68.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-CeEEEEeCCCCHHHHH--HHHHHHhhCCCccccccCCCCCCCCHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAG-WKFVLCSMENKVREHA--RKLLEKHIKKPFFEANYGGSAERMTVEE  370 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-~~vl~~s~E~~~~~~~--~r~~~~~~~~~~~~i~~~~~~~~l~~~~  370 (539)
                      +.+|+++++.|++|+||||.+..++......+| .+|.+++.+-..--..  -+..+...+++....        .++++
T Consensus       182 ~~~g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvpv~~~--------~~~~~  253 (767)
T PRK14723        182 LAQGGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGVPVHAV--------KDAAD  253 (767)
T ss_pred             cCCCeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCCCCcccc--------CCHHH
Confidence            456889999999999999999999988765556 5899999885321111  133455566665422        35666


Q ss_pred             HHHHHHHhhcc-ceeEeecCCC-CCCHHHHHHHHHHHHHHcC--CcEEEEc
Q 009230          371 FEQGKAWLSNT-FSLIRCENDS-LPSIKWVLDLAKAAVLRHG--VRGLVID  417 (539)
Q Consensus       371 ~~~~~~~l~~~-~~~i~~~~~~-~~~~~~i~~~i~~~~~~~~--~~~vvID  417 (539)
                      +.++.+.+.+. .++|  |..+ ++.-..+.+.+..+.....  -.++|+|
T Consensus       254 l~~al~~~~~~D~VLI--DTAGRs~~d~~l~eel~~l~~~~~p~e~~LVLs  302 (767)
T PRK14723        254 LRFALAALGDKHLVLI--DTVGMSQRDRNVSEQIAMLCGVGRPVRRLLLLN  302 (767)
T ss_pred             HHHHHHHhcCCCEEEE--eCCCCCccCHHHHHHHHHHhccCCCCeEEEEEC
Confidence            77766666654 3344  3222 2222345555554433222  2467777

>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein

Probab=97.35  E-value=0.0016  Score=61.99  Aligned_cols=35  Identities=26%  Similarity=0.459  Sum_probs=28.3

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        18 ~l~~isl~i~~G~~~~i~G~nGsGKSTLl~~l~G~~   53 (229)
T cd03254          18 VLKDINFSIKPGETVAIVGPTGAGKTTLINLLMRFY   53 (229)
T ss_pred             cccceEEEEcCCCEEEEECCCCCCHHHHHHHHhcCc
Confidence            3444444 9999999999999999999988887543

In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules

Probab=97.35  E-value=0.0015  Score=62.14  Aligned_cols=34  Identities=32%  Similarity=0.417  Sum_probs=28.0

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        29 ~l~~is~~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   63 (226)
T cd03248          29 VLQDVSFTLHPGEVTALVGPSGSGKSTVVALLENF   63 (226)
T ss_pred             cccceEEEEcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3555544 999999999999999999998877644

Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.

>PRK10744 pstB phosphate transporter ATP-binding protein; Provisional

Probab=97.35  E-value=0.0036  Score=60.86  Aligned_cols=33  Identities=18%  Similarity=0.257  Sum_probs=27.6

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        29 l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   62 (260)
T PRK10744         29 LKNINLDIAKNQVTAFIGPSGCGKSTLLRTFNRM   62 (260)
T ss_pred             eeceeEEEcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            444443 999999999999999999999888754

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=97.35  E-value=0.0038  Score=55.92  Aligned_cols=31  Identities=39%  Similarity=0.460  Sum_probs=26.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEH  324 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~  324 (539)
                      +..+.+++|.|+.|+|||+++..++......
T Consensus        18 ~~~~~~~~i~G~NgsGKS~~l~~i~~~~~~~   48 (162)
T cd03227          18 FGEGSLTIITGPNGSGKSTILDAIGLALGGA   48 (162)
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            3444699999999999999999988887765

These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.

>PRK13547 hmuV hemin importer ATP-binding subunit; Provisional

Probab=97.35  E-value=0.0041  Score=60.85  Aligned_cols=61  Identities=16%  Similarity=0.178  Sum_probs=41.5

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.       +.+ ......+.+.|++++++.+.+||+++|...                  .+...||.
T Consensus       171 ~~p~lllLDEPt~-------~LD-~~~~~~l~~~l~~~~~~~~~tviiisH~~~------------------~~~~~~d~  224 (272)
T PRK13547        171 QPPRYLLLDEPTA-------ALD-LAHQHRLLDTVRRLARDWNLGVLAIVHDPN------------------LAARHADR  224 (272)
T ss_pred             CCCCEEEEcCccc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEECCHH------------------HHHHhCCE
Confidence            4789999993322       122 234456778888888878999999999322                  13457788


Q ss_pred             EEEEEeC
Q 009230          489 GIVIHRN  495 (539)
Q Consensus       489 vl~l~r~  495 (539)
                      ++.|.+.
T Consensus       225 i~~l~~G  231 (272)
T PRK13547        225 IAMLADG  231 (272)
T ss_pred             EEEEECC
Confidence            8888653

>PRK14235 phosphate transporter ATP-binding protein; Provisional

Probab=97.35  E-value=0.012  Score=57.45  Aligned_cols=34  Identities=21%  Similarity=0.197  Sum_probs=27.8

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        35 l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   69 (267)
T PRK14235         35 LFDVDLDIPEKTVTAFIGPSGCGKSTFLRCLNRMN   69 (267)
T ss_pred             EEEEEEEEcCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            444433 9999999999999999999988877543

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=97.34  E-value=0.00099  Score=59.97  Aligned_cols=142  Identities=18%  Similarity=0.118  Sum_probs=89.9

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGK  375 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~  375 (539)
                      .|.|.+++|+-++|||+-+++-+.+.... |.+|+.|..+.+.+--... ++...|.+...                   
T Consensus         3 ~g~l~~i~gpM~SGKT~eLl~r~~~~~~~-g~~v~vfkp~iD~R~~~~~-V~Sr~G~~~~A-------------------   61 (201)
T COG1435           3 MGWLEFIYGPMFSGKTEELLRRARRYKEA-GMKVLVFKPAIDTRYGVGK-VSSRIGLSSEA-------------------   61 (201)
T ss_pred             eEEEEEEEccCcCcchHHHHHHHHHHHHc-CCeEEEEecccccccccce-eeeccCCcccc-------------------
Confidence            57899999999999999999999998886 9999999988655422111 12222222111                   


Q ss_pred             HHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEE
Q 009230          376 AWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVW  455 (539)
Q Consensus       376 ~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi  455 (539)
                             ..|    .   +-.++.+.+........+++|+||-. |.+.            .+++..|.++|.++|++|+
T Consensus        62 -------~~i----~---~~~~i~~~i~~~~~~~~~~~v~IDEa-QF~~------------~~~v~~l~~lad~lgi~Vi  114 (201)
T COG1435          62 -------VVI----P---SDTDIFDEIAALHEKPPVDCVLIDEA-QFFD------------EELVYVLNELADRLGIPVI  114 (201)
T ss_pred             -------eec----C---ChHHHHHHHHhcccCCCcCEEEEehh-HhCC------------HHHHHHHHHHHhhcCCEEE
Confidence                   112    1   23445555544333333789999933 3221            2577888999999999999


Q ss_pred             EEecCCCCCCCCCCCCCcccccccccchhccceEEEEE
Q 009230          456 FVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIH  493 (539)
Q Consensus       456 ~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~  493 (539)
                      +-.=...=        .-.-+.||..+-..||.+.-|.
T Consensus       115 ~~GL~~DF--------rgepFe~s~~Lla~ADkv~kL~  144 (201)
T COG1435         115 CYGLDTDF--------RGEPFEGSKYLLAIADKVTKLK  144 (201)
T ss_pred             Eecccccc--------ccCCCccHHHHHHHHHHHHHHH
Confidence            85431111        1122557777778888766443

>COG0411 LivG ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]

Probab=97.34  E-value=0.0039  Score=58.22  Aligned_cols=183  Identities=15%  Similarity=0.147  Sum_probs=96.6

Q ss_pred             Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC----CCHHHHHHHHHHHhhCCC--ccc
Q 009230          284 GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME----NKVREHARKLLEKHIKKP--FFE  356 (539)
Q Consensus       284 g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E----~~~~~~~~r~~~~~~~~~--~~~  356 (539)
                      |+..+|+..- +++|+++.|.||.|+||||+..-+.-. ..-....|. |..+    +++.++.++=++.-....  +..
T Consensus        16 Gl~Al~~Vsl~v~~Gei~~LIGPNGAGKTTlfNlitG~-~~P~~G~v~-~~G~~it~l~p~~iar~Gi~RTFQ~~rlF~~   93 (250)
T COG0411          16 GLTAVNDVSLEVRPGEIVGLIGPNGAGKTTLFNLITGF-YKPSSGTVI-FRGRDITGLPPHRIARLGIARTFQITRLFPG   93 (250)
T ss_pred             CEEEEeceeEEEcCCeEEEEECCCCCCceeeeeeeccc-ccCCCceEE-ECCcccCCCCHHHHHhccceeecccccccCC
Confidence            5667777766 999999999999999999985543322 222233443 4444    566665443221111000  000


Q ss_pred             ----------------cccCCCCCCC--CHHH-HHHHHHHhhcccee-EeecCCCCCCH--HHHHHHHHHHHHHcCCcEE
Q 009230          357 ----------------ANYGGSAERM--TVEE-FEQGKAWLSNTFSL-IRCENDSLPSI--KWVLDLAKAAVLRHGVRGL  414 (539)
Q Consensus       357 ----------------i~~~~~~~~l--~~~~-~~~~~~~l~~~~~~-i~~~~~~~~~~--~~i~~~i~~~~~~~~~~~v  414 (539)
                                      +...-.....  .+.+ .+++.++|..--+. .....-+..+-  ...++.++.++  .+|+++
T Consensus        94 lTVlENv~va~~~~~~~~~~l~~~~~~~~e~~~~e~A~~~Le~vgL~~~a~~~A~~LsyG~qR~LEIArALa--~~P~lL  171 (250)
T COG0411          94 LTVLENVAVGAHARLGLSGLLGRPRARKEEREARERARELLEFVGLGELADRPAGNLSYGQQRRLEIARALA--TQPKLL  171 (250)
T ss_pred             CcHHHHHHHHhhhhhhhhhhhccccchhhHHHHHHHHHHHHHHcCCchhhcchhhcCChhHhHHHHHHHHHh--cCCCEE
Confidence                            0000000001  1111 23344444321000 00001111221  22334444333  579999


Q ss_pred             EEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          415 VIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       415 vID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      ++|--+       .+.+. .+..++...++++.++.+++|+++=|.-+                  -+.+.||.|+.|..
T Consensus       172 LLDEPa-------AGln~-~e~~~l~~~i~~i~~~~g~tillIEHdM~------------------~Vm~l~dri~Vl~~  225 (250)
T COG0411         172 LLDEPA-------AGLNP-EETEELAELIRELRDRGGVTILLIEHDMK------------------LVMGLADRIVVLNY  225 (250)
T ss_pred             EecCcc-------CCCCH-HHHHHHHHHHHHHHhcCCcEEEEEEeccH------------------HHhhhccEEEeccC
Confidence            999221       23333 34567888888888889999999999422                  24579999999987


Q ss_pred             CC
Q 009230          495 NR  496 (539)
Q Consensus       495 ~~  496 (539)
                      -+
T Consensus       226 G~  227 (250)
T COG0411         226 GE  227 (250)
T ss_pred             Cc
Confidence            65

>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C

Probab=97.34  E-value=0.0029  Score=59.05  Aligned_cols=33  Identities=36%  Similarity=0.520  Sum_probs=27.3

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        21 l~~~s~~i~~G~~~~i~G~nG~GKSTLl~~i~G~   54 (204)
T cd03250          21 LKDINLEVPKGELVAIVGPVGSGKSSLLSALLGE   54 (204)
T ss_pred             eeeeeEEECCCCEEEEECCCCCCHHHHHHHHhCc
Confidence            444433 999999999999999999998877654

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>PRK14269 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.33  E-value=0.0053  Score=59.15  Aligned_cols=33  Identities=18%  Similarity=0.316  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        18 l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (246)
T PRK14269         18 LFDINMQIEQNKITALIGASGCGKSTFLRCFNRM   51 (246)
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            444433 999999999999999999998877653

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.33  E-value=0.0037  Score=59.71  Aligned_cols=36  Identities=19%  Similarity=0.332  Sum_probs=32.2

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ...+|.|+||+|||.++..++..+..+ |.+|+|++.
T Consensus       100 ~~~~l~G~~GtGKThLa~aia~~l~~~-g~~v~~it~  135 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAAICNELLLR-GKSVLIITV  135 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhc-CCeEEEEEH
Confidence            368899999999999999999998885 999999963

>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]

Probab=97.32  E-value=0.00095  Score=66.49  Aligned_cols=47  Identities=15%  Similarity=0.171  Sum_probs=36.4

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCC
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQ  462 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~  462 (539)
                      ..++.+.++|-+...+.       + .....+++.|.++|++.++++++++|+..
T Consensus       523 aerpn~~~iDEF~AhLD-------~-~TA~rVArkiselaRe~giTlivvThrpE  569 (593)
T COG2401         523 AERPNVLLIDEFAAHLD-------E-LTAVRVARKISELAREAGITLIVVTHRPE  569 (593)
T ss_pred             hcCCCcEEhhhhhhhcC-------H-HHHHHHHHHHHHHHHHhCCeEEEEecCHH
Confidence            35789999996665542       2 23457899999999999999999999543

>PLN03211 ABC transporter G-25; Provisional

Probab=97.31  E-value=0.0021  Score=70.78  Aligned_cols=34  Identities=38%  Similarity=0.520  Sum_probs=29.0

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      -|+.+.. +++|+++.|.|++|+|||||+.-++-.
T Consensus        83 iL~~vs~~i~~Ge~~aI~GpnGaGKSTLL~iLaG~  117 (659)
T PLN03211         83 ILNGVTGMASPGEILAVLGPSGSGKSTLLNALAGR  117 (659)
T ss_pred             eeeCCEEEEECCEEEEEECCCCCCHHHHHHHHhCC
Confidence            4666666 999999999999999999998877644

>PRK03695 vitamin B12-transporter ATPase; Provisional

Probab=97.31  E-value=0.0011  Score=63.96  Aligned_cols=33  Identities=27%  Similarity=0.345  Sum_probs=26.9

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++--
T Consensus        12 l~~vsl~i~~Gei~~l~G~nGsGKSTLl~~l~Gl   45 (248)
T PRK03695         12 LGPLSAEVRAGEILHLVGPNGAGKSTLLARMAGL   45 (248)
T ss_pred             ecceEEEEcCCCEEEEECCCCCCHHHHHHHHcCC
Confidence            444433 999999999999999999998877643

>TIGR03269 met_CoM_red_A2 methyl coenzyme M reductase system, component A2

Probab=97.31  E-value=0.0085  Score=64.54  Aligned_cols=34  Identities=24%  Similarity=0.235  Sum_probs=28.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        16 l~~is~~i~~Ge~~~iiG~nGsGKSTLl~~l~Gl~   50 (520)
T TIGR03269        16 LKNISFTIEEGEVLGILGRSGAGKSVLMHVLRGMD   50 (520)
T ss_pred             eeceeEEEcCCCEEEEECCCCCCHHHHHHHHhhcc
Confidence            444443 9999999999999999999998887653

The enzyme that catalyzes the final step in methanogenesis, methyl coenzyme M reductase, contains alpha, beta, and gamma chains. In older literature, the complex of alpha, beta, and gamma chains was termed component C, while this single chain protein was termed methyl coenzyme M reductase system component A2.

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=97.31  E-value=0.0087  Score=60.33  Aligned_cols=77  Identities=13%  Similarity=0.129  Sum_probs=57.5

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHH-HhcCCeEEEEeCCCC----HHHHHHHHHHHhhCCCccccccCCCCCCCCHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNIN-EHAGWKFVLCSMENK----VREHARKLLEKHIKKPFFEANYGGSAERMTVE  369 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a-~~~g~~vl~~s~E~~----~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~  369 (539)
                      .++.++++.||+|+||||-+..+|+... .....+|.++|++--    .+++  +..+...|+|+.-.        .++.
T Consensus       201 ~~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQL--k~Ya~im~vp~~vv--------~~~~  270 (407)
T COG1419         201 EQKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQL--KTYADIMGVPLEVV--------YSPK  270 (407)
T ss_pred             ccCcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHH--HHHHHHhCCceEEe--------cCHH
Confidence            4478999999999999999999999988 333689999999942    3333  44577788887643        4567


Q ss_pred             HHHHHHHHhhcc
Q 009230          370 EFEQGKAWLSNT  381 (539)
Q Consensus       370 ~~~~~~~~l~~~  381 (539)
                      ++..+...+.+.
T Consensus       271 el~~ai~~l~~~  282 (407)
T COG1419         271 ELAEAIEALRDC  282 (407)
T ss_pred             HHHHHHHHhhcC
Confidence            777776666654

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.31  E-value=0.01  Score=55.90  Aligned_cols=33  Identities=27%  Similarity=0.297  Sum_probs=26.9

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        27 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~i~G~   60 (214)
T PRK13543         27 FGPLDFHVDAGEALLVQGDNGAGKTTLLRVLAGL   60 (214)
T ss_pred             eecceEEECCCCEEEEEcCCCCCHHHHHHHHhCC
Confidence            343433 999999999999999999998877654

>TIGR02982 heterocyst_DevA ABC exporter ATP-binding subunit, DevA family

Probab=97.30  E-value=0.004  Score=58.87  Aligned_cols=59  Identities=12%  Similarity=0.317  Sum_probs=41.4

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|.-+.-       .+ ......+...|+.++++.+.+||+++|...                   +...||.
T Consensus       158 ~~p~illlDEP~~~-------LD-~~~~~~l~~~l~~~~~~~~~tii~~sh~~~-------------------~~~~~d~  210 (220)
T TIGR02982       158 HRPKLVLADEPTAA-------LD-SKSGRDVVELMQKLAREQGCTILIVTHDNR-------------------ILDVADR  210 (220)
T ss_pred             cCCCEEEEeCCCCc-------CC-HHHHHHHHHHHHHHHHHcCCEEEEEeCCHH-------------------HHhhCCE
Confidence            57899999933322       22 234557888888888878999999999421                   1247888


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|..
T Consensus       211 v~~l~~  216 (220)
T TIGR02982       211 IVHMED  216 (220)
T ss_pred             EEEEEC
Confidence            888864

Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The DevBCA proteins are thought export of either heterocyst-specific glycolipids or an enzyme essential for formation of the laminated layer found in heterocysts.

>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=97.30  E-value=6.6e-05  Score=70.26  Aligned_cols=165  Identities=15%  Similarity=0.149  Sum_probs=81.8

Q ss_pred             ccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh---cCCeEEEEeCCCCHHHHHHHHHHHhhCCCc
Q 009230          280 GISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEH---AGWKFVLCSMENKVREHARKLLEKHIKKPF  354 (539)
Q Consensus       280 gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~---~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~  354 (539)
                      .++.|...+..-+.  +....-++|+|.||+|||+++..++..++..   ....+..+.+-..  ++     +...+.+.
T Consensus        19 ~i~~g~~~~~~~v~~dl~~~~h~li~G~tgsGKS~~l~~ll~~l~~~~~p~~~~l~iiD~k~~--~l-----~~~~~~~~   91 (205)
T PF01580_consen   19 PIPVGVDQRGDPVVLDLKKNPHLLIAGATGSGKSTLLRTLLLSLALTYSPDDVQLYIIDPKGS--DL-----APLADLPH   91 (205)
T ss_dssp             EEEEEEETTS-EEEEEGGGS-SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSS--CC-----GGGTT-TT
T ss_pred             EEEecccCCCCEEEEEcCCCceEEEEcCCCCCccHHHHHHHHHHHHHhcCCccEEEEEcCCcc--cc-----chhhhhhh
Confidence            45555554333332  5555578899999999999999999999883   2556666665432  11     11111111


Q ss_pred             cccccCCCCCCCCHHHHHHHHHH----hhccceeEeecCCCCCCHHHHHHHHHHHHH---------HcCCcEEEEccccc
Q 009230          355 FEANYGGSAERMTVEEFEQGKAW----LSNTFSLIRCENDSLPSIKWVLDLAKAAVL---------RHGVRGLVIDPYNE  421 (539)
Q Consensus       355 ~~i~~~~~~~~l~~~~~~~~~~~----l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~---------~~~~~~vvID~~~~  421 (539)
                      ...  .  ...-+.++..++.++    +..+.-++.  ..+..+++........+..         ....-+++||.+..
T Consensus        92 ~~~--~--~~~~~~~~~~~~l~~l~~em~~R~~~l~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~iDe~~~  165 (205)
T PF01580_consen   92 VAA--V--AVATDPEEILRLLEELVEEMERRQALLR--EAGVRNIDDYNEERGELPDDIFADPWLKELPPIFIVIDEFAA  165 (205)
T ss_dssp             BSS-----S-B-SHHHHHHHHHHHHHHHHHHHHHHH--HCT-SSHHHHHHHHHHHHHTT----B-----EEEEEECTHHH
T ss_pred             hcc--c--cccccHHHHHHHHHHHHHHHHHHHHHHH--HcCccchhhHHHHhhhhccccccccccccCchHHHHhhhHHH
Confidence            100  0  001234444433322    222222221  1233334432222222111         23456889999998


Q ss_pred             cccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          422 LDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       422 l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                      +.....  ......+.+.+..|-+.++..||++|+.+|
T Consensus       166 l~~~~~--~~~~~~~~~~l~~i~~~gR~~Gi~li~~~Q  201 (205)
T PF01580_consen  166 LRDSAP--DDSKKEIMDLLARIARKGRAAGIHLILATQ  201 (205)
T ss_dssp             HHHHHH--HH----HHHHHHHHHHHCGGGTEEEEEEES
T ss_pred             HHhhcc--hhhHHHHHHHHHHHHHHHHhcCEEEEEEeC
Confidence            875321  011234566777777778899999999999

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.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=97.30  E-value=0.0018  Score=70.20  Aligned_cols=133  Identities=14%  Similarity=0.131  Sum_probs=80.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC---HHHHHHHHHHHhhCCCccccccCCCCCCCCHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK---VREHARKLLEKHIKKPFFEANYGGSAERMTVEE  370 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~---~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~  370 (539)
                      -....+++|.+|.|.||||++.|++. .+. .+..|.|+|++++   +.+++.++++.....-          +.+.++-
T Consensus        34 ~~~~RL~li~APAGfGKttl~aq~~~-~~~-~~~~v~Wlslde~dndp~rF~~yLi~al~~~~----------p~~~~~a  101 (894)
T COG2909          34 ANDYRLILISAPAGFGKTTLLAQWRE-LAA-DGAAVAWLSLDESDNDPARFLSYLIAALQQAT----------PTLGDEA  101 (894)
T ss_pred             CCCceEEEEeCCCCCcHHHHHHHHHH-hcC-cccceeEeecCCccCCHHHHHHHHHHHHHHhC----------ccccHHH
Confidence            44557999999999999999999988 444 3899999999866   6677788876543221          1222221


Q ss_pred             HHHHHHHhhccceeEeecCCCCCCHHHHHHHH-HHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009230          371 FEQGKAWLSNTFSLIRCENDSLPSIKWVLDLA-KAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQH  449 (539)
Q Consensus       371 ~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i-~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~  449 (539)
                      .     .+..+-        ...++..+.+.+ ..+..-.++=.+|||+|.-+-.+         .+.+.++.|-+-+ -
T Consensus       102 ~-----~l~q~~--------~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~---------~l~~~l~fLl~~~-P  158 (894)
T COG2909         102 Q-----TLLQKH--------QYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDP---------ALHEALRFLLKHA-P  158 (894)
T ss_pred             H-----HHHHhc--------ccccHHHHHHHHHHHHHhhcCceEEEeccccccCcc---------cHHHHHHHHHHhC-C
Confidence            1     222221        122344444333 34445567889999988755321         1333333332221 1


Q ss_pred             hCcEEEEEecCC
Q 009230          450 HACHVWFVAHPR  461 (539)
Q Consensus       450 ~~i~vi~~~q~r  461 (539)
                      -|++.|+++.++
T Consensus       159 ~~l~lvv~SR~r  170 (894)
T COG2909         159 ENLTLVVTSRSR  170 (894)
T ss_pred             CCeEEEEEeccC
Confidence            478888877644

>PRK14256 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.29  E-value=0.013  Score=56.61  Aligned_cols=33  Identities=15%  Similarity=0.215  Sum_probs=27.4

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++--
T Consensus        20 l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   53 (252)
T PRK14256         20 VKDVSMDFPENSVTAIIGPSGCGKSTVLRSINRM   53 (252)
T ss_pred             EecceEEEcCCCEEEEECCCCCCHHHHHHHHHhc
Confidence            444433 999999999999999999998887754

>PRK11231 fecE iron-dicitrate transporter ATP-binding subunit; Provisional

Probab=97.29  E-value=0.0035  Score=60.73  Aligned_cols=33  Identities=27%  Similarity=0.386  Sum_probs=26.8

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+-- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        18 l~~is~~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl   51 (255)
T PRK11231         18 LNDLSLSLPTGKITALIGPNGCGKSTLLKCFARL   51 (255)
T ss_pred             EeeeeeEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            444433 899999999999999999998877643

>TIGR03269 met_CoM_red_A2 methyl coenzyme M reductase system, component A2

Probab=97.28  E-value=0.0042  Score=66.87  Aligned_cols=61  Identities=10%  Similarity=0.169  Sum_probs=43.9

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|--+.       +.+ ......+++.|++++++.+.+||+++|....                  +.+.||
T Consensus       443 ~~~p~lLllDEPt~-------~LD-~~~~~~l~~~l~~l~~~~g~tvi~vsHd~~~------------------~~~~~d  496 (520)
T TIGR03269       443 IKEPRIVILDEPTG-------TMD-PITKVDVTHSILKAREEMEQTFIIVSHDMDF------------------VLDVCD  496 (520)
T ss_pred             hcCCCEEEEeCCcc-------cCC-HHHHHHHHHHHHHHHHHcCcEEEEEeCCHHH------------------HHHhCC
Confidence            35799999993222       222 3455678888889988889999999994221                  446789


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|+.
T Consensus       497 ~i~~l~~  503 (520)
T TIGR03269       497 RAALMRD  503 (520)
T ss_pred             EEEEEEC
Confidence            9998863

The enzyme that catalyzes the final step in methanogenesis, methyl coenzyme M reductase, contains alpha, beta, and gamma chains. In older literature, the complex of alpha, beta, and gamma chains was termed component C, while this single chain protein was termed methyl coenzyme M reductase system component A2.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=97.28  E-value=0.0029  Score=57.65  Aligned_cols=34  Identities=29%  Similarity=0.386  Sum_probs=27.9

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        18 l~~i~~~i~~Ge~~~i~G~nGsGKStLl~~l~G~~   52 (178)
T cd03247          18 LKNLSLELKQGEKIALLGRSGSGKSTLLQLLTGDL   52 (178)
T ss_pred             eEEEEEEEcCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            444433 9999999999999999999988877543

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.28  E-value=0.0018  Score=60.64  Aligned_cols=33  Identities=24%  Similarity=0.329  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        18 l~~is~~i~~Ge~~~i~G~nGsGKSTLl~~l~G~   51 (207)
T PRK13539         18 FSGLSFTLAAGEALVLTGPNGSGKTTLLRLIAGL   51 (207)
T ss_pred             EeceEEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            454443 899999999999999999998776643

>PRK15134 microcin C ABC transporter ATP-binding protein YejF; Provisional

Probab=97.28  E-value=0.0058  Score=65.94  Aligned_cols=61  Identities=20%  Similarity=0.303  Sum_probs=43.6

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|--+.       +. +......+++.|+.++++.+.+||+++|...                  .+...||
T Consensus       441 ~~~p~llllDEPt~-------~L-D~~~~~~l~~~l~~~~~~~~~tvi~vsHd~~------------------~~~~~~d  494 (529)
T PRK15134        441 ILKPSLIILDEPTS-------SL-DKTVQAQILALLKSLQQKHQLAYLFISHDLH------------------VVRALCH  494 (529)
T ss_pred             hCCCCEEEeeCCcc-------cc-CHHHHHHHHHHHHHHHHhhCCEEEEEeCCHH------------------HHHHhcC
Confidence            35799999993322       22 2344567888889998888999999999322                  1446789


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|+.
T Consensus       495 ~i~~l~~  501 (529)
T PRK15134        495 QVIVLRQ  501 (529)
T ss_pred             eEEEEEC
Confidence            9998874

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=97.28  E-value=0.0031  Score=68.94  Aligned_cols=169  Identities=15%  Similarity=0.134  Sum_probs=85.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHHHHhhCCC---ccccccCCC---CC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLLEKHIKKP---FFEANYGGS---AE  364 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~---~~~i~~~~~---~~  364 (539)
                      +++|+.+.|.|++|+|||||+.-++--.--. ...|.+-.-+   .+.+.+..+ ++....-+   ...++++-.   ..
T Consensus       366 i~~G~~~aIvG~sGsGKSTLl~ll~gl~~p~-~G~I~i~g~~i~~~~~~~~~~~-i~~v~Q~~~lf~~Ti~~Ni~~~~~~  443 (582)
T PRK11176        366 IPAGKTVALVGRSGSGKSTIANLLTRFYDID-EGEILLDGHDLRDYTLASLRNQ-VALVSQNVHLFNDTIANNIAYARTE  443 (582)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHHhccCCC-CceEEECCEEhhhcCHHHHHhh-ceEEccCceeecchHHHHHhcCCCC
Confidence            8999999999999999999987776543322 3444432222   223333322 22211111   111111100   11


Q ss_pred             CCCHHHHHHHHH------Hhhccc---eeEeecCCCCCCHHH--HHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHH
Q 009230          365 RMTVEEFEQGKA------WLSNTF---SLIRCENDSLPSIKW--VLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTET  433 (539)
Q Consensus       365 ~l~~~~~~~~~~------~l~~~~---~~i~~~~~~~~~~~~--i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~  433 (539)
                      ..+++++.++.+      ++...+   ....-+.....+-.+  -+..+|.+.  .+++++++|.-+.-+       +. 
T Consensus       444 ~~~~~~i~~al~~~~l~~~i~~lp~Gldt~ig~~g~~LSGGqrQRi~LARall--~~~~ililDEptsaL-------D~-  513 (582)
T PRK11176        444 QYSREQIEEAARMAYAMDFINKMDNGLDTVIGENGVLLSGGQRQRIAIARALL--RDSPILILDEATSAL-------DT-  513 (582)
T ss_pred             CCCHHHHHHHHHHhCcHHHHHhcccccCceeCCCCCcCCHHHHHHHHHHHHHH--hCCCEEEEECccccC-------CH-
Confidence            356676655432      222211   111001111122222  233334333  378999999444332       11 


Q ss_pred             HHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          434 EYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       434 ~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                      +.-..+.+.|+++.  .+.++|+++|.-.                   ....||.|+.|...
T Consensus       514 ~t~~~i~~~l~~~~--~~~tvI~VtHr~~-------------------~~~~~D~Ii~l~~g  554 (582)
T PRK11176        514 ESERAIQAALDELQ--KNRTSLVIAHRLS-------------------TIEKADEILVVEDG  554 (582)
T ss_pred             HHHHHHHHHHHHHh--CCCEEEEEecchH-------------------HHHhCCEEEEEECC
Confidence            22235667776653  3699999999321                   23468999999753

>PRK13644 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.28  E-value=0.0048  Score=60.50  Aligned_cols=34  Identities=29%  Similarity=0.227  Sum_probs=27.8

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        17 ~l~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (274)
T PRK13644         17 ALENINLVIKKGEYIGIIGKNGSGKSTLALHLNGL   51 (274)
T ss_pred             eeeeeEEEEeCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3444444 999999999999999999998877643

>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=97.28  E-value=0.00077  Score=67.28  Aligned_cols=36  Identities=17%  Similarity=0.381  Sum_probs=30.2

Q ss_pred             Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          284 GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       284 g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++..+|++-- +.+||++.|-|||||||||++.-||-
T Consensus        17 ~~~av~~isl~i~~Gef~~lLGPSGcGKTTlLR~IAG   53 (352)
T COG3842          17 DFTAVDDISLDIKKGEFVTLLGPSGCGKTTLLRMIAG   53 (352)
T ss_pred             CeeEEecceeeecCCcEEEEECCCCCCHHHHHHHHhC
Confidence            3566776655 99999999999999999999887763

>TIGR01189 ccmA heme ABC exporter, ATP-binding protein CcmA

Probab=97.27  E-value=0.0058  Score=56.75  Aligned_cols=33  Identities=27%  Similarity=0.252  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        16 l~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~l~G~   49 (198)
T TIGR01189        16 FEGLSFTLNAGEALQVTGPNGIGKTTLLRILAGL   49 (198)
T ss_pred             EeeeeEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            444433 999999999999999999998876653

This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c.

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=97.27  E-value=0.00053  Score=68.02  Aligned_cols=25  Identities=24%  Similarity=0.482  Sum_probs=23.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      +..||+.+|.||+||||||++.-||
T Consensus        26 i~~Gef~vllGPSGcGKSTlLr~IA   50 (338)
T COG3839          26 IEDGEFVVLLGPSGCGKSTLLRMIA   50 (338)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHh
Confidence            9999999999999999999988766

>TIGR00972 3a0107s01c2 phosphate ABC transporter, ATP-binding protein

Probab=97.26  E-value=0.0027  Score=61.17  Aligned_cols=33  Identities=21%  Similarity=0.288  Sum_probs=26.6

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        17 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~l~G~   50 (247)
T TIGR00972        17 LKNINLDIPKNQVTALIGPSGCGKSTLLRSLNRM   50 (247)
T ss_pred             ecceeEEECCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            444433 999999999999999999998876633

This model represents the ATP-binding protein of a family of ABC transporters for inorganic phosphate. In the model species Escherichia coli, a constitutive transporter for inorganic phosphate, with low affinity, is also present. The high affinity transporter that includes this polypeptide is induced when extracellular phosphate concentrations are low. The proteins most similar to the members of this family but not included appear to be amino acid transporters.

>TIGR03415 ABC_choXWV_ATP choline ABC transporter, ATP-binding protein

Probab=97.26  E-value=0.0028  Score=64.77  Aligned_cols=43  Identities=14%  Similarity=0.110  Sum_probs=31.9

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                      .+++++++|.-..       +.+ .....++.+.|.++.++.+.+||+++|
T Consensus       181 ~~P~ILLlDEPts-------~LD-~~~r~~l~~~L~~l~~~~~~TII~iTH  223 (382)
T TIGR03415       181 MDADILLMDEPFS-------ALD-PLIRTQLQDELLELQAKLNKTIIFVSH  223 (382)
T ss_pred             cCCCEEEEECCCc-------cCC-HHHHHHHHHHHHHHHHhcCCEEEEEeC
Confidence            5799999993332       222 234457888888888888999999999

Members of this protein family are the ATP-binding subunit of a three-protein transporter. This family belongs, more broadly, to the family of proline and glycine-betaine transporters, but members have been identified by direct characterization and by bioinformatic means as choline transporters. Many species have several closely-related members of this family, probably with variable abilities to act additionally on related quaternary amines.

>PRK13540 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.26  E-value=0.008  Score=55.88  Aligned_cols=33  Identities=18%  Similarity=0.284  Sum_probs=26.8

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        17 l~~~s~~i~~Ge~~~l~G~nGsGKSTLl~~i~G~   50 (200)
T PRK13540         17 LQQISFHLPAGGLLHLKGSNGAGKTTLLKLIAGL   50 (200)
T ss_pred             EeeeeEEECCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            444433 999999999999999999998866543

>PRK13642 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.25  E-value=0.0032  Score=61.79  Aligned_cols=35  Identities=26%  Similarity=0.220  Sum_probs=28.3

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .|+.+-- +.+|+.+.|.|++|+|||||+.-++-..
T Consensus        22 ~l~~v~l~i~~Ge~~~I~G~nGsGKSTLl~~l~Gl~   57 (277)
T PRK13642         22 QLNGVSFSITKGEWVSIIGQNGSGKSTTARLIDGLF   57 (277)
T ss_pred             eeeeeEEEEcCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            4555544 9999999999999999999988776443

>PLN03140 ABC transporter G family member; Provisional

Probab=97.25  E-value=0.0019  Score=76.99  Aligned_cols=34  Identities=35%  Similarity=0.543  Sum_probs=28.9

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      -|+.+.+ +.+|+++.|.|++|+|||||+.-++-.
T Consensus       895 iL~~vs~~i~~Gel~aL~G~sGaGKTTLL~~LaG~  929 (1470)
T PLN03140        895 LLREVTGAFRPGVLTALMGVSGAGKTTLMDVLAGR  929 (1470)
T ss_pred             EeeCcEEEEECCeEEEEECCCCCCHHHHHHHHcCC
Confidence            4566666 999999999999999999998877654

>PRK15439 autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional

Probab=97.25  E-value=0.0018  Score=69.56  Aligned_cols=33  Identities=21%  Similarity=0.274  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        27 l~~vsl~i~~Ge~~~liG~NGsGKSTLl~~l~Gl   60 (510)
T PRK15439         27 LKGIDFTLHAGEVHALLGGNGAGKSTLMKIIAGI   60 (510)
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            444444 999999999999999999998776643

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=97.25  E-value=0.0061  Score=57.21  Aligned_cols=32  Identities=22%  Similarity=0.291  Sum_probs=25.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+| ++.|.|++|+|||||+.-++-.
T Consensus        16 l~~vs~~i~~g-~~~i~G~nGsGKSTLl~~l~Gl   48 (211)
T cd03264          16 LDGVSLTLGPG-MYGLLGPNGAGKTTLMRILATL   48 (211)
T ss_pred             EcceeEEEcCC-cEEEECCCCCCHHHHHHHHhCC
Confidence            444433 8899 9999999999999998877643

The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK13768 GTPase; Provisional

Probab=97.25  E-value=0.0028  Score=61.21  Aligned_cols=40  Identities=23%  Similarity=0.408  Sum_probs=35.1

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV  338 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~  338 (539)
                      -+++++|++|+||||++.+++..++.+ |.+|+++.++...
T Consensus         3 ~~i~v~G~~G~GKTt~~~~~~~~l~~~-g~~v~~i~~D~~~   42 (253)
T PRK13768          3 YIVFFLGTAGSGKTTLTKALSDWLEEQ-GYDVAIVNLDPAV   42 (253)
T ss_pred             EEEEEECCCCccHHHHHHHHHHHHHhc-CCceEEEECCCcc
Confidence            368899999999999999999998875 9999999988553

>PRK06921 hypothetical protein; Provisional

Probab=97.24  E-value=0.0069  Score=58.91  Aligned_cols=38  Identities=18%  Similarity=0.292  Sum_probs=33.2

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +.-++|.|+||+|||.|+..++..+..+.|..|+|++.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~  154 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPF  154 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEH
Confidence            56788999999999999999998887644899999995

>PRK13632 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.24  E-value=0.0028  Score=62.06  Aligned_cols=34  Identities=29%  Similarity=0.280  Sum_probs=27.6

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        24 il~~isl~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl   58 (271)
T PRK13632         24 ALKNVSFEINEGEYVAILGHNGSGKSTISKILTGL   58 (271)
T ss_pred             ceeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3555544 999999999999999999998766644

>cd03231 ABC_CcmA_heme_exporter CcmA, the ATP-binding component of the bacterial CcmAB transporter

Probab=97.24  E-value=0.0055  Score=57.03  Aligned_cols=33  Identities=30%  Similarity=0.311  Sum_probs=26.8

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        16 l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~l~G~   49 (201)
T cd03231          16 FSGLSFTLAAGEALQVTGPNGSGKTTLLRILAGL   49 (201)
T ss_pred             eccceEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            444443 899999999999999999998766643

The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE is a periplasmic heme chaperone that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH. The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE.

>cd03252 ABCC_Hemolysin The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E

Probab=97.24  E-value=0.0015  Score=62.47  Aligned_cols=34  Identities=26%  Similarity=0.360  Sum_probs=27.5

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        18 l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (237)
T cd03252          18 LDNISLRIKPGEVVGIVGRSGSGKSTLTKLIQRFY   52 (237)
T ss_pred             eeceEEEEcCCCEEEEECCCCCCHHHHHHHHhcCc
Confidence            444433 8999999999999999999988777443

coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.

>PRK09580 sufC cysteine desulfurase ATPase component; Reviewed

Probab=97.24  E-value=0.006  Score=58.81  Aligned_cols=33  Identities=36%  Similarity=0.435  Sum_probs=27.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        17 l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   50 (248)
T PRK09580         17 LRGLNLEVRPGEVHAIMGPNGSGKSTLSATLAGR   50 (248)
T ss_pred             eecceeEEcCCCEEEEECCCCCCHHHHHHHHcCC
Confidence            444444 899999999999999999998877654

>PRK14237 phosphate transporter ATP-binding protein; Provisional

Probab=97.24  E-value=0.017  Score=56.34  Aligned_cols=33  Identities=21%  Similarity=0.293  Sum_probs=27.5

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        36 l~~vsl~i~~Ge~~~I~G~nGsGKSTLl~~l~Gl   69 (267)
T PRK14237         36 IKGIDMQFEKNKITALIGPSGSGKSTYLRSLNRM   69 (267)
T ss_pred             EeeeEEEEcCCCEEEEECCCCCCHHHHHHHHHhc
Confidence            444444 999999999999999999999887654

>PRK14268 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.24  E-value=0.016  Score=56.31  Aligned_cols=32  Identities=25%  Similarity=0.348  Sum_probs=26.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        28 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~i~G   60 (258)
T PRK14268         28 LKNVSMQIPKNSVTALIGPSGCGKSTFIRCLNR   60 (258)
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            444433 99999999999999999999887764

>PRK07773 replicative DNA helicase; Validated

Probab=97.24  E-value=0.00041  Score=78.99  Aligned_cols=60  Identities=18%  Similarity=0.187  Sum_probs=49.1

Q ss_pred             ccccccchhccceEEEEEeCCCC--CCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          476 ISGSAHFINKCDNGIVIHRNRDP--EAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       476 l~gs~~i~~~aD~vl~l~r~~~~--~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      |--...|+|.||.|++|||++..  +....+..+++|.|||||++|++   .+.|++++.||.+.
T Consensus       822 ~~~hn~i~~dAD~v~~l~r~~~y~~~~~~~g~~e~ii~K~R~g~~g~~---~~~~~~~~~~f~~~  883 (886)
T PRK07773        822 IIVHNSIEQDADVVILLYRPDYYDRDDPRGGEAEFIVAKHRNGPTGTV---TLAFQLHLSRFANL  883 (886)
T ss_pred             eEecCceeccCCEEEEEechhhcCCCCCCCCceEEEEeccCCCCCceE---EEEEecCcceeecc
Confidence            33456799999999999997732  22334789999999999999986   79999999999875

>PRK14267 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.23  E-value=0.013  Score=56.63  Aligned_cols=34  Identities=12%  Similarity=0.131  Sum_probs=27.8

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        19 ~l~~is~~i~~Ge~~~l~G~nGsGKSTLl~~l~G~   53 (253)
T PRK14267         19 VIKGVDLKIPQNGVFALMGPSGCGKSTLLRTFNRL   53 (253)
T ss_pred             eeecceEEEcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            3555544 999999999999999999998876644

>PRK14242 phosphate transporter ATP-binding protein; Provisional

Probab=97.23  E-value=0.011  Score=57.17  Aligned_cols=32  Identities=22%  Similarity=0.344  Sum_probs=26.8

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        22 l~~is~~i~~Ge~~~i~G~nGsGKSTLl~~l~G   54 (253)
T PRK14242         22 LHDISLEFEQNQVTALIGPSGCGKSTFLRCLNR   54 (253)
T ss_pred             ecceeEEEeCCCEEEEECCCCCCHHHHHHHHHh
Confidence            444443 99999999999999999999888764

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=97.23  E-value=0.0033  Score=68.90  Aligned_cols=166  Identities=14%  Similarity=0.116  Sum_probs=87.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHhhCCCc---cccccCCC--CCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---ENKVREHARKLLEKHIKKPF---FEANYGGS--AER  365 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---E~~~~~~~~r~~~~~~~~~~---~~i~~~~~--~~~  365 (539)
                      +++|+.+.|.|++|+||||++.-++... -. ...+.+-.-   +.+.+.+.+. ++....-+.   ..++++-.  .+.
T Consensus       373 i~~G~~vaIvG~SGsGKSTL~~lL~g~~-p~-~G~I~i~g~~i~~~~~~~lr~~-i~~v~Q~~~LF~~TI~eNI~~g~~~  449 (588)
T PRK11174        373 LPAGQRIALVGPSGAGKTSLLNALLGFL-PY-QGSLKINGIELRELDPESWRKH-LSWVGQNPQLPHGTLRDNVLLGNPD  449 (588)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC-CC-CcEEEECCEecccCCHHHHHhh-eEEecCCCcCCCcCHHHHhhcCCCC
Confidence            8999999999999999999988777655 32 334443321   3445544433 222211110   11111110  124


Q ss_pred             CCHHHHHHHHH------Hhhccc---e-eEeecCCCCCCH--HHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHH
Q 009230          366 MTVEEFEQGKA------WLSNTF---S-LIRCENDSLPSI--KWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTET  433 (539)
Q Consensus       366 l~~~~~~~~~~------~l~~~~---~-~i~~~~~~~~~~--~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~  433 (539)
                      .+++++.++.+      ++...+   . .+. +.....+=  .+-+..+|.+.  .+++++++|.-+.-++        .
T Consensus       450 ~~~eei~~al~~a~l~~~i~~lp~G~dT~vg-e~G~~LSGGQrQRialARAll--~~~~IliLDE~TSaLD--------~  518 (588)
T PRK11174        450 ASDEQLQQALENAWVSEFLPLLPQGLDTPIG-DQAAGLSVGQAQRLALARALL--QPCQLLLLDEPTASLD--------A  518 (588)
T ss_pred             CCHHHHHHHHHHhCHHHHHHhcccccccccc-cCCCCCCHHHHHHHHHHHHHh--cCCCEEEEeCCccCCC--------H
Confidence            67777766532      232221   1 110 10111221  22333344333  4789999995443321        1


Q ss_pred             HHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          434 EYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       434 ~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      +.-..+.+.|+++.  .+.++|+++|.-.                   .-..||.++.|..
T Consensus       519 ~te~~i~~~l~~~~--~~~TvIiItHrl~-------------------~i~~aD~Iivl~~  558 (588)
T PRK11174        519 HSEQLVMQALNAAS--RRQTTLMVTHQLE-------------------DLAQWDQIWVMQD  558 (588)
T ss_pred             HHHHHHHHHHHHHh--CCCEEEEEecChH-------------------HHHhCCEEEEEeC
Confidence            22235666666654  4688999999321                   1246899999864

>PRK14274 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.23  E-value=0.022  Score=55.26  Aligned_cols=33  Identities=27%  Similarity=0.387  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        28 l~~vs~~i~~Ge~~~l~G~nGsGKSTLl~~l~G~   61 (259)
T PRK14274         28 LKNINLSIPENEVTAIIGPSGCGKSTFIKTLNLM   61 (259)
T ss_pred             EEeeEEEEcCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            444433 899999999999999999999877744

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=97.23  E-value=0.0023  Score=59.88  Aligned_cols=34  Identities=32%  Similarity=0.294  Sum_probs=27.5

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        23 ~l~~isl~i~~G~~~~i~G~nGsGKSTLl~~l~Gl   57 (207)
T cd03369          23 VLKNVSFKVKAGEKIGIVGRTGAGKSTLILALFRF   57 (207)
T ss_pred             cccCceEEECCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            3444433 999999999999999999998877644

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>PRK14245 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.22  E-value=0.014  Score=56.26  Aligned_cols=32  Identities=16%  Similarity=0.227  Sum_probs=26.5

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        19 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~i~G   51 (250)
T PRK14245         19 LKGISMEIEEKSVVAFIGPSGCGKSTFLRLFNR   51 (250)
T ss_pred             EeeeeEEEeCCCEEEEECCCCCCHHHHHHHHhh
Confidence            344433 99999999999999999999888863

>PRK14247 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.22  E-value=0.0068  Score=58.53  Aligned_cols=33  Identities=21%  Similarity=0.249  Sum_probs=27.4

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        19 l~~is~~i~~Ge~~~i~G~nGsGKSTLl~~i~G~   52 (250)
T PRK14247         19 LDGVNLEIPDNTITALMGPSGSGKSTLLRVFNRL   52 (250)
T ss_pred             eecceeEEcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            444444 899999999999999999998877754

>PRK10762 D-ribose transporter ATP binding protein; Provisional

Probab=97.22  E-value=0.0031  Score=67.58  Aligned_cols=34  Identities=29%  Similarity=0.376  Sum_probs=27.6

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        19 ~l~~is~~i~~Ge~~~l~G~NGsGKSTLl~~l~G~   53 (501)
T PRK10762         19 ALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGI   53 (501)
T ss_pred             EeeeeeEEEcCCeEEEEECCCCCCHHHHHHHHhCC
Confidence            3555544 999999999999999999998776644

>PRK14240 phosphate transporter ATP-binding protein; Provisional

Probab=97.22  E-value=0.009  Score=57.69  Aligned_cols=26  Identities=23%  Similarity=0.385  Sum_probs=24.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +.+|+++.|.|++|+|||||+.-++-
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~~i~G   51 (250)
T PRK14240         26 IEENQVTALIGPSGCGKSTFLRTLNR   51 (250)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            89999999999999999999887764

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.20  E-value=0.0032  Score=59.09  Aligned_cols=34  Identities=24%  Similarity=0.367  Sum_probs=27.2

Q ss_pred             chhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          285 WRALNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       285 ~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      ...|+++-- +.+||++.|.|+|||||||++.-+|
T Consensus        16 ~~vl~~i~L~v~~GEfvsilGpSGcGKSTLLriiA   50 (248)
T COG1116          16 VEVLEDINLSVEKGEFVAILGPSGCGKSTLLRLIA   50 (248)
T ss_pred             eEEeccceeEECCCCEEEEECCCCCCHHHHHHHHh
Confidence            444555543 9999999999999999999977655

>TIGR02324 CP_lyasePhnL phosphonate C-P lyase system protein PhnL

Probab=97.20  E-value=0.0066  Score=57.54  Aligned_cols=33  Identities=30%  Similarity=0.450  Sum_probs=27.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        24 l~~vs~~i~~Ge~~~l~G~nGsGKSTLl~~i~G~   57 (224)
T TIGR02324        24 LKNVSLTVNAGECVALSGPSGAGKSTLLKSLYAN   57 (224)
T ss_pred             EecceEEECCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            444444 999999999999999999998876644

Members of this family are the PhnL protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lysase complex. This protein (PhnL) and the adjacent-encoded PhnK (TIGR02323) resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this C-P lyase complex rather than part of a transporter per se.

>PRK14273 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.17  E-value=0.017  Score=55.85  Aligned_cols=33  Identities=27%  Similarity=0.417  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        23 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   56 (254)
T PRK14273         23 LNNINIKILKNSITALIGPSGCGKSTFLRTLNRM   56 (254)
T ss_pred             ecceeeEEcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            444433 999999999999999999998877643

>PRK14241 phosphate transporter ATP-binding protein; Provisional

Probab=97.17  E-value=0.018  Score=55.96  Aligned_cols=34  Identities=24%  Similarity=0.298  Sum_probs=28.1

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        19 ~l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~laGl   53 (258)
T PRK14241         19 AVEDVNLNIEPRSVTAFIGPSGCGKSTVLRTLNRM   53 (258)
T ss_pred             eeeeeeEEEcCCcEEEEECCCCCCHHHHHHHHhcc
Confidence            3455544 999999999999999999998887754

>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]

Probab=97.17  E-value=0.0018  Score=54.33  Aligned_cols=73  Identities=21%  Similarity=0.271  Sum_probs=53.7

Q ss_pred             CCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCccchHHHH
Q 009230          123 ESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAE  202 (539)
Q Consensus       123 ~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~~G~~~~~  202 (539)
                      .+.|+||||--|..++-+++...++.+.+++.+..              ..+. .+....+.+.|+|.+|.|.+|.+-.+
T Consensus         9 ~~~vIVVEGK~D~~~l~~~~~~~~i~~~g~~i~~~--------------~~ie-~i~~~~~~k~VIILTD~D~~Ge~Irk   73 (127)
T COG1658           9 LKEVIVVEGKDDTASLKRLGDAGVIITNGSAINSL--------------ETIE-LIKKAQKYKGVIILTDPDRKGERIRK   73 (127)
T ss_pred             cCceEEEeCCcHHHHHHHhcCCceEEEcCCccchH--------------HHHH-HHHHhhccCCEEEEeCCCcchHHHHH
Confidence            36899999999999999999887776543332211              0100 11222347889999999999999999


Q ss_pred             HHHHHhcC
Q 009230          203 ELARRVGR  210 (539)
Q Consensus       203 ~~~~~l~~  210 (539)
                      .+.+.|+.
T Consensus        74 ~l~~~l~~   81 (127)
T COG1658          74 KLKEYLPG   81 (127)
T ss_pred             HHHHHhcc
Confidence            99999976

>PRK14271 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.17  E-value=0.0069  Score=59.43  Aligned_cols=33  Identities=21%  Similarity=0.290  Sum_probs=27.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        37 l~~vs~~i~~Ge~~~I~G~nGsGKSTLl~~l~Gl   70 (276)
T PRK14271         37 LDQVSMGFPARAVTSLMGPTGSGKTTFLRTLNRM   70 (276)
T ss_pred             eeeeEEEEcCCcEEEEECCCCCCHHHHHHHHhcc
Confidence            444433 999999999999999999998888754

>PRK14259 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.16  E-value=0.013  Score=57.29  Aligned_cols=33  Identities=21%  Similarity=0.369  Sum_probs=27.3

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        29 l~~is~~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl   62 (269)
T PRK14259         29 VKNVFCDIPRGKVTALIGPSGCGKSTVLRSLNRM   62 (269)
T ss_pred             EcceEEEEcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            444443 999999999999999999998877643

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=97.16  E-value=0.0068  Score=54.32  Aligned_cols=146  Identities=14%  Similarity=0.093  Sum_probs=83.2

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC-----CCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM-----ENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEE  370 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~-----E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~  370 (539)
                      +| ++.|.+++|.||||.++-++..++.+ |.+|+++-+     .......+.++     ++.+.....+          
T Consensus         5 ~G-li~v~~g~GkGKtt~a~g~a~ra~~~-g~~v~ivQFlKg~~~~GE~~~l~~~-----~~~~~~~g~g----------   67 (173)
T TIGR00708         5 RG-IIIVHTGNGKGKTTAAFGMALRALGH-GKKVGVIQFIKGAWPNGERAAFEPH-----GVEFQVMGTG----------   67 (173)
T ss_pred             cc-EEEEECCCCCChHHHHHHHHHHHHHC-CCeEEEEEEecCCcccChHHHHHhc-----CcEEEECCCC----------
Confidence            35 77777789999999999999999884 999987732     22223333332     3333322111          


Q ss_pred             HHHHHHHhhccceeEeecCCCCC---CHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHH
Q 009230          371 FEQGKAWLSNTFSLIRCENDSLP---SIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFA  447 (539)
Q Consensus       371 ~~~~~~~l~~~~~~i~~~~~~~~---~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA  447 (539)
                                 +.+.. . +...   ...+..+.++..+....+++||+|-++..+.-.  --+    .+++++.|+  .
T Consensus        68 -----------~~~~~-~-~~~~~~~~~~~~~~~a~~~l~~~~~DlvVLDEi~~A~~~g--li~----~~~v~~lL~--~  126 (173)
T TIGR00708        68 -----------FTWET-Q-NREADTAIAKAAWQHAKEMLADPELDLVLLDELTYALKYG--YLD----VEEVVEALQ--E  126 (173)
T ss_pred             -----------CeecC-C-CcHHHHHHHHHHHHHHHHHHhcCCCCEEEehhhHHHHHCC--CcC----HHHHHHHHH--h
Confidence                       11110 0 0000   012233444455555679999999887665431  112    234555554  2


Q ss_pred             HHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          448 QHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       448 ~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      +.-++.||++-++.                 ...+-..||.|--+...+
T Consensus       127 rp~~~evVlTGR~~-----------------p~~l~e~AD~VTEm~~vK  158 (173)
T TIGR00708       127 RPGHQHVIITGRGC-----------------PQDLLELADLVTEMRPVK  158 (173)
T ss_pred             CCCCCEEEEECCCC-----------------CHHHHHhCceeeeecccc
Confidence            45678888875521                 124667889887776544

Alternate name: corrinoid adenosyltransferase.

>PTZ00293 thymidine kinase; Provisional

Probab=97.16  E-value=0.0029  Score=58.58  Aligned_cols=139  Identities=15%  Similarity=0.148  Sum_probs=80.0

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG  374 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~  374 (539)
                      ..|.|.+++||-++|||+-+++.+.+.... |.+++.|-.-.+.+.-....+..+.|...                    
T Consensus         2 ~~G~i~vi~GpMfSGKTteLLr~i~~y~~a-g~kv~~~kp~~DtR~~~~~~I~Sh~g~~~--------------------   60 (211)
T PTZ00293          2 YRGTISVIIGPMFSGKTTELMRLVKRFTYS-EKKCVVIKYSKDTRYSDEQNISSHDKQML--------------------   60 (211)
T ss_pred             CceEEEEEECCCCChHHHHHHHHHHHHHHc-CCceEEEEecccccCCCCCcEEecCCCcc--------------------
Confidence            458999999999999999777777777664 88999887654433100000000001000                    


Q ss_pred             HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEE
Q 009230          375 KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHV  454 (539)
Q Consensus       375 ~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~v  454 (539)
                            .-+.+       ..+.++.+.+      .++++|+||-.              +.+..+.+....++ ..|++|
T Consensus        61 ------~a~~v-------~~~~e~~~~~------~~~dvI~IDEa--------------QFf~~i~~~~~~l~-~~g~~V  106 (211)
T PTZ00293         61 ------KAIKV-------SKLKEVLETA------KNYDVIAIDEG--------------QFFPDLVEFSEAAA-NLGKIV  106 (211)
T ss_pred             ------eeEEc-------CCHHHHHHhc------cCCCEEEEEch--------------HhhHhHHHHHHHHH-HCCCeE
Confidence                  00111       1233333322      36899999922              22333333333333 789999


Q ss_pred             EEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          455 WFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       455 i~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      ++..-...-.+        .-+.++..+-..||.|.-|...-
T Consensus       107 ivaGLd~Df~~--------~~F~~~~~Ll~~AD~V~kl~aiC  140 (211)
T PTZ00293        107 IVAALDGTFQR--------KPFGQILNLIPLAERVTKLTAVC  140 (211)
T ss_pred             EEEecCccccc--------CcCccHHHHHHhhCEEEEcceEc
Confidence            88766322221        12567788889999998776543

>COG1135 AbcC ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.16  E-value=0.0098  Score=57.48  Aligned_cols=160  Identities=17%  Similarity=0.158  Sum_probs=88.2

Q ss_pred             Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-cCCeEEEEe---CCCCHHHHHHHHHHHhhCCCccccc
Q 009230          284 GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEH-AGWKFVLCS---MENKVREHARKLLEKHIKKPFFEAN  358 (539)
Q Consensus       284 g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-~g~~vl~~s---~E~~~~~~~~r~~~~~~~~~~~~i~  358 (539)
                      .+..||++.- +.+|+++.|.|+||+||||++.-  .|.... ....|.+..   ...+...+.  ...+..|+=+..+.
T Consensus        18 ~~~al~~vsL~I~~GeI~GIIG~SGAGKSTLiR~--iN~Le~PtsG~v~v~G~di~~l~~~~Lr--~~R~~IGMIFQhFn   93 (339)
T COG1135          18 TVTALDDVSLEIPKGEIFGIIGYSGAGKSTLLRL--INLLERPTSGSVFVDGQDLTALSEAELR--QLRQKIGMIFQHFN   93 (339)
T ss_pred             ceeeeccceEEEcCCcEEEEEcCCCCcHHHHHHH--HhccCCCCCceEEEcCEecccCChHHHH--HHHhhccEEecccc
Confidence            4567777765 99999999999999999999773  344332 235666665   334444332  22222222111110


Q ss_pred             ------------cCCCCCCCCHHHHHH-HHHHhh-----ccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcccc
Q 009230          359 ------------YGGSAERMTVEEFEQ-GKAWLS-----NTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYN  420 (539)
Q Consensus       359 ------------~~~~~~~l~~~~~~~-~~~~l~-----~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~  420 (539)
                                  +.-....++.++.++ ..+.+.     ++..-+  ...=+....+-...++.++  .+|++++-|--+
T Consensus        94 LLssrTV~~NvA~PLeiag~~k~ei~~RV~elLelVgL~dk~~~y--P~qLSGGQKQRVaIARALa--~~P~iLL~DEaT  169 (339)
T COG1135          94 LLSSRTVFENVAFPLELAGVPKAEIKQRVAELLELVGLSDKADRY--PAQLSGGQKQRVAIARALA--NNPKILLCDEAT  169 (339)
T ss_pred             ccccchHHhhhhhhHhhcCCCHHHHHHHHHHHHHHcCChhhhccC--chhcCcchhhHHHHHHHHh--cCCCEEEecCcc
Confidence                        000001233444332 222221     111000  0011112334445555444  579999999555


Q ss_pred             ccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          421 ELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       421 ~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                      +.+.        .+-...+++-|+.+-+++|++|++++|
T Consensus       170 SALD--------P~TT~sIL~LL~~In~~lglTIvlITH  200 (339)
T COG1135         170 SALD--------PETTQSILELLKDINRELGLTIVLITH  200 (339)
T ss_pred             ccCC--------hHHHHHHHHHHHHHHHHcCCEEEEEec
Confidence            4432        233567999999999999999999999

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.15  E-value=0.018  Score=58.92  Aligned_cols=40  Identities=18%  Similarity=0.258  Sum_probs=34.5

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHh---cCCeEEEEeCCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEH---AGWKFVLCSMEN  336 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~---~g~~vl~~s~E~  336 (539)
                      +.++++.|++|+||||.+..+|..+...   .|.+|++++.+-
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt  216 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDN  216 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccC
Confidence            3589999999999999999999887642   378999999985

>cd03114 ArgK-like The function of this protein family is unkown

Probab=97.15  E-value=0.0012  Score=58.10  Aligned_cols=37  Identities=35%  Similarity=0.583  Sum_probs=33.0

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.+.|++|+|||||+.+++..+... |.+++.+..+..
T Consensus         2 i~~~G~~GsGKTt~~~~l~~~~~~~-g~~v~ii~~D~~   38 (148)
T cd03114           2 IGITGVPGAGKSTLIDALITALRAR-GKRVAVLAIDPS   38 (148)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHC-CCEEEEEEeCCC
Confidence            5788999999999999999888775 999999998864

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.

>KOG0065 consensus Pleiotropic drug resistance proteins (PDR1-15), ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]

Probab=97.15  E-value=0.0039  Score=71.00  Aligned_cols=55  Identities=22%  Similarity=0.210  Sum_probs=39.3

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC------HHHHHHHHH
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK------VREHARKLL  346 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~------~~~~~~r~~  346 (539)
                      .-|+.+.| ++||.||.|.|.+|+|||||+.=+|-      .....|++.|+.      .++.+.|..
T Consensus       805 qLL~~V~G~~kPG~LTALMG~SGAGKTTLLdvLA~------R~t~G~I~Gdi~i~G~p~~q~tF~R~~  866 (1391)
T KOG0065|consen  805 QLLNNVSGAFKPGVLTALMGESGAGKTTLLDVLAG------RKTGGYIEGDILISGFPKDQETFARVS  866 (1391)
T ss_pred             EhhhcCceEecCCceeehhcCCCCchHHHHHHHhc------CcccceEEeEEEECCeeCchhhhcccc
Confidence            34677778 99999999999999999999655442      345567777743      224555554

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.15  E-value=0.01  Score=55.38  Aligned_cols=33  Identities=24%  Similarity=0.321  Sum_probs=26.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        17 l~~vs~~i~~Ge~~~l~G~nGsGKSTLl~~l~G~   50 (204)
T PRK13538         17 FSGLSFTLNAGELVQIEGPNGAGKTSLLRILAGL   50 (204)
T ss_pred             EecceEEECCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            444433 999999999999999999998876643

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=97.15  E-value=0.0079  Score=56.76  Aligned_cols=37  Identities=22%  Similarity=0.312  Sum_probs=30.4

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHh-cCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEH-AGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~-~g~~vl~~s~E  335 (539)
                      .+.|.|++|+|||.|+..++..+... .+.+|+|++.+
T Consensus        36 ~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~   73 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAE   73 (219)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHH
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHH
Confidence            56799999999999999998887764 36899999865

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.

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=97.14  E-value=0.028  Score=56.91  Aligned_cols=141  Identities=16%  Similarity=0.185  Sum_probs=92.9

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HH-HHHHHHHHHhhCCCccccccCCCCCCCCHHHH-HHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VR-EHARKLLEKHIKKPFFEANYGGSAERMTVEEF-EQG  374 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~-~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~-~~~  374 (539)
                      .+++++|--|+||||.+-.+|..+.. .|++|+.++++.- |. .-..+.++...++++.....     .-++-++ .++
T Consensus       101 ~vImmvGLQGsGKTTt~~KLA~~lkk-~~~kvllVaaD~~RpAA~eQL~~La~q~~v~~f~~~~-----~~~Pv~Iak~a  174 (451)
T COG0541         101 TVILMVGLQGSGKTTTAGKLAKYLKK-KGKKVLLVAADTYRPAAIEQLKQLAEQVGVPFFGSGT-----EKDPVEIAKAA  174 (451)
T ss_pred             eEEEEEeccCCChHhHHHHHHHHHHH-cCCceEEEecccCChHHHHHHHHHHHHcCCceecCCC-----CCCHHHHHHHH
Confidence            68999999999999999999999988 5999999999954 22 11234567778888765421     2233333 344


Q ss_pred             HHHhhcc-ceeEeecCCCCCCHH-HHHHHHHHHHHHcCCc--EEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHh
Q 009230          375 KAWLSNT-FSLIRCENDSLPSIK-WVLDLAKAAVLRHGVR--GLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHH  450 (539)
Q Consensus       375 ~~~l~~~-~~~i~~~~~~~~~~~-~i~~~i~~~~~~~~~~--~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~  450 (539)
                      .++.... .-++-++.-+...+| ++.+.+..+...-.|+  ++|||..+        +       ......-+.|-+..
T Consensus       175 l~~ak~~~~DvvIvDTAGRl~ide~Lm~El~~Ik~~~~P~E~llVvDam~--------G-------QdA~~~A~aF~e~l  239 (451)
T COG0541         175 LEKAKEEGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAMI--------G-------QDAVNTAKAFNEAL  239 (451)
T ss_pred             HHHHHHcCCCEEEEeCCCcccccHHHHHHHHHHHhhcCCCeEEEEEeccc--------c-------hHHHHHHHHHhhhc
Confidence            4554443 222223545666665 4777777776666664  78888222        1       12334446677788


Q ss_pred             CcEEEEEec
Q 009230          451 ACHVWFVAH  459 (539)
Q Consensus       451 ~i~vi~~~q  459 (539)
                      +++-++++-
T Consensus       240 ~itGvIlTK  248 (451)
T COG0541         240 GITGVILTK  248 (451)
T ss_pred             CCceEEEEc
Confidence            999999876

>cd03279 ABC_sbcCD SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends

Probab=97.12  E-value=0.0085  Score=56.32  Aligned_cols=24  Identities=29%  Similarity=0.425  Sum_probs=20.8

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      ..|++++|.|++|+||||++..++
T Consensus        26 ~~~~~~~i~G~NGsGKSTll~~i~   49 (213)
T cd03279          26 DNNGLFLICGPTGAGKSTILDAIT   49 (213)
T ss_pred             CccCEEEEECCCCCCHHHHHHHhe
Confidence            347899999999999999987664

They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.

>PRK14262 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.12  E-value=0.0072  Score=58.37  Aligned_cols=32  Identities=13%  Similarity=0.339  Sum_probs=26.5

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        19 l~~i~~~i~~Ge~~~i~G~nGsGKSTLl~~i~G   51 (250)
T PRK14262         19 VKNVTMKIFKNQITAIIGPSGCGKTTLLRSINR   51 (250)
T ss_pred             EeeeeEeecCCCEEEEECCCCCCHHHHHHHHhc
Confidence            444433 89999999999999999999887763

>TIGR00956 3a01205 Pleiotropic Drug Resistance (PDR) Family protein

Probab=97.12  E-value=0.0093  Score=71.34  Aligned_cols=34  Identities=38%  Similarity=0.630  Sum_probs=29.5

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      -|+.+.+ +.+|+++.|.|++|+|||||+.-++-.
T Consensus        76 iL~~vs~~i~~Ge~~aIlG~nGsGKSTLLk~LaG~  110 (1394)
T TIGR00956        76 ILKPMDGLIKPGELTVVLGRPGSGCSTLLKTIASN  110 (1394)
T ss_pred             eeeCCEEEEECCEEEEEECCCCCCHHHHHHHHhCC
Confidence            4666767 999999999999999999998887754

>PRK15056 manganese/iron transporter ATP-binding protein; Provisional

Probab=97.12  E-value=0.0025  Score=62.45  Aligned_cols=33  Identities=33%  Similarity=0.402  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        23 l~~vsl~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl   56 (272)
T PRK15056         23 LRDASFTVPGGSIAALVGVNGSGKSTLFKALMGF   56 (272)
T ss_pred             EEeeEEEEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            444443 899999999999999999998877643

>PRK15439 autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional

Probab=97.11  E-value=0.0056  Score=65.74  Aligned_cols=33  Identities=24%  Similarity=0.369  Sum_probs=27.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus       279 l~~isl~i~~Ge~~~l~G~NGsGKSTLl~~i~Gl  312 (510)
T PRK15439        279 FRNISLEVRAGEILGLAGVVGAGRTELAETLYGL  312 (510)
T ss_pred             ccceeEEEcCCcEEEEECCCCCCHHHHHHHHcCC
Confidence            455433 999999999999999999998877643

>TIGR00956 3a01205 Pleiotropic Drug Resistance (PDR) Family protein

Probab=97.11  E-value=0.0062  Score=72.78  Aligned_cols=35  Identities=31%  Similarity=0.547  Sum_probs=29.3

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      -|+.+.. +.+|+++.|.|++|+|||||+.-++-..
T Consensus       778 iL~~vs~~i~~Ge~~aI~G~sGaGKSTLL~~Lag~~  813 (1394)
T TIGR00956       778 ILNNVDGWVKPGTLTALMGASGAGKTTLLNVLAERV  813 (1394)
T ss_pred             eeeCCEEEEECCEEEEEECCCCCCHHHHHHHHhCCC
Confidence            4566666 9999999999999999999988776543

>PRK14270 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.11  E-value=0.023  Score=54.93  Aligned_cols=27  Identities=22%  Similarity=0.383  Sum_probs=24.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+++.|.|++|+|||||+.-++-.
T Consensus        27 i~~Ge~~~i~G~nGsGKSTLl~~l~G~   53 (251)
T PRK14270         27 IYENKITALIGPSGCGKSTFLRCLNRM   53 (251)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHhc
Confidence            899999999999999999999888743

>PRK14244 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.11  E-value=0.014  Score=56.29  Aligned_cols=34  Identities=21%  Similarity=0.279  Sum_probs=27.7

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        20 ~l~~is~~i~~Ge~~~I~G~nGsGKSTLl~~i~G~   54 (251)
T PRK14244         20 ILFDINLDIYKREVTAFIGPSGCGKSTFLRCFNRM   54 (251)
T ss_pred             eeeeeEEEEcCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            3444444 999999999999999999998877654

>PRK14253 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.11  E-value=0.0069  Score=58.47  Aligned_cols=33  Identities=21%  Similarity=0.270  Sum_probs=27.4

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        19 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   52 (249)
T PRK14253         19 LKSINLPIPARQVTALIGPSGCGKSTLLRCLNRM   52 (249)
T ss_pred             eecceEEecCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            444444 999999999999999999998887653

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=97.10  E-value=0.0038  Score=58.17  Aligned_cols=28  Identities=25%  Similarity=0.444  Sum_probs=25.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +.+|++++|+|++|+|||||+..++...
T Consensus        26 l~~~~~~~l~G~Ng~GKStll~~i~~~~   53 (202)
T cd03243          26 LGSGRLLLITGPNMGGKSTYLRSIGLAV   53 (202)
T ss_pred             EcCCeEEEEECCCCCccHHHHHHHHHHH
Confidence            6788999999999999999999998554

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.10  E-value=0.0077  Score=62.40  Aligned_cols=50  Identities=14%  Similarity=0.233  Sum_probs=36.6

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhc-CCeEEEEeCC--CCHHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHA-GWKFVLCSME--NKVREHARKLLEK  348 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~-g~~vl~~s~E--~~~~~~~~r~~~~  348 (539)
                      .++|.|+||+|||+++..++.++.... +..++|+++.  .+...++.+++..
T Consensus        57 ~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~  109 (394)
T PRK00411         57 NVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQ  109 (394)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHHH
Confidence            568999999999999999998876542 4778888764  2344555555443

>PRK09700 D-allose transporter ATP-binding protein; Provisional

Probab=97.10  E-value=0.0032  Score=67.63  Aligned_cols=33  Identities=30%  Similarity=0.433  Sum_probs=27.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        21 l~~vs~~i~~Ge~~~liG~nGsGKSTLl~~i~Gl   54 (510)
T PRK09700         21 LKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGI   54 (510)
T ss_pred             eeeeeEEEcCCcEEEEECCCCCCHHHHHHHHcCC
Confidence            455444 999999999999999999998776643

>PRK14272 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.09  E-value=0.031  Score=54.03  Aligned_cols=33  Identities=18%  Similarity=0.325  Sum_probs=27.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        20 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~i~G~   53 (252)
T PRK14272         20 VKNVNLDVQRGTVNALIGPSGCGKTTFLRAINRM   53 (252)
T ss_pred             eccceEEEcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            444433 899999999999999999998877654

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.09  E-value=0.023  Score=59.53  Aligned_cols=61  Identities=18%  Similarity=0.208  Sum_probs=44.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-CeEEEEeCCCC---HHHHHHHHHHHhhCCCcc
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAG-WKFVLCSMENK---VREHARKLLEKHIKKPFF  355 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-~~vl~~s~E~~---~~~~~~r~~~~~~~~~~~  355 (539)
                      +..|.++++.|++|+||||.+..|+......+| .+|.+++.+-.   ..+-+ +..+...|++..
T Consensus       253 ~~~g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQL-r~~AeilGVpv~  317 (484)
T PRK06995        253 LDRGGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQL-RIYGKILGVPVH  317 (484)
T ss_pred             ccCCcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHH-HHHHHHhCCCee
Confidence            456889999999999999999999988865556 48999988743   21221 334555666654

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=97.08  E-value=0.021  Score=50.58  Aligned_cols=144  Identities=13%  Similarity=0.063  Sum_probs=79.0

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEE---eC--CCCHHHHHHHHHHHhhCCCccccccCCCCC-CCCHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLC---SM--ENKVREHARKLLEKHIKKPFFEANYGGSAE-RMTVEEFE  372 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~---s~--E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~-~l~~~~~~  372 (539)
                      ++.|..++|.|||+.++-++..++.+ |.+|+++   -.  +.....++.++    -++.......+.... .-.+++..
T Consensus         4 ~i~vy~g~G~Gkt~~a~g~~~ra~~~-g~~v~~vQFlKg~~~~gE~~~l~~l----~~v~~~~~g~~~~~~~~~~~~~~~   78 (159)
T cd00561           4 LIQVYTGNGKGKTTAALGLALRALGH-GYRVGVVQFLKGGWKYGELKALERL----PNIEIHRMGRGFFWTTENDEEDIA   78 (159)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-CCeEEEEEEeCCCCccCHHHHHHhC----CCcEEEECCCCCccCCCChHHHHH
Confidence            77788888999999999999999985 9999994   33  23333333333    233332211110000 00000000


Q ss_pred             HHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCc
Q 009230          373 QGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHAC  452 (539)
Q Consensus       373 ~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i  452 (539)
                      .                     .....+.++..+....+++||+|-++..+.-.   .-+   .+++++.|+.  +--++
T Consensus        79 ~---------------------a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~g---li~---~~~v~~ll~~--rp~~~  129 (159)
T cd00561          79 A---------------------AAEGWAFAKEAIASGEYDLVILDEINYALGYG---LLD---VEEVVDLLKA--KPEDL  129 (159)
T ss_pred             H---------------------HHHHHHHHHHHHhcCCCCEEEEechHhHhhCC---CCC---HHHHHHHHHc--CCCCC
Confidence            0                     11223344444555679999999887765432   112   2345554442  34578


Q ss_pred             EEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEE
Q 009230          453 HVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIH  493 (539)
Q Consensus       453 ~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~  493 (539)
                      .||++.++-.                 ..+...||.|--+.
T Consensus       130 evIlTGr~~p-----------------~~l~e~AD~VTEm~  153 (159)
T cd00561         130 ELVLTGRNAP-----------------KELIEAADLVTEMR  153 (159)
T ss_pred             EEEEECCCCC-----------------HHHHHhCceeeecc
Confidence            8888766311                 23566778766554

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PRK14252 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.08  E-value=0.0072  Score=58.92  Aligned_cols=32  Identities=22%  Similarity=0.339  Sum_probs=26.5

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |..+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        32 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~l~G   64 (265)
T PRK14252         32 LKNINMMVHEKQVTALIGPSGCGKSTFLRCFNR   64 (265)
T ss_pred             eeeeEEEEcCCcEEEEECCCCCCHHHHHHHHhc
Confidence            444433 89999999999999999999887764

>PRK14236 phosphate transporter ATP-binding protein; Provisional

Probab=97.08  E-value=0.027  Score=55.12  Aligned_cols=27  Identities=19%  Similarity=0.233  Sum_probs=24.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+++.|.|++|+|||||+.-++-.
T Consensus        48 i~~Ge~~~I~G~nGsGKSTLl~~laGl   74 (272)
T PRK14236         48 IPKNRVTAFIGPSGCGKSTLLRCFNRM   74 (272)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHhc
Confidence            899999999999999999998887643

>PRK11288 araG L-arabinose transporter ATP-binding protein; Provisional

Probab=97.07  E-value=0.0045  Score=66.36  Aligned_cols=27  Identities=30%  Similarity=0.432  Sum_probs=24.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +++|+.+.|.|++|+|||||+.-++-.
T Consensus       276 i~~Ge~~~iiG~NGsGKSTLlk~l~G~  302 (501)
T PRK11288        276 VRAGEIVGLFGLVGAGRSELMKLLYGA  302 (501)
T ss_pred             EeCCcEEEEEcCCCCCHHHHHHHHcCC
Confidence            899999999999999999998877744

>PRK14260 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.07  E-value=0.029  Score=54.42  Aligned_cols=33  Identities=21%  Similarity=0.344  Sum_probs=27.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        23 l~~isl~i~~Ge~~~l~G~nGsGKSTLlk~l~Gl   56 (259)
T PRK14260         23 IEGISMDIYRNKVTAIIGPSGCGKSTFIKTLNRI   56 (259)
T ss_pred             ecceEEEEcCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            333433 999999999999999999998887754

>PRK10762 D-ribose transporter ATP binding protein; Provisional

Probab=97.07  E-value=0.0047  Score=66.15  Aligned_cols=59  Identities=12%  Similarity=0.249  Sum_probs=40.5

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|--+.       +.+ ......+.+.|+.++++ +.+||+++|.-.                  .+.+.||.
T Consensus       412 ~~p~lllLDEPt~-------~LD-~~~~~~l~~~l~~~~~~-g~tviivtHd~~------------------~~~~~~d~  464 (501)
T PRK10762        412 TRPKVLILDEPTR-------GVD-VGAKKEIYQLINQFKAE-GLSIILVSSEMP------------------EVLGMSDR  464 (501)
T ss_pred             hCCCEEEEcCCCC-------CCC-HhHHHHHHHHHHHHHHC-CCEEEEEcCCHH------------------HHHhhCCE
Confidence            5789999993332       222 23455677778888765 899999999422                  24567899


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      ++.|..
T Consensus       465 v~~l~~  470 (501)
T PRK10762        465 ILVMHE  470 (501)
T ss_pred             EEEEEC
Confidence            998874

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=97.06  E-value=0.0033  Score=63.71  Aligned_cols=45  Identities=31%  Similarity=0.423  Sum_probs=32.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVRE  340 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~  340 (539)
                      ..++.+++|+|++|+||||++..++..+....+.+  +++.|.+.+.
T Consensus       119 ~~~~g~ili~G~tGSGKTT~l~al~~~i~~~~~~~--i~tiEdp~E~  163 (343)
T TIGR01420       119 ERPRGLILVTGPTGSGKSTTLASMIDYINKNAAGH--IITIEDPIEY  163 (343)
T ss_pred             hhcCcEEEEECCCCCCHHHHHHHHHHhhCcCCCCE--EEEEcCChhh
Confidence            34567999999999999999988876654322334  4466887663

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.

>PRK14257 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.06  E-value=0.013  Score=58.96  Aligned_cols=33  Identities=24%  Similarity=0.319  Sum_probs=27.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |..+.- +.+|+++.|.|++|+|||||+.-++..
T Consensus        98 L~~is~~I~~Ge~v~IvG~~GsGKSTLl~~L~g~  131 (329)
T PRK14257         98 LHDLNLDIKRNKVTAFIGPSGCGKSTFLRNLNQL  131 (329)
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            444444 999999999999999999999887754

>PRK14255 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.06  E-value=0.026  Score=54.51  Aligned_cols=32  Identities=25%  Similarity=0.329  Sum_probs=26.6

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        21 l~~vs~~i~~Ge~~~l~G~nGsGKSTLl~~l~G   53 (252)
T PRK14255         21 LKGIDLDFNQNEITALIGPSGCGKSTYLRTLNR   53 (252)
T ss_pred             EecceEEEcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            444433 89999999999999999999888764

>PRK09700 D-allose transporter ATP-binding protein; Provisional

Probab=97.06  E-value=0.0035  Score=67.34  Aligned_cols=33  Identities=24%  Similarity=0.409  Sum_probs=27.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus       279 l~~isl~i~~Ge~~~l~G~NGsGKSTLlk~i~Gl  312 (510)
T PRK09700        279 VRDISFSVCRGEILGFAGLVGSGRTELMNCLFGV  312 (510)
T ss_pred             ccceeEEEcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            444433 999999999999999999998877743

>PRK14251 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.06  E-value=0.027  Score=54.39  Aligned_cols=33  Identities=27%  Similarity=0.300  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        20 l~~~sl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   53 (251)
T PRK14251         20 LHGISLDFEEKELTALIGPSGCGKSTFLRCLNRM   53 (251)
T ss_pred             eeeeeEEEcCCCEEEEECCCCCCHHHHHHHHhhc
Confidence            443433 999999999999999999998887754

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.05  E-value=0.0052  Score=61.47  Aligned_cols=39  Identities=13%  Similarity=0.213  Sum_probs=33.9

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .+.-.+|.|+||+|||.|+..+|..+..+ |..|+|++..
T Consensus       182 ~~~~Lll~G~~GtGKThLa~aIa~~l~~~-g~~V~y~t~~  220 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLSNCIAKELLDR-GKSVIYRTAD  220 (329)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHC-CCeEEEEEHH
Confidence            34678899999999999999999988875 9999999853

>PRK10636 putative ABC transporter ATP-binding protein; Provisional

Probab=97.05  E-value=0.0062  Score=67.10  Aligned_cols=27  Identities=30%  Similarity=0.409  Sum_probs=24.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+.+.|.|++|+|||||+.-++-.
T Consensus       335 i~~Ge~~~l~G~NGsGKSTLlk~l~G~  361 (638)
T PRK10636        335 LVPGSRIGLLGRNGAGKSTLIKLLAGE  361 (638)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999999998887754

>PRK14249 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.05  E-value=0.023  Score=54.85  Aligned_cols=33  Identities=24%  Similarity=0.290  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        20 l~~~s~~i~~G~~~~i~G~nGsGKSTLl~~l~Gl   53 (251)
T PRK14249         20 LKNINMDFPERQITAIIGPSGCGKSTLLRALNRM   53 (251)
T ss_pred             ecceEEEEcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            444433 899999999999999999998877653

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=97.05  E-value=0.0033  Score=68.84  Aligned_cols=26  Identities=31%  Similarity=0.480  Sum_probs=23.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +.+|+.+.|.|++|+|||||+.-++-
T Consensus       358 i~~G~~v~IvG~sGsGKSTLl~lL~g  383 (588)
T PRK13657        358 AKPGQTVAIVGPTGAGKSTLINLLQR  383 (588)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhc
Confidence            89999999999999999999866553

>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase

Probab=97.04  E-value=0.0025  Score=51.98  Aligned_cols=81  Identities=30%  Similarity=0.371  Sum_probs=51.8

Q ss_pred             cEEEEechhhHHHHHHhCC---CceEEcCCCCCCCCCCCCCCChhh-hhhhHHHHhHHHHhccCCEEEEEecCCccchHH
Q 009230          125 DIIIVEGEMDKLSMEEAGF---LNCVSVPDGAPSSVSKKNVPSEEQ-DTKYQYLWNCKMYLKQASRIILATDGDPPGQAL  200 (539)
Q Consensus       125 ~v~i~EG~~Dalsl~~~g~---~~~v~l~~g~~~~~~~~~l~~~~~-~~~~~~l~~~~~~l~~~~~ivl~~DnD~~G~~~  200 (539)
                      +|+|+||..|+-++.++..   ..++++ .|......   .|.... ..+...+......+.+..+||+|.|+|..|+..
T Consensus         1 ~liIvE~ps~a~~i~~~l~~~~~~v~~~-~Ghl~~~~---~~~~~~~~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~I   76 (100)
T PF01751_consen    1 ELIIVEKPSDAKAIAKALGGEEYIVIAT-SGHLLELA---KPEDYDPKDKKKQIKNLKKLLKKADEIIIATDPDREGELI   76 (100)
T ss_dssp             EEEEESSHHHHHHHHHHSSTTTEEEEEE-SSSSEEST---TSSHHHCHTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHH
T ss_pred             CEEEEeCHHHHHHHHHHcCCCCEEEEEe-CCcccccc---cccccccccccccchhhHHHhhhccEeeecCCCChHHHHH
Confidence            4899999999999999976   333332 34332111   111100 111222333445566789999999999999999


Q ss_pred             HHHHHHHhc
Q 009230          201 AEELARRVG  209 (539)
Q Consensus       201 ~~~~~~~l~  209 (539)
                      +..+.+.++
T Consensus        77 a~~i~~~~~   85 (100)
T PF01751_consen   77 AWEIIELLG   85 (100)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999988884

This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=97.04  E-value=0.0026  Score=63.10  Aligned_cols=118  Identities=17%  Similarity=0.133  Sum_probs=64.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccc--cCCCCCCCCHHH-HHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEAN--YGGSAERMTVEE-FEQG  374 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~--~~~~~~~l~~~~-~~~~  374 (539)
                      .+++++|.-|+||||++..+|.++|.. |.+|+.+|++-... +.. ++....+-....+.  .+-....++.+. +++.
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~~A~~-G~rtLlvS~Dpa~~-L~d-~l~~~~~~~~~~v~~~~~L~a~eid~~~~~~~~   78 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALALARR-GKRTLLVSTDPAHS-LSD-VLGQKLGGEPTKVEGVPNLSAMEIDPEAELEEY   78 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHT-TS-EEEEESSTTTH-HHH-HHTS--BSS-EEETTCSSEEEEE--HHHHHHHH
T ss_pred             eEEEEecCCCCCcHHHHHHHHHHHhhC-CCCeeEeecCCCcc-HHH-HhCCcCCCCCeEecCCCCceeeecCHHHHHHHH
Confidence            378999999999999999999999996 99999999996543 222 22222222222332  110111233332 2222


Q ss_pred             HHHh----hccce------eEeecCCCCCCHHHHH--HHHHHHHHHcCCcEEEEcc
Q 009230          375 KAWL----SNTFS------LIRCENDSLPSIKWVL--DLAKAAVLRHGVRGLVIDP  418 (539)
Q Consensus       375 ~~~l----~~~~~------~i~~~~~~~~~~~~i~--~~i~~~~~~~~~~~vvID~  418 (539)
                      .+.+    .....      ++...-...|.++++.  ..+..+......++||+|.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~PG~~E~~~l~~l~~~~~~~~~D~IVvDt  134 (305)
T PF02374_consen   79 WEEVQKDLSSLLPLIGLERILDEELSSLPGLDELAALLRLADLLESGEYDLIVVDT  134 (305)
T ss_dssp             HHHHHHGCSTCHHCHHHHHHHHHHTTSSTTHHHHHHHHHHHHHHHHCSTSEEEEES
T ss_pred             HHHHHhhhccchhhhhhHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCEEEECC
Confidence            1111    11000      0001112346777754  4555666677899999993

...

>PRK11288 araG L-arabinose transporter ATP-binding protein; Provisional

Probab=97.03  E-value=0.0053  Score=65.77  Aligned_cols=34  Identities=26%  Similarity=0.397  Sum_probs=27.8

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        19 il~~isl~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl   53 (501)
T PRK11288         19 ALDDISFDCRAGQVHALMGENGAGKSTLLKILSGN   53 (501)
T ss_pred             EEeeeeEEEeCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3555544 999999999999999999998877643

>PRK14246 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.03  E-value=0.0075  Score=58.49  Aligned_cols=34  Identities=24%  Similarity=0.267  Sum_probs=27.6

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        26 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~iaG~~   60 (257)
T PRK14246         26 LKDITIKIPNNSIFGIMGPSGSGKSTLLKVLNRLI   60 (257)
T ss_pred             EeceEEEEcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            444444 8999999999999999999988777543

>PRK14243 phosphate transporter ATP-binding protein; Provisional

Probab=97.03  E-value=0.032  Score=54.38  Aligned_cols=32  Identities=16%  Similarity=0.298  Sum_probs=26.8

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        26 l~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~l~G   58 (264)
T PRK14243         26 VKNVWLDIPKNQITAFIGPSGCGKSTILRCFNR   58 (264)
T ss_pred             eecceEEEcCCCEEEEECCCCCCHHHHHHHHHh
Confidence            444433 99999999999999999999987774

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=97.02  E-value=0.0045  Score=59.73  Aligned_cols=36  Identities=28%  Similarity=0.524  Sum_probs=31.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      |++|+|.||+||||++.+++..+... +.+|.+++.+
T Consensus         1 LIvl~G~pGSGKST~a~~La~~l~~~-~~~v~~i~~D   36 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKKLSEK-NIDVIILGTD   36 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHc-CCceEEEccH
Confidence            58999999999999999999887664 7888888764

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>CHL00131 ycf16 sulfate ABC transporter protein; Validated

Probab=97.02  E-value=0.0055  Score=59.24  Aligned_cols=32  Identities=28%  Similarity=0.356  Sum_probs=26.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        23 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~i~G   55 (252)
T CHL00131         23 LKGLNLSINKGEIHAIMGPNGSGKSTLSKVIAG   55 (252)
T ss_pred             eecceeEEcCCcEEEEECCCCCCHHHHHHHHcC
Confidence            444433 99999999999999999999987664

>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=97.01  E-value=0.0026  Score=60.19  Aligned_cols=35  Identities=17%  Similarity=0.371  Sum_probs=26.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      -++|.|++|+|||+|++.+..+...  ....+|+..+
T Consensus        15 r~viIG~sGSGKT~li~~lL~~~~~--~f~~I~l~t~   49 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKSLLYYLRH--KFDHIFLITP   49 (241)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhhcc--cCCEEEEEec
Confidence            4679999999999999999987654  3444444444

This is thought to be an ATPase involved in viral DNA packaging [].

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.01  E-value=0.0076  Score=64.60  Aligned_cols=173  Identities=23%  Similarity=0.314  Sum_probs=88.7

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCC----C-------c
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKK----P-------F  354 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~----~-------~  354 (539)
                      -|+++.- ++||+.+.+.||+|+||||++.=+. ++-.-....++.=.  .+-.++=.+.+....|.    |       .
T Consensus       483 Vlk~lsfti~pGe~vALVGPSGsGKSTiasLL~-rfY~PtsG~IllDG--~~i~~~~~~~lr~~Ig~V~QEPvLFs~sI~  559 (716)
T KOG0058|consen  483 VLKNLSFTIRPGEVVALVGPSGSGKSTIASLLL-RFYDPTSGRILLDG--VPISDINHKYLRRKIGLVGQEPVLFSGSIR  559 (716)
T ss_pred             hhcCceeeeCCCCEEEEECCCCCCHHHHHHHHH-HhcCCCCCeEEECC--eehhhcCHHHHHHHeeeeeccceeecccHH
Confidence            4555554 9999999999999999999865443 33332344444321  22222222222222111    1       1


Q ss_pred             cccccCCCCCCCCHHHHHHHH------HHhhccceeEe--ecCCC---CCCHHHHHHHHHHHHHHcCCcEEEEccccccc
Q 009230          355 FEANYGGSAERMTVEEFEQGK------AWLSNTFSLIR--CENDS---LPSIKWVLDLAKAAVLRHGVRGLVIDPYNELD  423 (539)
Q Consensus       355 ~~i~~~~~~~~l~~~~~~~~~------~~l~~~~~~i~--~~~~~---~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~  423 (539)
                      +.|.+|-  ...++|++..+.      +.+.+.+.=+.  +.+.+   +....+=++.+|.++  .+|.++|+|.-+..+
T Consensus       560 eNI~YG~--~~~t~e~i~~AAk~ANah~FI~~~p~gY~T~VGEkG~qLSGGQKQRIAIARALl--r~P~VLILDEATSAL  635 (716)
T KOG0058|consen  560 ENIAYGL--DNATDEEIEAAAKMANAHEFITNFPDGYNTVVGEKGSQLSGGQKQRIAIARALL--RNPRVLILDEATSAL  635 (716)
T ss_pred             HHHhcCC--CCCCHHHHHHHHHHhChHHHHHhCccccccccCCccccccchHHHHHHHHHHHh--cCCCEEEEechhhhc
Confidence            2233442  246677776543      33433221110  11111   112233444455544  478999999666554


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          424 HQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      +    .++|. .+.+   .|.++.++  -+|++++| -..                    -+.||.|.++.+-+
T Consensus       636 D----aeSE~-lVq~---aL~~~~~~--rTVlvIAHRLST--------------------V~~Ad~Ivvi~~G~  679 (716)
T KOG0058|consen  636 D----AESEY-LVQE---ALDRLMQG--RTVLVIAHRLST--------------------VRHADQIVVIDKGR  679 (716)
T ss_pred             c----hhhHH-HHHH---HHHHhhcC--CeEEEEehhhhH--------------------hhhccEEEEEcCCe
Confidence            3    23332 2233   33333333  88999999 321                    24678888887654

>PRK14265 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.00  E-value=0.023  Score=55.67  Aligned_cols=31  Identities=16%  Similarity=0.241  Sum_probs=26.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      |+.+.- +.+|+.+.|.|++|+|||||+.-++
T Consensus        36 l~~vs~~i~~Ge~~~IiG~nGsGKSTLl~~l~   67 (274)
T PRK14265         36 LVDVHLKIPAKKIIAFIGPSGCGKSTLLRCFN   67 (274)
T ss_pred             EeeeeeEEcCCCEEEEECCCCCCHHHHHHHHh
Confidence            444433 9999999999999999999988776

>PRK14238 phosphate transporter ATP-binding protein; Provisional

Probab=97.00  E-value=0.018  Score=56.30  Aligned_cols=34  Identities=26%  Similarity=0.408  Sum_probs=27.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        40 l~~vsl~i~~Ge~~~I~G~nGsGKSTLl~~i~Gl~   74 (271)
T PRK14238         40 LKNINLDIHENEVTAIIGPSGCGKSTYIKTLNRMV   74 (271)
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            444433 9999999999999999999998887543

>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C

Probab=97.00  E-value=0.004  Score=58.88  Aligned_cols=34  Identities=32%  Similarity=0.381  Sum_probs=27.9

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        19 ~l~~i~~~i~~Ge~~~i~G~nGsGKSTLl~~l~G~   53 (221)
T cd03244          19 VLKNISFSIKPGEKVGIVGRTGSGKSSLLLALFRL   53 (221)
T ss_pred             cccceEEEECCCCEEEEECCCCCCHHHHHHHHHcC
Confidence            3454444 999999999999999999998877654

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>PRK10982 galactose/methyl galaxtoside transporter ATP-binding protein; Provisional

Probab=97.00  E-value=0.0041  Score=66.50  Aligned_cols=33  Identities=12%  Similarity=0.320  Sum_probs=26.9

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus       264 l~~vsl~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl  297 (491)
T PRK10982        264 IRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGI  297 (491)
T ss_pred             cceeeEEEeCCcEEEEecCCCCCHHHHHHHHcCC
Confidence            444433 999999999999999999998877643

>PRK00889 adenylylsulfate kinase; Provisional

Probab=97.00  E-value=0.0012  Score=59.90  Aligned_cols=40  Identities=23%  Similarity=0.317  Sum_probs=35.0

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ++|++++|.|.||+||||++..++..+... |..+.++..+
T Consensus         2 ~~g~~i~~~G~~GsGKST~a~~la~~l~~~-g~~v~~id~D   41 (175)
T PRK00889          2 QRGVTVWFTGLSGAGKTTIARALAEKLREA-GYPVEVLDGD   41 (175)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEEcCc
Confidence            578999999999999999999999888664 7888888765

>PRK10982 galactose/methyl galaxtoside transporter ATP-binding protein; Provisional

Probab=96.99  E-value=0.008  Score=64.23  Aligned_cols=33  Identities=24%  Similarity=0.360  Sum_probs=27.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        14 l~~vs~~i~~Ge~~~liG~nGsGKSTLl~~l~Gl   47 (491)
T PRK10982         14 LDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGI   47 (491)
T ss_pred             eeeeeEEEcCCcEEEEECCCCCCHHHHHHHHcCC
Confidence            444443 999999999999999999998877643

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=96.99  E-value=0.0028  Score=58.99  Aligned_cols=30  Identities=23%  Similarity=0.235  Sum_probs=25.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINE  323 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~  323 (539)
                      ...|++++|.|++|+|||+++..++.....
T Consensus        26 ~~~~~~~~l~G~n~~GKstll~~i~~~~~l   55 (204)
T cd03282          26 RGSSRFHIITGPNMSGKSTYLKQIALLAIM   55 (204)
T ss_pred             eCCCcEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            677899999999999999999988765544

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PF09807 DUF2348: Uncharacterized conserved protein (DUF2348); InterPro: IPR018627 Members of this family of putative uncharacterised proteins have no known function

Probab=96.98  E-value=0.017  Score=55.51  Aligned_cols=191  Identities=16%  Similarity=0.234  Sum_probs=117.5

Q ss_pred             chhhhhhhc-----cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCcccccc
Q 009230          285 WRALNELYN-----VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANY  359 (539)
Q Consensus       285 ~~~LD~~~~-----l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~  359 (539)
                      |++|+.+++     .++|.+++|... ++-=|.++.+++....+ .|.+|+++++..+.... .+. ++-.|+++...+.
T Consensus         2 f~eln~ll~~~~~~~~~g~~ili~d~-~~dgsFLlh~~L~~~Lk-~~~~V~fv~~~q~~~HY-~~v-~~KLG~NL~~~~~   77 (249)
T PF09807_consen    2 FPELNSLLNWSPDSVPPGKLILIEDC-ETDGSFLLHHFLSQYLK-AGCKVCFVAFSQSFSHY-NNV-AQKLGVNLSAAKE   77 (249)
T ss_pred             chHHHHHhcCCCCCCCCCeEEEEEcC-CCCchhHHHHHHHHHhc-CCCcEEEEEccCCHHHH-HHH-HHhhEecchHhcc
Confidence            466776663     789999999999 88888888888888877 49999999999886632 222 3335776654432


Q ss_pred             CCCCCCCCH-HHHHHHHHHhh-----c--cc-eeEeecCCCCCCHHHHHHHHHHHHHH---cCCcEEEEccccccccCCC
Q 009230          360 GGSAERMTV-EEFEQGKAWLS-----N--TF-SLIRCENDSLPSIKWVLDLAKAAVLR---HGVRGLVIDPYNELDHQRP  427 (539)
Q Consensus       360 ~~~~~~l~~-~~~~~~~~~l~-----~--~~-~~i~~~~~~~~~~~~i~~~i~~~~~~---~~~~~vvID~~~~l~~~~~  427 (539)
                      .+   ++.- +-+....+.+-     +  .+ -+++ . .+...+..+.+.|+.....   .+..+||||++.-|...  
T Consensus        78 ~g---ql~fiD~l~~~~~~l~~~~~~~~~~~~~~l~-~-~~~~~L~~L~~~I~~~l~~~~~~~~~~liIDdls~Ll~l--  150 (249)
T PF09807_consen   78 KG---QLVFIDGLKSSLDLLFDEDSSDEPNPLKFLR-E-DNASSLRSLYEFIQEALSPADSNGSVVLIIDDLSVLLSL--  150 (249)
T ss_pred             CC---cEEEeehhhhhhhhhhccccccCCccccccc-c-CCcchHHHHHHHHHHHHhhccCCCCeEEEEeCHHHHHHc--
Confidence            21   2110 11111111111     1  11 1111 1 2223467777777665554   34689999998888752  


Q ss_pred             CCCCHHHHHHHHHHHHH-HHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          428 VSQTETEYVSQMLTMVK-RFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       428 ~~~~~~~~~~~~~~~Lk-~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                       +.+. ..+-.++..++ .++.+.+..++++.| .-....   ....  .  =...+.+.||.+|.+..-
T Consensus       151 -G~s~-~~vldF~~ycra~l~~~~~~~lVvl~h~d~~~~~---e~~~--~--l~~~L~h~a~l~i~v~~L  211 (249)
T PF09807_consen  151 -GVSS-NDVLDFIHYCRATLCSESNGSLVVLVHCDIDDED---EEND--L--LLNSLAHMADLVITVEPL  211 (249)
T ss_pred             -CCCH-HHHHHHHHHHHHHhccccCCCEEEEEecCCCCcc---chHH--H--HHHHHHHHhcEEEEecCC
Confidence             2233 34667899998 688888888888888 322211   1111  0  124688999999988753

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=96.98  E-value=0.014  Score=52.54  Aligned_cols=33  Identities=33%  Similarity=0.498  Sum_probs=27.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        17 l~~i~l~i~~Ge~~~i~G~nGsGKSTLl~~l~G~   50 (166)
T cd03223          17 LKDLSFEIKPGDRLLITGPSGTGKSSLFRALAGL   50 (166)
T ss_pred             eecCeEEECCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            444433 999999999999999999998877654

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=96.98  E-value=0.0063  Score=67.01  Aligned_cols=171  Identities=18%  Similarity=0.189  Sum_probs=89.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC---HHHHHHHHHHHhhCCCc---cccccCC--CCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK---VREHARKLLEKHIKKPF---FEANYGG--SAER  365 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~---~~~~~~r~~~~~~~~~~---~~i~~~~--~~~~  365 (539)
                      +++|+.+.|.|++||||||++.-+.--.-- ....+.+=..+.+   ...+. |-+.....-++   ..++.+-  ..+.
T Consensus       496 I~~Ge~vaIvG~SGsGKSTL~KLL~gly~p-~~G~I~~dg~dl~~i~~~~lR-~~ig~V~Q~~~Lf~gSI~eNi~l~~p~  573 (709)
T COG2274         496 IPPGEKVAIVGRSGSGKSTLLKLLLGLYKP-QQGRILLDGVDLNDIDLASLR-RQVGYVLQDPFLFSGSIRENIALGNPE  573 (709)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhcCCCC-CCceEEECCEeHHhcCHHHHH-hheeEEcccchhhcCcHHHHHhcCCCC
Confidence            999999999999999999997655432222 1334444433322   23222 22211111110   1111110  1233


Q ss_pred             CCHHHHHHH------HHHhhccceeEee-cCCCCCC----HHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHH
Q 009230          366 MTVEEFEQG------KAWLSNTFSLIRC-ENDSLPS----IKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETE  434 (539)
Q Consensus       366 l~~~~~~~~------~~~l~~~~~~i~~-~~~~~~~----~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~  434 (539)
                      .+.|++.++      .+.+...|.=+.. -.++..+    ..+.+..+|.+.  .+|+++++|--+.-++        .+
T Consensus       574 ~~~e~i~~A~~~ag~~~fI~~lP~gy~t~v~E~G~~LSGGQrQrlalARaLl--~~P~ILlLDEaTSaLD--------~~  643 (709)
T COG2274         574 ATDEEIIEAAQLAGAHEFIENLPMGYDTPVGEGGANLSGGQRQRLALARALL--SKPKILLLDEATSALD--------PE  643 (709)
T ss_pred             CCHHHHHHHHHHhCcHHHHHhcccccccccccCCCCCCHHHHHHHHHHHHhc--cCCCEEEEeCcccccC--------Hh
Confidence            455555443      2444443321100 0122222    344555555443  5799999994443221        12


Q ss_pred             HHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC
Q 009230          435 YVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD  497 (539)
Q Consensus       435 ~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~  497 (539)
                      .-..+++.|.++.  .++++|+++|....                   -..||.++.++..+-
T Consensus       644 sE~~I~~~L~~~~--~~~T~I~IaHRl~t-------------------i~~adrIiVl~~Gki  685 (709)
T COG2274         644 TEAIILQNLLQIL--QGRTVIIIAHRLST-------------------IRSADRIIVLDQGKI  685 (709)
T ss_pred             HHHHHHHHHHHHh--cCCeEEEEEccchH-------------------hhhccEEEEccCCce
Confidence            2245777777665  45899999993322                   347899999987653

>COG1101 PhnK ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=96.98  E-value=0.012  Score=53.81  Aligned_cols=151  Identities=19%  Similarity=0.327  Sum_probs=84.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHH--HHHHhhCCCccccccCCCCC
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARK--LLEKHIKKPFFEANYGGSAE  364 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r--~~~~~~~~~~~~i~~~~~~~  364 (539)
                      |+.+.- +..|++++|.|..|+|||||+.-++-.+... +..|..-.-..+.....+|  +++....-+...     ..+
T Consensus        22 l~~~sL~I~~g~FvtViGsNGAGKSTlln~iaG~l~~t-~G~I~Idg~dVtk~~~~~RA~~larVfQdp~~g-----t~~   95 (263)
T COG1101          22 LNGLSLEIAEGDFVTVIGSNGAGKSTLLNAIAGDLKPT-SGQILIDGVDVTKKSVAKRANLLARVFQDPLAG-----TAP   95 (263)
T ss_pred             HhcCceeecCCceEEEEcCCCccHHHHHHHhhCccccC-CceEEECceecccCCHHHHhhHHHHHhcchhhC-----Ccc
Confidence            444433 8999999999999999999999888777664 5555544444332222222  233333222211     112


Q ss_pred             CCCHHH-HH--------------------H-HHHHh-----------hccceeEeecCCCCCCHHHHHHHHHHHHHHcCC
Q 009230          365 RMTVEE-FE--------------------Q-GKAWL-----------SNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGV  411 (539)
Q Consensus       365 ~l~~~~-~~--------------------~-~~~~l-----------~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~  411 (539)
                      .|+-+| +.                    + ..+.+           .++.-++    .+  ...+.++.+  ++.-+++
T Consensus        96 ~lTieENl~la~~Rg~~rgl~~~ln~~~~~~f~~~l~~l~lgLenrL~~~iglL----SG--GQRQalsL~--MAtl~~p  167 (263)
T COG1101          96 ELTIEENLALAESRGKKRGLSSALNERRRSSFRERLARLGLGLENRLSDRIGLL----SG--GQRQALSLL--MATLHPP  167 (263)
T ss_pred             cccHHHHHHHHHhcCcccccchhhhHHHHHHHHHHHhhcccchhhhhcChhhhc----cc--hHHHHHHHH--HHhcCCC
Confidence            333332 10                    0 01111           1111111    11  112222222  3445789


Q ss_pred             cEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          412 RGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       412 ~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      +++++|.++.-..+.        .-..+++.-.++..+.+++.+++.||
T Consensus       168 kiLLLDEHTAALDPk--------ta~~vm~lT~kiV~~~klTtlMVTHn  208 (263)
T COG1101         168 KILLLDEHTAALDPK--------TAEFVMELTAKIVEEHKLTTLMVTHN  208 (263)
T ss_pred             cEEEecchhhcCCcc--------hHHHHHHHHHHHHHhcCCceEEEecc
Confidence            999999887765432        12456777777889999999999995

>PRK14261 phosphate ABC transporter ATP-binding protein; Provisional

Probab=96.98  E-value=0.023  Score=54.90  Aligned_cols=32  Identities=19%  Similarity=0.272  Sum_probs=26.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        22 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~l~G   54 (253)
T PRK14261         22 LYDITISIPKNRVTALIGPSGCGKSTLLRCFNR   54 (253)
T ss_pred             eeeeEEEECCCcEEEEECCCCCCHHHHHHHHhc
Confidence            444433 99999999999999999999888763

>TIGR03689 pup_AAA proteasome ATPase

Probab=96.98  E-value=0.0022  Score=67.51  Aligned_cols=33  Identities=21%  Similarity=0.389  Sum_probs=24.9

Q ss_pred             hhccCCCcEEEEEcCCCCChhHHHHHHHHHHHH
Q 009230          291 LYNVLPGELTIVTGVPNSGKSEWIDALICNINE  323 (539)
Q Consensus       291 ~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~  323 (539)
                      ..++.+..-++|.||||+|||+++..++..+..
T Consensus       210 ~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~  242 (512)
T TIGR03689       210 EYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQ  242 (512)
T ss_pred             hccCCCCcceEEECCCCCcHHHHHHHHHHhhcc
Confidence            334433345889999999999999988877654

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.

>TIGR02633 xylG D-xylose ABC transporter, ATP-binding protein

Probab=96.97  E-value=0.0088  Score=64.09  Aligned_cols=34  Identities=32%  Similarity=0.352  Sum_probs=27.8

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        16 il~~isl~i~~Ge~~~liG~nGsGKSTLl~~i~G~   50 (500)
T TIGR02633        16 ALDGIDLEVRPGECVGLCGENGAGKSTLMKILSGV   50 (500)
T ss_pred             eecceEEEEeCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3555544 999999999999999999998877643

Several bacterial species have enzymes xylose isomerase and xylulokinase enzymes for xylose utilization. Members of this protein family are the ATP-binding cassette (ABC) subunit of the known or predicted high-affinity xylose ABC transporter for xylose import. These genes, which closely resemble other sugar transport ABC transporter genes, typically are encoded near xylose utilization enzymes and regulatory proteins. Note that this form of the transporter contains two copies of the ABC transporter domain (pfam00005).

>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function

Probab=96.97  E-value=0.0014  Score=60.72  Aligned_cols=35  Identities=37%  Similarity=0.612  Sum_probs=26.3

Q ss_pred             Cchhh-hhhh-ccCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          284 GWRAL-NELY-NVLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       284 g~~~L-D~~~-~l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +|..+ +.+. .+.+| +++|.|++|+|||||+..++.
T Consensus         8 ~fr~~~~~~~l~~~~g-~~~i~G~nGsGKStll~al~~   44 (197)
T cd03278           8 GFKSFADKTTIPFPPG-LTAIVGPNGSGKSNIIDAIRW   44 (197)
T ss_pred             CCcCcCCCeeeecCCC-cEEEECCCCCCHHHHHHHHHH
Confidence            44445 3332 28889 999999999999999987753

Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w

>PRK09183 transposase/IS protein; Provisional

Probab=96.97  E-value=0.00097  Score=64.61  Aligned_cols=40  Identities=20%  Similarity=0.183  Sum_probs=35.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +..|+.++|.|+||+|||+++..++..++.+ |.+|+|++.
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~-G~~v~~~~~  138 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALGYEAVRA-GIKVRFTTA  138 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHHHHHHHc-CCeEEEEeH
Confidence            7889999999999999999999998777664 999999974

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=96.96  E-value=0.006  Score=59.70  Aligned_cols=35  Identities=26%  Similarity=0.392  Sum_probs=28.6

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .|+.+.- +.+|+.+.|.|++|+|||||+.-++...
T Consensus        19 ~l~~isl~I~~Ge~~~IvG~nGsGKSTLl~~L~gl~   54 (275)
T cd03289          19 VLENISFSISPGQRVGLLGRTGSGKSTLLSAFLRLL   54 (275)
T ss_pred             ceeceEEEEcCCCEEEEECCCCCCHHHHHHHHhhhc
Confidence            3444444 9999999999999999999988876554

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

>TIGR03797 NHPM_micro_ABC2 NHPM bacteriocin system ABC transporter, ATP-binding protein

Probab=96.96  E-value=0.0065  Score=67.80  Aligned_cols=165  Identities=18%  Similarity=0.122  Sum_probs=83.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHHHHhhCCCc---cccccCCC-CCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLLEKHIKKPF---FEANYGGS-AERM  366 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~~---~~i~~~~~-~~~l  366 (539)
                      +++|+.+.|.|++|+|||||+.-++--..-. ...+.+-.-+   .+...+.+++ +....-+.   ..++++-. ....
T Consensus       476 i~~Ge~vaIvG~sGsGKSTLlklL~gl~~p~-~G~I~idg~~i~~~~~~~lr~~i-~~v~Q~~~lf~gTI~eNi~~~~~~  553 (686)
T TIGR03797       476 IEPGEFVAIVGPSGSGKSTLLRLLLGFETPE-SGSVFYDGQDLAGLDVQAVRRQL-GVVLQNGRLMSGSIFENIAGGAPL  553 (686)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCCCCC-CCEEEECCEEcCcCCHHHHHhcc-EEEccCCccCcccHHHHHhcCCCC
Confidence            8999999999999999999977666443322 3444433222   3444443332 21111110   11111100 0115


Q ss_pred             CHHHHHHHHH------Hhhccce----eEeecCCCCCCHH--HHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHH
Q 009230          367 TVEEFEQGKA------WLSNTFS----LIRCENDSLPSIK--WVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETE  434 (539)
Q Consensus       367 ~~~~~~~~~~------~l~~~~~----~i~~~~~~~~~~~--~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~  434 (539)
                      +++++.++.+      .+...+.    .+. +.....+-.  +-+..+|.+.  .+++++++|.-+.-+       +. .
T Consensus       554 ~~e~i~~al~~a~l~~~i~~lp~G~dt~ig-e~G~~LSGGQrQRialARAll--~~p~iLiLDEpTS~L-------D~-~  622 (686)
T TIGR03797       554 TLDEAWEAARMAGLAEDIRAMPMGMHTVIS-EGGGTLSGGQRQRLLIARALV--RKPRILLFDEATSAL-------DN-R  622 (686)
T ss_pred             CHHHHHHHHHHcCcHHHHHhcccccccccc-CCCCCCCHHHHHHHHHHHHHh--cCCCEEEEeCCccCC-------CH-H
Confidence            6666655532      2322221    110 101112222  2333444333  578999999444322       21 2


Q ss_pred             HHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          435 YVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       435 ~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      .-..+.+.|+++    +.++|+++|.-.                   .-..||.|+.|..
T Consensus       623 te~~i~~~L~~~----~~T~IiItHr~~-------------------~i~~~D~Iivl~~  659 (686)
T TIGR03797       623 TQAIVSESLERL----KVTRIVIAHRLS-------------------TIRNADRIYVLDA  659 (686)
T ss_pred             HHHHHHHHHHHh----CCeEEEEecChH-------------------HHHcCCEEEEEEC
Confidence            223566666654    679999999311                   1246899999964

Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=96.96  E-value=0.012  Score=56.71  Aligned_cols=151  Identities=15%  Similarity=0.124  Sum_probs=79.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-cCCeEEEEeCC---CCHHHHHHHHHHHhhCCCccccccCC---CCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEH-AGWKFVLCSME---NKVREHARKLLEKHIKKPFFEANYGG---SAERM  366 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~~~~i~~~~---~~~~l  366 (539)
                      ..| -+.+|.||+|+|||.|+.++...-..+ ....|.|++.|   .+++++...-... ..-++..-..|+   ..+.+
T Consensus        85 ~qP-~I~~VYGPTG~GKSqLlRNLis~~lI~P~PETVfFItP~~~mIpp~E~~aW~~Ql-~EgNY~~~~~gTi~P~t~t~  162 (369)
T PF02456_consen   85 LQP-FIGVVYGPTGSGKSQLLRNLISCQLIQPPPETVFFITPQKDMIPPQEITAWETQL-CEGNYDCGPDGTIVPQTGTF  162 (369)
T ss_pred             CCc-eEEEEECCCCCCHHHHHHHhhhcCcccCCCCceEEECCCCCCCCHHHHHHHHHHH-HhcCCCCCCCCeeccccccc
Confidence            444 278899999999999999886543332 36789999999   4466665554332 222222111110   01223


Q ss_pred             CHHHHHHHHHHh-hccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHH-HHHHH
Q 009230          367 TVEEFEQGKAWL-SNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQM-LTMVK  444 (539)
Q Consensus       367 ~~~~~~~~~~~l-~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~-~~~Lk  444 (539)
                      .++-++-..+.+ .+..+       +-.+++.|...+    .+.|+=.||+|--+.-+.+.   .+-....-.+ ++-..
T Consensus       163 ~P~Fv~msy~e~t~~~Nl-------dI~~p~NiF~~A----a~~GPiaIImDECMe~Lg~~---~~is~fFHAlPSKL~~  228 (369)
T PF02456_consen  163 RPKFVEMSYDEATSPENL-------DITNPNNIFAQA----AKKGPIAIIMDECMEKLGSH---KSISKFFHALPSKLHD  228 (369)
T ss_pred             cccceeecHhhhCCcccc-------CCCCchHHHHHH----HhcCCEEEEhHHHHHHhcCC---CChhHHHhcCcHHHhh
Confidence            332222111111 11111       112345555433    45789999999666544322   1111111112 22234


Q ss_pred             HHHHHhCcEEEEEecC
Q 009230          445 RFAQHHACHVWFVAHP  460 (539)
Q Consensus       445 ~lA~~~~i~vi~~~q~  460 (539)
                      ++++=++-.|++|-||
T Consensus       229 rfp~CTgy~VfVVLHN  244 (369)
T PF02456_consen  229 RFPKCTGYYVFVVLHN  244 (369)
T ss_pred             hccCCceeEEEEEecc
Confidence            4666688899999993

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

>PRK15064 ABC transporter ATP-binding protein; Provisional

Probab=96.95  E-value=0.0099  Score=64.18  Aligned_cols=32  Identities=22%  Similarity=0.344  Sum_probs=26.4

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus       335 l~~is~~i~~Ge~~~l~G~NGsGKSTLl~~i~G  367 (530)
T PRK15064        335 FKNLNLLLEAGERLAIIGENGVGKTTLLRTLVG  367 (530)
T ss_pred             ecCcEEEECCCCEEEEECCCCCCHHHHHHHHhC
Confidence            344433 89999999999999999999887764

>PRK13549 xylose transporter ATP-binding subunit; Provisional

Probab=96.95  E-value=0.0068  Score=65.02  Aligned_cols=34  Identities=29%  Similarity=0.374  Sum_probs=28.0

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        20 il~~isl~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl   54 (506)
T PRK13549         20 ALDNVSLKVRAGEIVSLCGENGAGKSTLMKVLSGV   54 (506)
T ss_pred             eecceeEEEeCCeEEEEECCCCCCHHHHHHHHhCC
Confidence            3555544 999999999999999999998877653

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=96.94  E-value=0.014  Score=63.59  Aligned_cols=172  Identities=20%  Similarity=0.242  Sum_probs=88.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe---CCCCHHHHHHHHHHHhhCCC-------ccc
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS---MENKVREHARKLLEKHIKKP-------FFE  356 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s---~E~~~~~~~~r~~~~~~~~~-------~~~  356 (539)
                      |+++.- +++|+.+.|.|++|+||||++.-++.-.--+ ...+++-.   -+.+...+.+++ +....-+       ..-
T Consensus       345 l~~is~~i~~Ge~vaiVG~sGsGKSTl~~LL~r~~~~~-~G~I~idg~dI~~i~~~~lr~~I-~~V~Qd~~LF~~TI~~N  422 (567)
T COG1132         345 LKDISFSIEPGEKVAIVGPSGSGKSTLIKLLLRLYDPT-SGEILIDGIDIRDISLDSLRKRI-GIVSQDPLLFSGTIREN  422 (567)
T ss_pred             ccCceEEEcCCCEEEEECCCCCCHHHHHHHHhccCCCC-CCeEEECCEehhhcCHHHHHHhc-cEEcccceeecccHHHH
Confidence            444443 9999999999999999999987666544322 34555411   123344343333 2211111       011


Q ss_pred             cccCCCCCCCCHHHHHHHH------HHhhccc---eeEeecCCCC--CC--HHHHHHHHHHHHHHcCCcEEEEccccccc
Q 009230          357 ANYGGSAERMTVEEFEQGK------AWLSNTF---SLIRCENDSL--PS--IKWVLDLAKAAVLRHGVRGLVIDPYNELD  423 (539)
Q Consensus       357 i~~~~~~~~l~~~~~~~~~------~~l~~~~---~~i~~~~~~~--~~--~~~i~~~i~~~~~~~~~~~vvID~~~~l~  423 (539)
                      +..+  .+..+++++.++.      +.+.+.|   ... .. ++.  .+  ..+.+..+|.+.  .+++++|+|.-+.-.
T Consensus       423 I~~g--~~~at~eei~~a~k~a~~~d~I~~lp~g~dt~-vg-e~G~~LSgGQrQrlaiARall--~~~~ILILDEaTSal  496 (567)
T COG1132         423 IALG--RPDATDEEIEEALKLANAHEFIANLPDGYDTI-VG-ERGVNLSGGQRQRLAIARALL--RNPPILILDEATSAL  496 (567)
T ss_pred             HhcC--CCCCCHHHHHHHHHHhChHHHHHhCcccccce-ec-CCCccCCHHHHHHHHHHHHHh--cCCCEEEEecccccc
Confidence            2222  1236777776653      2333322   111 11 121  12  233444444433  467999999544332


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          424 HQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      +    ..++    ..+.+.++++.+.  -++++++|.-+.                  +. .||.++.+...+
T Consensus       497 D----~~tE----~~I~~~l~~l~~~--rT~iiIaHRlst------------------i~-~aD~IiVl~~G~  540 (567)
T COG1132         497 D----TETE----ALIQDALKKLLKG--RTTLIIAHRLST------------------IK-NADRIIVLDNGR  540 (567)
T ss_pred             C----HHhH----HHHHHHHHHHhcC--CEEEEEeccHhH------------------HH-hCCEEEEEECCE
Confidence            1    1122    3455555555533  477789883221                  23 499999998654

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.94  E-value=0.0055  Score=65.61  Aligned_cols=38  Identities=18%  Similarity=0.192  Sum_probs=32.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHh-cCCeEEEEeCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEH-AGWKFVLCSMEN  336 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~-~g~~vl~~s~E~  336 (539)
                      -.+|.|++|+|||.|+..++..+... .|.+|+|++.+.
T Consensus       316 pL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaee  354 (617)
T PRK14086        316 PLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEE  354 (617)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHH
Confidence            47899999999999999999887653 378999999764

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=96.94  E-value=0.0044  Score=69.27  Aligned_cols=166  Identities=19%  Similarity=0.190  Sum_probs=83.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHhhCCC-------ccccccCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---ENKVREHARKLLEKHIKKP-------FFEANYGGSA  363 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---E~~~~~~~~r~~~~~~~~~-------~~~i~~~~~~  363 (539)
                      +++|+.+.|.|++|+|||||+.-++--.--. ...+.+-.-   +.+...+.+.+ +....-+       .+.+..+  .
T Consensus       488 i~~G~~iaIvG~sGsGKSTLlklL~gl~~p~-~G~I~idg~~l~~~~~~~lr~~i-~~v~Q~~~lf~~TI~eNi~~~--~  563 (694)
T TIGR03375       488 IRPGEKVAIIGRIGSGKSTLLKLLLGLYQPT-EGSVLLDGVDIRQIDPADLRRNI-GYVPQDPRLFYGTLRDNIALG--A  563 (694)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCCCCC-CceEEECCEEhhhCCHHHHHhcc-EEECCChhhhhhhHHHHHhCC--C
Confidence            8999999999999999999987665433222 233333221   12333332222 1111100       0011111  1


Q ss_pred             CCCCHHHHHHHH------HHhhccce----eEeecCCCCCCH--HHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCC
Q 009230          364 ERMTVEEFEQGK------AWLSNTFS----LIRCENDSLPSI--KWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQT  431 (539)
Q Consensus       364 ~~l~~~~~~~~~------~~l~~~~~----~i~~~~~~~~~~--~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~  431 (539)
                      +..+++++.++.      +++...+.    .+. +.....+-  .+-+..++.+.  .+++++++|.-+.-+       +
T Consensus       564 ~~~~~~~i~~a~~~~~l~~~i~~lp~gl~T~i~-e~G~~LSgGQrQRlalARall--~~p~iliLDE~Ts~L-------D  633 (694)
T TIGR03375       564 PYADDEEILRAAELAGVTEFVRRHPDGLDMQIG-ERGRSLSGGQRQAVALARALL--RDPPILLLDEPTSAM-------D  633 (694)
T ss_pred             CCCCHHHHHHHHHHcChHHHHHhCcccccceec-CCCCCCCHHHHHHHHHHHHHh--cCCCEEEEeCCCCCC-------C
Confidence            135666665543      23322221    110 10111222  23344444433  478999999443322       2


Q ss_pred             HHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          432 ETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       432 ~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                      . +.-..+.+.|+++.+  +.++|+++|.-.                   ....||.|+.|...
T Consensus       634 ~-~te~~i~~~l~~~~~--~~T~iiItHrl~-------------------~~~~~D~iivl~~G  675 (694)
T TIGR03375       634 N-RSEERFKDRLKRWLA--GKTLVLVTHRTS-------------------LLDLVDRIIVMDNG  675 (694)
T ss_pred             H-HHHHHHHHHHHHHhC--CCEEEEEecCHH-------------------HHHhCCEEEEEeCC
Confidence            1 222456666666543  789999999321                   12578999999643

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase

Probab=96.93  E-value=0.0039  Score=58.38  Aligned_cols=42  Identities=21%  Similarity=0.232  Sum_probs=34.6

Q ss_pred             cEEEEE-cCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH
Q 009230          298 ELTIVT-GVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR  339 (539)
Q Consensus       298 ~l~~i~-G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~  339 (539)
                      .++.|+ +..|+||||++.++|..++...|.+|+.+.++....
T Consensus        36 ~vi~v~s~kgG~GkSt~a~nLA~~la~~~g~~VLlvD~D~~~~   78 (207)
T TIGR03018        36 NLIMVTSSLPGEGKSFTAINLAISLAQEYDKTVLLIDADLRRP   78 (207)
T ss_pred             eEEEEECCCCCCCHHHHHHHHHHHHHHhcCCeEEEEECCCCCh
Confidence            345554 688999999999999999874599999999997654

Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=96.92  E-value=0.0071  Score=60.42  Aligned_cols=41  Identities=32%  Similarity=0.445  Sum_probs=35.7

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR  339 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~  339 (539)
                      -++.|+|+||+|||||+..++..+... |.+|.+++.+.+..
T Consensus        57 ~~igi~G~~GaGKSTl~~~l~~~l~~~-g~~v~vi~~Dp~s~   97 (332)
T PRK09435         57 LRIGITGVPGVGKSTFIEALGMHLIEQ-GHKVAVLAVDPSST   97 (332)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHC-CCeEEEEEeCCCcc
Confidence            478899999999999999999888764 99999999997643

>PRK10522 multidrug transporter membrane component/ATP-binding component; Provisional

Probab=96.92  E-value=0.0051  Score=66.66  Aligned_cols=167  Identities=13%  Similarity=0.085  Sum_probs=81.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHHHHhhCCC---ccccccCCCCCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLLEKHIKKP---FFEANYGGSAERMT  367 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~---~~~i~~~~~~~~l~  367 (539)
                      +++|+.+.|.|++|+|||||+.-++-..-- ....+.+-..+   .+...+..++ +....-+   ...+..+  ....+
T Consensus       346 i~~G~~~aivG~sGsGKSTL~~ll~g~~~~-~~G~i~~~g~~~~~~~~~~~~~~i-~~v~q~~~lf~~ti~~n--~~~~~  421 (547)
T PRK10522        346 IKRGELLFLIGGNGSGKSTLAMLLTGLYQP-QSGEILLDGKPVTAEQPEDYRKLF-SAVFTDFHLFDQLLGPE--GKPAN  421 (547)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCCC-CCeEEEECCEECCCCCHHHHhhhe-EEEecChhHHHHhhccc--cCchH
Confidence            899999999999999999998666533222 12334332222   2333333221 1110000   0001111  11233


Q ss_pred             HHHHHHHHHHhhccceeEeecC----CCCCCHHH--HHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHH
Q 009230          368 VEEFEQGKAWLSNTFSLIRCEN----DSLPSIKW--VLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLT  441 (539)
Q Consensus       368 ~~~~~~~~~~l~~~~~~i~~~~----~~~~~~~~--i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~  441 (539)
                      ++++.++.+.+.-.. .+...+    ....+-.+  -+..++.+  -.+++++++|.-+.-+       +. +.-..+.+
T Consensus       422 ~~~~~~~~~~~~l~~-~~~~~~~~~~G~~LSgGq~qRl~lARal--~~~~~ililDE~ts~L-------D~-~~~~~i~~  490 (547)
T PRK10522        422 PALVEKWLERLKMAH-KLELEDGRISNLKLSKGQKKRLALLLAL--AEERDILLLDEWAADQ-------DP-HFRREFYQ  490 (547)
T ss_pred             HHHHHHHHHHcCCch-hhhccccCCCCCCCCHHHHHHHHHHHHH--hcCCCEEEEECCCCCC-------CH-HHHHHHHH
Confidence            444444443332111 110000    01222222  22233332  3578999999444322       22 22235566


Q ss_pred             HHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          442 MVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       442 ~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      .|....++.+.+||+++|.-.                   ....||.++.+..
T Consensus       491 ~l~~~~~~~~~tvi~itH~~~-------------------~~~~~d~i~~l~~  524 (547)
T PRK10522        491 VLLPLLQEMGKTIFAISHDDH-------------------YFIHADRLLEMRN  524 (547)
T ss_pred             HHHHHHHhCCCEEEEEEechH-------------------HHHhCCEEEEEEC
Confidence            666555556899999999321                   1246888888864

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=96.92  E-value=0.0083  Score=61.61  Aligned_cols=26  Identities=31%  Similarity=0.360  Sum_probs=23.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +.+|+...|.||+|+||||++.-+.-
T Consensus       359 l~~G~~lgIIGPSgSGKSTLaR~lvG  384 (580)
T COG4618         359 LQAGEALGIIGPSGSGKSTLARLLVG  384 (580)
T ss_pred             ecCCceEEEECCCCccHHHHHHHHHc
Confidence            89999999999999999999887764

>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein

Probab=96.92  E-value=0.013  Score=64.10  Aligned_cols=29  Identities=31%  Similarity=0.464  Sum_probs=25.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      +.+|+.+.|.|++|+|||||+.-++--..
T Consensus       363 i~~Ge~i~IvG~sGsGKSTLlklL~gl~~  391 (576)
T TIGR02204       363 VRPGETVALVGPSGAGKSTLFQLLLRFYD  391 (576)
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHHhccC
Confidence            89999999999999999999887775543

This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=96.89  E-value=0.012  Score=60.65  Aligned_cols=28  Identities=21%  Similarity=0.360  Sum_probs=22.7

Q ss_pred             ccCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          293 NVLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       293 ~l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.++.-++|.|+||+|||+++..+|..
T Consensus       175 Gl~~pkgvLL~GppGTGKT~LAkalA~~  202 (398)
T PTZ00454        175 GIDPPRGVLLYGPPGTGKTMLAKAVAHH  202 (398)
T ss_pred             CCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            4555567889999999999998887754

>PRK13549 xylose transporter ATP-binding subunit; Provisional

Probab=96.89  E-value=0.0084  Score=64.34  Aligned_cols=34  Identities=18%  Similarity=0.408  Sum_probs=27.8

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus       277 vl~~vsl~i~~Ge~~~l~G~NGsGKSTLlk~i~Gl  311 (506)
T PRK13549        277 RVDDVSFSLRRGEILGIAGLVGAGRTELVQCLFGA  311 (506)
T ss_pred             cccceeeEEcCCcEEEEeCCCCCCHHHHHHHHhCC
Confidence            3555433 999999999999999999998887743

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.88  E-value=0.053  Score=55.91  Aligned_cols=79  Identities=14%  Similarity=0.123  Sum_probs=50.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-CeEEEEeCCCCH---HHHHHHHHHHhhCCCccccccCCCCCCCCHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAG-WKFVLCSMENKV---REHARKLLEKHIKKPFFEANYGGSAERMTVE  369 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-~~vl~~s~E~~~---~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~  369 (539)
                      +..|+.+.+.|++|+||||++.-++......++ .++.+++.+...   .+. .+..+...|++....        .+..
T Consensus       188 ~~~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rigalEQ-L~~~a~ilGvp~~~v--------~~~~  258 (420)
T PRK14721        188 IEQGGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQ-LRIYGKLLGVSVRSI--------KDIA  258 (420)
T ss_pred             cCCCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchhHHHH-HHHHHHHcCCceecC--------CCHH
Confidence            467899999999999999999999986654433 577777766432   211 233455667776533        2334


Q ss_pred             HHHHHHHHhhcc
Q 009230          370 EFEQGKAWLSNT  381 (539)
Q Consensus       370 ~~~~~~~~l~~~  381 (539)
                      ++..+...+.+.
T Consensus       259 dl~~al~~l~~~  270 (420)
T PRK14721        259 DLQLMLHELRGK  270 (420)
T ss_pred             HHHHHHHHhcCC
Confidence            444444555543

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=96.88  E-value=0.0025  Score=60.31  Aligned_cols=30  Identities=23%  Similarity=0.216  Sum_probs=26.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINE  323 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~  323 (539)
                      ...+++++|.|++|+|||+++..++.....
T Consensus        27 ~~~~~~~~l~G~n~~GKstll~~i~~~~~l   56 (222)
T cd03285          27 RGKSRFLIITGPNMGGKSTYIRQIGVIVLM   56 (222)
T ss_pred             ecCCeEEEEECCCCCChHHHHHHHHHHHHH
Confidence            567899999999999999999999866443

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PRK14266 phosphate ABC transporter ATP-binding protein; Provisional

Probab=96.88  E-value=0.037  Score=53.38  Aligned_cols=32  Identities=25%  Similarity=0.346  Sum_probs=26.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        19 l~~~s~~i~~Ge~~~i~G~nGsGKSTLl~~l~G   51 (250)
T PRK14266         19 LKNVNLDIPKNSVTALIGPSGCGKSTFIRTLNR   51 (250)
T ss_pred             EeeeEEEEcCCCEEEEECCCCCCHHHHHHHHHh
Confidence            444433 89999999999999999999888874

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=96.88  E-value=0.025  Score=52.31  Aligned_cols=27  Identities=26%  Similarity=0.454  Sum_probs=24.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+++.|.|++|+|||||+.-++-.
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~l~G~   49 (195)
T PRK13541         23 FLPSAITYIKGANGCGKSSLLRMIAGI   49 (195)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhcC
Confidence            899999999999999999998877654

>PRK14275 phosphate ABC transporter ATP-binding protein; Provisional

Probab=96.86  E-value=0.011  Score=58.19  Aligned_cols=32  Identities=22%  Similarity=0.392  Sum_probs=26.8

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        55 l~~vsl~i~~Ge~~~l~G~nGsGKSTLl~~L~G   87 (286)
T PRK14275         55 VKKVNADILSKYVTAIIGPSGCGKSTFLRAINR   87 (286)
T ss_pred             EeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            444433 99999999999999999999887764

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=96.86  E-value=0.011  Score=63.84  Aligned_cols=33  Identities=30%  Similarity=0.349  Sum_probs=26.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+++.- +++|+.+.|.|++|+||||++.-++..
T Consensus       351 L~~isl~i~~G~~vaIvG~SGsGKSTLl~lL~g~  384 (529)
T TIGR02868       351 LDGVSLDLPPGERVAILGPSGSGKSTLLMLLTGL  384 (529)
T ss_pred             eecceEEEcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            343333 899999999999999999998666543

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK10263 DNA translocase FtsK; Provisional

Probab=96.86  E-value=0.009  Score=68.30  Aligned_cols=44  Identities=14%  Similarity=0.274  Sum_probs=35.3

Q ss_pred             cEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CC
Q 009230          412 RGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PR  461 (539)
Q Consensus       412 ~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r  461 (539)
                      -+||||.+..|+...      ...+.+.+..|.+.++..|||+|+.+| +.
T Consensus      1142 IVVIIDE~AdLm~~~------~kevE~lI~rLAqkGRAaGIHLILATQRPs 1186 (1355)
T PRK10263       1142 IVVLVDEFADLMMTV------GKKVEELIARLAQKARAAGIHLVLATQRPS 1186 (1355)
T ss_pred             EEEEEcChHHHHhhh------hHHHHHHHHHHHHHhhhcCeEEEEEecCcc
Confidence            389999999987531      124667888899999999999999999 54

>PRK14263 phosphate ABC transporter ATP-binding protein; Provisional

Probab=96.86  E-value=0.011  Score=57.53  Aligned_cols=33  Identities=21%  Similarity=0.187  Sum_probs=26.9

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+.+.|.|++|+|||||+.-++-.
T Consensus        24 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   57 (261)
T PRK14263         24 VRDSHVPIRKNEITGFIGPSGCGKSTVLRSLNRM   57 (261)
T ss_pred             EeeeEEEEcCCCEEEEECCCCCCHHHHHHHHHcc
Confidence            444433 999999999999999999998876533

>TIGR01846 type_I_sec_HlyB type I secretion system ABC transporter, HlyB family

Probab=96.85  E-value=0.0069  Score=67.67  Aligned_cols=168  Identities=17%  Similarity=0.147  Sum_probs=85.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHhhCCC---ccccccCC--CCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---ENKVREHARKLLEKHIKKP---FFEANYGG--SAER  365 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---E~~~~~~~~r~~~~~~~~~---~~~i~~~~--~~~~  365 (539)
                      +++|+.+.|.|++|+|||||+.-++-...-. ...+.+-..   +.+...+.+++ +....-+   ...++.+-  ..+.
T Consensus       480 i~~G~~vaivG~sGsGKSTL~~ll~g~~~p~-~G~I~idg~~i~~~~~~~~r~~i-~~v~q~~~lf~~ti~eNi~~~~~~  557 (694)
T TIGR01846       480 IKPGEFIGIVGPSGSGKSTLTKLLQRLYTPQ-HGQVLVDGVDLAIADPAWLRRQM-GVVLQENVLFSRSIRDNIALCNPG  557 (694)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCCCCC-CceEEECCEehhhCCHHHHHHhC-eEEccCCeehhhhHHHHHhcCCCC
Confidence            8999999999999999999977666543322 334443322   23333333222 1111100   00111100  0123


Q ss_pred             CCHHHHHHHH------HHhhccc----eeEeecCCCCCCHHH--HHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHH
Q 009230          366 MTVEEFEQGK------AWLSNTF----SLIRCENDSLPSIKW--VLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTET  433 (539)
Q Consensus       366 l~~~~~~~~~------~~l~~~~----~~i~~~~~~~~~~~~--i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~  433 (539)
                      .+++++.++.      +.+...+    ..+. +.....+-.+  -+..++.+.  .+++++++|.-+.-+       + .
T Consensus       558 ~~~~~i~~a~~~~~l~~~i~~lp~gl~t~i~-~~g~~LSgGq~qri~lARall--~~~~ililDEpts~L-------D-~  626 (694)
T TIGR01846       558 APFEHVIHAAKLAGAHDFISELPQGYNTEVG-EKGANLSGGQRQRIAIARALV--GNPRILIFDEATSAL-------D-Y  626 (694)
T ss_pred             CCHHHHHHHHHHcChHHHHHhCcCccCcEec-CCCCCCCHHHHHHHHHHHHHH--hCCCEEEEECCCcCC-------C-H
Confidence            5566655443      2222211    1111 1111222222  233334333  578999999444322       2 1


Q ss_pred             HHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          434 EYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       434 ~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                      ..-..+.+.|+.+.  .+.++|+++|.-..                  + ..+|.++.|...
T Consensus       627 ~~~~~i~~~l~~~~--~~~t~i~itH~~~~------------------~-~~~d~ii~l~~G  667 (694)
T TIGR01846       627 ESEALIMRNMREIC--RGRTVIIIAHRLST------------------V-RACDRIIVLEKG  667 (694)
T ss_pred             HHHHHHHHHHHHHh--CCCEEEEEeCChHH------------------H-HhCCEEEEEeCC
Confidence            22345677777664  47899999993211                  2 358999998653

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.

>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=96.85  E-value=0.0052  Score=67.34  Aligned_cols=173  Identities=16%  Similarity=0.090  Sum_probs=85.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC---CHHHHHHHHHHHhhCCCc---cccccC
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN---KVREHARKLLEKHIKKPF---FEANYG  360 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~---~~~~~~~r~~~~~~~~~~---~~i~~~  360 (539)
                      |+++.- +++|+.+.|.|++|+|||||+.-++--.-- ....+.+-.-+.   +.+.+.+++ +....-+.   ..++++
T Consensus       357 l~~i~l~i~~Ge~iaIvG~SGsGKSTLl~lL~gl~~p-~~G~I~idg~~i~~~~~~~l~~~i-~~v~Q~~~lF~~Ti~~N  434 (592)
T PRK10790        357 LQNINLSVPSRGFVALVGHTGSGKSTLASLLMGYYPL-TEGEIRLDGRPLSSLSHSVLRQGV-AMVQQDPVVLADTFLAN  434 (592)
T ss_pred             eeceeEEEcCCCEEEEECCCCCCHHHHHHHHhcccCC-CCceEEECCEEhhhCCHHHHHhhe-EEEccCCccccchHHHH
Confidence            443333 999999999999999999997766543322 234554433222   233333332 21111110   111110


Q ss_pred             CC-CCCCCHHHHHHHHH------Hhhccc----eeEeecCCCCCCHH--HHHHHHHHHHHHcCCcEEEEccccccccCCC
Q 009230          361 GS-AERMTVEEFEQGKA------WLSNTF----SLIRCENDSLPSIK--WVLDLAKAAVLRHGVRGLVIDPYNELDHQRP  427 (539)
Q Consensus       361 ~~-~~~l~~~~~~~~~~------~l~~~~----~~i~~~~~~~~~~~--~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~  427 (539)
                      -. ....+++++.++.+      ++...+    ..+. +.....+-.  +-+..+|.+.  .+++++++|.-+.-+    
T Consensus       435 I~~~~~~~d~~i~~a~~~~gl~~~i~~lp~Gldt~i~-e~g~~LSGGqrQRialARaLl--~~~~illlDEpts~L----  507 (592)
T PRK10790        435 VTLGRDISEEQVWQALETVQLAELARSLPDGLYTPLG-EQGNNLSVGQKQLLALARVLV--QTPQILILDEATANI----  507 (592)
T ss_pred             HHhCCCCCHHHHHHHHHHcCcHHHHHhcccccccccc-CCCCCCCHHHHHHHHHHHHHH--hCCCEEEEeCCcccC----
Confidence            00 01345666555432      222211    1110 111122222  2333444443  478999999333222    


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          428 VSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       428 ~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                         +. +.-..+.+.|+++..  +++||+++|.-.                   ....+|.|+.|..
T Consensus       508 ---D~-~t~~~i~~~l~~~~~--~~tvIivtHr~~-------------------~l~~~D~ii~l~~  549 (592)
T PRK10790        508 ---DS-GTEQAIQQALAAVRE--HTTLVVIAHRLS-------------------TIVEADTILVLHR  549 (592)
T ss_pred             ---CH-HHHHHHHHHHHHHhC--CCEEEEEecchH-------------------HHHhCCEEEEEEC
Confidence               22 223456677776643  689999999321                   1235788888864

>PLN03140 ABC transporter G family member; Provisional

Probab=96.84  E-value=0.009  Score=71.45  Aligned_cols=38  Identities=26%  Similarity=0.457  Sum_probs=32.6

Q ss_pred             Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          284 GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       284 g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +..-|+++.+ +.+|++++|.|+||+|||||+.-++-..
T Consensus       177 ~~~IL~~vs~~i~~Ge~~~llGpnGSGKSTLLk~LaG~l  215 (1470)
T PLN03140        177 KLTILKDASGIIKPSRMTLLLGPPSSGKTTLLLALAGKL  215 (1470)
T ss_pred             cceeccCCeEEEeCCeEEEEEcCCCCCHHHHHHHHhCCC
Confidence            4566788878 9999999999999999999988877543

>PRK10789 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=96.84  E-value=0.0059  Score=66.50  Aligned_cols=28  Identities=25%  Similarity=0.440  Sum_probs=24.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +++|+.+.|.|++|+|||||+.-++-..
T Consensus       338 i~~G~~~~ivG~sGsGKSTLl~ll~g~~  365 (569)
T PRK10789        338 LKPGQMLGICGPTGSGKSTLLSLIQRHF  365 (569)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            8999999999999999999987766443

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=96.84  E-value=0.0043  Score=58.41  Aligned_cols=25  Identities=20%  Similarity=0.343  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      ++++|.|++|+|||||+..++....
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~~~~   55 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVALIAL   55 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHHHHH
Confidence            7999999999999999999976443

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam

>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=96.83  E-value=0.011  Score=64.52  Aligned_cols=174  Identities=17%  Similarity=0.103  Sum_probs=86.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHhhCCC---ccccccC
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---ENKVREHARKLLEKHIKKP---FFEANYG  360 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---E~~~~~~~~r~~~~~~~~~---~~~i~~~  360 (539)
                      |+.+.- +++|+.+.|.|++|+|||||+.-++...--. ...+.+-..   +.+...+.+. ++....-+   ...++++
T Consensus       356 l~~i~~~i~~G~~~aivG~sGsGKSTL~~ll~g~~~p~-~G~I~i~g~~i~~~~~~~~r~~-i~~v~Q~~~lf~~ti~~N  433 (574)
T PRK11160        356 LKGLSLQIKAGEKVALLGRTGCGKSTLLQLLTRAWDPQ-QGEILLNGQPIADYSEAALRQA-ISVVSQRVHLFSATLRDN  433 (574)
T ss_pred             eecceEEECCCCEEEEECCCCCCHHHHHHHHhcCCCCC-CceEEECCEEhhhCCHHHHHhh-eeEEcccchhhcccHHHH
Confidence            444433 8999999999999999999987776544322 334443222   2233333222 11111111   0111111


Q ss_pred             CC--CCCCCHHHHHHHHHH------hhccceeEe---ecCCCCCCHHH--HHHHHHHHHHHcCCcEEEEccccccccCCC
Q 009230          361 GS--AERMTVEEFEQGKAW------LSNTFSLIR---CENDSLPSIKW--VLDLAKAAVLRHGVRGLVIDPYNELDHQRP  427 (539)
Q Consensus       361 ~~--~~~l~~~~~~~~~~~------l~~~~~~i~---~~~~~~~~~~~--i~~~i~~~~~~~~~~~vvID~~~~l~~~~~  427 (539)
                      -.  .+..+++++.++.+.      +.. +.=+.   -+.....+-.+  -+..++.+.  .+++++++|.-+.-+    
T Consensus       434 i~~~~~~~~~~~i~~al~~~~l~~~i~~-p~GldT~vge~g~~LSgGqrqRialARall--~~~~ililDE~ts~l----  506 (574)
T PRK11160        434 LLLAAPNASDEALIEVLQQVGLEKLLED-DKGLNAWLGEGGRQLSGGEQRRLGIARALL--HDAPLLLLDEPTEGL----  506 (574)
T ss_pred             hhcCCCccCHHHHHHHHHHcCCHHHHcC-ccccCchhcCCCCCCCHHHHHHHHHHHHHh--cCCCEEEEeCCcccC----
Confidence            00  123466666555332      222 11000   00011122222  233333333  478999999444322    


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          428 VSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       428 ~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                         +. +.-..+.+.|+.+.  .+.++|+++|.-..                  + ..||.++.|+..
T Consensus       507 ---D~-~t~~~i~~~l~~~~--~~~tviiitHr~~~------------------~-~~~d~i~~l~~G  549 (574)
T PRK11160        507 ---DA-ETERQILELLAEHA--QNKTVLMITHRLTG------------------L-EQFDRICVMDNG  549 (574)
T ss_pred             ---CH-HHHHHHHHHHHHHc--CCCEEEEEecChhH------------------H-HhCCEEEEEeCC
Confidence               21 22345666676664  37899999993211                  2 358999998753

>cd03245 ABCC_bacteriocin_exporters ABC-type bacteriocin exporters

Probab=96.82  E-value=0.0077  Score=56.89  Aligned_cols=33  Identities=27%  Similarity=0.324  Sum_probs=26.9

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus        20 l~~i~~~i~~G~~~~i~G~nGsGKSTLl~~i~G~   53 (220)
T cd03245          20 LDNVSLTIRAGEKVAIIGRVGSGKSTLLKLLAGL   53 (220)
T ss_pred             ccceEEEEcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            444433 899999999999999999998877643

Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=96.82  E-value=0.018  Score=61.39  Aligned_cols=139  Identities=19%  Similarity=0.145  Sum_probs=71.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc-------CCeEEEEeCC--CCHHHHHHHHHHHhhCCCccccccCCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHA-------GWKFVLCSME--NKVREHARKLLEKHIKKPFFEANYGGSAE  364 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~-------g~~vl~~s~E--~~~~~~~~r~~~~~~~~~~~~i~~~~~~~  364 (539)
                      +++|+-.+|.|++|+|||+|...++-=.--..       +..++|++=+  ++...+ +..++           +.....
T Consensus       416 v~~G~~llI~G~SG~GKTsLlRaiaGLWP~g~G~I~~P~~~~~lflpQ~PY~p~GtL-re~l~-----------YP~~~~  483 (604)
T COG4178         416 VRPGERLLITGESGAGKTSLLRALAGLWPWGSGRISMPADSALLFLPQRPYLPQGTL-REALC-----------YPNAAP  483 (604)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhccCccCCCceecCCCCceEEecCCCCCCCccH-HHHHh-----------CCCCCC
Confidence            89999999999999999999887763221111       2234555433  333322 22221           222222


Q ss_pred             CCCHHHHHHHHHH-----hhccceeEeecCCCCCCHHH--HHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHH
Q 009230          365 RMTVEEFEQGKAW-----LSNTFSLIRCENDSLPSIKW--VLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVS  437 (539)
Q Consensus       365 ~l~~~~~~~~~~~-----l~~~~~~i~~~~~~~~~~~~--i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~  437 (539)
                      .++++++.++..+     +.++.--.. .=+.-.+.++  -++.++-  .-++|++||+|.-+.-+.       +     
T Consensus       484 ~~~d~~l~~vL~~vgL~~L~~rl~~~~-~W~~vLS~GEqQRlafARi--lL~kP~~v~LDEATsALD-------e-----  548 (604)
T COG4178         484 DFSDAELVAVLHKVGLGDLAERLDEED-RWDRVLSGGEQQRLAFARL--LLHKPKWVFLDEATSALD-------E-----  548 (604)
T ss_pred             CCChHHHHHHHHHcCcHHHHHHHhccC-cHhhhcChhHHHHHHHHHH--HHcCCCEEEEecchhccC-------h-----
Confidence            4777776665322     222110000 0001111221  1222222  236899999995554332       2     


Q ss_pred             HHHHHHHHHHHH--hCcEEEEEec
Q 009230          438 QMLTMVKRFAQH--HACHVWFVAH  459 (539)
Q Consensus       438 ~~~~~Lk~lA~~--~~i~vi~~~q  459 (539)
                      +.-..|.++.++  .+++||-|+|
T Consensus       549 ~~e~~l~q~l~~~lp~~tvISV~H  572 (604)
T COG4178         549 ETEDRLYQLLKEELPDATVISVGH  572 (604)
T ss_pred             HHHHHHHHHHHhhCCCCEEEEecc
Confidence            112334444556  7999999999

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=96.82  E-value=0.013  Score=64.01  Aligned_cols=167  Identities=19%  Similarity=0.180  Sum_probs=84.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHHHHhhCCC---ccccccCC---CCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLLEKHIKKP---FFEANYGG---SAE  364 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~---~~~i~~~~---~~~  364 (539)
                      +++|+.+.|.|++|+|||||+.-++-..-- ....+.+-.-+   .+...+... ++....-+   ...++.+-   ...
T Consensus       355 i~~G~~v~IvG~sGsGKSTLl~lL~gl~~~-~~G~I~i~g~~i~~~~~~~~~~~-i~~v~Q~~~lf~~Ti~~Ni~~~~~~  432 (571)
T TIGR02203       355 IEPGETVALVGRSGSGKSTLVNLIPRFYEP-DSGQILLDGHDLADYTLASLRRQ-VALVSQDVVLFNDTIANNIAYGRTE  432 (571)
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHHhccCC-CCCeEEECCEeHHhcCHHHHHhh-ceEEccCcccccccHHHHHhcCCCC
Confidence            899999999999999999998876644322 23444443322   233333222 12111111   11111110   011


Q ss_pred             CCCHHHHHHHHH------Hhhccc----eeEeecCCCCCCHHH--HHHHHHHHHHHcCCcEEEEccccccccCCCCCCCH
Q 009230          365 RMTVEEFEQGKA------WLSNTF----SLIRCENDSLPSIKW--VLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTE  432 (539)
Q Consensus       365 ~l~~~~~~~~~~------~l~~~~----~~i~~~~~~~~~~~~--i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~  432 (539)
                      ..+++++.++.+      ++.+.+    ..+. +.....+-.+  -+..+|.+.  .+++++++|.-+.-+       + 
T Consensus       433 ~~~~~~i~~~l~~~~l~~~i~~lp~gldt~i~-~~g~~LSgGqrQRiaLARall--~~~~illLDEpts~L-------D-  501 (571)
T TIGR02203       433 QADRAEIERALAAAYAQDFVDKLPLGLDTPIG-ENGVLLSGGQRQRLAIARALL--KDAPILILDEATSAL-------D-  501 (571)
T ss_pred             CCCHHHHHHHHHHcChHHHHHhCcCcccceec-CCCCcCCHHHHHHHHHHHHHh--cCCCEEEEeCccccC-------C-
Confidence            456666655432      222211    1120 1111223333  333344333  478999999433222       2 


Q ss_pred             HHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          433 TEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       433 ~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      ...-..+++.|++++  -+.++|+++|...                   +...||.|+.+..
T Consensus       502 ~~~~~~i~~~L~~~~--~~~tiIiitH~~~-------------------~~~~~D~ii~l~~  542 (571)
T TIGR02203       502 NESERLVQAALERLM--QGRTTLVIAHRLS-------------------TIEKADRIVVMDD  542 (571)
T ss_pred             HHHHHHHHHHHHHHh--CCCEEEEEehhhH-------------------HHHhCCEEEEEeC
Confidence            222345677777664  3689999999422                   2346888888853

This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.

>TIGR01526 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase, NadR type

Probab=96.82  E-value=0.015  Score=58.42  Aligned_cols=48  Identities=10%  Similarity=0.126  Sum_probs=31.2

Q ss_pred             cEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          412 RGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       412 ~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                      -++++++...-........+..+....+.+.|+++.+++|+++++|+|
T Consensus       271 l~~l~~p~~~~~~D~~R~~~~~~~R~~~~~ll~~~l~~~G~~~v~Vtg  318 (325)
T TIGR01526       271 LTLLLKPNTEWVDDGLRSLGSQKQRQEFQQLLKKLLDEYGVPFVVIES  318 (325)
T ss_pred             EEEECCCCCCCccCCcccCchHHHHHHHHHHHHHHHHHcCCcEEEEeC
Confidence            456677665533221122222234456777999999999999999999

E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this model share that activity.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.82  E-value=0.0098  Score=61.87  Aligned_cols=38  Identities=26%  Similarity=0.236  Sum_probs=31.5

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhc-CCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHA-GWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~-g~~vl~~s~E  335 (539)
                      ...+|.|++|+|||.|+..++..+..+. +..|+|++.+
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~  175 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSE  175 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHH
Confidence            4578999999999999999988877642 6889999754

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).

>PRK13409 putative ATPase RIL; Provisional

Probab=96.82  E-value=0.0083  Score=65.26  Aligned_cols=26  Identities=23%  Similarity=0.234  Sum_probs=23.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +.+|+++.|.|++|+||||++.-++-
T Consensus        96 i~~Gev~gLvG~NGaGKSTLlkiL~G  121 (590)
T PRK13409         96 PKEGKVTGILGPNGIGKTTAVKILSG  121 (590)
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHhC
Confidence            89999999999999999999876654

>TIGR00957 MRP_assoc_pro multi drug resistance-associated protein (MRP)

Probab=96.81  E-value=0.0097  Score=71.97  Aligned_cols=168  Identities=18%  Similarity=0.161  Sum_probs=89.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHHHHhhCCCc---cccccCCC-CCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLLEKHIKKPF---FEANYGGS-AERM  366 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~~---~~i~~~~~-~~~l  366 (539)
                      +.+|+.+.|.|++|+||||++.-+..-.-- ....+.+-..+   .+...+..++ +....-+.   ..++.+-. .+..
T Consensus      1309 I~~GekiaIVGrTGsGKSTL~~lL~rl~~~-~~G~I~IdG~dI~~i~~~~LR~~i-~iVpQdp~LF~gTIr~NLdp~~~~ 1386 (1522)
T TIGR00957      1309 IHGGEKVGIVGRTGAGKSSLTLGLFRINES-AEGEIIIDGLNIAKIGLHDLRFKI-TIIPQDPVLFSGSLRMNLDPFSQY 1386 (1522)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCccC-CCCeEEECCEEccccCHHHHHhcC-eEECCCCcccCccHHHHcCcccCC
Confidence            899999999999999999998877654322 23344443322   3445444443 22111111   12222211 2356


Q ss_pred             CHHHHHHHHH------Hhhccc---e-eEeecCCCCCCH--HHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHH
Q 009230          367 TVEEFEQGKA------WLSNTF---S-LIRCENDSLPSI--KWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETE  434 (539)
Q Consensus       367 ~~~~~~~~~~------~l~~~~---~-~i~~~~~~~~~~--~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~  434 (539)
                      +++++.++.+      .+...+   . .+ -+.....+-  .+.+..+|.+.  .+++++++|.-+.-++      .+++
T Consensus      1387 sdeei~~al~~a~l~~~I~~lp~GLdt~v-~e~G~~LSgGQrQrl~LARALL--r~~~ILiLDEaTSalD------~~Te 1457 (1522)
T TIGR00957      1387 SDEEVWWALELAHLKTFVSALPDKLDHEC-AEGGENLSVGQRQLVCLARALL--RKTKILVLDEATAAVD------LETD 1457 (1522)
T ss_pred             CHHHHHHHHHHcCcHHHHhhCccCCCcee-cCCCCcCCHHHHHHHHHHHHHH--cCCCEEEEECCcccCC------HHHH
Confidence            7777665532      222211   1 11 011122332  34555555554  4689999995443321      1221


Q ss_pred             HHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          435 YVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       435 ~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                        ..+.+.|++..  -+++||+++|.-..                   -..+|.|+.|...
T Consensus      1458 --~~Iq~~l~~~~--~~~TvI~IAHRl~t-------------------i~~~DrIlVld~G 1495 (1522)
T TIGR00957      1458 --NLIQSTIRTQF--EDCTVLTIAHRLNT-------------------IMDYTRVIVLDKG 1495 (1522)
T ss_pred             --HHHHHHHHHHc--CCCEEEEEecCHHH-------------------HHhCCEEEEEECC
Confidence              23445555432  47999999992111                   2368999999753

This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved.

>TIGR01194 cyc_pep_trnsptr cyclic peptide transporter

Probab=96.81  E-value=0.02  Score=62.13  Aligned_cols=27  Identities=19%  Similarity=0.345  Sum_probs=24.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+.+.|.|++|+||||++.-++..
T Consensus       365 i~~G~~~aivG~sGsGKSTl~~ll~g~  391 (555)
T TIGR01194       365 IAQGDIVFIVGENGCGKSTLAKLFCGL  391 (555)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999999998776643

This model describes cyclic peptide transporter in bacteria. Bacteria have elaborate pathways for the production of toxins and secondary metabolites. Many such compounds, including syringomycin and pyoverdine are synthesized on non-ribosomal templates consisting of a multienzyme complex. On several occasions the proteins of the complex and transporter protein are present on the same operon. Often times these compounds cross the biological membrane by specific transporters. Syringomycin is an amphipathic, cylclic lipodepsipeptide when inserted into host causes formation of channels, permeable to variety of cations. On the other hand, pyoverdine is a cyclic octa-peptidyl dihydroxyquinoline, which is efficient in sequestering iron for uptake.

>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit

Probab=96.80  E-value=0.0084  Score=64.75  Aligned_cols=158  Identities=17%  Similarity=0.147  Sum_probs=76.6

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHHHHhhCCC---ccccccC
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLLEKHIKKP---FFEANYG  360 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~---~~~i~~~  360 (539)
                      |+.+.- +++|+.+.|.|++|+|||||+.-++...-- ....+.+-.-+   .+...+.+++ +....-+   ...++++
T Consensus       338 l~~i~l~i~~G~~~~ivG~sGsGKSTL~~ll~g~~~~-~~G~I~~~g~~i~~~~~~~lr~~i-~~v~Q~~~lf~~ti~~N  415 (529)
T TIGR02857       338 LRPVSFTVPPGERVALVGPSGAGKSTLLNLLLGFVDP-TEGSIAVNGVPLADADADSWRDQI-AWVPQHPFLFAGTIAEN  415 (529)
T ss_pred             ccceeEEECCCCEEEEECCCCCCHHHHHHHHhcCCCC-CCcEEEECCEehhhCCHHHHHhhe-EEEcCCCcccCcCHHHH
Confidence            444333 999999999999999999998776543322 23344433222   3344433332 2111111   0111111


Q ss_pred             CC--CCCCCHHHHHHHHH------Hhhccc---e-eEeecCCCCCCHH--HHHHHHHHHHHHcCCcEEEEccccccccCC
Q 009230          361 GS--AERMTVEEFEQGKA------WLSNTF---S-LIRCENDSLPSIK--WVLDLAKAAVLRHGVRGLVIDPYNELDHQR  426 (539)
Q Consensus       361 ~~--~~~l~~~~~~~~~~------~l~~~~---~-~i~~~~~~~~~~~--~i~~~i~~~~~~~~~~~vvID~~~~l~~~~  426 (539)
                      -.  .+..+++++.++.+      ++...+   . .+. +.....+-.  +-+..+|.+.  .+++++++|.-+.-+   
T Consensus       416 i~~~~~~~~~~~i~~a~~~~~l~~~i~~lp~Gldt~v~-e~g~~LSgGq~qri~laRal~--~~~~ililDE~ts~l---  489 (529)
T TIGR02857       416 IRLARPDASDAEIRRALERAGLDEFVAALPQGLDTLIG-EGGAGLSGGQAQRLALARAFL--RDAPLLLLDEPTAHL---  489 (529)
T ss_pred             HhccCCCCCHHHHHHHHHHcCcHHHHHhCcccccchhc-cccccCCHHHHHHHHHHHHHh--cCCCEEEEeCccccc---
Confidence            00  12345666555432      222211   1 110 001111212  2233333332  478999999444322   


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          427 PVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       427 ~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                          +. +.-..+.+.|+.+.  .+.++|+++|.
T Consensus       490 ----D~-~~~~~i~~~l~~~~--~~~t~i~itH~  516 (529)
T TIGR02857       490 ----DA-ETEALVTEALRALA--QGRTVLLVTHR  516 (529)
T ss_pred             ----CH-HHHHHHHHHHHHhc--CCCEEEEEecC
Confidence                11 22234666666554  57999999993

Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD

>cd03290 ABCC_SUR1_N The SUR domain 1

Probab=96.80  E-value=0.027  Score=53.07  Aligned_cols=34  Identities=26%  Similarity=0.483  Sum_probs=27.5

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        17 l~~vs~~i~~Ge~~~i~G~nGsGKSTLl~~i~G~~   51 (218)
T cd03290          17 LSNINIRIPTGQLTMIVGQVGCGKSSLLLAILGEM   51 (218)
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            444433 9999999999999999999988776443

The sulfonylurea receptor SUR is an ATP transporter of the ABCC/MRP family with tandem ATPase binding domains. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.

>PRK04017 hypothetical protein; Provisional

Probab=96.80  E-value=0.0034  Score=53.08  Aligned_cols=71  Identities=24%  Similarity=0.301  Sum_probs=50.9

Q ss_pred             CCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCccchHHHH
Q 009230          123 ESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAE  202 (539)
Q Consensus       123 ~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~~G~~~~~  202 (539)
                      ...++||||--|.-++.++|+...+-+.+|.+-       ....     +      ......+.|+|..|.|.+|.+-++
T Consensus        22 ~g~vIVVEGk~D~~~L~~lGv~~~iI~t~g~~~-------~~~~-----e------~ia~~~r~VIILTD~D~~GekIr~   83 (132)
T PRK04017         22 AGAPIIVEGKRDVESLRKLGVEGEIIKVSRTPL-------AEIA-----E------LIASRGKEVIILTDFDRKGEELAK   83 (132)
T ss_pred             CCCEEEEeCccHHHHHHHcCCCccEEEECCeec-------chHH-----H------HHHhcCCeEEEEECCCcchHHHHH
Confidence            457899999999999999998533333333321       1000     0      123467899999999999999999


Q ss_pred             HHHHHhcCC
Q 009230          203 ELARRVGRE  211 (539)
Q Consensus       203 ~~~~~l~~~  211 (539)
                      ++.+.|...
T Consensus        84 ~l~~~l~~~   92 (132)
T PRK04017         84 KLSEYLQGY   92 (132)
T ss_pred             HHHHHHHhC
Confidence            999988553

>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein

Probab=96.79  E-value=0.0064  Score=68.16  Aligned_cols=165  Identities=17%  Similarity=0.134  Sum_probs=82.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHHHHhhCCC---ccccccCC--CCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLLEKHIKKP---FFEANYGG--SAER  365 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~---~~~i~~~~--~~~~  365 (539)
                      +++|+.+.|.|++|+|||||+.-++-...-. ...+.+-..+   .+...+.+++ +....-+   ...++.+-  ..+.
T Consensus       502 i~~Ge~vaIvG~sGsGKSTLlklL~gl~~p~-~G~I~idg~~i~~~~~~~lr~~i-~~v~Q~~~lf~gTi~eNi~l~~~~  579 (710)
T TIGR03796       502 LQPGQRVALVGGSGSGKSTIAKLVAGLYQPW-SGEILFDGIPREEIPREVLANSV-AMVDQDIFLFEGTVRDNLTLWDPT  579 (710)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCCCCC-CcEEEECCEeHHHCCHHHHHhhe-eEEecCChhhhccHHHHhhCCCCC
Confidence            8999999999999999999987665443322 3344432211   2333333222 2111111   01111110  0123


Q ss_pred             CCHHHHHHHHH------Hhhccc----eeEeecCCCCCCH--HHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHH
Q 009230          366 MTVEEFEQGKA------WLSNTF----SLIRCENDSLPSI--KWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTET  433 (539)
Q Consensus       366 l~~~~~~~~~~------~l~~~~----~~i~~~~~~~~~~--~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~  433 (539)
                      .+++++.++.+      .+...+    ..+. +.....+-  .+-+..+|.+.  .+++++++|.-+.-+       +. 
T Consensus       580 ~~~~~i~~al~~~~l~~~i~~lp~gl~t~i~-e~G~~LSGGQrQRiaLARall--~~p~iliLDEptS~L-------D~-  648 (710)
T TIGR03796       580 IPDADLVRACKDAAIHDVITSRPGGYDAELA-EGGANLSGGQRQRLEIARALV--RNPSILILDEATSAL-------DP-  648 (710)
T ss_pred             CCHHHHHHHHHHhCCHHHHHhCcCcccceec-cCCCCCCHHHHHHHHHHHHHh--hCCCEEEEECccccC-------CH-
Confidence            56666655432      222221    1111 11111221  23334444443  478999999444322       21 


Q ss_pred             HHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          434 EYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       434 ~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      ..-..+++.|++    .+.++|+++|.-.                   .-..||.++.|..
T Consensus       649 ~te~~i~~~l~~----~~~T~IiitHrl~-------------------~i~~~D~Iivl~~  686 (710)
T TIGR03796       649 ETEKIIDDNLRR----RGCTCIIVAHRLS-------------------TIRDCDEIIVLER  686 (710)
T ss_pred             HHHHHHHHHHHh----cCCEEEEEecCHH-------------------HHHhCCEEEEEeC
Confidence            222356666653    5899999999321                   1245899999964

This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.

>TIGR01192 chvA glucan exporter ATP-binding protein

Probab=96.78  E-value=0.0084  Score=65.50  Aligned_cols=27  Identities=22%  Similarity=0.337  Sum_probs=24.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+.+.|.|++|+|||||+.-++..
T Consensus       358 i~~G~~~~ivG~sGsGKSTL~~ll~g~  384 (585)
T TIGR01192       358 AKAGQTVAIVGPTGAGKTTLINLLQRV  384 (585)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHccC
Confidence            899999999999999999998766643

This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related.

>PRK10938 putative molybdenum transport ATP-binding protein ModF; Provisional

Probab=96.77  E-value=0.016  Score=61.86  Aligned_cols=32  Identities=31%  Similarity=0.392  Sum_probs=26.9

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus       276 l~~vsl~i~~Ge~~~i~G~NGsGKSTLl~~l~G  308 (490)
T PRK10938        276 LHNLSWQVNPGEHWQIVGPNGAGKSTLLSLITG  308 (490)
T ss_pred             EeeceEEEcCCCEEEEECCCCCCHHHHHHHHcC
Confidence            444433 99999999999999999999888775

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=96.77  E-value=0.0019  Score=54.58  Aligned_cols=28  Identities=32%  Similarity=0.617  Sum_probs=23.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      .++|+|+||+||||++.+++...    |.+++
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~----~~~~i   28 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERL----GFPVI   28 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH----TCEEE
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH----CCeEE
Confidence            47899999999999998887654    66665

...

>cd03288 ABCC_SUR2 The SUR domain 2

Probab=96.77  E-value=0.012  Score=57.02  Aligned_cols=34  Identities=26%  Similarity=0.341  Sum_probs=27.4

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-..
T Consensus        37 l~~isl~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   71 (257)
T cd03288          37 LKHVKAYIKPGQKVGICGRTGSGKSSLSLAFFRMV   71 (257)
T ss_pred             eeEEEEEEcCCCEEEEECCCCCCHHHHHHHHHccc
Confidence            444433 9999999999999999999988776543

The sulfonylurea receptor SUR is an ATP binding cassette (ABC) protein of the ABCC/MRP family. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.

>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=96.76  E-value=0.0061  Score=57.89  Aligned_cols=44  Identities=14%  Similarity=0.167  Sum_probs=32.1

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      ..|+++..|.=+.-+.        ...-.+++..|.+|.++.++||+-|+|+
T Consensus       145 t~P~LLLmDEPLaSLD--------~~RK~EilpylERL~~e~~IPIlYVSHS  188 (352)
T COG4148         145 TAPELLLMDEPLASLD--------LPRKREILPYLERLRDEINIPILYVSHS  188 (352)
T ss_pred             cCCCeeeecCchhhcc--------cchhhHHHHHHHHHHHhcCCCEEEEecC
Confidence            4689999993322111        1123578899999999999999999993

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=96.76  E-value=0.0037  Score=60.35  Aligned_cols=66  Identities=24%  Similarity=0.223  Sum_probs=54.2

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREH  341 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~  341 (539)
                      .....+.||+..+|-++-+.+|+=..|.|++|+|||+++.+++.++..++...++|....+..+++
T Consensus        48 ~~~e~L~TGIr~ID~l~pig~GQr~~If~~~G~GKTtLa~~i~~~i~~~~~~~~V~~~iGer~~Ev  113 (274)
T cd01133          48 TKTEILETGIKVIDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNIAKAHGGYSVFAGVGERTREG  113 (274)
T ss_pred             CcCcccccCceeeeccCCcccCCEEEEecCCCCChhHHHHHHHHHHHhcCCCEEEEEEeccCcHHH
Confidence            344578999999999888999999999999999999999999999887544456666666666554

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.76  E-value=0.0071  Score=58.52  Aligned_cols=124  Identities=15%  Similarity=0.179  Sum_probs=70.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-CeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAG-WKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFE  372 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~  372 (539)
                      +.-..|+++.||||+|||+++-.+|.++..+.. .----.-.|.....++.++.+- +|             +       
T Consensus       174 It~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsE-Sg-------------K-------  232 (423)
T KOG0744|consen  174 ITWNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSE-SG-------------K-------  232 (423)
T ss_pred             eeeeeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehhHHHHHHHhh-hh-------------h-------
Confidence            555679999999999999999998888765411 0000112366666666665431 11             1       


Q ss_pred             HHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCC-cEEEEccccccccCCC---CC---CCHHHHHHHHHHHHHH
Q 009230          373 QGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGV-RGLVIDPYNELDHQRP---VS---QTETEYVSQMLTMVKR  445 (539)
Q Consensus       373 ~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~-~~vvID~~~~l~~~~~---~~---~~~~~~~~~~~~~Lk~  445 (539)
                                           .+..+...|..++...|+ =+|.||-.-.|...+.   ++   .+.-..+..++.+|-+
T Consensus       233 ---------------------lV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDr  291 (423)
T KOG0744|consen  233 ---------------------LVAKMFQKIQELVEDRGNLVFVLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDR  291 (423)
T ss_pred             ---------------------HHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHH
Confidence                                 122233333334333332 2344554433322110   11   1223456778888888


Q ss_pred             HHHHhCcEEEEEec
Q 009230          446 FAQHHACHVWFVAH  459 (539)
Q Consensus       446 lA~~~~i~vi~~~q  459 (539)
                      +-+.-|+-++.++.
T Consensus       292 lK~~~NvliL~TSN  305 (423)
T KOG0744|consen  292 LKRYPNVLILATSN  305 (423)
T ss_pred             hccCCCEEEEeccc
Confidence            88888988888776

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=96.75  E-value=0.0058  Score=58.64  Aligned_cols=59  Identities=17%  Similarity=0.291  Sum_probs=41.4

Q ss_pred             hhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-Ce-EEEEeCC--CCHHHHHHHH
Q 009230          287 ALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAG-WK-FVLCSME--NKVREHARKL  345 (539)
Q Consensus       287 ~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-~~-vl~~s~E--~~~~~~~~r~  345 (539)
                      .+|-++.+.+|+-++|.|++|+||||++..++.+....+. .. +++.+.|  ....++...+
T Consensus         6 ~id~~~~i~~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~~fdv~~~v~vI~er~~ev~el~~~I   68 (249)
T cd01128           6 VVDLFAPIGKGQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEEVTDMQRSV   68 (249)
T ss_pred             heeeecccCCCCEEEEECCCCCCHHHHHHHHHhccccccCCeEEEEEEccCCCccHHHHHHHh
Confidence            4565666899999999999999999999888877655322 22 3344555  4555565554

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.

>TIGR02633 xylG D-xylose ABC transporter, ATP-binding protein

Probab=96.74  E-value=0.011  Score=63.48  Aligned_cols=34  Identities=24%  Similarity=0.430  Sum_probs=27.6

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-.
T Consensus       275 ~l~~is~~i~~Ge~~~l~G~NGsGKSTLl~~l~G~  309 (500)
T TIGR02633       275 RVDDVSFSLRRGEILGVAGLVGAGRTELVQALFGA  309 (500)
T ss_pred             ccccceeEEeCCcEEEEeCCCCCCHHHHHHHHhCC
Confidence            3454433 999999999999999999998877643

Several bacterial species have enzymes xylose isomerase and xylulokinase enzymes for xylose utilization. Members of this protein family are the ATP-binding cassette (ABC) subunit of the known or predicted high-affinity xylose ABC transporter for xylose import. These genes, which closely resemble other sugar transport ABC transporter genes, typically are encoded near xylose utilization enzymes and regulatory proteins. Note that this form of the transporter contains two copies of the ABC transporter domain (pfam00005).

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=96.74  E-value=0.0047  Score=60.32  Aligned_cols=58  Identities=12%  Similarity=0.162  Sum_probs=36.3

Q ss_pred             cCCC-cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEE-EeCCCCHHHHHHHHHHHhhCCC
Q 009230          294 VLPG-ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVL-CSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       294 l~~G-~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~-~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      ++++ .+++|.|++|+||||++..++...... +..+.+ +....++.++...+. ...|.+
T Consensus        39 ~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~~~-~~~~~~~~~~~~~~~~~l~~i~-~~lG~~   98 (269)
T TIGR03015        39 LSQREGFILITGEVGAGKTTLIRNLLKRLDQE-RVVAAKLVNTRVDAEDLLRMVA-ADFGLE   98 (269)
T ss_pred             HhcCCCEEEEEcCCCCCHHHHHHHHHHhcCCC-CeEEeeeeCCCCCHHHHHHHHH-HHcCCC
Confidence            4444 489999999999999999987665422 333322 345566666654443 333443

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.

>PF02492 cobW: CobW/HypB/UreG, nucleotide-binding domain; InterPro: IPR003495 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt

Probab=96.73  E-value=0.0066  Score=55.29  Aligned_cols=58  Identities=26%  Similarity=0.309  Sum_probs=41.9

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCcccccc
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANY  359 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~  359 (539)
                      +++|+|..|+|||||+.+++.  ....|.++.++-.|+....+=.+++.. .+++...+..
T Consensus         2 v~ii~GfLGsGKTTli~~ll~--~~~~~~~~~vI~ne~g~~~iD~~~l~~-~~~~v~~l~~   59 (178)
T PF02492_consen    2 VIIITGFLGSGKTTLINHLLK--RNRQGERVAVIVNEFGEVNIDAELLQE-DGVPVVELNN   59 (178)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH--HHTTTS-EEEEECSTTSTHHHHHHHHT-TT-EEEEECT
T ss_pred             EEEEEcCCCCCHHHHHHHHHH--HhcCCceeEEEEccccccccchhhhcc-cceEEEEecC
Confidence            689999999999999999997  333599999999999866555555543 2555555543

Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [].; PDB: 2WSM_B 1NIJ_A 2HF9_A 2HF8_B.

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=96.73  E-value=0.0026  Score=57.88  Aligned_cols=47  Identities=21%  Similarity=0.359  Sum_probs=35.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKL  345 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~  345 (539)
                      +..+.-.+|.|+||+|||.++..++.+++.. |.+|+|++.    .+++.++
T Consensus        44 ~~~~~~l~l~G~~G~GKThLa~ai~~~~~~~-g~~v~f~~~----~~L~~~l   90 (178)
T PF01695_consen   44 IENGENLILYGPPGTGKTHLAVAIANEAIRK-GYSVLFITA----SDLLDEL   90 (178)
T ss_dssp             -SC--EEEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEH----HHHHHHH
T ss_pred             cccCeEEEEEhhHhHHHHHHHHHHHHHhccC-CcceeEeec----Cceeccc
Confidence            6667788999999999999999999998884 999999974    3455554

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.

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=96.73  E-value=0.12  Score=48.08  Aligned_cols=38  Identities=16%  Similarity=0.323  Sum_probs=33.6

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.|+|.-|+||||++.-++..++.++|+.|+.+..+.+
T Consensus         3 IaI~GKGG~GKTtiaalll~~l~~~~~~~VLvVDaDpd   40 (255)
T COG3640           3 IAITGKGGVGKTTIAALLLKRLLSKGGYNVLVVDADPD   40 (255)
T ss_pred             EEEecCCCccHHHHHHHHHHHHHhcCCceEEEEeCCCC
Confidence            67999999999999999899998876799999987753

>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter

Probab=96.73  E-value=0.011  Score=66.40  Aligned_cols=165  Identities=18%  Similarity=0.155  Sum_probs=82.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHhhCCC---ccc----cccCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---ENKVREHARKLLEKHIKKP---FFE----ANYGGSA  363 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---E~~~~~~~~r~~~~~~~~~---~~~----i~~~~~~  363 (539)
                      +++|+.+.|.|++|+|||||+.-++.-..-. ...+.+-..   +.+...+.+++ +....-+   ...    +..+ ..
T Consensus       497 i~~G~~vaIvG~SGsGKSTLlklL~gl~~p~-~G~I~idg~~i~~~~~~~lr~~i-~~v~Q~~~lf~gTI~eNi~l~-~~  573 (708)
T TIGR01193       497 IKMNSKTTIVGMSGSGKSTLAKLLVGFFQAR-SGEILLNGFSLKDIDRHTLRQFI-NYLPQEPYIFSGSILENLLLG-AK  573 (708)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhccCCCC-CcEEEECCEEHHHcCHHHHHHhe-EEEecCceehhHHHHHHHhcc-CC
Confidence            8999999999999999999987665433222 233333221   23333333322 1111100   001    1111 01


Q ss_pred             CCCCHHHHHHHHH------Hhhccce----eEeecCCCCCCH--HHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCC
Q 009230          364 ERMTVEEFEQGKA------WLSNTFS----LIRCENDSLPSI--KWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQT  431 (539)
Q Consensus       364 ~~l~~~~~~~~~~------~l~~~~~----~i~~~~~~~~~~--~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~  431 (539)
                      ...+++++.++.+      .+...+.    .+. +.....+-  .+-+..+|.+.  .+++++++|.-+.-+       +
T Consensus       574 ~~~~~~~i~~a~~~a~l~~~i~~lp~gldt~i~-e~G~~LSgGQrQRialARall--~~p~iliLDE~Ts~L-------D  643 (708)
T TIGR01193       574 ENVSQDEIWAACEIAEIKDDIENMPLGYQTELS-EEGSSISGGQKQRIALARALL--TDSKVLILDESTSNL-------D  643 (708)
T ss_pred             CCCCHHHHHHHHHHhCCHHHHHhcccccCcEec-CCCCCCCHHHHHHHHHHHHHh--hCCCEEEEeCccccC-------C
Confidence            2356666655432      2322221    110 11111222  23334444433  478999999444322       2


Q ss_pred             HHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          432 ETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       432 ~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      . +.-..+.+.|+.+   .+.++|+++|.-.                   ....||.++.|..
T Consensus       644 ~-~te~~i~~~L~~~---~~~T~IiitHr~~-------------------~~~~~D~i~~l~~  683 (708)
T TIGR01193       644 T-ITEKKIVNNLLNL---QDKTIIFVAHRLS-------------------VAKQSDKIIVLDH  683 (708)
T ss_pred             H-HHHHHHHHHHHHh---cCCEEEEEecchH-------------------HHHcCCEEEEEEC
Confidence            2 2224566667654   3789999999321                   1246899998864

This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.

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

Probab=96.72  E-value=0.017  Score=51.81  Aligned_cols=142  Identities=16%  Similarity=0.181  Sum_probs=76.0

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhc-CCeEEEEeCCCC-HHHHHHHHHHHhhC--CCccccccCCCCCCCCHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHA-GWKFVLCSMENK-VREHARKLLEKHIK--KPFFEANYGGSAERMTVEEF  371 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~-g~~vl~~s~E~~-~~~~~~r~~~~~~~--~~~~~i~~~~~~~~l~~~~~  371 (539)
                      .|.-.+|.|++|+|||+.+.-.+.+...+. ...++++..... .++...++......  +....+. +    ..+..  
T Consensus        13 ~~~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~-~----~~~~~--   85 (169)
T PF00270_consen   13 SGKNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLH-G----GQSIS--   85 (169)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEES-T----TSCHH--
T ss_pred             cCCCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeeccccccccccccccccccccccccccc-c----ccccc--
Confidence            466788999999999999888777766652 237888876644 44555555443332  1222221 1    23322  


Q ss_pred             HHHHHHhhc-cceeEeecCCCCCCHHHHHHHHHHH-HHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009230          372 EQGKAWLSN-TFSLIRCENDSLPSIKWVLDLAKAA-VLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQH  449 (539)
Q Consensus       372 ~~~~~~l~~-~~~~i~~~~~~~~~~~~i~~~i~~~-~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~  449 (539)
                      .....++.. ..+++.       +++.+...+... ..-..+++||||....+...     .....+..+++.++.   .
T Consensus        86 ~~~~~~~~~~~~ilv~-------T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~-----~~~~~~~~i~~~~~~---~  150 (169)
T PF00270_consen   86 EDQREVLSNQADILVT-------TPEQLLDLISNGKINISRLSLIVIDEAHHLSDE-----TFRAMLKSILRRLKR---F  150 (169)
T ss_dssp             HHHHHHHHTTSSEEEE-------EHHHHHHHHHTTSSTGTTESEEEEETHHHHHHT-----THHHHHHHHHHHSHT---T
T ss_pred             cccccccccccccccc-------CcchhhccccccccccccceeeccCcccccccc-----cHHHHHHHHHHHhcC---C
Confidence            111223332 233331       456555555430 01133899999966665531     222233344443332   2


Q ss_pred             hCcEEEEEec
Q 009230          450 HACHVWFVAH  459 (539)
Q Consensus       450 ~~i~vi~~~q  459 (539)
                      .++++++++-
T Consensus       151 ~~~~~i~~SA  160 (169)
T PF00270_consen  151 KNIQIILLSA  160 (169)
T ss_dssp             TTSEEEEEES
T ss_pred             CCCcEEEEee
Confidence            2788888876

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 ....

>COG4987 CydC ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]

Probab=96.71  E-value=0.034  Score=57.74  Aligned_cols=176  Identities=20%  Similarity=0.152  Sum_probs=88.6

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC---HHHHHHHH--HHHhhCCCccccccC
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK---VREHARKL--LEKHIKKPFFEANYG  360 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~---~~~~~~r~--~~~~~~~~~~~i~~~  360 (539)
                      .|+.+.- +.+||=+.|.|++||||||++.-++.+.--+ ...+.+=..|+.   +..+.+.+  +.+-...=...++++
T Consensus       353 ~L~~~~l~l~~GEkvAIlG~SGsGKSTllqLl~~~~~~~-~G~i~~~g~~~~~l~~~~~~e~i~vl~Qr~hlF~~Tlr~N  431 (573)
T COG4987         353 ALKNFNLTLAQGEKVAILGRSGSGKSTLLQLLAGAWDPQ-QGSITLNGVEIASLDEQALRETISVLTQRVHLFSGTLRDN  431 (573)
T ss_pred             hhhccceeecCCCeEEEECCCCCCHHHHHHHHHhccCCC-CCeeeECCcChhhCChhhHHHHHhhhccchHHHHHHHHHH
Confidence            3444443 9999999999999999999988777655443 234444443432   33333333  111111111111111


Q ss_pred             C--CCCCCCHHHHHHHHHH------hhccc----eeEeecCCCCCCH--HHHHHHHHHHHHHcCCcEEEEccccccccCC
Q 009230          361 G--SAERMTVEEFEQGKAW------LSNTF----SLIRCENDSLPSI--KWVLDLAKAAVLRHGVRGLVIDPYNELDHQR  426 (539)
Q Consensus       361 ~--~~~~l~~~~~~~~~~~------l~~~~----~~i~~~~~~~~~~--~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~  426 (539)
                      -  ..+.-++|++.++.+.      +.+.+    -++  + ++...+  .+.....-.-+--++..++++|-=+.=.   
T Consensus       432 L~lA~~~AsDEel~~aL~qvgL~~l~~~~p~gl~t~l--g-e~G~~LSGGE~rRLAlAR~LL~dapl~lLDEPTegL---  505 (573)
T COG4987         432 LRLANPDASDEELWAALQQVGLEKLLESAPDGLNTWL--G-EGGRRLSGGERRRLALARALLHDAPLWLLDEPTEGL---  505 (573)
T ss_pred             HhhcCCCCCHHHHHHHHHHcCHHHHHHhChhhhhchh--c-cCCCcCCchHHHHHHHHHHHHcCCCeEEecCCcccC---
Confidence            0  1234677877665332      22221    122  1 222211  2322211111123488999999222110   


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          427 PVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       427 ~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                       +..++    .++++.|..-++  +-++++++| -+..                    ..+|.|+++..-+
T Consensus       506 -D~~TE----~~vL~ll~~~~~--~kTll~vTHrL~~l--------------------e~~drIivl~~Gk  549 (573)
T COG4987         506 -DPITE----RQVLALLFEHAE--GKTLLMVTHRLRGL--------------------ERMDRIIVLDNGK  549 (573)
T ss_pred             -ChhhH----HHHHHHHHHHhc--CCeEEEEecccccH--------------------hhcCEEEEEECCe
Confidence             11223    345555544443  788999988 5443                    3678888887654

>cd03275 ABC_SMC1_euk Eukaryotic SMC1 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains

Probab=96.70  E-value=0.0048  Score=59.46  Aligned_cols=60  Identities=13%  Similarity=0.209  Sum_probs=40.9

Q ss_pred             CCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceE
Q 009230          410 GVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNG  489 (539)
Q Consensus       410 ~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~v  489 (539)
                      .++++++|.-+.-+       + ......+.+.|+.++++ +.+||+++|...                   +...||.+
T Consensus       177 ~p~~lllDEPt~~L-------D-~~~~~~l~~~i~~~~~~-g~~vi~isH~~~-------------------~~~~~d~i  228 (247)
T cd03275         177 PAPFFVLDEVDAAL-------D-NTNVGKVASYIREQAGP-NFQFIVISLKEE-------------------FFSKADAL  228 (247)
T ss_pred             CCCEEEEecccccC-------C-HHHHHHHHHHHHHhccC-CcEEEEEECCHH-------------------HHhhCCeE
Confidence            47899999333222       2 23345667777777654 899999999421                   23479999


Q ss_pred             EEEEeCCC
Q 009230          490 IVIHRNRD  497 (539)
Q Consensus       490 l~l~r~~~  497 (539)
                      +.++++.+
T Consensus       229 ~~~~~~~~  236 (247)
T cd03275         229 VGVYRDQE  236 (247)
T ss_pred             EEEEecCC
Confidence            99998875

Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (for

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=96.70  E-value=0.03  Score=57.30  Aligned_cols=53  Identities=13%  Similarity=0.119  Sum_probs=38.0

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhc-C----CeEEEEeCCC--CHHHHHHHHHHHhh
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHA-G----WKFVLCSMEN--KVREHARKLLEKHI  350 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~-g----~~vl~~s~E~--~~~~~~~r~~~~~~  350 (539)
                      ..++|.|+||+|||+++..++.++.... +    ..++|+.+..  +...++.++.....
T Consensus        41 ~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~  100 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLR  100 (365)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4689999999999999999988765421 1    5788888642  35567777665543

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.

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=96.69  E-value=0.017  Score=54.43  Aligned_cols=35  Identities=26%  Similarity=0.205  Sum_probs=28.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHH-hcCCe
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINE-HAGWK  328 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~-~~g~~  328 (539)
                      +.+|++++|.|++|+|||+|+..++..... +.|..
T Consensus        28 ~~~g~~~~itG~N~~GKStll~~i~~~~~la~~G~~   63 (222)
T cd03287          28 AEGGYCQIITGPNMGGKSSYIRQVALITIMAQIGSF   63 (222)
T ss_pred             ecCCcEEEEECCCCCCHHHHHHHHHHHHHHHhCCCE
Confidence            678999999999999999999999884433 33543

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>COG4674 Uncharacterized ABC-type transport system, ATPase component [General function prediction only]

Probab=96.68  E-value=0.0035  Score=56.33  Aligned_cols=59  Identities=27%  Similarity=0.415  Sum_probs=40.4

Q ss_pred             Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe-CC---CCHHHHHH
Q 009230          284 GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS-ME---NKVREHAR  343 (539)
Q Consensus       284 g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s-~E---~~~~~~~~  343 (539)
                      ||..|+++.- +.+|+|-+|.||.|.|||||+--|.-..-- ....|+|-. .+   ++..++++
T Consensus        17 GF~Aln~ls~~v~~Gelr~lIGpNGAGKTT~mD~ItGKtrp-~~G~v~f~g~~dl~~~~e~~IAr   80 (249)
T COG4674          17 GFKALNDLSFSVDPGELRVLIGPNGAGKTTLMDVITGKTRP-QEGEVLFDGDTDLTKLPEHRIAR   80 (249)
T ss_pred             ceeeeeeeEEEecCCeEEEEECCCCCCceeeeeeecccCCC-CcceEEEcCchhhccCCHHHHHH
Confidence            6888888876 999999999999999999996655433221 124555544 44   33444443

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.68  E-value=0.012  Score=62.19  Aligned_cols=38  Identities=24%  Similarity=0.205  Sum_probs=32.0

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhc-CCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHA-GWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~-g~~vl~~s~E  335 (539)
                      .-.+|.|+||+|||.|+..++..+..+. +..|+|++.+
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~  187 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSE  187 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHH
Confidence            3578999999999999999998877642 6789999865

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.68  E-value=0.009  Score=61.52  Aligned_cols=38  Identities=29%  Similarity=0.404  Sum_probs=27.4

Q ss_pred             hhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          291 LYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       291 ~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +=| |++|  +++.||||+|||.|+..+|-.    .|.|..|.|.
T Consensus       332 LGGKLPKG--VLLvGPPGTGKTlLARAvAGE----A~VPFF~~sG  370 (752)
T KOG0734|consen  332 LGGKLPKG--VLLVGPPGTGKTLLARAVAGE----AGVPFFYASG  370 (752)
T ss_pred             ccCcCCCc--eEEeCCCCCchhHHHHHhhcc----cCCCeEeccc
Confidence            335 9998  779999999999997665533    3666655543

>COG4988 CydD ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]

Probab=96.68  E-value=0.026  Score=59.29  Aligned_cols=169  Identities=17%  Similarity=0.151  Sum_probs=85.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEE---eCCCCHHHHHHHHHHHhhCCC---ccccccCC--CCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLC---SMENKVREHARKLLEKHIKKP---FFEANYGG--SAER  365 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~---s~E~~~~~~~~r~~~~~~~~~---~~~i~~~~--~~~~  365 (539)
                      +++|+++.|.|++|+||||++.-++--..-. .....+=   .-+.+.+...+.+ +....-+   ...++.+-  ....
T Consensus       344 ~~~g~~talvG~SGaGKSTLl~lL~G~~~~~-~G~I~vng~~l~~l~~~~~~k~i-~~v~Q~p~lf~gTireNi~l~~~~  421 (559)
T COG4988         344 IKAGQLTALVGASGAGKSTLLNLLLGFLAPT-QGEIRVNGIDLRDLSPEAWRKQI-SWVSQNPYLFAGTIRENILLARPD  421 (559)
T ss_pred             ecCCcEEEEECCCCCCHHHHHHHHhCcCCCC-CceEEECCccccccCHHHHHhHe-eeeCCCCccccccHHHHhhccCCc
Confidence            9999999999999999999987666443322 2222222   1234455444443 2222222   11222110  0123


Q ss_pred             CCHHHHHHHHH------Hhhc--cce-eEeecCCCCCCHHHHH--HHHHHHHHHcCCcEEEEccccccccCCCCCCCHHH
Q 009230          366 MTVEEFEQGKA------WLSN--TFS-LIRCENDSLPSIKWVL--DLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETE  434 (539)
Q Consensus       366 l~~~~~~~~~~------~l~~--~~~-~i~~~~~~~~~~~~i~--~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~  434 (539)
                      .+++++.++.+      ++..  ... .+ -+.....+..+.-  ..+|.+  -.+++++++|--+.=++    .+++  
T Consensus       422 ~s~e~i~~al~~a~l~~~v~~p~GLdt~i-ge~G~~LSgGQ~QRlaLARAl--l~~~~l~llDEpTA~LD----~etE--  492 (559)
T COG4988         422 ASDEEIIAALDQAGLLEFVPKPDGLDTVI-GEGGAGLSGGQAQRLALARAL--LSPASLLLLDEPTAHLD----AETE--  492 (559)
T ss_pred             CCHHHHHHHHHHhcHHHhhcCCCcccchh-ccCCCCCCHHHHHHHHHHHHh--cCCCCEEEecCCccCCC----HhHH--
Confidence            56677665532      2222  111 11 0111122333322  222222  24589999993332111    1122  


Q ss_pred             HHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC
Q 009230          435 YVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD  497 (539)
Q Consensus       435 ~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~  497 (539)
                        ..+.+.|.+++++  -+|++++| .-                    ....+|.|+.|..-+.
T Consensus       493 --~~i~~~l~~l~~~--ktvl~itHrl~--------------------~~~~~D~I~vld~G~l  532 (559)
T COG4988         493 --QIILQALQELAKQ--KTVLVITHRLE--------------------DAADADRIVVLDNGRL  532 (559)
T ss_pred             --HHHHHHHHHHHhC--CeEEEEEcChH--------------------HHhcCCEEEEecCCce
Confidence              3466777777776  67888888 21                    2347899999886553

>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.67  E-value=0.03  Score=56.39  Aligned_cols=148  Identities=16%  Similarity=0.183  Sum_probs=78.2

Q ss_pred             cccCchhhhhhhc-----cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-------cCCeEEEEe--------CCCCHHH
Q 009230          281 ISTGWRALNELYN-----VLPGELTIVTGVPNSGKSEWIDALICNINEH-------AGWKFVLCS--------MENKVRE  340 (539)
Q Consensus       281 i~tg~~~LD~~~~-----l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-------~g~~vl~~s--------~E~~~~~  340 (539)
                      +.+|+++-+-++.     +-..+-+.|.||.|+|||||+.-+.-.+--+       +..++.||.        .|.++.+
T Consensus       592 VtFgy~gqkpLFkkldFGiDmdSRiaIVGPNGVGKSTlLkLL~Gkl~P~~GE~RKnhrL~iG~FdQh~~E~L~~Eetp~E  671 (807)
T KOG0066|consen  592 VTFGYPGQKPLFKKLDFGIDMDSRIAIVGPNGVGKSTLLKLLIGKLDPNDGELRKNHRLRIGWFDQHANEALNGEETPVE  671 (807)
T ss_pred             ccccCCCCCchhhcccccccccceeEEECCCCccHHHHHHHHhcCCCCCcchhhccceeeeechhhhhHHhhccccCHHH
Confidence            3466766665553     3444678999999999999987766543322       335677763        5666666


Q ss_pred             HHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHH--hhccceeEe-ecCCCCCCHHHHHHHHHHHHHHcCCcEEEEc
Q 009230          341 HARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAW--LSNTFSLIR-CENDSLPSIKWVLDLAKAAVLRHGVRGLVID  417 (539)
Q Consensus       341 ~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~--l~~~~~~i~-~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID  417 (539)
                      .+.|..    .+++              ++.+.....  |..+-+.|. ++-.+.......  .+ .+ .-.+++++|+|
T Consensus       672 yLqr~F----Nlpy--------------q~ARK~LG~fGL~sHAHTikikdLSGGQKaRVa--la-eL-al~~PDvlILD  729 (807)
T KOG0066|consen  672 YLQRKF----NLPY--------------QEARKQLGTFGLASHAHTIKIKDLSGGQKARVA--LA-EL-ALGGPDVLILD  729 (807)
T ss_pred             HHHHhc----CCCh--------------HHHHHHhhhhhhhhccceEeeeecCCcchHHHH--HH-HH-hcCCCCEEEec
Confidence            655542    2222              222221111  112222221 222333322221  11 12 23579999999


Q ss_pred             cccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCC
Q 009230          418 PYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQ  462 (539)
Q Consensus       418 ~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~  462 (539)
                      .-+.-+        +-+    -+..|...-.+|+-.||+|+| -|-
T Consensus       730 EPTNNL--------DIE----SIDALaEAIney~GgVi~VsHDeRL  763 (807)
T KOG0066|consen  730 EPTNNL--------DIE----SIDALAEAINEYNGGVIMVSHDERL  763 (807)
T ss_pred             CCCCCc--------chh----hHHHHHHHHHhccCcEEEEecccce
Confidence            322111        112    234444445689999999999 553

>TIGR01271 CFTR_protein cystic fibrosis transmembrane conductor regulator (CFTR)

Probab=96.67  E-value=0.015  Score=70.07  Aligned_cols=150  Identities=15%  Similarity=0.099  Sum_probs=79.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC---CHHHHHHHHHHHhhCCC---ccccccCC-CCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN---KVREHARKLLEKHIKKP---FFEANYGG-SAERM  366 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~---~~~~~~~r~~~~~~~~~---~~~i~~~~-~~~~l  366 (539)
                      +++|+-+.|.|++|+|||||+.-++.-.. . ...+++-..+.   +...+..++ +....-+   ...++.+- .....
T Consensus      1242 I~~GekvaIvGrSGsGKSTLl~lL~rl~~-~-~G~I~IdG~di~~i~~~~lR~~i-s~IpQdp~LF~GTIR~NLdp~~~~ 1318 (1490)
T TIGR01271      1242 VEGGQRVGLLGRTGSGKSTLLSALLRLLS-T-EGEIQIDGVSWNSVTLQTWRKAF-GVIPQKVFIFSGTFRKNLDPYEQW 1318 (1490)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhhhcC-C-CcEEEECCEEcccCCHHHHHhce-EEEeCCCccCccCHHHHhCcccCC
Confidence            89999999999999999999988876653 3 45555444333   344444433 2111111   01122111 11235


Q ss_pred             CHHHHHHHHHH------hhccc---e-eEeecCCCCCCH--HHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHH
Q 009230          367 TVEEFEQGKAW------LSNTF---S-LIRCENDSLPSI--KWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETE  434 (539)
Q Consensus       367 ~~~~~~~~~~~------l~~~~---~-~i~~~~~~~~~~--~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~  434 (539)
                      +++++.++.+.      +...+   . .+ -+.....+-  .+.+..+|.+.  .+++++++|--+.-++        .+
T Consensus      1319 tdeei~~aL~~~~L~~~i~~lp~GLdt~v-~e~G~nLSgGQrQrL~LARALL--r~~~ILlLDEaTS~lD--------~~ 1387 (1490)
T TIGR01271      1319 SDEEIWKVAEEVGLKSVIEQFPDKLDFVL-VDGGYVLSNGHKQLMCLARSIL--SKAKILLLDEPSAHLD--------PV 1387 (1490)
T ss_pred             CHHHHHHHHHHCCCHHHHHhCcccccccc-ccCCCcCCHHHHHHHHHHHHHh--CCCCEEEEeCCcccCC--------HH
Confidence            67776555332      22211   1 11 011112333  34555555544  4689999994443321        11


Q ss_pred             HHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          435 YVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       435 ~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                      .-..+.+.|+...  -+++||+++|
T Consensus      1388 Te~~I~~~L~~~~--~~~TvI~IaH 1410 (1490)
T TIGR01271      1388 TLQIIRKTLKQSF--SNCTVILSEH 1410 (1490)
T ss_pred             HHHHHHHHHHHHc--CCCEEEEEec
Confidence            2234556665543  4799999999

The model describes the cystis fibrosis transmembrane conductor regulator (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	539
1q57_A	503	The Crystal Structure Of The Bifunctional Primase-h		3e-11
1e0j_A	289	Gp4d Helicase From Phage T7 Adpnp Complex Length =		5e-06
1cr0_A	296	Crystal Structure Of The Helicase Domain Of The Gen		5e-06

>pdb|1Q57|A Chain A, The Crystal Structure Of The Bifunctional Primase-helicase Of Bacteriophage T7 Length = 503

Iteration: 1
 Score = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 113/474 (23%), Positives = 182/474 (38%), Gaps = 75/474 (15%)
Query: 88  RNGKLVNCKYRDFNKKFWQEKDTEK-VFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNC 146
           +NG +V+ K RD +K F      +    +G     G   I++ EGE+D L++ E      
Sbjct: 51  QNGNIVSQKVRDKDKNFKTTGSHKSDALFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKY 110
Query: 147 VSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELAX 206
             V  G  +S +KK   +  +            Y  Q  +IIL  D D  G+   EE A 
Sbjct: 111 PVVSLGHGASAAKKTCAANYE------------YFDQFEQIILMFDMDEAGRKAVEEAAQ 158
Query: 207 XXXXXXXXXXXXPKKNDVDHFKDANEVLMYLGPGALKEVVENAELY---PIMGLFNFRDY 263
                       P        KDANE  +      + E V NA  +    ++   + R+ 
Sbjct: 159 VLPAGKVRVAVLP-------CKDANECHLNGHDREIMEQVWNAGPWIPDGVVSALSLRER 211
Query: 264 FDEIDAYYHRTSGDEFGIS-TGWRALNE-LYNVLPGELTIVTGVPNSGKSEWIDALICNI 321
             E     H +S +  G+  +G   +N+       GE+ +VT       S ++       
Sbjct: 212 IRE-----HLSSEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMVMSTFVRQQALQW 266
Query: 322 NEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVE--EFEQGKAWLS 379
               G K  L  +E  V E A  L+  H +    +++   S +R  +E  +F+Q   W  
Sbjct: 267 GTAMGKKVGLAMLEESVEETAEDLIGLHNRVRLRQSD---SLKREIIENGKFDQ---WFD 320
Query: 380 NTF---------SLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQ 430
             F         S    E D L        LAK A +R G+   VI     LDH   V  
Sbjct: 321 ELFGNDTFHLYDSFAEAETDRL--------LAKLAYMRSGLGCDVI----ILDHISIVVS 368
Query: 431 T-----ETEYVSQMLTMVKRFAQHHACHVWFVAHPR-----QLHNWVGEPPNLYDISGSA 480
                 E + +  ++T +K FA+     +  + H +     + H   G P ++ D+ GS 
Sbjct: 369 ASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHLKNPDKGKAHE-EGRPVSITDLRGSG 427
Query: 481 HFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEA-FLSYNRVTG 533
                 D  I + RN+  +   +    V VR ++ +  G  G A ++ YN+ TG
Sbjct: 428 ALRQLSDTIIALERNQQGDMPNL----VLVRILKCRFTGDTGIAGYMEYNKETG 477

>pdb|1E0J|A Chain A, Gp4d Helicase From Phage T7 Adpnp Complex Length = 289

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 65/259 (25%), Positives = 104/259 (40%), Gaps = 45/259 (17%)
Query: 297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFE 356
           GE+ +VT     GKS ++           G K  L  +E  V E A  L+  H +    +
Sbjct: 45  GEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVRLRQ 104
Query: 357 ANYGGSAERMTVE--EFEQGKAWLSNTF---------SLIRCENDSLPSIKWVLDLAKAA 405
           ++   S +R  +E  +F+Q   W    F         S    E D L        LAK A
Sbjct: 105 SD---SLKREIIENGKFDQ---WFDELFGNDTFHLYDSFAEAETDRL--------LAKLA 150
Query: 406 VLRHGVRGLVIDPYNELDHQRPVSQT-----ETEYVSQMLTMVKRFAQHHACHVWFVAHP 460
            +R G+   VI     LDH   V        E + +  ++T +K FA+     +  + H 
Sbjct: 151 YMRSGLGCDVII----LDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHL 206
Query: 461 R-----QLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRN 515
           +     + H   G P ++ D+ GS       D  I + RN+  +   +    V VR ++ 
Sbjct: 207 KNPDKGKAHEE-GRPVSITDLRGSGALRQLSDTIIALERNQQGDMPNL----VLVRILKC 261
Query: 516 KVVGTIGEA-FLSYNRVTG 533
           +  G  G A ++ YN+ TG
Sbjct: 262 RFTGDTGIAGYMEYNKETG 280

>pdb|1CR0|A Chain A, Crystal Structure Of The Helicase Domain Of The Gene4 Protein Of Bacteriophage T7 Length = 296

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 65/259 (25%), Positives = 104/259 (40%), Gaps = 45/259 (17%)
Query: 297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFE 356
           GE+ +VT     GKS ++           G K  L  +E  V E A  L+  H +    +
Sbjct: 35  GEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVRLRQ 94
Query: 357 ANYGGSAERMTVE--EFEQGKAWLSNTF---------SLIRCENDSLPSIKWVLDLAKAA 405
           ++   S +R  +E  +F+Q   W    F         S    E D L        LAK A
Sbjct: 95  SD---SLKREIIENGKFDQ---WFDELFGNDTFHLYDSFAEAETDRL--------LAKLA 140
Query: 406 VLRHGVRGLVIDPYNELDHQRPVSQT-----ETEYVSQMLTMVKRFAQHHACHVWFVAHP 460
            +R G+   VI     LDH   V        E + +  ++T +K FA+     +  + H 
Sbjct: 141 YMRSGLGCDVI----ILDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHL 196
Query: 461 R-----QLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRN 515
           +     + H   G P ++ D+ GS       D  I + RN+  +   +    V VR ++ 
Sbjct: 197 KNPDKGKAHEE-GRPVSITDLRGSGALRQLSDTIIALERNQQGDMPNL----VLVRILKC 251
Query: 516 KVVGTIGEA-FLSYNRVTG 533
           +  G  G A ++ YN+ TG
Sbjct: 252 RFTGDTGIAGYMEYNKETG 270

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	539
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	1e-101
1nui_A	255	DNA primase/helicase; zinc-biding domain, toprim f	4e-21
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	2e-08
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	2e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
4edg_A	329	DNA primase; catalytic domain, nucleoside triphosp	2e-06
2au3_A	407	DNA primase; zinc ribbon, toprim, RNA polymerase,	7e-06
1dd9_A	338	DNA primase, DNAG; toprim, 3-helix bundle, DNA-bin	2e-05
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	2e-04

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2 Length = 503

 Score =  314 bits (806), Expect = e-101
 Identities = 98/494 (19%), Positives = 181/494 (36%), Gaps = 38/494 (7%)

Query: 54  AYFAERLISAETLRRNRV-MQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEK 112
           +    R IS ET ++    + K  G    +A    +NG +V+ K RD +K F      + 
Sbjct: 16  SALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKS 75

Query: 113 V-FYGLDDIEGESDIIIVEGEMDKLSMEEAGFLN--CVSVPDGAPSSVSKKNVPSEEQDT 169
              +G     G   I++ EGE+D L++ E        VS+  GA +              
Sbjct: 76  DALFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASA-------------- 121

Query: 170 KYQYLWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKD 229
             +       Y  Q  +IIL  D D  G+   EE A+ +   +      P        KD
Sbjct: 122 AKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLP-------CKD 174

Query: 230 ANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALN 289
           ANE  +      + E V NA  +   G+ +     + I  +          + +G   +N
Sbjct: 175 ANECHLNGHDREIMEQVWNAGPWIPDGVVSALSLRERIREHLSSE-ESVGLLFSGCTGIN 233

Query: 290 ELYNVL-PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEK 348
           +       GE+ +VT       S ++           G K  L  +E  V E A  L+  
Sbjct: 234 DKTLGARGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGL 293

Query: 349 HIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLR 408
           H +    +++     E +   +F+Q    L    +    ++ +      +L         
Sbjct: 294 HNRVRLRQSDS-LKREIIENGKFDQWFDELFGNDTFHLYDSFAEAETDRLLAKLAYMRSG 352

Query: 409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPR----QLH 464
            G   +++D +  +         E + +  ++T +K FA+     +  + H +       
Sbjct: 353 LGCDVIILD-HISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHLKNPDKGKA 411

Query: 465 NWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEA 524
           +  G P ++ D+ GS       D  I + RN+  +   +  V++    ++ +  G  G A
Sbjct: 412 HEEGRPVSITDLRGSGALRQLSDTIIALERNQQGDMPNLVLVRI----LKCRFTGDTGIA 467

Query: 525 -FLSYNRVTGEYMD 537
            ++ YN+ TG    
Sbjct: 468 GYMEYNKETGWLEP 481

>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2 Length = 255

 Score = 92.1 bits (227), Expect = 4e-21
 Identities = 54/250 (21%), Positives = 86/250 (34%), Gaps = 34/250 (13%)

Query: 1   MCFRAKCGWKGSTSALVDNNRSQSSLKKFSKMKTIREITEDSLELEPLGNELRAYFAERL 60
            C+   C    +       N          K    +  T +        N   +    R 
Sbjct: 35  FCYV--CEKWTA------GNEDTKERASKRKPSGGKPGTYNVWNF-GESNGRYSALTARG 85

Query: 61  ISAETLRRNRV-MQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKD-TEKVFYGLD 118
           IS ET ++    + K  G    +A    +NG +V+ K RD +K F           +G  
Sbjct: 86  ISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFGKH 145

Query: 119 DIEGESDIIIVEGEMDKLSMEEA--GFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWN 176
              G   I++ EGE+D L++ E        VS+  GA ++         ++     Y + 
Sbjct: 146 LWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASAA---------KKTCAANYEY- 195

Query: 177 CKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMY 236
                 Q  +IIL  D D  G+   EE A+ +   +      P        KDANE  + 
Sbjct: 196 ----FDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLP-------CKDANECHLN 244

Query: 237 LGPGALKEVV 246
                + E V
Sbjct: 245 GHDREIMEQV 254

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A* Length = 296

 Score = 54.6 bits (132), Expect = 2e-08
 Identities = 59/290 (20%), Positives = 110/290 (37%), Gaps = 43/290 (14%)

Query: 265 DEIDAYYHRTSGDEFGISTGWRALNELYNVL-PGELTIVTGVPNSGKSEWIDALICNINE 323
           + I  +          + +G   +N+       GE+ +VT     GKS      +     
Sbjct: 3   ERIREHLSSEESVG-LLFSGCTGINDKTLGARGGEVIMVTSGSGMGKS----TFVRQQAL 57

Query: 324 HAGWKF----VLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQ--GKAW 377
             G        L  +E  V E A  L+  H +    +++     E +   +F+Q   + +
Sbjct: 58  QWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVRLRQSDS-LKREIIENGKFDQWFDELF 116

Query: 378 LSNTFSLIRCENDSLPSIKWVLDL-AKAAVLR--HGVRGLVIDPYNELDHQRPVSQTETE 434
            ++TF L     DS    +    L AK A +R   G   +++D +  +         E +
Sbjct: 117 GNDTFHLY----DSFAEAE-TDRLLAKLAYMRSGLGCDVIILD-HISIVVSASGESDERK 170

Query: 435 YVSQMLTMVKRFAQHHACHVWFVAH----PRQLHNWVGEPPNLYDI--SGS----AHFIN 484
            +  ++T +K FA+     +  + H     +   +  G P ++ D+  SG+    +  I 
Sbjct: 171 MIDNLMTKLKGFAKSTGVVLVVICHLKNPDKGKAHEEGRPVSITDLRGSGALRQLSDTI- 229

Query: 485 KCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEAF-LSYNRVTG 533
                I + RN+  +    + V V + K R    G  G A  + YN+ TG
Sbjct: 230 -----IALERNQQGDMP--NLVLVRILKCRFT--GDTGIAGYMEYNKETG 270

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A Length = 279

 Score = 52.0 bits (124), Expect = 2e-07
 Identities = 30/217 (13%), Positives = 61/217 (28%), Gaps = 31/217 (14%)

Query: 293 NVLPGELTIVTGVPNSGKSEWIDALICNINEHAGW---------KFVLCSMENKVREHAR 343
           N++ G +  +     +GKS     L   I                 +    E+       
Sbjct: 26  NMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHH 85

Query: 344 KLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAK 403
           +L    +            A+ +                 LI+    SLP+I        
Sbjct: 86  RL--HALGAHLSAEERQAVADGL-----------------LIQPLIGSLPNIMAPEWFDG 126

Query: 404 AAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQL 463
                 G R +V+D       +   +      ++Q++  ++  A    C + F+ H  + 
Sbjct: 127 LKRAAEGRRLMVLDTLRRFHIEEENASGP---MAQVIGRMEAIAADTGCSIVFLHHASKG 183

Query: 464 HNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEA 500
              +G         GS+  ++       +      EA
Sbjct: 184 AAMMGAGDQQQASRGSSVLVDNIRWQSYLSSMTSAEA 220

>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 = 50.2 bits (119), Expect = 1e-06
 Identities = 70/550 (12%), Positives = 163/550 (29%), Gaps = 163/550 (29%)

Query: 104 FW----QEKDTEKVFYGLDDIEGESDIII--VEGEMDKLSMEEAGFLNCVSVPDGAPSSV 157
           FW    ++++  + F   + +      ++  ++ E  + SM    ++             
Sbjct: 68  FWTLLSKQEEMVQKFVE-EVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF 126

Query: 158 SKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPG---QALAEELAR--RVGRER 212
           +K NV   +    Y  L    + L+ A  +++  DG   G     +A ++    +V  + 
Sbjct: 127 AKYNVSRLQ---PYLKLRQALLELRPAKNVLI--DGVL-GSGKTWVALDVCLSYKVQCKM 180

Query: 213 CWRVRWPKKNDVDHFKDANEVLMYL----------------GPGALKEVVENAELYPIMG 256
            +++ W     + +      VL  L                    +K  + + +   +  
Sbjct: 181 DFKIFWLN---LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE-LRR 236

Query: 257 LFNFRDY------FDEIDAYYHRTSGDEFGIS------TGWRAL-NELYNVLPGELTIVT 303
           L   + Y         +    +  + + F +S      T ++ + + L       +++  
Sbjct: 237 LLKSKPYENCLLVLLNV---QNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH 293

Query: 304 GVPNSGKSE-------WID-------ALICNIN------------EHAG----WKFVLCS 333
                   E       ++D         +   N            +       WK V C 
Sbjct: 294 HSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCD 353

Query: 334 MENKVREHARKLLEKHIKKPFFEA--------------------NYGGSAERMTVEEFEQ 373
               + E +  +LE    +  F+                     +   S   + V +  +
Sbjct: 354 KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK 413

Query: 374 GKAWLSNTFSLIRCEND----SLPSIKWVLDLAKAAVLRHGVRGLVIDPYN---ELDHQR 426
                   +SL+  +      S+PSI   L+L       + +   ++D YN     D   
Sbjct: 414 --------YSLVEKQPKESTISIPSIY--LELKVKLENEYALHRSIVDHYNIPKTFDSDD 463

Query: 427 PVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLY-DISGSAHFI-N 484
            +     +Y          F  H   H   + +             ++ D      F+  
Sbjct: 464 LIPPYLDQY----------FYSHIGHH---LKNIEHPERM-TLFRMVFLDF----RFLEQ 505

Query: 485 KCDNGIVIHR--NRDPEAGPIDRVQVCVRKVRN----------KVVGTIGEAFL---SYN 529
           K     + H     +     ++ +Q  ++  +           ++V  I + FL     N
Sbjct: 506 K-----IRHDSTAWNASGSILNTLQQ-LKFYKPYICDNDPKYERLVNAILD-FLPKIEEN 558

Query: 530 RVTGEYMDIV 539
            +  +Y D++
Sbjct: 559 LICSKYTDLL 568

>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 = 49.5 bits (117), Expect = 2e-06
 Identities = 52/297 (17%), Positives = 88/297 (29%), Gaps = 84/297 (28%)

Query: 131 GEM-----DKLSMEEAGF---LNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLK 182
           GE      D LS+ E  F    +C  V D        K++ S+E+             + 
Sbjct: 12  GEHQYQYKDILSVFEDAFVDNFDCKDVQD------MPKSILSKEE---------IDHIIM 56

Query: 183 QASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGAL 242
                                   R+     W +   ++  V  F +    + Y     L
Sbjct: 57  SKDA---------------VSGTLRL----FWTLLSKQEEMVQKFVEEVLRINY---KFL 94

Query: 243 KEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWR-----ALNE-LYNVLP 296
              ++  +  P M     R Y ++ D  Y       F      R      L + L  + P
Sbjct: 95  MSPIKTEQRQPSM---MTRMYIEQRDRLY--NDNQVFAKYNVSRLQPYLKLRQALLELRP 149

Query: 297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV-------REHARKLLEK- 348
            +  ++ GV  SGK+ W+   +C   +      V C M+ K+             +LE  
Sbjct: 150 AKNVLIDGVLGSGKT-WVALDVCLSYK------VQCKMDFKIFWLNLKNCNSPETVLEML 202

Query: 349 -----HIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLD 400
                 I   +   +   S  ++ +      +A L         EN  L     VL 
Sbjct: 203 QKLLYQIDPNWTSRSDHSSNIKLRIHSI---QAELRRLLKSKPYENCLL-----VLL 251

>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 = 47.5 bits (112), Expect = 1e-05
 Identities = 41/281 (14%), Positives = 79/281 (28%), Gaps = 88/281 (31%)

Query: 18  DNNRSQSSLK-KFSKMKTIREITEDSLE-LEPLGNELRAYFAERL--------ISAETLR 67
                 +       K+ TI E    SL  LEP   E R  F +RL        I    L 
Sbjct: 340 GLATWDNWKHVNCDKLTTIIES---SLNVLEP--AEYRKMF-DRLSVFPPSAHIPTILLS 393

Query: 68  RNRVMQKRHGHEVVIAFPYWRNGK------LVNCKYRDFNKKFWQEKDTEKVFYGLDDIE 121
                              W +        +VN      +K    EK  ++    +  I 
Sbjct: 394 L-----------------IWFDVIKSDVMVVVN----KLHKYSLVEKQPKESTISIPSI- 431

Query: 122 GESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMY- 180
                + ++ +++         ++  ++P    S      +P       Y ++     + 
Sbjct: 432 ----YLELKVKLENEYALHRSIVDHYNIPKTFDSD---DLIPPYLDQYFYSHI----GHH 480

Query: 181 LKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPG 240
           LK                     L R V  +     R+ ++      K  ++   +   G
Sbjct: 481 LKNI------------EHPERMTLFRMVFLD----FRFLEQ------KIRHDSTAWNASG 518

Query: 241 ALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGD--EF 279
           ++   ++  + Y        + Y  + D  Y R      +F
Sbjct: 519 SILNTLQQLKFY--------KPYICDNDPKYERLVNAILDF 551

>4edg_A DNA primase; catalytic domain, nucleoside triphosphate, nucleoside polyph protein-ligand complex, transferase; HET: DNA ATP; 2.00A {Staphylococcus aureus} PDB: 4edk_A* 4edr_A* 4edt_A* 4edv_A* 4ee1_A* Length = 329

 Score = 48.8 bits (117), Expect = 2e-06
 Identities = 47/264 (17%), Positives = 77/264 (29%), Gaps = 86/264 (32%)

Query: 36  REITEDSLELEPLG------NELRAYFAERLISAETLR------------------RNRV 71
           R  T+  ++   +G      +    +  ++    E                     RNR+
Sbjct: 39  RGFTDALIKERGIGFAPDSSHFCHDFLQKKGYDIELAYEAGLLSRNEENFSYYDRFRNRI 98

Query: 72  M---QKRHGHEVVIAFP--YWRNGKLVNCKYRD------FNKKFWQEKDTEKVFYGLD-- 118
           M   +   G   ++ +    +   +    KY +      F K+        K+ Y LD  
Sbjct: 99  MFPLKNAQGR--IVGYSGRTYTGQE---PKYLNSPETPIFQKR--------KLLYNLDKA 145

Query: 119 --DIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWN 176
              I    +I+++EG MD +  + AG  N V     A          S+E          
Sbjct: 146 RKSIRKLDEIVLLEGFMDVIKSDTAGLKNVV-----ATMGTQL----SDEH--------- 187

Query: 177 CKMYLKQASRIILATDGDPPGQALAE---ELARRVGRERCWRVRW---PKKNDVDHFKDA 230
                K  S I L  DGD  G        +   + G      V     P   D D +   
Sbjct: 188 ITFIRKLTSNITLMFDGDFAGSEATLKTGQHLLQQGLN----VFVIQLPSGMDPDEYIGK 243

Query: 231 NEVLMYLGPGALKEVVENAELYPI 254
                  G  A    V+N +    
Sbjct: 244 Y------GNDAFTTFVKNDKKSFA 261

>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transf; HET: DNA; 2.00A {Aquifex aeolicus} Length = 407

 Score = 47.5 bits (114), Expect = 7e-06
 Identities = 49/254 (19%), Positives = 74/254 (29%), Gaps = 86/254 (33%)

Query: 47  PLGNELRAYFAERLISAETLR----------------RNRVM---QKRHGHEVVIAFPYW 87
           P    L     E  +    L                   RV+   +   G   VI F   
Sbjct: 149 PSSEALVKVLKENDLLEAYLETKNLLSPTKGVYRDLFLRRVVIPIKDPRGR--VIGF--- 203

Query: 88  RNGKLVN----CKY------RDFNKKFWQEKDTEKVFYGLD----DIEGESDIIIVEGEM 133
             G+ +      KY      R F K         +  +GL      I+ E   I+VEG  
Sbjct: 204 -GGRRIVEDKSPKYINSPDSRVFKKG--------ENLFGLYEAKEYIKEEGFAILVEGYF 254

Query: 134 DKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDG 193
           D L +   G  N V     AP   +     ++ Q           +  K   ++ +  DG
Sbjct: 255 DLLRLFSEGIRNVV-----APLGTAL----TQNQ---------ANLLSKFTKKVYILYDG 296

Query: 194 DPPGQALAE---ELARRVGRERCWRVRW---PKKNDVDHFKDANEVLMYLGPGALKEVVE 247
           D  G+   +    L    G E    V     P+  D D F          G   L+ ++ 
Sbjct: 297 DDAGRKAMKSAIPLLLSAGVE----VYPVYLPEGYDPDEFIKEF------GKEELRRLIN 346

Query: 248 NAELYPIMGLFNFR 261
           ++       LF   
Sbjct: 347 SS-----GELFETL 355

>1dd9_A DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein, transferase; HET: DNA; 1.60A {Escherichia coli} SCOP: e.13.1.1 PDB: 1dde_A* 1eqn_A* 3b39_A* Length = 338

 Score = 45.8 bits (109), Expect = 2e-05
 Identities = 46/265 (17%), Positives = 83/265 (31%), Gaps = 96/265 (36%)

Query: 36  REITEDSLELEPLG------NELRAYFAERLISAETLR-----------------RNRVM 72
           R ++ + +    +G      + +   F     + ++L                  R RVM
Sbjct: 51  RGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSYDRFRERVM 110

Query: 73  ---QKRHGHEVVIAF---------PYWRNGKLVNCKYRD------FNKKFWQEKDTEKVF 114
              + + G   VI F         P          KY +      F+K         +  
Sbjct: 111 FPIRDKRGR--VIGFGGRVLGNDTP----------KYLNSPETDIFHKG--------RQL 150

Query: 115 YGLD----DIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTK 170
           YGL     D    + +++VEG MD +++ + G    V     A    S     + +    
Sbjct: 151 YGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAV-----ASLGTST----TADH--- 198

Query: 171 YQYLWNCKMYLKQASRIILATDGDPPGQALAE---ELARRVGRERCWRVRW---PKKNDV 224
                  ++  +  + +I   DGD  G+  A    E A     +   ++R+   P   D 
Sbjct: 199 ------IQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGR-QLRFMFLPDGEDP 251

Query: 225 DHFKDANEVLMYLGPGALKEVVENA 249
           D            G  A +  +E A
Sbjct: 252 DTLVRKE------GKEAFEARMEQA 270

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori} Length = 338

 Score = 42.7 bits (101), Expect = 2e-04
 Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 5/66 (7%)

Query: 261 RDYFDEIDAYYHRTSGDEFGISTGWRALNELYNVL-PGELTIVTGVPNSGKSEWIDALIC 319
               D I     + S +  GI TG+  L+   +    G L I+   P+ GK+    +L+ 
Sbjct: 9   ESAMDLITENQRKGSLEVTGIPTGFVQLDNYTSGFNKGSLVIIGARPSMGKT----SLMM 64

Query: 320 NINEHA 325
           N+   A
Sbjct: 65  NMVLSA 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	539
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	100.0
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	100.0
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	100.0
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	100.0
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	100.0
2r6a_A	454	DNAB helicase, replicative helicase; replication,	100.0
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	99.97
1nui_A	255	DNA primase/helicase; zinc-biding domain, toprim f	99.96
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	99.95
2au3_A	407	DNA primase; zinc ribbon, toprim, RNA polymerase,	99.95
4edg_A	329	DNA primase; catalytic domain, nucleoside triphosp	99.94
1dd9_A	338	DNA primase, DNAG; toprim, 3-helix bundle, DNA-bin	99.94
1xp8_A	366	RECA protein, recombinase A; recombination, radior	99.89
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	99.89
2z43_A	324	DNA repair and recombination protein RADA; archaea	99.89
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	99.88
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	99.88
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	99.88
2cvh_A	220	DNA repair and recombination protein RADB; filamen	99.87
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	99.87
1u94_A	356	RECA protein, recombinase A; homologous recombinat	99.87
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	99.87
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	99.85
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	99.84
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	99.84
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	99.84
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	99.83
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	99.81
3io5_A	333	Recombination and repair protein; storage dimer, i	99.76
4a74_A	231	DNA repair and recombination protein RADA; hydrola	99.74
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	99.72
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	99.71
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	99.64
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	99.62
3bs4_A	260	Uncharacterized protein PH0321; structural genomic	99.61
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	99.16
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	99.09
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	98.75
1t6t_1	118	Putative protein; structural genomics, PSI, protei	98.54
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	97.97
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.9
2fcj_A	119	Small toprim domain protein; structural genomics,	97.88
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	97.86
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.8
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.79
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	97.78
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	97.78
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	97.76
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	97.76
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	97.73
1g6h_A	257	High-affinity branched-chain amino acid transport	97.72
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	97.69
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	97.69
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	97.66
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	97.62
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	97.62
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	97.6
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	97.6
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	97.58
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	97.58
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	97.57
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	97.57
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	97.56
1b0u_A	262	Histidine permease; ABC transporter, transport pro	97.55
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	97.54
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	97.52
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	97.46
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	97.46
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	97.44
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	97.43
1ji0_A	240	ABC transporter; ATP binding protein, structural g	97.43
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	97.42
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	97.42
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	97.4
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	97.4
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	97.38
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	97.36
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	97.35
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	97.34
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	97.34
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	97.34
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	97.3
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	97.3
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	97.28
2og2_A	359	Putative signal recognition particle receptor; nuc	97.28
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	97.28
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.26
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	97.24
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	97.24
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	97.24
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	97.23
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	97.23
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	97.21
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	97.21
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	97.2
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	97.15
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	97.13
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	97.13
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	97.09
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	97.09
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	97.05
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	97.04
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	97.04
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	97.01
1sgw_A	214	Putative ABC transporter; structural genomics, P p	96.99
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	96.98
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	96.97
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	96.94
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	96.9
2xxa_A	433	Signal recognition particle protein; protein trans	96.9
3pih_A	916	Uvrabc system protein A; hydrolase, ABC ATPase, DN	96.82
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	96.8
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	96.76
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.76
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	96.75
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.74
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	96.7
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	96.7
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.68
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.68
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	96.66
3ice_A	422	Transcription termination factor RHO; transcriptio	96.65
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.62
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.61
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	96.6
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	96.57
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	96.56
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	96.55
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	96.52
3bos_A	242	Putative DNA replication factor; P-loop containing	96.52
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	96.45
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	96.44
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	96.43
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.42
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.41
3qxc_A	242	Dethiobiotin synthetase; DTBS, structural genomics	96.4
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.39
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	96.36
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	96.35
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.35
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	96.32
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	96.29
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	96.26
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	96.25
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.23
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.21
4aby_A	415	DNA repair protein RECN; hydrolase, double strand	96.21
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	96.2
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.19
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	96.18
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.18
3igf_A	374	ALL4481 protein; two-domained protein consisting o	96.13
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.13
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	96.13
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.12
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	96.11
2vf7_A	842	UVRA2, excinuclease ABC, subunit A.; DNA-binding p	96.1
3ux8_A	670	Excinuclease ABC, A subunit; UVRA, nucleotide exci	96.1
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	96.08
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	96.08
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	96.07
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	96.06
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	96.04
2yl4_A	595	ATP-binding cassette SUB-family B member 10, mitoc	96.03
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	96.01
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.97
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	95.97
3l0o_A	427	Transcription termination factor RHO; helicase, RH	95.96
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	95.93
2qgz_A	308	Helicase loader, putative primosome component; str	95.92
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	95.92
2woj_A	354	ATPase GET3; tail-anchored, membrane protein, targ	95.92
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.91
2iw3_A	986	Elongation factor 3A; acetylation, ATP-binding, pr	95.89
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	95.89
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	95.89
3end_A	307	Light-independent protochlorophyllide reductase ir	95.84
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.81
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.8
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	95.78
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	95.78
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	95.77
3ux8_A	670	Excinuclease ABC, A subunit; UVRA, nucleotide exci	95.74
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	95.73
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.72
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	95.7
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	95.68
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.66
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	95.65
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.65
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	95.64
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.64
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	95.63
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	95.63
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	95.61
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.6
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	95.59
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	95.58
3bfv_A	271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	95.57
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	95.57
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	95.56
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	95.52
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	95.49
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	95.49
1tue_A	212	Replication protein E1; helicase, replication, E1E	95.48
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	95.48
3cio_A	299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	95.46
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	95.43
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	95.41
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	95.4
1g3q_A	237	MIND ATPase, cell division inhibitor; alpha-beta-a	95.38
1hyq_A	263	MIND, cell division inhibitor (MIND-1); MINC, FTSZ	95.37
2woo_A	329	ATPase GET3; tail-anchored, membrane protein, targ	95.35
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	95.35
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	95.31
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.3
3fwy_A	314	Light-independent protochlorophyllide reductase I	95.29
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.26
2ph1_A	262	Nucleotide-binding protein; alpha-beta protein, st	95.24
3q9l_A	260	Septum site-determining protein MIND; ATPase, bact	95.23
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	95.21
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	95.21
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	95.2
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	95.2
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	95.19
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.18
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	95.17
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	95.16
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	95.16
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.13
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	95.12
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	95.11
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	95.11
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	95.08
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	95.08
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	95.08
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	95.08
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	95.07
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	95.07
3la6_A	286	Tyrosine-protein kinase WZC; P-loop protein, nucle	95.07
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	95.06
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	95.06
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	95.06
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	95.05
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.02
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	95.0
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	94.98
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	94.97
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	94.97
2ewv_A	372	Twitching motility protein PILT; pilus retraction	94.97
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.96
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.96
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.94
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.93
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	94.93
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	94.92
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	94.91
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	94.91
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	94.91
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	94.91
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	94.9
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	94.89
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	94.89
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	94.88
3cwq_A	209	Para family chromosome partitioning protein; alpha	94.86
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	94.85
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.83
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	94.79
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	94.79
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	94.78
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	94.71
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	94.71
1byi_A	224	Dethiobiotin synthase; biotin synthesis, cyclo-lig	94.69
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	94.68
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	94.65
3kta_A	182	Chromosome segregation protein SMC; structural mai	94.63
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	94.62
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	94.57
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	94.55
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	94.53
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	94.53
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	94.52
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.47
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	94.46
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	94.44
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	94.44
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	94.44
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	94.43
2oze_A	298	ORF delta'; para, walker type atpases, DNA segrega	94.42
1wcv_1	257	SOJ, segregation protein; ATPase, bacterial, chrom	94.41
1p9r_A	418	General secretion pathway protein E; bacterial typ	94.37
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	94.36
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	94.34
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	94.34
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	94.33
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	94.33
2xj4_A	286	MIPZ; replication, cell division, ATPase, WACA; 1.	94.32
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	94.32
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	94.23
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	94.2
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	94.16
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	94.14
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	94.14
3b6e_A	216	Interferon-induced helicase C domain-containing P;	94.11
2vli_A	183	Antibiotic resistance protein; transferase, tunica	94.1
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	94.1
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	94.08
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	94.02
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	94.0
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	93.98
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	93.98
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	93.96
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	93.94
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	93.93
3pg5_A	361	Uncharacterized protein; structural genomics, PSI-	93.93
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	93.89
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	93.87
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	93.84
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	93.84
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	93.82
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	93.81
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	93.8
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	93.79
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	93.79
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	93.75
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	93.7
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	93.66
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	93.64
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	93.61
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	93.61
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	93.59
1via_A	175	Shikimate kinase; structural genomics, transferase	93.57
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	93.55
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	93.55
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	93.55
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	93.53
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	93.51
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	93.5
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	93.49
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	93.48
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	93.47
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	93.4
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	93.34
3gqb_A	578	V-type ATP synthase alpha chain; A3B3, V-ATPase, A	93.31
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	93.3
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	93.28
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	93.25
2chg_A	226	Replication factor C small subunit; DNA-binding pr	93.24
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	93.21
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	93.19
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	93.18
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	93.14
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	93.1
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	93.09
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	93.09
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	93.08
2fna_A	357	Conserved hypothetical protein; structural genomic	93.08
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	93.06
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	93.06
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	93.04
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	93.01
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	93.01
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	93.0
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	92.98
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	92.97
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	92.95
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	92.89
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	92.88
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	92.86
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	92.84
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	92.83
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	92.82
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	92.78
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	92.78
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	92.76
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	92.74
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	92.69
3ez2_A	398	Plasmid partition protein A; type IA, DNA binding,	92.63
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	92.63
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	92.63
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	92.62
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	92.58
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	92.48
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	92.45
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	92.44
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	92.43
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	92.42
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	92.4
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	92.38
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	92.38
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	92.28
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	92.27
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	92.26
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	92.18
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	92.18
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	92.16
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	92.15
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	92.09
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	92.08
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	92.02
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	92.01
4a8j_A	361	Elongator complex protein 4; transcription; 2.10A	92.0
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	91.94
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	91.9
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	91.84
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	91.78
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	91.71
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	91.69
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	91.68
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	91.66
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	91.65
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	91.64
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	91.63
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	91.59
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	91.49
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	91.42
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	91.41
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	91.38
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	91.36
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	91.36
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	91.22
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	91.17
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	91.16
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	91.01
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	91.01
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	90.9
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	90.85
3ez9_A	403	Para; DNA binding, winged-HTH, partition, biosynth	90.81
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	90.79
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	90.79
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	90.78
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	90.77
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	90.76
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	90.75
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	90.65
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	90.65
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	90.62
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	90.54
3of5_A	228	Dethiobiotin synthetase; structural genomics, cent	90.52
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	90.51
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	90.43
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	90.29
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	90.28
2vf7_A	842	UVRA2, excinuclease ABC, subunit A.; DNA-binding p	90.28
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	90.24
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	90.23
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	90.13
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	90.13
3pvs_A	447	Replication-associated recombination protein A; ma	90.07
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	90.04
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	89.94
2hf9_A	226	Probable hydrogenase nickel incorporation protein	89.89
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	89.67
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	89.58
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	89.49
2wji_A	165	Ferrous iron transport protein B homolog; membrane	89.37
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	89.35
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	89.3
2r44_A	331	Uncharacterized protein; putative ATPase, structur	89.21
3co5_A	143	Putative two-component system transcriptional RES	89.18
1ni3_A	392	YCHF GTPase, YCHF GTP-binding protein; structural	89.0
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	88.98
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	88.91
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	88.9
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	88.82
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	88.8
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	88.75
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	88.74
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	88.71
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	88.65
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	88.64
2o5v_A	359	DNA replication and repair protein RECF; ABC ATPas	88.59
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	88.55
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	88.51
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	88.43
1e69_A	322	Chromosome segregation SMC protein; structural mai	88.42
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	88.39
1yks_A	440	Genome polyprotein [contains: flavivirin protease	88.28
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	88.24
1w1w_A	430	Structural maintenance of chromosome 1; cohesin, c	88.16
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	88.15
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	88.14
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	88.11
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	88.07
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	87.97
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	87.91
3fgn_A	251	Dethiobiotin synthetase; biotin biosynthesis, BIOD	87.91
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	87.84
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	87.77
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	87.77
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	87.68
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	87.68
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	87.65
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	87.65
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	87.61
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	87.58
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	87.57
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	87.52
2ged_A	193	SR-beta, signal recognition particle receptor beta	87.5
4a0g_A	831	Adenosylmethionine-8-amino-7-oxononanoate aminotra	87.45

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=100.00  E-value=1.1e-67  Score=561.88  Aligned_cols=453  Identities=22%  Similarity=0.239  Sum_probs=372.9

Q ss_pred             HHHHHHhcCCCHHHHHHcCcccccCCceeEEEEeEe-eCCEEEEEEeecCCCccccc-CCCCCccccccccCCCCcEEEE
Q 009230           52 LRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYW-RNGKLVNCKYRDFNKKFWQE-KDTEKVFYGLDDIEGESDIIIV  129 (539)
Q Consensus        52 ~~~Yl~~Rgi~~~~~~~~~~~~~~~~~~~~i~fP~~-~~G~~~~~~~R~~~~~~~~~-~~~~~~l~g~~~~~~~~~v~i~  129 (539)
                      +++||.+|||+.+++++|++++.+..+..+++|||+ ..|+++++++|..++.|++. +.+...+||++...+.++|+||
T Consensus        14 ~~~YL~~Rgi~~~~~~~~~~~~~~~~g~~~i~fp~~d~~G~~~g~~~R~~~~~~ky~~~~k~~~lyg~~~~~~~~~v~i~   93 (503)
T 1q57_A           14 RYSALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFGKHLWNGGKKIVVT   93 (503)
T ss_dssp             BCCCBTTTTBCHHHHHHHTEEECCBTTBCEEEEEEECTTSCEEEEEEEETTTEEEEEECCCTTCEETGGGCSSEEEEEEE
T ss_pred             HHHHHHHCCCCHHHHHHcCeEEECCCCcEEEEEEEECCCCCEEEEEeECCCCCceEecCCCCCceECccccCCCCEEEEE
Confidence            678999999999999999987665445578999988 88999999999876555542 2345789999988777899999


Q ss_pred             echhhHHHHHHh-CC-CceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCccchHHHHHHHHH
Q 009230          130 EGEMDKLSMEEA-GF-LNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELARR  207 (539)
Q Consensus       130 EG~~Dalsl~~~-g~-~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~~G~~~~~~~~~~  207 (539)
                      ||++|+||++|+ |. .++++++++....              ...+.+++++|+++++|++|+|||+||+++++++++.
T Consensus        94 EG~~D~ls~~~~~g~~~~v~slg~~~~~~--------------~~~l~~~l~~l~~~~~ivl~~D~D~aG~~aa~~~~~~  159 (503)
T 1q57_A           94 EGEIDMLTVMELQDCKYPVVSLGHGASAA--------------KKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQV  159 (503)
T ss_dssp             SSHHHHHHHTTTTTTCSCEEEESSTTTTH--------------HHHHHTTHHHHHTEEEEEEECCSSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHhcCCCcEEEECCcccchh--------------HHHHHHHHHhhcCCCEEEEEeCCCHHHHHHHHHHHHh
Confidence            999999999999 76 3566765443321              1234445677888899999999999999999999999


Q ss_pred             hcCCceEEEecCCCCCCCCCCChHHHHHhcCcchHHHHHHhccccCccccccccchHHHHHHHhhccCCCcccccc-Cch
Q 009230          208 VGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGIST-GWR  286 (539)
Q Consensus       208 l~~~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~~~~~~~A~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~gi~t-g~~  286 (539)
                      |...+|+++.+|       +|||||+|++.|.+++.+++++|.++.+.+++++.++++++++.+.  .+...+++| ||+
T Consensus       160 l~~~~~~~~~~p-------~kD~nd~l~~~g~~~~~~~i~~a~~~~~~~i~~~~~~~~~i~~~~~--~~~~~~i~t~G~~  230 (503)
T 1q57_A          160 LPAGKVRVAVLP-------CKDANECHLNGHDREIMEQVWNAGPWIPDGVVSALSLRERIREHLS--SEESVGLLFSGCT  230 (503)
T ss_dssp             SCGGGEEECCCS-------SSSHHHHHTTSCHHHHHHHHTTCCCCCCSSEEEGGGGHHHHHHHHH--HSCTTCSCCSSCT
T ss_pred             cccCcEEEEeCC-------CCCHHHHHHhcCHHHHHHHHHhcCCCCHHHhcChHHHHHHHHhhhc--ccccCCccccchh
Confidence            976578777654       8999999999999999999999999999999999999999988764  356789999 999


Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccc---cccCCC
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFE---ANYGGS  362 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~---i~~~~~  362 (539)
                      .||++++ +++|++++|+|+||+|||+|++|++.+++.++|.+|+|||+||+++++..|+++..+++++.+   ++.+  
T Consensus       231 ~LD~~lgGl~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~E~s~~~l~~r~~~~~~~~~~~~~~~~~~g--  308 (503)
T 1q57_A          231 GINDKTLGARGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVRLRQSDSLKRE--  308 (503)
T ss_dssp             THHHHHCCCCTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEESSSCHHHHHHHHHHHHTTSCCTTCHHHHHH--
T ss_pred             hhhHhhcccCCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEeccCCHHHHHHHHHHHHcCCChhhccccccC--
Confidence            9999998 999999999999999999999999999998558999999999999999999999999998764   4332  


Q ss_pred             CCCCCHHHHHHHHHHh-hccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHH
Q 009230          363 AERMTVEEFEQGKAWL-SNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLT  441 (539)
Q Consensus       363 ~~~l~~~~~~~~~~~l-~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~  441 (539)
                        .++++++.++.+.+ ....+++. +..+..+++++...++.++.++++++||||++. ++.......++.+.+.++++
T Consensus       309 --~l~~~~~~~~~~~~~~~~~l~i~-~~~~~~~~~~i~~~i~~~~~~~~~~lvVID~l~-~l~~~~~~~~~~~~~~~~~~  384 (503)
T 1q57_A          309 --IIENGKFDQWFDELFGNDTFHLY-DSFAEAETDRLLAKLAYMRSGLGCDVIILDHIS-IVVSASGESDERKMIDNLMT  384 (503)
T ss_dssp             --HHHTSHHHHHHHHHHTTTCEEEE-CCC---CHHHHHHHHHHHHHTTCCSEEEEECTT-CCCSCCSCCCHHHHHHHHHH
T ss_pred             --CCCHHHHHHHHHHHhccCCEEEE-CCCCCCCHHHHHHHHHHHHHhcCCCEEEEccch-hcCCCCCCCCHHHHHHHHHH
Confidence              45555666665554 34445552 222347899999999999999999999999555 44433223577788999999


Q ss_pred             HHHHHHHHhCcEEEEEec-CCCCCCC----CCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEee-C
Q 009230          442 MVKRFAQHHACHVWFVAH-PRQLHNW----VGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVR-N  515 (539)
Q Consensus       442 ~Lk~lA~~~~i~vi~~~q-~r~~~~~----~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R-~  515 (539)
                      .|+.||+++||+||+++| ++ .+++    .+++|.++|++||+.|++.||+||+|++++..+  .++.+++.|.|+| +
T Consensus       385 ~Lk~lak~~~i~vi~~~q~~r-~~~~~~~~~~~~p~l~dlr~s~~ie~~aD~vi~l~r~~~~~--~~~~~~l~v~K~R~~  461 (503)
T 1q57_A          385 KLKGFAKSTGVVLVVICHLKN-PDKGKAHEEGRPVSITDLRGSGALRQLSDTIIALERNQQGD--MPNLVLVRILKCRFT  461 (503)
T ss_dssp             HHHHHHHHHTCEEEEEEECCC-CSSSSCSTTCCCCCSSSCSSSSHHHHHCSEEEEEEECSSSS--CTTEEEEEEEEETTT
T ss_pred             HHHHHHHHHCCeEEEEEcCCc-hhccCccccCCCCChhhhccchHhhecCcEEEEEEeCCcCC--CCCeEEEEEEeccCC
Confidence            999999999999999999 76 4433    367899999999999999999999999987533  2357899999999 8


Q ss_pred             CCcceeeeEEEEEeCCCceeccC
Q 009230          516 KVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       516 g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      |++|.+  +.+.|+++++||.++
T Consensus       462 G~~g~~--~~l~f~~~~~~f~~~  482 (503)
T 1q57_A          462 GDTGIA--GYMEYNKETGWLEPS  482 (503)
T ss_dssp             CCCEEE--EEEEECTTTCCEEEE
T ss_pred             CCCCce--EEEEEEcCCceEecC
Confidence            988764  379999999999875

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=100.00  E-value=8.9e-47  Score=374.43  Aligned_cols=267  Identities=21%  Similarity=0.261  Sum_probs=228.4

Q ss_pred             cchHHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH
Q 009230          261 RDYFDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR  339 (539)
Q Consensus       261 ~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~  339 (539)
                      .++++++++++++..+...|+||||+.||++++ |++|+|++|+|+||+|||+|+++++.+++.+ |.+|+|||+||+++
T Consensus         9 ~~~~~~~~~~~~~~~~~~~gi~TG~~~LD~~~gGl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~-g~~Vl~fSlEms~~   87 (338)
T 4a1f_A            9 ESAMDLITENQRKGSLEVTGIPTGFVQLDNYTSGFNKGSLVIIGARPSMGKTSLMMNMVLSALND-DRGVAVFSLEMSAE   87 (338)
T ss_dssp             HHHHHHHHHHHHHTTTCCCSBCCSCHHHHHHHCSBCTTCEEEEEECTTSCHHHHHHHHHHHHHHT-TCEEEEEESSSCHH
T ss_pred             HHHHHHHHHHHhcCCCCcCcccCCChHHHHHhcCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHc-CCeEEEEeCCCCHH
Confidence            455677877766235678999999999999998 9999999999999999999999999999985 99999999999999


Q ss_pred             HHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHc-CCcEEE
Q 009230          340 EHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRH-GVRGLV  415 (539)
Q Consensus       340 ~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~-~~~~vv  415 (539)
                      ++..|+++..++++..+++.+    .++.+++.++   ...+.+.+++|.  +.+..++++|.+.+++++.++ ++++||
T Consensus        88 ql~~Rlls~~~~v~~~~l~~g----~Ls~~e~~~l~~a~~~l~~~~l~I~--d~~~~si~~i~~~ir~l~~~~gg~~lIV  161 (338)
T 4a1f_A           88 QLALRALSDLTSINMHDLESG----RLDDDQWENLAKCFDHLSQKKLFFY--DKSYVRIEQIRLQLRKLKSQHKELGIAF  161 (338)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHT----CCCHHHHHHHHHHHHHHHHSCEEEE--CCTTCCHHHHHHHHHHHHHHCTTEEEEE
T ss_pred             HHHHHHHHHhhCCCHHHHhcC----CCCHHHHHHHHHHHHHHhcCCeEEe--CCCCCcHHHHHHHHHHHHHhcCCCCEEE
Confidence            999999999999999999876    7999988765   455666677773  356678999999999999998 899999


Q ss_pred             EccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          416 IDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       416 ID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      || |++++.......++.+++.++++.||.||+++|||||+++| +|..+++.+++|.++||+||++|+|.||+|++|+|
T Consensus       162 ID-yLqlm~~~~~~~~r~~ei~~isr~LK~lAkel~vpVi~lsQl~R~~e~r~dkrP~lsDLreSg~IeqdAD~Vl~l~R  240 (338)
T 4a1f_A          162 ID-YLQLMSGSKATKERHEQIAEISRELKTLARELEIPIIALVQLNRSLENRDDKRPILSDIKDSGGIEQDADIVLFLYR  240 (338)
T ss_dssp             EE-EEECCCTHHHHHHCCCCHHHHHHHHHHHHHHHTSCEEEEEECCGGGGGSSSCSCCGGGSEETTEECCCCSEEEEEEC
T ss_pred             Ee-chHHhcCCCCCCChHHHHHHHHHHHHHHHHHcCCeEEEEEecCccccccccCCCChHhcccchhhhhhCcEEEEEec
Confidence            99 77777542111233356889999999999999999999999 99988888899999999999999999999999999


Q ss_pred             CCCC--------------CC----------------------CCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          495 NRDP--------------EA----------------------GPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       495 ~~~~--------------~~----------------------~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      ++..              +.                      ..++.++|+|.|||||++|++   .+.|++++.||.+.
T Consensus       241 ~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eiiiaK~R~G~~g~v---~l~f~~~~~~F~~~  317 (338)
T 4a1f_A          241 GYIYQMRAEDNKIDKLKKEGKIEEAQELYLKVNEERRIHKQNGSIEEAEIIVAKNRNGATGTV---YTRFNAPFTRYEDM  317 (338)
T ss_dssp             HHHHHHHHHHHHHHHHHGGGCHHHHHHHHHHHHHHHHHHHHTTSEEEEEEEEEEETTSCCEEE---EEEEEGGGTEECCC
T ss_pred             chhcccccccccccccccccccccccchhhhhhhhhcccccccCCCceEEEEEeccCCCCceE---EEEEccccceeccc
Confidence            7521              11                      125679999999999999875   79999999999874

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=100.00  E-value=6e-42  Score=341.20  Aligned_cols=272  Identities=17%  Similarity=0.237  Sum_probs=222.3

Q ss_pred             ccccccchHHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          256 GLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       256 ~~~~~~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +..++.++++++.+.+++..+...++||||+.||++++ |++|++++|+|+||+|||+|++|++.+++.+ |.+|+|||+
T Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~i~TG~~~LD~~lgGl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~-g~~vl~~sl  104 (315)
T 3bh0_A           26 DDGSIDEALVTVYEEIESADGNITGVPSGFTELDRMTYGYKRRNFVLIAARPSMGKTAFALKQAKNMSDN-DDVVNLHSL  104 (315)
T ss_dssp             CCCCCHHHHHHHHHHHHTCSSSCCSBCCSCHHHHHHHSSBCTTCEEEEECCTTSSHHHHHHHHHHHHHTT-TCEEEEEES
T ss_pred             CcccHHHHHHHHHHHHHhccCCCCCccCChHHHHhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHc-CCeEEEEEC
Confidence            34455666555444443324556899999999999998 9999999999999999999999999999986 899999999


Q ss_pred             CCCHHHHHHHHHHHhhCCCccccccCCCCCC--CCHHHHHH---HHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHc
Q 009230          335 ENKVREHARKLLEKHIKKPFFEANYGGSAER--MTVEEFEQ---GKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRH  409 (539)
Q Consensus       335 E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~--l~~~~~~~---~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~  409 (539)
                      ||+++++..|+++..++++..+++.+    .  ++.+++.+   +...+...++++.  +....++++|.+.+++++.++
T Consensus       105 E~s~~~l~~R~~~~~~~i~~~~l~~~----~~~l~~~~~~~l~~a~~~l~~~~i~i~--d~~~~~~~~i~~~i~~l~~~~  178 (315)
T 3bh0_A          105 EMGKKENIKRLIVTAGSINAQKIKAA----RRDFASEDWGKLSMAIGEISNSNINIF--DKAGQSVNYIWSKTRQTKRKN  178 (315)
T ss_dssp             SSCHHHHHHHHHHHHTTCCHHHHHSC----HHHHCSSCHHHHHHHHHHHHTSCEEEE--CCSCCBHHHHHHHHHHHHHTS
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHhcC----CCCCCHHHHHHHHHHHHHHhCCCEEEE--CCCCCCHHHHHHHHHHHHHhc
Confidence            99999999999999999998877644    3  55555543   4455655566652  245578999999999999989


Q ss_pred             CCc--EEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhcc
Q 009230          410 GVR--GLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKC  486 (539)
Q Consensus       410 ~~~--~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~a  486 (539)
                      +++  +|||| +++++.......++.+.+.++++.|+.+|+++|||||+++| +|..+++.+++|.++|++||+.|+|.|
T Consensus       179 ~~~~~lVVID-~l~~l~~~~~~~~r~~~i~~~~~~Lk~lAk~~~i~vi~lsql~r~~e~r~~~~p~l~dlr~sg~ie~~a  257 (315)
T 3bh0_A          179 PGKRVIVMID-YLQLLEPAKANDSRTNQISQISRDLKKMARELDVVVIALSQLSRQVEQRQDKRPMLSDLRESGQLEQDA  257 (315)
T ss_dssp             SSCCEEEEEE-CGGGSBCSCTTSCHHHHHHHHHHHHHHHHHHHTCEEEEEECCCGGGTTSSSCCCCGGGGTTTSHHHHHC
T ss_pred             CCCCeEEEEe-CchhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEEeecCcccccCCCCCCCHHHhhhhhhhHhhC
Confidence            999  99999 55555433233567788999999999999999999999999 888877778899999999999999999


Q ss_pred             ceEEEEEeCCC--CCCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          487 DNGIVIHRNRD--PEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       487 D~vl~l~r~~~--~~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      |+||+|+|++.  ++...++.+++.|.|||+|++|++   .+.|+++++||.+.
T Consensus       258 D~vi~L~r~~~~~~~~~~~~~~~l~v~K~R~G~~g~~---~l~f~~~~~~f~~~  308 (315)
T 3bh0_A          258 DIIEFLYRDDYYDKESESKNIVEVIIAKHRDGPVGTV---SLAFIKEYGNFVNL  308 (315)
T ss_dssp             SEEEEEEEHHHHCTTCTTTTEEEEEEEEETTSCCEEE---EEEEEGGGTEEEEC
T ss_pred             CEEEEEecccccCccccCCCcEEEEEECCcCCCCceE---EEEEECCCCeEecC
Confidence            99999999752  222234578999999999998865   69999999999875

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=100.00  E-value=1.6e-41  Score=352.06  Aligned_cols=272  Identities=17%  Similarity=0.234  Sum_probs=225.5

Q ss_pred             ccccccchHHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          256 GLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       256 ~~~~~~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +..++.++..+..+.++...+...|+||||+.||++++ |++|++++|+|+||+|||+|++|++.+++.+ |.+|+|||+
T Consensus       155 ~~~~~~~~~~~~~~~i~~~~~~~~gi~TG~~~LD~~lgGl~~G~liiIaG~pG~GKTtlal~ia~~~a~~-g~~vl~fSl  233 (444)
T 3bgw_A          155 DDGSIDEALVTVYEEIESADGNITGVPSGFTELDRMTYGYKRRNFVLIAARPSMGKTAFALKQAKNMSDN-DDVVNLHSL  233 (444)
T ss_dssp             CCCCCHHHHHHHHHHHHTCCSSCCSBCCSCHHHHHHHSSBCSSCEEEEEECSSSSHHHHHHHHHHHHHHT-TCEEEEECS
T ss_pred             CCccHHHHHHHHHHHHHHhhcCCCCcCCCcHHHHhhcCCCCCCcEEEEEeCCCCChHHHHHHHHHHHHHc-CCEEEEEEC
Confidence            44455555544333332211557899999999999998 9999999999999999999999999999997 999999999


Q ss_pred             CCCHHHHHHHHHHHhhCCCccccccCCCCCC--CCHHHHHH---HHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHc
Q 009230          335 ENKVREHARKLLEKHIKKPFFEANYGGSAER--MTVEEFEQ---GKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRH  409 (539)
Q Consensus       335 E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~--l~~~~~~~---~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~  409 (539)
                      ||+++++..|+++..++++..+++.+    .  ++.++|.+   +...+...++++.  +.+..++++|.+.+++++.++
T Consensus       234 Ems~~ql~~R~~~~~~~i~~~~l~~g----~~~l~~~~~~~l~~a~~~l~~~~l~i~--d~~~~s~~~i~~~ir~l~~~~  307 (444)
T 3bgw_A          234 EMGKKENIKRLIVTAGSINAQKIKAA----RRDFASEDWGKLSMAIGEISNSNINIF--DKAGQSVNYIWSKTRQTKRKN  307 (444)
T ss_dssp             SSCTTHHHHHHHHHHSCCCHHHHHHT----GGGTCCSCHHHHHHHHHHHHTSCEEEE--CCSSCBHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHhcc----cCCCCHHHHHHHHHHHHHHhcCCEEEE--CCCCCCHHHHHHHHHHHHHHh
Confidence            99999999999999999998888755    4  66555544   4556666667763  245678999999999999999


Q ss_pred             CCc--EEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhcc
Q 009230          410 GVR--GLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKC  486 (539)
Q Consensus       410 ~~~--~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~a  486 (539)
                      +++  +|||| +++++.......++.+.+.++++.|+.+|+++|||||+++| +|..+.+.+++|.++|++||++|+|.|
T Consensus       308 ~~~~~lIVID-~Lq~~~~~~~~~~r~~~i~~i~~~Lk~lAke~~v~vi~lsql~r~~e~r~~krp~lsdlr~Sg~ieq~a  386 (444)
T 3bgw_A          308 PGKRVIVMID-YLQLLEPAKANDSRTNQISQISRDLKKMARELDVVVIALSQLSRQVEQRQDKRPMLSDLRESGQLEQDA  386 (444)
T ss_dssp             CSSCEEEEEE-CSTTSBCSCSSSCHHHHHHHHHHHHHHHHHHHTCEEEEEEECCGGGGGSSCCCCCGGGCCSCSHHHHHC
T ss_pred             CCCCeEEEEe-cHHhccCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEEecCCccccccCCCCCchhhhhhhhhHHhhC
Confidence            999  99999 66666543223577788999999999999999999999999 998887778999999999999999999


Q ss_pred             ceEEEEEeCCCC--CCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          487 DNGIVIHRNRDP--EAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       487 D~vl~l~r~~~~--~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      |+|++|+|++..  +...++..++.|.|||+|++|++   .+.|+++++||.+.
T Consensus       387 D~Vi~L~r~~~~~~~~~~~~~~~l~i~K~R~G~~g~v---~l~f~~~~~rf~~~  437 (444)
T 3bgw_A          387 DIIEFLYRDDYYDKESESKNIVEVIIAKHRDGPVGTV---SLAFIKEYGNFVNL  437 (444)
T ss_dssp             SEEEECCBGGGTCTTCSSTTEEEEEEEEESSSCCEEE---EEEEETTTTEEECC
T ss_pred             CEEEEEeccccccccccCCCeEEEEEEcccCCCCeEE---EEEEEcCccEEecC
Confidence            999999998642  22234678999999999998865   79999999999885

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=100.00  E-value=1.6e-39  Score=339.27  Aligned_cols=254  Identities=19%  Similarity=0.264  Sum_probs=212.8

Q ss_pred             CCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          275 SGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       275 ~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      .+...++||||+.||.+++ |++|++++|+|+||+|||+|+++++.+++.+.|.+|+|||+||+++++..|+++..++++
T Consensus       177 ~~~~~~i~tG~~~LD~~lgGl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~slE~~~~~l~~R~~~~~~~i~  256 (444)
T 2q6t_A          177 KGEVAGVRTGFKELDQLIGTLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSLEMPAAQLTLRMMCSEARID  256 (444)
T ss_dssp             ------CCCSCHHHHHHHCCCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEESSSCHHHHHHHHHHHHTTCC
T ss_pred             CCCCCcccCCCHhhhhhcCCcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEECCCCHHHHHHHHHHHHcCCC
Confidence            3456899999999999998 999999999999999999999999999998558999999999999999999999999999


Q ss_pred             ccccccCCCCCCCCHHHHHHHH---HHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCC--C-
Q 009230          354 FFEANYGGSAERMTVEEFEQGK---AWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQR--P-  427 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~---~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~--~-  427 (539)
                      ..+++.+    .+++++|.++.   +.+...++++.  +.+..+++++.+.+++++.++++++|||| +.+++...  . 
T Consensus       257 ~~~l~~g----~l~~~~~~~~~~a~~~l~~~~l~i~--d~~~~s~~~l~~~~~~l~~~~~~~lIvID-~l~~~~~~~~~~  329 (444)
T 2q6t_A          257 MNRVRLG----QLTDRDFSRLVDVASRLSEAPIYID--DTPDLTLMEVRARARRLVSQNQVGLIIID-YLQLMSGPGSGK  329 (444)
T ss_dssp             TTTCCGG----GCCHHHHHHHHHHHHHHHTSCEEEE--CCTTCBHHHHHHHHHHHHHHSCCCEEEEE-CGGGCBCC----
T ss_pred             HHHHhCC----CCCHHHHHHHHHHHHHHhcCCEEEE--CCCCCCHHHHHHHHHHHHHHcCCCEEEEc-ChhhcCCCcCCC
Confidence            9888765    78988887653   45555566662  24566899999999999999999999999 55555432  1 


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCC--CCCCCC
Q 009230          428 VSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDP--EAGPID  504 (539)
Q Consensus       428 ~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~--~~~~~~  504 (539)
                      ...++.+.+.++++.|+.+|+++|||||+++| +|..+.+.+++|.++|++||++|++.||+|++|+|++..  +...++
T Consensus       330 ~~~~r~~~i~~i~~~Lk~lAke~~v~vi~lsql~r~~e~r~~~~p~l~dlr~Sg~ie~~aD~vi~L~r~~~~~~~~~~~~  409 (444)
T 2q6t_A          330 SGENRQQEIAAISRGLKALARELGIPIIALSQLSRAVEARPNKRPMLSDLRESGSIEQDADLVMFIYRDEYYNPHSEKAG  409 (444)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHTSCEEEEEECCGGGGSSSSCSCCGGGGGGGCTTGGGCSEEEEEEEGGGTCSSSSCCS
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHhCCeEEEEecCCcccccCCCCCCChHHhcchhHHHHhCCEEEEEecccccCCcCCCCC
Confidence            22467788999999999999999999999999 888877778899999999999999999999999998743  222346


Q ss_pred             cEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          505 RVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       505 ~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      .+++.|.|+|+|++|++   .+.|+++++||.+.
T Consensus       410 ~~~l~i~K~R~g~~g~~---~l~f~~~~~~f~~~  440 (444)
T 2q6t_A          410 IAEIIVGKQRNGPTGTV---ELQFHASHVRFNDL  440 (444)
T ss_dssp             EEEEEEEECSSSCCEEE---EEEEETTTTEEECC
T ss_pred             eEEEEEEecCCCCceEE---EEEEECCccEEecC
Confidence            78999999999998864   79999999999875

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=100.00  E-value=1.5e-37  Score=325.17  Aligned_cols=266  Identities=19%  Similarity=0.271  Sum_probs=217.2

Q ss_pred             chHHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHH
Q 009230          262 DYFDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVRE  340 (539)
Q Consensus       262 ~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~  340 (539)
                      ++++++++.+++ .+...++||||+.||++++ |++|++++|+|+||+|||+|+++++.+++...|.+|+|||+||+.++
T Consensus       168 ~~~~~~~~~~~~-~~~~~~i~tG~~~LD~~~gGl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~E~s~~~  246 (454)
T 2r6a_A          168 QTYDNIEMLHNR-DGEITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQ  246 (454)
T ss_dssp             HHHHHHHHHHSC-CCCCCSBCCSCHHHHHHHSSBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEESSSCHHH
T ss_pred             HHHHHHHHHHhC-CCCCCCCCCCcHHHHhhcCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEECCCCHHH
Confidence            445666665443 4567899999999999998 99999999999999999999999999999865889999999999999


Q ss_pred             HHHHHHHHhhCCCccccccCCCCCCCCHHHHHHH---HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEc
Q 009230          341 HARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG---KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVID  417 (539)
Q Consensus       341 ~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~---~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID  417 (539)
                      +..|+++..++++..+++.+    .++.+++..+   .+.+...++++.  +.+..+++++...++.++.++++++||||
T Consensus       247 l~~r~~~~~~~~~~~~l~~g----~l~~~~~~~~~~a~~~l~~~~l~i~--d~~~~s~~~i~~~~~~l~~~~~~~livID  320 (454)
T 2r6a_A          247 LVMRMLCAEGNINAQNLRTG----KLTPEDWGKLTMAMGSLSNAGIYID--DTPSIRVSDIRAKCRRLKQESGLGMIVID  320 (454)
T ss_dssp             HHHHHHHHHHTCCHHHHHTS----CCCHHHHHHHHHHHHHHHSSCEEEE--CCTTCCHHHHHHHHHHHHTTTCCCEEEEE
T ss_pred             HHHHHHHHHcCCCHHHHhcC----CCCHHHHHHHHHHHHHHhcCCEEEE--CCCCCCHHHHHHHHHHHHHHcCCCEEEEc
Confidence            99999998999999888655    7888887664   345555566663  24566899999999999888899999999


Q ss_pred             cccccccCCC-CCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          418 PYNELDHQRP-VSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       418 ~~~~l~~~~~-~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                       +.+++.... ...++.+.+.++++.|+.+|+++||+||+++| +|..+.+.+++|.++|++||+.+++.||.|++|+++
T Consensus       321 -~l~~~~~~~~~~~~~~~~i~~i~~~Lk~lAke~~i~vi~~sql~r~~e~~~~~~p~lsdlr~Sg~ie~~aD~vi~l~r~  399 (454)
T 2r6a_A          321 -YLQLIQGSGRSKENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDIRESGSIEQDADIVAFLYRD  399 (454)
T ss_dssp             -CGGGSCCSCC----CHHHHHHHHHHHHHHHHHHTCCEEEEECCCTTSTTC---CCCTHHHHTTCSHHHHCSEEEEEEET
T ss_pred             -cHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEEecCCcccccCCCCCCcHHHhhccchhHhhCCEEEEEecc
Confidence             555544321 12356678899999999999999999999999 888877777889999999999999999999999998


Q ss_pred             CCCC--CCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceeccC
Q 009230          496 RDPE--AGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       496 ~~~~--~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      +..+  ...++.+++.|.|||+|++|++   .+.|+++++||.+.
T Consensus       400 ~~~~~~~~~~~~~~l~i~K~R~G~~g~v---~l~f~~~~~~f~~~  441 (454)
T 2r6a_A          400 DYYNKDSENKNIIEIIIAKQRNGPVGTV---QLAFIKEYNKFVNL  441 (454)
T ss_dssp             TC-------CCEEEEEEEEESSSCCEEE---EEEEETTTTEEECC
T ss_pred             cccCcccCCCCeEEEEEecccCCCCeEE---EEEEEcCccEEeCC
Confidence            7532  1234678999999999998865   79999999999875

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=99.97  E-value=1.7e-30  Score=257.15  Aligned_cols=264  Identities=19%  Similarity=0.220  Sum_probs=182.5

Q ss_pred             HHHHHHHhhccCCCcccccc-Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHH
Q 009230          264 FDEIDAYYHRTSGDEFGIST-GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREH  341 (539)
Q Consensus       264 ~~~i~~~~~~~~~~~~gi~t-g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~  341 (539)
                      ++.+++.++.  ....+++| |++.||.+++ +++|++++|+|+||+|||||+.+++..++...|.+|+|+++|++..++
T Consensus         2 ~~~l~~~~~~--~~~~~i~t~g~~~Ld~i~~~l~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~~e~~~~~~   79 (296)
T 1cr0_A            2 RERIREHLSS--EESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEET   79 (296)
T ss_dssp             HHHHHHHHHH--CCCCCBCCCSCTTHHHHHCSBCTTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEESSSCHHHH
T ss_pred             hhHhhhhhcc--CCcCCcccCCHHHHHHHhcCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEeCcCCHHHH
Confidence            3455554433  66789999 9999999998 999999999999999999999999999887657799999999999999


Q ss_pred             HHHHHHHhhCCCccc---cccCCCCCCCCHHHHHHHHHHh-hccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEc
Q 009230          342 ARKLLEKHIKKPFFE---ANYGGSAERMTVEEFEQGKAWL-SNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVID  417 (539)
Q Consensus       342 ~~r~~~~~~~~~~~~---i~~~~~~~~l~~~~~~~~~~~l-~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID  417 (539)
                      ..|+.+...+.++..   +..+    .++.+++.++.+.+ ....+++. +.....++.++...++.++..+++++||||
T Consensus        80 ~~r~~~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~l~~~~l~i~-~~~~~~~~~~l~~~~~a~~~~~~p~llilD  154 (296)
T 1cr0_A           80 AEDLIGLHNRVRLRQSDSLKRE----IIENGKFDQWFDELFGNDTFHLY-DSFAEAETDRLLAKLAYMRSGLGCDVIILD  154 (296)
T ss_dssp             HHHHHHHHTTCCGGGCHHHHHH----HHHHTHHHHHHHHHHSSSCEEEE-CCCCSCCHHHHHHHHHHHHHTTCCSEEEEE
T ss_pred             HHHHHHHHcCCChhhccccccC----CCCHHHHHHHHHHHhccCCEEEE-CCCCCCCHHHHHHHHHHHHHhcCCCEEEEc
Confidence            999888777766432   1111    12334444444443 32234442 212456788888888876777899999999


Q ss_pred             cccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCC---CCCCCCCCcccccccccchhccceEEEEE
Q 009230          418 PYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLH---NWVGEPPNLYDISGSAHFINKCDNGIVIH  493 (539)
Q Consensus       418 ~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~---~~~~~~~~~~~l~gs~~i~~~aD~vl~l~  493 (539)
                      ..+.+.... ...++...+.++++.|+.+|+++|++||+++| +|...   .+.+++|.++|++||+.+++.||.|++|+
T Consensus       155 ept~~~~~~-~~~d~~~~~~~i~~~L~~la~~~~~~vi~vsh~~r~~~~~~~~~~~~p~l~dl~~s~~i~~~aD~vi~L~  233 (296)
T 1cr0_A          155 HISIVVSAS-GESDERKMIDNLMTKLKGFAKSTGVVLVVICHLKNPDKGKAHEEGRPVSITDLRGSGALRQLSDTIIALE  233 (296)
T ss_dssp             EEC------------CHHHHHHHHHHHHHHHHHCCEEEEEEECC-----------------CCC---CHHHHCSEEEEEE
T ss_pred             CccccCCCC-CCCCHHHHHHHHHHHHHHHHHHhCCeEEEEEecCccccccccccCCCCCHHHhcccHHhHhhCcEEEEEe
Confidence            666544221 11233356788999999999999999999999 65221   13468899999999999999999999999


Q ss_pred             eCCCCCCCCCCcEEEEEEEee-CCCcceeeeEEEEEeCCCceeccCC
Q 009230          494 RNRDPEAGPIDRVQVCVRKVR-NKVVGTIGEAFLSYNRVTGEYMDIV  539 (539)
Q Consensus       494 r~~~~~~~~~~~~~l~i~K~R-~g~~G~~~~~~l~fd~~~~rf~~~~  539 (539)
                      +.+..+  .++..++.+.|+| +|+.|.+  ..+.|++++++|.++.
T Consensus       234 ~~~~~~--~~~~~~l~i~K~R~~g~~g~~--~~~~f~~~~~~f~~~~  276 (296)
T 1cr0_A          234 RNQQGD--MPNLVLVRILKCRFTGDTGIA--GYMEYNKETGWLEPSS  276 (296)
T ss_dssp             EC---------CEEEEEEEETTTCCCEEE--EEEEECTTTCCEEECC
T ss_pred             cCcccC--CCCeEEEEEEccccCCCCCce--EEEEEEcCccEEecCC
Confidence            987532  1357899999999 7988864  2799999999998863

>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2

Probab=99.96  E-value=5.7e-29  Score=239.76  Aligned_cols=186  Identities=25%  Similarity=0.269  Sum_probs=142.0

Q ss_pred             cccCCCCCCcHHHHHHHHhcCCCHHHHHHcCcccccCCceeEEEEeEe-eCCEEEEEEeecCCCccccc-CCCCCccccc
Q 009230           40 EDSLELEPLGNELRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYW-RNGKLVNCKYRDFNKKFWQE-KDTEKVFYGL  117 (539)
Q Consensus        40 ~~~~~~~p~~~~~~~Yl~~Rgi~~~~~~~~~~~~~~~~~~~~i~fP~~-~~G~~~~~~~R~~~~~~~~~-~~~~~~l~g~  117 (539)
                      .+.+...|.. .+.+||.+|||+.++++.|++......+...++||+. .+|+++++++|..++.|++. +.+...+||+
T Consensus        66 ~~~~~~~~~~-~~~~YL~~RGi~~~~i~~f~~~~~~~~g~~~i~fp~~d~~G~vvg~~~R~~~~~~Ky~~s~k~~~lyg~  144 (255)
T 1nui_A           66 YNVWNFGESN-GRYSALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFGK  144 (255)
T ss_dssp             BCCBCGGGTT-CBCCCBGGGTBCHHHHHHHTEEEEEETTEEEEEEEEECTTSCEEEEEEECTTCCCEEEECCCTTCCTTG
T ss_pred             cccccccccH-HHHHHHHHcCCCHHHHHHhCeEEEccCCcEEEEEEEECCCCCEEEEEEECCCCCceEecCCCCccccCc
Confidence            3334444433 3678999999999999999886432223456999988 78999999999876666642 2355689999


Q ss_pred             cccCCCCcEEEEechhhHHHHHHh-CC-CceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCc
Q 009230          118 DDIEGESDIIIVEGEMDKLSMEEA-GF-LNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDP  195 (539)
Q Consensus       118 ~~~~~~~~v~i~EG~~Dalsl~~~-g~-~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~  195 (539)
                      +...+.++|+||||++|+||++|+ |. .++++++++....              ..+|.+++..|.++++||||+|||+
T Consensus       145 ~~~~~~~~v~i~EG~~Dals~~~~~g~~~~v~slg~~~~~~--------------~~~l~~~~~~l~~~~~iil~~D~D~  210 (255)
T 1nui_A          145 HLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASAA--------------KKTCAANYEYFDQFEQIILMFDMDE  210 (255)
T ss_dssp             GGCCCBSCCEEESSHHHHHHHHHHHTTCSCEECCTTTTTTH--------------HHHHHHTHHHHTTBSCEEEECCSSH
T ss_pred             cccCCCCEEEEEeCHHHHHHHHHhhCCCcEEEECCCccchh--------------HHHHHHHHHHhcCCCEEEEEeCCCH
Confidence            988767889999999999999999 64 3456654333220              1234455677888899999999999


Q ss_pred             cchHHHHHHHHHhcCCceEEEecCCCCCCCCCCChHHHHHhcCcchHHHHHH
Q 009230          196 PGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVE  247 (539)
Q Consensus       196 ~G~~~~~~~~~~l~~~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~~~~~~  247 (539)
                      ||+++++++++.|...+|+++.+|       +|||||+|+++|.+++.++|+
T Consensus       211 aG~~aa~~~~~~l~~~~v~~~~~p-------~kD~nd~l~~~g~~~~~~~i~  255 (255)
T 1nui_A          211 AGRKAVEEAAQVLPAGKVRVAVLP-------CKDANECHLNGHDREIMEQVW  255 (255)
T ss_dssp             HHHHHHHHHHHHSCTTTEEECCCS-------SSSHHHHHTTTTHHHHHHHHC
T ss_pred             HHHHHHHHHHHhccCCCEEEEeCC-------CCCHHHHHHhcCHHHHHHHhC
Confidence            999999999999965477766643       899999999999999988874

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=99.95  E-value=7.1e-28  Score=232.19  Aligned_cols=222  Identities=15%  Similarity=0.135  Sum_probs=157.9

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      .+..++|||++.||++++  |++|++++|+|+||+|||+|++|++.+.+.+.+.+|+|+|+||+++++..|+.+...+. 
T Consensus         7 ~~i~ri~TGi~~LD~~l~GGl~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~E~~~~~~~~~~~~~~~~~-   85 (251)
T 2zts_A            7 QPVRRVKSGIPGFDELIEGGFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLEERARDLRREMASFGWDF-   85 (251)
T ss_dssp             -CCCEECCSCTTTGGGTTTSEETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEESSSCHHHHHHHHHTTTCCH-
T ss_pred             CCCCeecCCcHHHHHhhcCCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeecccCCHHHHHHHHHHcCCCh-
Confidence            577899999999999994  99999999999999999999999999987766899999999999999999986543222 


Q ss_pred             ccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHH
Q 009230          354 FFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTET  433 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~  433 (539)
                       ......+   .+...++............+   ........+.+.+.+..++..+++++||||++..+....    .+.
T Consensus        86 -~~~~~~~---~~~~~d~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~vviD~~~~l~~~~----~~~  154 (251)
T 2zts_A           86 -EKYEKEG---KIAIVDGVSSVVGLPSEEKF---VLEDRFNVDNFLRYIYRVVKAINAKRLVIDSIPSIALRL----EEE  154 (251)
T ss_dssp             -HHHHHTT---SEEEEC----------------------CCHHHHHHHHHHHHHHTTCSEEEEECHHHHHHHS----SSG
T ss_pred             -HHHHhcC---cchhhhhHHHHhhcccchhc---cccccccHHHHHHHHHHHHHhcCCcEEEEEcHHHHhhhc----cCh
Confidence             1111000   11000000000000000111   113455778899999999999999999999888776432    122


Q ss_pred             HHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEe
Q 009230          434 EYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKV  513 (539)
Q Consensus       434 ~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~  513 (539)
                      ..+.+++..|+.+|+++||+|++++|...        +...++++++.+++.||.||.|++.+....   ....+.|.|+
T Consensus       155 ~~~~~~~~~L~~~a~~~~i~vi~~~q~~~--------~~~~~~~~~~~~~~~aD~vi~l~~~~~~~~---~~R~l~I~K~  223 (251)
T 2zts_A          155 RKIREVLLKLNTILLEMGVTTILTTEAPD--------PQHGKLSRYGIEEFIARGVIVLDLQEKNIE---LKRYVLIRKM  223 (251)
T ss_dssp             GGHHHHHHHHHHHHHHHCCEEEEEECCC------------CCSSSSSCGGGGCSEEEEEEEEECSSS---EEEEEEEEEE
T ss_pred             HHHHHHHHHHHHHHHHcCCCeEEEEEEec--------ccccccccCCceeEEeeEEEEEEEEecCCe---EEEEEEEEEc
Confidence            34678899999999999999999999321        234567889999999999999998765332   2467999999


Q ss_pred             eCCCcce
Q 009230          514 RNKVVGT  520 (539)
Q Consensus       514 R~g~~G~  520 (539)
                      |+++.+.
T Consensus       224 R~~~~~~  230 (251)
T 2zts_A          224 RETRHSM  230 (251)
T ss_dssp             TTCCCCC
T ss_pred             CCCCCCC
Confidence            9987654

>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transf; HET: DNA; 2.00A {Aquifex aeolicus}

Probab=99.95  E-value=2.8e-28  Score=249.86  Aligned_cols=178  Identities=19%  Similarity=0.248  Sum_probs=142.7

Q ss_pred             cHHHHHHHHhcCCCHHHHHHcCcccccC---------------------------------CceeEEEEeEe-eCCEEEE
Q 009230           49 GNELRAYFAERLISAETLRRNRVMQKRH---------------------------------GHEVVIAFPYW-RNGKLVN   94 (539)
Q Consensus        49 ~~~~~~Yl~~Rgi~~~~~~~~~~~~~~~---------------------------------~~~~~i~fP~~-~~G~~~~   94 (539)
                      ...+.+||.+|||+.++++.|++++...                                 ..+++|+||++ ..|++++
T Consensus       123 ~~~a~~YL~~RGi~~~~i~~f~lGyap~~~~l~~~l~~~~~~~~~l~~~Gl~~~~~g~~~d~f~~ri~fPi~d~~G~vig  202 (407)
T 2au3_A          123 NREASEYVKSRGIDPKVARKFDLGYAPSSEALVKVLKENDLLEAYLETKNLLSPTKGVYRDLFLRRVVIPIKDPRGRVIG  202 (407)
T ss_dssp             CHHHHHHHHHTTCCHHHHHHTTCEECCCHHHHHHHHHHHTCHHHHHTTTCEECSSTTCCEETTTTEEEEEEECTTSCEEE
T ss_pred             ChHHHHHHHHcCCCHHHHHHhCCCCCCchHHHHHHHHhcCCCHHHHHHCCceEecCCCcccccCCeEEEEEECCCCCEEE
Confidence            3568899999999999999998753321                                 11469999988 8899999


Q ss_pred             EEee-cC---CCcccccC-----CCCCccccccccC----CCCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCC
Q 009230           95 CKYR-DF---NKKFWQEK-----DTEKVFYGLDDIE----GESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKN  161 (539)
Q Consensus        95 ~~~R-~~---~~~~~~~~-----~~~~~l~g~~~~~----~~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~  161 (539)
                      +++| .+   .+||.+.+     .+...+||++.+.    +.++|+||||++|+||++|+|+.++|+.. |++.      
T Consensus       203 f~gRr~l~~~~pKylnspet~~f~k~~~lygl~~a~~~i~~~~~viivEG~~Dvlsl~q~G~~n~VA~l-Gtal------  275 (407)
T 2au3_A          203 FGGRRIVEDKSPKYINSPDSRVFKKGENLFGLYEAKEYIKEEGFAILVEGYFDLLRLFSEGIRNVVAPL-GTAL------  275 (407)
T ss_dssp             EEEEECSCCSSCSEEECCCCSSCCGGGCEETHHHHHHHHHHHTCEEECSSHHHHHHHHHTTCCSEEEES-SSSC------
T ss_pred             EEEEEecCCCCCeeecCCCCCCCCCCccccChHHHHHHhccCCeEEEEechHhHHHHHHCCCCcEEEcC-cccC------
Confidence            9999 55   46788754     3456789998653    35789999999999999999999888864 5432      


Q ss_pred             CCChhhhhhhHHHHhHHHHhccC-CEEEEEecCCccchHHHHHHHHHhc--CCceEEEecCCCCCCCCCCChHHHHHhcC
Q 009230          162 VPSEEQDTKYQYLWNCKMYLKQA-SRIILATDGDPPGQALAEELARRVG--RERCWRVRWPKKNDVDHFKDANEVLMYLG  238 (539)
Q Consensus       162 l~~~~~~~~~~~l~~~~~~l~~~-~~ivl~~DnD~~G~~~~~~~~~~l~--~~~~~~~~~p~~~~~~~~kD~nd~l~~~g  238 (539)
                       +           ..++..|.++ ++|++|+|||.||++|+.++++.|.  +..++++.+|      .+|||||+++++|
T Consensus       276 -t-----------~~~~~~L~r~~~~vil~~D~D~AG~~Aa~r~~~~l~~~g~~~~v~~lP------~gkDpdd~l~~~g  337 (407)
T 2au3_A          276 -T-----------QNQANLLSKFTKKVYILYDGDDAGRKAMKSAIPLLLSAGVEVYPVYLP------EGYDPDEFIKEFG  337 (407)
T ss_dssp             -C-----------HHHHHHHHTTCSEEEEECCSSHHHHHHHHHHHHHHHHTTCEEEEECCC------TTCCHHHHHHHHC
T ss_pred             -C-----------HHHHHHHHhcCCeEEEEEcCCHHHHHHHHHHHHHHHhCCCeEEEEECC------CCCChHHHHHhcC
Confidence             1           1124566665 7999999999999999999999884  3467788887      5799999999999


Q ss_pred             cchHHHHHHhccc
Q 009230          239 PGALKEVVENAEL  251 (539)
Q Consensus       239 ~~~~~~~~~~A~~  251 (539)
                      .+++.+++++|.+
T Consensus       338 ~~~~~~~l~~a~~  350 (407)
T 2au3_A          338 KEELRRLINSSGE  350 (407)
T ss_dssp             HHHHHHHHHHCCC
T ss_pred             HHHHHHHHHcCCC
Confidence            9999999999874

>4edg_A DNA primase; catalytic domain, nucleoside triphosphate, nucleoside polyph protein-ligand complex, transferase; HET: DNA ATP; 2.00A {Staphylococcus aureus} PDB: 4e2k_A* 4edk_A* 4edr_A* 4edt_A* 4edv_A* 4ee1_A*

Probab=99.94  E-value=1.8e-27  Score=233.53  Aligned_cols=191  Identities=21%  Similarity=0.335  Sum_probs=149.0

Q ss_pred             hhcccccCCCCCCcHHHHHHHHhcCCCHHHHHHcCcccccCC------------------------------------ce
Q 009230           36 REITEDSLELEPLGNELRAYFAERLISAETLRRNRVMQKRHG------------------------------------HE   79 (539)
Q Consensus        36 ~~~~~~~~~~~p~~~~~~~Yl~~Rgi~~~~~~~~~~~~~~~~------------------------------------~~   79 (539)
                      ..+....+.-.|....+++||.+|||++++++.|++++...+                                    .+
T Consensus        16 ~~~y~~~L~~~~~g~~a~~YL~~Rgl~~e~i~~f~lGyap~~~~~l~~~l~~~g~~~~~l~~~GL~~~~~~g~~~yd~Fr   95 (329)
T 4edg_A           16 QEFYYYALTKTVEGEQALTYLQERGFTDALIKERGIGFAPDSSHFCHDFLQKKGYDIELAYEAGLLSRNEENFSYYDRFR   95 (329)
T ss_dssp             HHHHHHHHHHSSTTHHHHHHHHHTTCCHHHHHHHTCEEECSSSCHHHHHHHHTTCCHHHHHHTTSEEEETTTTEEEESCC
T ss_pred             HHHHHHHHccCcccHHHHHHHHHcCCCHHHHHhCCeeeccCcHHHHHHHHHHCCCCHHHHHHCCCeEECCCCCccccccC
Confidence            333333333345666799999999999999999988543211                                    13


Q ss_pred             eEEEEeEe-eCCEEEEEEeecC---CCcccccC-----CCCCccccccccC----CCCcEEEEechhhHHHHHHhCCCce
Q 009230           80 VVIAFPYW-RNGKLVNCKYRDF---NKKFWQEK-----DTEKVFYGLDDIE----GESDIIIVEGEMDKLSMEEAGFLNC  146 (539)
Q Consensus        80 ~~i~fP~~-~~G~~~~~~~R~~---~~~~~~~~-----~~~~~l~g~~~~~----~~~~v~i~EG~~Dalsl~~~g~~~~  146 (539)
                      ++|+||++ ..|++++|.+|.+   .+||.+++     +++..|||++...    +.++|+||||++|+||++|+|+.++
T Consensus        96 ~Ri~fPI~d~~G~vigF~gR~l~~~~pKYlNspet~~f~K~~~Lygl~~a~~~i~~~~~vivvEG~~Dvial~q~Gi~na  175 (329)
T 4edg_A           96 NRIMFPLKNAQGRIVGYSGRTYTGQEPKYLNSPETPIFQKRKLLYNLDKARKSIRKLDEIVLLEGFMDVIKSDTAGLKNV  175 (329)
T ss_dssp             SEEEEEEECTTSCEEEEEEECSSSCSSSEEECCCCSSCCTTTCCBTHHHHHHHHHHHTCEEEESCHHHHHHHHHHTCCSE
T ss_pred             CEEEEEEECCCCCEEEEEeEECCCCCCeEeCCCCcccccccchhccHHHHHHHhccCCcEEEEecHHHHHHHHHcCCCeE
Confidence            69999988 7899999999998   37888866     3577899998764    4678999999999999999999998


Q ss_pred             EEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhcc-CCEEEEEecCCccchHHHHHHHHHhc--CCceEEEecCCCCC
Q 009230          147 VSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQ-ASRIILATDGDPPGQALAEELARRVG--RERCWRVRWPKKND  223 (539)
Q Consensus       147 v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~-~~~ivl~~DnD~~G~~~~~~~~~~l~--~~~~~~~~~p~~~~  223 (539)
                      |+. .|++-       ..           .++..|.+ .++||+|+|+|+||++|+.++.+.|.  +..++++.+|    
T Consensus       176 VA~-lGTal-------t~-----------~~~~~L~r~~~~Vil~~D~D~AG~~Aa~r~~~~l~~~g~~v~v~~lP----  232 (329)
T 4edg_A          176 VAT-MGTQL-------SD-----------EHITFIRKLTSNITLMFDGDFAGSEATLKTGQHLLQQGLNVFVIQLP----  232 (329)
T ss_dssp             EEC-SSSCC-------CH-----------HHHHHHHHHCSEEEECCCSSHHHHHHHHHHHHHHHHTTCEEEECCCC----
T ss_pred             EEC-CccCC-------CH-----------HHHHHHHhcCCeEEEEeCCCHHHHHHHHHHHHHHHhcCCeEEEEECC----
Confidence            885 45532       11           12445555 47999999999999999999999884  3467888887    


Q ss_pred             CCCCCChHHHHHhcCcchHHHHH-Hhccc
Q 009230          224 VDHFKDANEVLMYLGPGALKEVV-ENAEL  251 (539)
Q Consensus       224 ~~~~kD~nd~l~~~g~~~~~~~~-~~A~~  251 (539)
                        .+|||||+++++|.+++.+++ +++.+
T Consensus       233 --~gkDpdd~l~~~G~~~~~~~i~~~~~~  259 (329)
T 4edg_A          233 --SGMDPDEYIGKYGNDAFTTFVKNDKKS  259 (329)
T ss_dssp             --TTCCHHHHHHHHCHHHHHHHHHHCCEE
T ss_pred             --CCCCHHHHHHHhCHHHHHHHHHhcCCC
Confidence              579999999999999999985 55654

>1dd9_A DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein, transferase; HET: DNA; 1.60A {Escherichia coli} SCOP: e.13.1.1 PDB: 1dde_A* 1eqn_A* 3b39_A*

Probab=99.94  E-value=1.3e-26  Score=229.21  Aligned_cols=180  Identities=21%  Similarity=0.320  Sum_probs=144.1

Q ss_pred             CCcHHHHHHHHhcCCCHHHHHHcCcccccCC-----------------------------------ceeEEEEeEe-eCC
Q 009230           47 PLGNELRAYFAERLISAETLRRNRVMQKRHG-----------------------------------HEVVIAFPYW-RNG   90 (539)
Q Consensus        47 p~~~~~~~Yl~~Rgi~~~~~~~~~~~~~~~~-----------------------------------~~~~i~fP~~-~~G   90 (539)
                      |....+.+||.+|||++++++.|++++...+                                   ..++|+||+. ..|
T Consensus        39 ~~~~~a~~YL~~RGls~e~i~~f~lGyap~~~~~L~~~l~~~g~~~~~l~~~GL~~~~~~g~~yd~Fr~Ri~fPI~d~~G  118 (338)
T 1dd9_A           39 PVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSYDRFRERVMFPIRDKRG  118 (338)
T ss_dssp             GGGHHHHHHHHHTTCCHHHHHHHTCEEECSSSCHHHHHHCSSHHHHHHHHHTTSEEEC---CEEESCCSEEEEEEECTTS
T ss_pred             CccHHHHHHHHHcCCCHHHHHHcceeeccccHHHHHHHHHHcCCCHHHHHHCCCeeecCCCccccccCCEEEEEEECCCC
Confidence            5567799999999999999999998643211                                   1358999988 789


Q ss_pred             EEEEEEeecC---CCcccccCC-----CCCccccccc----cCCCCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCC
Q 009230           91 KLVNCKYRDF---NKKFWQEKD-----TEKVFYGLDD----IEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVS  158 (539)
Q Consensus        91 ~~~~~~~R~~---~~~~~~~~~-----~~~~l~g~~~----~~~~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~  158 (539)
                      ++++|.+|.+   .+||.+++.     +...+||++.    +.+.++|+||||++|+||++|+|+.++|++. |++.   
T Consensus       119 ~vigf~gR~l~~~~pKYlnspet~if~K~~~Lygl~~A~~~i~~~~~viIvEG~~Dvlsl~q~G~~~aVA~l-Gtal---  194 (338)
T 1dd9_A          119 RVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASL-GTST---  194 (338)
T ss_dssp             CEEEEEEEESSSCSCSEEECCCCSSCCTTTCCBTHHHHHHTCSSCSCEEEESSHHHHHHHHHTTCCCEEECC-C-CC---
T ss_pred             cEEEEEEEeCCCCCCceecCCCCcccccCccccCccHHHHhhccCCeEEEEechHhHHHHHHcCCCcEEEeC-cccc---
Confidence            9999999998   367887663     5678999875    3457899999999999999999999888854 5542   


Q ss_pred             CCCCCChhhhhhhHHHHhHHHHhcc-CCEEEEEecCCccchHHHHHHHHH---hc--CCceEEEecCCCCCCCCCCChHH
Q 009230          159 KKNVPSEEQDTKYQYLWNCKMYLKQ-ASRIILATDGDPPGQALAEELARR---VG--RERCWRVRWPKKNDVDHFKDANE  232 (539)
Q Consensus       159 ~~~l~~~~~~~~~~~l~~~~~~l~~-~~~ivl~~DnD~~G~~~~~~~~~~---l~--~~~~~~~~~p~~~~~~~~kD~nd  232 (539)
                          +.           .++..|.+ .++||||+|||+||++|+.++.+.   +.  +..++++.+|      .+|||||
T Consensus       195 ----t~-----------~~~~~L~r~~~~Vil~~D~D~AG~~Aa~r~~~~~~~l~~~g~~v~v~~lP------~gkDpdd  253 (338)
T 1dd9_A          195 ----TA-----------DHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLP------DGEDPDT  253 (338)
T ss_dssp             ----CH-----------HHHHHHHHHCSEEEEEEESSHHHHHHHHHHHHHHGGGCCTTCEEEEEEEC------TTCCHHH
T ss_pred             ----CH-----------HHHHHHHhcCCeEEEEeCCCHHHHHHHHHHHHHHHHHHhCCCEEEEecCC------CCCChHH
Confidence                11           12344543 489999999999999999999987   42  3467888888      5899999


Q ss_pred             HHHhcCcchHHHHHHhccc
Q 009230          233 VLMYLGPGALKEVVENAEL  251 (539)
Q Consensus       233 ~l~~~g~~~~~~~~~~A~~  251 (539)
                      +++++|.+++.+++++|.+
T Consensus       254 ~l~~~G~~~~~~~l~~a~~  272 (338)
T 1dd9_A          254 LVRKEGKEAFEARMEQAMP  272 (338)
T ss_dssp             HHHHHHHHHHHHHHTTCEE
T ss_pred             HHHHhcHHHHHHHHHcCCC
Confidence            9999999999999988875

>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=99.89  E-value=7.8e-23  Score=205.77  Aligned_cols=223  Identities=13%  Similarity=0.120  Sum_probs=156.7

Q ss_pred             CCccccccCchhhhhhhc---cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCC
Q 009230          276 GDEFGISTGWRALNELYN---VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKK  352 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~---l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~  352 (539)
                      ....++|||++.||.+++   |++|++++|+|+||+|||+|+++++.+++.. |.+|+||++|++..++.    +...|+
T Consensus        50 ~~~~~i~TG~~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~~~~~-g~~vlyi~~E~s~~~~~----a~~~g~  124 (366)
T 1xp8_A           50 LDVQVVSTGSLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKA-GGTCAFIDAEHALDPVY----ARALGV  124 (366)
T ss_dssp             CCCCEECCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT-TCCEEEEESSCCCCHHH----HHHTTC
T ss_pred             ccCceecCCCHHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHHHHHC-CCeEEEEECCCChhHHH----HHHcCC
Confidence            456789999999999984   9999999999999999999999999999885 89999999999877653    222344


Q ss_pred             CccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCC-CC--
Q 009230          353 PFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRP-VS--  429 (539)
Q Consensus       353 ~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~-~~--  429 (539)
                      +..                         .+++.     ...+.+++.+.++.++...++++||||++..+..... .+  
T Consensus       125 d~~-------------------------~l~i~-----~~~~~e~~l~~l~~l~~~~~~~lVVIDsl~~l~~~~e~~g~~  174 (366)
T 1xp8_A          125 NTD-------------------------ELLVS-----QPDNGEQALEIMELLVRSGAIDVVVVDSVAALTPRAEIEGDM  174 (366)
T ss_dssp             CGG-------------------------GCEEE-----CCSSHHHHHHHHHHHHTTTCCSEEEEECTTTCCCSTTC----
T ss_pred             CHH-------------------------Hceee-----cCCcHHHHHHHHHHHHhcCCCCEEEEeChHHhcccccccccc
Confidence            321                         12222     2346788888888887778899999997777653111 00  


Q ss_pred             -C----CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC-C-CCC
Q 009230          430 -Q----TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD-P-EAG  501 (539)
Q Consensus       430 -~----~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~-~-~~~  501 (539)
                       .    .....+.++++.|+.+|+++||+||+++| +++.....+ .|  ....|+..+++.||+++.|+|.+. . +..
T Consensus       175 gd~~~~~~~r~~~~~lr~L~~~a~~~~~~VI~~nq~~~~~~~~fg-~p--~~~~gg~al~~~a~~rl~L~r~~~~~k~~~  251 (366)
T 1xp8_A          175 GDSLPGLQARLMSQALRKLTAILSKTGTAAIFINQVREKIGVMYG-NP--ETTTGGRALKFYASVRLDVRKIGQPTKVGN  251 (366)
T ss_dssp             ----CCHHHHHHHHHHHHHHHHHTTTCCEEEEEEEC------------------CHHHHHHHCSEEEEEEEESCCC----
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHcCCEEEEEEecccccCcccC-Cc--cccCCcchhhheeeEEEEEEecchhcccCc
Confidence             0    12235678999999999999999999999 665543211 11  112468899999999999999763 1 111


Q ss_pred             --CCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceec
Q 009230          502 --PIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYM  536 (539)
Q Consensus       502 --~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~  536 (539)
                        ..+.+++.|.|||+++.+....+.+.|+..-.+|.
T Consensus       252 ~~~g~~~~v~v~Knr~~p~~~~~~f~i~~~~Gi~~~~  288 (366)
T 1xp8_A          252 DAVANTVKIKTVKNKVAAPFKEVELALVYGKGFDQLS  288 (366)
T ss_dssp             --CEEEEEEEEEEESSSCCCCEEEEEEETTTEECHHH
T ss_pred             cccCCEEEEEEEcCCCCCCCceEEEEEEeCCCcccch
Confidence              12468999999999987655556666665544443

>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=99.89  E-value=2e-22  Score=201.46  Aligned_cols=237  Identities=12%  Similarity=0.124  Sum_probs=164.9

Q ss_pred             chHHHHHHhccccCccccccccchHHHHHHHhhccCCCccccccCchhhhhhh-c-cCCCcEEEEEcCCCCChhHHHHHH
Q 009230          240 GALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELY-N-VLPGELTIVTGVPNSGKSEWIDAL  317 (539)
Q Consensus       240 ~~~~~~~~~A~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~-~-l~~G~l~~i~G~~G~GKT~~~~~l  317 (539)
                      +.+.+++..|....+.+..+..++.+.        .....+++||++.||.++ | +++|++++|+|+||+|||+|++++
T Consensus        47 ~~a~~~i~~a~~~~~~~~~~~~~~~~~--------~~~~~~i~TG~~~LD~~l~GGl~~g~i~~i~G~~gsGKT~la~~l  118 (322)
T 2i1q_A           47 KAAAKMIMGARDLCDLGFKSGIDLLKQ--------RSTVWKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQS  118 (322)
T ss_dssp             HHHHHHHHHHHHHTTCSCCCTHHHHHH--------HTTCCEECCSCHHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhcCCcHHHHHHH--------hccCCeecCCChhHHHhcCCCccCCeEEEEECCCCCCHHHHHHHH
Confidence            456666776665444556665665431        134578999999999999 4 999999999999999999999999


Q ss_pred             HHHHHHh-----------cC----CeEEEEeCCCC--HHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhc
Q 009230          318 ICNINEH-----------AG----WKFVLCSMENK--VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSN  380 (539)
Q Consensus       318 a~~~a~~-----------~g----~~vl~~s~E~~--~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~  380 (539)
                      +.+++..           .|    .+|+||++|++  ++++..++..  .+++              .+++      + +
T Consensus       119 a~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~~~~--~g~~--------------~~~~------~-~  175 (322)
T 2i1q_A          119 CVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEH--AGID--------------GQTV------L-D  175 (322)
T ss_dssp             HHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHHHHH--HTCC--------------HHHH------H-H
T ss_pred             HHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHHHHH--cCCC--------------HHHH------h-c
Confidence            9886432           24    79999999997  8888776532  3332              2211      1 2


Q ss_pred             cceeEeecCCCCCCHH---HHHHHHHHHHHH-cCCcEEEEccccccccCCCC--CC--CHHHHHHHHHHHHHHHHHHhCc
Q 009230          381 TFSLIRCENDSLPSIK---WVLDLAKAAVLR-HGVRGLVIDPYNELDHQRPV--SQ--TETEYVSQMLTMVKRFAQHHAC  452 (539)
Q Consensus       381 ~~~~i~~~~~~~~~~~---~i~~~i~~~~~~-~~~~~vvID~~~~l~~~~~~--~~--~~~~~~~~~~~~Lk~lA~~~~i  452 (539)
                      +.++..     ..+.+   ++...+..++.+ .++++||||++..+......  +.  ++...+.+++..|+.+|+++|+
T Consensus       176 ~l~~~~-----~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~l~~~~~~~~~~~~~r~~~~~~~~~~L~~la~~~~~  250 (322)
T 2i1q_A          176 NTFVAR-----AYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTSTFRNEYTGRGKLAERQQKLGRHMATLNKLADLFNC  250 (322)
T ss_dssp             TEEEEE-----CSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSSHHHHHHCCCTTSHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CEEEEe-----CCCHHHHHHHHHHHHHHHhhccCccEEEEECcHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            233331     22333   455666666776 78999999988877542110  11  1234678999999999999999


Q ss_pred             EEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCCCccee
Q 009230          453 HVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       453 ~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~G~~  521 (539)
                      +||+++| +++.....+   ......|+..+++.+|++|.|++.+.      ....+.+.|+|+++.|.+
T Consensus       251 ~vi~~nq~~~~~~~~~g---~~~~~~g~~~~~~~~d~~i~l~~~~~------~~r~~~v~k~~~~p~~~~  311 (322)
T 2i1q_A          251 VVLVTNQVSAKPDAFFG---MAEQAIGGHIVGHAATFRFFVRKGKG------DKRVAKLYDSPHLPDAEA  311 (322)
T ss_dssp             EEEEEECEECC----------CCEESSHHHHHHHCSEEEEEEECST------TEEEEEEEECSSSCCEEE
T ss_pred             EEEEECceeecCCCCCC---CCcCCCCcHHHHhcCcEEEEEEecCC------CeEEEEEEECCCCCCeEE
Confidence            9999999 665432110   11234577789999999999998752      245899999999988764

>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=99.89  E-value=3.1e-22  Score=199.89  Aligned_cols=236  Identities=15%  Similarity=0.119  Sum_probs=143.7

Q ss_pred             chHHHHHHhccccCccccccccchHHHHHHHhhccCCCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHH
Q 009230          240 GALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDAL  317 (539)
Q Consensus       240 ~~~~~~~~~A~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~l  317 (539)
                      +.+..+++.|....+.+..+..++.+.        .....+++||++.||.+++  +++|++++|+|+||+|||+|++++
T Consensus        56 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~i~TG~~~LD~~L~GGl~~G~i~~i~G~~GsGKT~la~~l  127 (324)
T 2z43_A           56 STAQKIIKEARDALDIRFKTALEVKKE--------RMNVKKISTGSQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQL  127 (324)
T ss_dssp             ----------------CCCCHHHHHHH--------HCSCCEECCSCHHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcccCccchhhhhhh--------hccCCcccCCchhHHHhcCCCCCCCcEEEEECCCCCCHhHHHHHH
Confidence            455566666655444555555555321        1346789999999999994  999999999999999999999999


Q ss_pred             HHHHHHhc-----CCeEEEEeCCCC--HHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCC
Q 009230          318 ICNINEHA-----GWKFVLCSMENK--VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCEND  390 (539)
Q Consensus       318 a~~~a~~~-----g~~vl~~s~E~~--~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~  390 (539)
                      +.+++...     +.+|+||++|++  ++++..++..  .+++              .+++      + ++.++..    
T Consensus       128 a~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~~~~~--~g~~--------------~~~~------~-~~l~~~~----  180 (324)
T 2z43_A          128 SVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKA--LGLD--------------IDNV------M-NNIYYIR----  180 (324)
T ss_dssp             HHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHH--TTCC--------------HHHH------H-HTEEEEE----
T ss_pred             HHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHH--hCCC--------------HHHH------h-ccEEEEe----
Confidence            99876532     679999999997  7877766432  2322              2221      1 2333332    


Q ss_pred             CCCCHH---HHHHHHHHHHHH-cCCcEEEEccccccccCCC--CCC--CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CC
Q 009230          391 SLPSIK---WVLDLAKAAVLR-HGVRGLVIDPYNELDHQRP--VSQ--TETEYVSQMLTMVKRFAQHHACHVWFVAH-PR  461 (539)
Q Consensus       391 ~~~~~~---~i~~~i~~~~~~-~~~~~vvID~~~~l~~~~~--~~~--~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r  461 (539)
                       ..+.+   ++...+..++.+ .++++||||++..+.....  .+.  ++...+.++++.|+.+|+++|++||+++| ++
T Consensus       181 -~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~l~~~~~~~~g~~~~r~~~~~~~l~~L~~la~~~~~~Vi~~nq~~~  259 (324)
T 2z43_A          181 -AINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFRAEYPGRENLAVRQQKLNKHLHQLTRLAEVYDIAVIITNQVMA  259 (324)
T ss_dssp             -CCSHHHHHHHHHHHHHHHHHCTTEEEEEETTTTHHHHHHSCTTTSHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEEC--
T ss_pred             -CCCHHHHHHHHHHHHHHHHhccCCCEEEEeCcHHHhhhhhcCcccHHHHHHHHHHHHHHHHHHHHHhCCEEEEEcceee
Confidence             22333   456667777777 7899999998887764211  011  12346789999999999999999999999 65


Q ss_pred             CCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCCCcce
Q 009230          462 QLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGT  520 (539)
Q Consensus       462 ~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~G~  520 (539)
                      +.....   .......|+..+++.+|++|.|++.+.      ....+.+.|+|+++.|.
T Consensus       260 ~~~~~~---~~~~~~~gg~~l~~~~d~~l~l~r~~~------~~r~~~v~k~~~~p~~~  309 (324)
T 2z43_A          260 RPDMFY---GDPTVAVGGHTLYHVPGIRIQLKKSRG------NRRIARVVDAPHLPEGE  309 (324)
T ss_dssp             -------------------------CEEEEEEECST------TEEEEEEEECSSSCCEE
T ss_pred             cCCCcC---CCCCCCCchHHHHhhCcEEEEEEEcCC------CeEEEEEEECCCCCceE
Confidence            543211   011123567789999999999998652      24689999999998775

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=99.88  E-value=5.6e-22  Score=199.37  Aligned_cols=243  Identities=14%  Similarity=0.118  Sum_probs=152.2

Q ss_pred             chHHHHHHhccccCccccccccchHHHHHHHhhccCCCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHH
Q 009230          240 GALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDAL  317 (539)
Q Consensus       240 ~~~~~~~~~A~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~l  317 (539)
                      +.+.++++.|......+..+..++.+.        .....+++||++.||.+++  +++|++++|+|+||+|||+|++++
T Consensus        71 ~~~~~~~~~a~~~~~~~~~~~~~~~~~--------~~~~~~i~TG~~~LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~l  142 (343)
T 1v5w_A           71 AKVDKIKEAANKLIEPGFLTAFEYSEK--------RKMVFHITTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTL  142 (343)
T ss_dssp             ---------------CCSEEHHHHHHH--------GGGCCCBCCSCHHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcccCCCcHHHHHhh--------hcccceeecCChhHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHH
Confidence            345555666654444445544444321        1235689999999999994  999999999999999999999999


Q ss_pred             HHHHHHh-----cCCeEEEEeCCCC--HHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCC
Q 009230          318 ICNINEH-----AGWKFVLCSMENK--VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCEND  390 (539)
Q Consensus       318 a~~~a~~-----~g~~vl~~s~E~~--~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~  390 (539)
                      +.+++..     .+.+|+||++|++  ++++..++..  .+++              .++   +   +. ++++..  ..
T Consensus       143 a~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~~~~~--~g~~--------------~~~---~---l~-~l~~~~--~~  197 (343)
T 1v5w_A          143 CVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADR--FNVD--------------HDA---V---LD-NVLYAR--AY  197 (343)
T ss_dssp             HHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHHHHHH--TTCC--------------HHH---H---HH-TEEEEE--CC
T ss_pred             HHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHH--cCCC--------------HHH---H---Hh-ceeEee--cC
Confidence            9987652     2789999999996  7777766532  2322              211   1   22 233332  12


Q ss_pred             CCCCHHHHHHHHHHHHHH--cCCcEEEEccccccccCCCC--CC--CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCC
Q 009230          391 SLPSIKWVLDLAKAAVLR--HGVRGLVIDPYNELDHQRPV--SQ--TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQL  463 (539)
Q Consensus       391 ~~~~~~~i~~~i~~~~~~--~~~~~vvID~~~~l~~~~~~--~~--~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~  463 (539)
                      ....+.++...++.++.+  .++++||||++..+....-.  +.  ++...+.++++.|+.+|+++|++||+++| +++.
T Consensus       198 ~~e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~l~~~~~~~~g~~~~r~~~l~~~l~~L~~la~~~~~~Vi~~nq~~~~~  277 (343)
T 1v5w_A          198 TSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAERQQKLAQMLSRLQKISEEYNVAVFVTNQMTADP  277 (343)
T ss_dssp             STTHHHHHHHHHHHHHHHSCSSEEEEEEETSGGGHHHHCCGGGCHHHHHHHHHHHHHHHHHHHHHHTCEEEEEECC----
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCccEEEEechHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHhCCEEEEEeeceecC
Confidence            223344566667777777  78999999988877643111  11  12345789999999999999999999999 6655


Q ss_pred             CCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCCCccee
Q 009230          464 HNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       464 ~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~G~~  521 (539)
                      ..+..-..+...-.|+..+++.||++|.|++.+.      ....+.|.|+|+++.|.+
T Consensus       278 ~~~~~~~g~~~~~~gg~~i~~~ad~~l~l~r~~~------~~r~~~v~K~r~~p~~~~  329 (343)
T 1v5w_A          278 GATMTFQADPKKPIGGHILAHASTTRISLRKGRG------ELRIAKIYDSPEMPENEA  329 (343)
T ss_dssp             ---------------CCTTTTSSSEEEEEEESST------TEEEEEEEECTTCCSSCE
T ss_pred             CCccccCCCCCcCCchHHHHHhCCEEEEEEEcCC------CEEEEEEEECCCCCCeeE
Confidence            3310000000112356689999999999998652      256899999999988763

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=99.88  E-value=2e-21  Score=186.43  Aligned_cols=213  Identities=15%  Similarity=0.200  Sum_probs=147.1

Q ss_pred             cccccCchhhhhhh-c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccc
Q 009230          279 FGISTGWRALNELY-N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFE  356 (539)
Q Consensus       279 ~gi~tg~~~LD~~~-~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~  356 (539)
                      .+++||++.||+++ + +++|++++|+|+||+|||+|+++++.+.+.. |.+|+|+++|++..++..|+.  ..|.++..
T Consensus         3 ~~i~tG~~~LD~~l~gGl~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~-~~~v~~~~~e~~~~~~~~~~~--~~g~~~~~   79 (247)
T 2dr3_A            3 RRVKTGIPGVDEILHGGIPERNVVLLSGGPGTGKTIFSQQFLWNGLKM-GEPGIYVALEEHPVQVRQNMA--QFGWDVKP   79 (247)
T ss_dssp             CEECCCCTTHHHHTTTSEETTCEEEEEECTTSSHHHHHHHHHHHHHHT-TCCEEEEESSSCHHHHHHHHH--TTTCCCHH
T ss_pred             ccccCCchhHHHHcCCCCCCCcEEEEECCCCCCHHHHHHHHHHHHHhc-CCeEEEEEccCCHHHHHHHHH--HcCCCHHH
Confidence            47999999999997 4 9999999999999999999999999999885 899999999999998888874  24444322


Q ss_pred             cccCCCCCCCCHHH-HHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHH
Q 009230          357 ANYGGSAERMTVEE-FEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEY  435 (539)
Q Consensus       357 i~~~~~~~~l~~~~-~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~  435 (539)
                      +...+   .+...+ .......+.....++ .  ....+++++...+..++.+.++++||||++..+...     +. ..
T Consensus        80 ~~~~~---~l~~~~~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~~i~~~~~~~~~~~vviD~~~~l~~~-----~~-~~  147 (247)
T 2dr3_A           80 YEEKG---MFAMVDAFTAGIGKSKEYEKYI-V--HDLTDIREFIEVLRQAIRDINAKRVVVDSVTTLYIN-----KP-AM  147 (247)
T ss_dssp             HHHHT---SEEEEECSTTTTCC--CCCSCB-C--SCCSSHHHHHHHHHHHHHHHTCCEEEEETSGGGTTT-----CG-GG
T ss_pred             HhhCC---cEEEEecchhhccccccccccc-c--cCccCHHHHHHHHHHHHHHhCCCEEEECCchHhhcC-----CH-HH
Confidence            11000   000000 000000000001111 0  233567888888888888889999999988877521     11 13


Q ss_pred             HHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEee
Q 009230          436 VSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVR  514 (539)
Q Consensus       436 ~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R  514 (539)
                      ..+++..|.++++++|++|++++| ++...          +++++ .+++.||.|+.|++.+...   .....+.|.|+|
T Consensus       148 ~~~~l~~l~~~~~~~~~~vi~~~h~~~~~~----------~~~~~-~~~~~~D~vi~L~~~~~~~---~~~r~l~v~K~R  213 (247)
T 2dr3_A          148 ARSIILQLKRVLAGTGCTSIFVSQVSVGER----------GFGGP-GVEHGVDGIIRLDLDEIDG---ELKRSLIVWKMR  213 (247)
T ss_dssp             HHHHHHHHHHHHHHTTCEEEEEEECC--------------CCC-C-CHHHHSSEEEEEEEEEETT---EEEEEEEEEEET
T ss_pred             HHHHHHHHHHHHHHCCCeEEEEecCCCCcc----------ccccc-ccceeEEEEEEEEEEccCC---eeEEEEEEEECC
Confidence            456778889999999999999999 55321          11222 4789999999999875421   236789999999


Q ss_pred             CCCcce
Q 009230          515 NKVVGT  520 (539)
Q Consensus       515 ~g~~G~  520 (539)
                      +++.+.
T Consensus       214 ~~~~~~  219 (247)
T 2dr3_A          214 GTSHSM  219 (247)
T ss_dssp             TSCCCC
T ss_pred             CCCCCC
Confidence            998763

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=99.88  E-value=5.4e-22  Score=229.90  Aligned_cols=214  Identities=15%  Similarity=0.112  Sum_probs=162.0

Q ss_pred             CCccccccCchhhhhhhc---cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCC
Q 009230          276 GDEFGISTGWRALNELYN---VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKK  352 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~---l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~  352 (539)
                      ....+++||++.||++++   +++|++++|+|+||+|||+|+++++.+++.+ |.+|+|||+||+..++.    +...|+
T Consensus       708 ~~~~~i~TG~~eLD~lLg~GGl~~G~lVlI~G~PG~GKTtLal~lA~~aa~~-g~~VlyiS~Ees~~ql~----A~~lGv  782 (1706)
T 3cmw_A          708 MDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE-GKTCAFIDAEHALDPIY----ARKLGV  782 (1706)
T ss_dssp             GSCCEECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEECTTSCCCHHH----HHHTTC
T ss_pred             ccccccccCcHHHHHHhccCCcCCCceEEEECCCCCCcHHHHHHHHHHHHHc-CCCeEEEeccchHHHHH----HHHcCC
Confidence            356789999999999994   9999999999999999999999999999985 89999999999988764    444454


Q ss_pred             CccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcccccccc-C---CCC
Q 009230          353 PFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDH-Q---RPV  428 (539)
Q Consensus       353 ~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~-~---~~~  428 (539)
                      +..                         .+++.     ...+++++.+.+++++.++++++||||++..+.. .   ...
T Consensus       783 d~~-------------------------~L~i~-----~~~~leei~~~l~~lv~~~~~~lVVIDsLq~l~~~~e~~~~~  832 (1706)
T 3cmw_A          783 DID-------------------------NLLCS-----QPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEI  832 (1706)
T ss_dssp             CGG-------------------------GCEEE-----CCSSHHHHHHHHHHHHHHTCCSEEEESCSTTCCCHHHHHSCT
T ss_pred             Chh-------------------------heEEe-----cCCcHHHHHHHHHHHHHccCCCEEEEechhhhcccccccccc
Confidence            432                         12332     2337889999999988889999999996665542 1   011


Q ss_pred             CC----CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC---CCC
Q 009230          429 SQ----TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD---PEA  500 (539)
Q Consensus       429 ~~----~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~---~~~  500 (539)
                      +.    .....+.+++..|+.+|+++|++||+++| ++......+ .|.  .-.||+.+++.||+++.|+|++.   .+.
T Consensus       833 G~~~~~~q~reis~~Lr~Lk~lAke~gi~VIlinql~r~~g~~~G-dp~--~p~gs~~Leq~ADvvl~L~R~~~~~~g~~  909 (1706)
T 3cmw_A          833 GDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKIGVMFG-NPE--TTTGGNALKFYASVRLDIRRIGAVKEGEN  909 (1706)
T ss_dssp             TCCCTTHHHHHHHHHHHHHHHHHHHHTCEEEEEECEEECTTCCSS-CCE--EESSCSHHHHHEEEEEEEEEEEEEEETTE
T ss_pred             CccchhHHHHHHHHHHHHHHHHHHHcCCEEEEEecCCCccccccC-Ccc--ccCCcchhhheeeEEEEEEeccccccccc
Confidence            11    13345788899999999999999999999 776554332 221  12368999999999999998752   111


Q ss_pred             CCCCcEEEEEEEeeCCCcceeeeEEEE
Q 009230          501 GPIDRVQVCVRKVRNKVVGTIGEAFLS  527 (539)
Q Consensus       501 ~~~~~~~l~i~K~R~g~~G~~~~~~l~  527 (539)
                      ...+.+.+.+.|||+|++|+.+.+.+.
T Consensus       910 ~~g~~r~l~V~KnR~gp~~~~~~F~I~  936 (1706)
T 3cmw_A          910 VVGSETRVKVVKNKIAAPFKQAEFQIL  936 (1706)
T ss_dssp             EEEEEEEEEEEEESSSCSCCEEEEEEE
T ss_pred             ccCcEEEEEEEecCCCCCCceEEEEEE
Confidence            112368899999999999987655553

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=99.87  E-value=9.3e-21  Score=178.53  Aligned_cols=201  Identities=19%  Similarity=0.189  Sum_probs=142.8

Q ss_pred             ccccCchhhhhhh-c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC--CHHHHHHHHHHHhhCCCcc
Q 009230          280 GISTGWRALNELY-N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN--KVREHARKLLEKHIKKPFF  355 (539)
Q Consensus       280 gi~tg~~~LD~~~-~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~--~~~~~~~r~~~~~~~~~~~  355 (539)
                      .++||++.||+++ | +++|++++|.|+||+|||||+.+++.   . .+.+|+|++.|+  +..++...+ . ..+    
T Consensus         1 ri~tG~~~LD~~l~Ggi~~G~~~~i~G~~GsGKTtl~~~l~~---~-~~~~v~~i~~~~~~~~~~~~~~~-~-~~~----   70 (220)
T 2cvh_A            1 MLSTGTKSLDSLLGGGFAPGVLTQVYGPYASGKTTLALQTGL---L-SGKKVAYVDTEGGFSPERLVQMA-E-TRG----   70 (220)
T ss_dssp             CBCCSCHHHHHHTTSSBCTTSEEEEECSTTSSHHHHHHHHHH---H-HCSEEEEEESSCCCCHHHHHHHH-H-TTT----
T ss_pred             CcccCcHHHHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHH---H-cCCcEEEEECCCCCCHHHHHHHH-H-hcC----
Confidence            3799999999999 4 99999999999999999999999998   3 389999999998  776654422 1 111    


Q ss_pred             ccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHH
Q 009230          356 EANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEY  435 (539)
Q Consensus       356 ~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~  435 (539)
                                +..+++      + +...+.  ...+......+.+.++.++.+ ++++||||+...++.......++...
T Consensus        71 ----------~~~~~~------~-~~~~~~--~~~~~~~~~~~~~~~~~l~~~-~~~lliiD~~~~~l~~~~~~~~~~~~  130 (220)
T 2cvh_A           71 ----------LNPEEA------L-SRFILF--TPSDFKEQRRVIGSLKKTVDS-NFALVVVDSITAHYRAEENRSGLIAE  130 (220)
T ss_dssp             ----------CCHHHH------H-HHEEEE--CCTTTSHHHHHHHHHHHHCCT-TEEEEEEECCCCCTTGGGGSSTTHHH
T ss_pred             ----------CChHHH------h-hcEEEE--ecCCHHHHHHHHHHHHHHhhc-CCCEEEEcCcHHHhhhcCchHHHHHH
Confidence                      222221      1 122222  112222233445555555444 79999999888776432212344567


Q ss_pred             HHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEee
Q 009230          436 VSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVR  514 (539)
Q Consensus       436 ~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R  514 (539)
                      +.++++.|+.++++++++||+++| ++.... .+.+|     .+|..+++.||.++.|++.+..     +...+.|.|+|
T Consensus       131 ~~~~~~~L~~l~~~~~~~vi~~~h~~~~~~~-~~~~p-----~~~~~~~~~~d~vi~l~~~~~~-----~~r~l~v~K~r  199 (220)
T 2cvh_A          131 LSRQLQVLLWIARKHNIPVIVINQVHFDSRT-EMTKP-----VAEQTLGYRCKDILRLDKLPKP-----GLRVAVLERHR  199 (220)
T ss_dssp             HHHHHHHHHHHHHHHTCCEEEEECSSSSCTT-SSCCS-----CCCHHHHHTSSEEEEEEECSST-----TEEEEEEEECS
T ss_pred             HHHHHHHHHHHHHHcCCEEEEEeeEEEcCCC-Ccccc-----CCCcceeecCcEEEEEEEecCC-----CEEEEEEEeCC
Confidence            788999999999999999999999 654432 12233     4567899999999999988631     36789999999


Q ss_pred             CCCccee
Q 009230          515 NKVVGTI  521 (539)
Q Consensus       515 ~g~~G~~  521 (539)
                      +++.|..
T Consensus       200 ~~~~~~~  206 (220)
T 2cvh_A          200 FRPEGLM  206 (220)
T ss_dssp             SSCTTCE
T ss_pred             CCCCCce
Confidence            9988763

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=99.87  E-value=5.6e-22  Score=231.75  Aligned_cols=222  Identities=16%  Similarity=0.124  Sum_probs=163.9

Q ss_pred             CCccccccCchhhhhhhc---cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCC
Q 009230          276 GDEFGISTGWRALNELYN---VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKK  352 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~---l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~  352 (539)
                      ....++|||++.||.+++   |++|++++|+|+||+|||+|++|++.+++.+ |.+|+|||+||+..++.    +...|+
T Consensus       359 ~~~~~I~TG~~~LD~lLG~GGl~~G~lilI~G~pGsGKTtLaLqia~~~a~~-G~~vlyis~E~s~~~~~----a~~lGv  433 (2050)
T 3cmu_A          359 MDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE-GKTCAFIDAEHALDPIY----ARKLGV  433 (2050)
T ss_dssp             TSCCEECCSCHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTT-TCCEEEECTTSCCCHHH----HHHTTC
T ss_pred             cCCceeeCCCHHHHHHhccCCccCCcEEEEEeCCCCCHHHHHHHHHHHHHhc-CCeEEEEEcCCCHHHHH----HHHcCC
Confidence            346789999999999994   9999999999999999999999999999875 89999999999988764    333454


Q ss_pred             CccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcccccccc-CC---CC
Q 009230          353 PFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDH-QR---PV  428 (539)
Q Consensus       353 ~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~-~~---~~  428 (539)
                      +..                         + +++.    ...+++++.+.++.++.+.++++||||++..+.. ..   ..
T Consensus       434 d~~-------------------------~-L~I~----~~~~~e~il~~~~~lv~~~~~~lIVIDSL~al~~~~e~eg~~  483 (2050)
T 3cmu_A          434 DID-------------------------N-LLCS----QPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEI  483 (2050)
T ss_dssp             CTT-------------------------T-CEEE----CCSSHHHHHHHHHHHHHHTCCSEEEESCGGGCCCHHHHHSCT
T ss_pred             CHH-------------------------H-eEEe----CCCCHHHHHHHHHHHHHhcCCcEEEECCHHHhhccccccccc
Confidence            321                         1 2231    2346788999999888889999999997766653 10   00


Q ss_pred             CC----CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC---CCC
Q 009230          429 SQ----TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD---PEA  500 (539)
Q Consensus       429 ~~----~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~---~~~  500 (539)
                      ++    .....+.+.++.|+.+|+++||+||+++| +++...+.+ .|  ..-.|+.++++.||++|.|+|.+.   .+.
T Consensus       484 Gd~~~~~q~R~is~~Lr~L~~lake~~i~VIlinQl~~~vg~~~g-~p--~~psGg~ale~~ADv~l~L~R~~~~~~g~~  560 (2050)
T 3cmu_A          484 GDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKIGVMFG-NP--ETTTGGNALKFYASVRLDIRRIGAVKEGEN  560 (2050)
T ss_dssp             TCCCTTHHHHHHHHHHHHHHHHHHTTTCEEEEEECCEECTTCCSS-CC--EECSSHHHHHHHEEEEEEEEEEEEEEETTE
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHcCCeEEEEeecccccccccC-CC--cCCCCcchhhhhCCEEEEEEecccccCCcc
Confidence            11    13345677888888889999999999999 766543311 11  122588899999999999999752   111


Q ss_pred             CCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCcee
Q 009230          501 GPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEY  535 (539)
Q Consensus       501 ~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf  535 (539)
                      ...+.+++.+.|||+|+.|..+.+.+.|+..-.+|
T Consensus       561 ~~g~~~~v~V~KnR~gp~g~~~~f~I~~~~Gi~~~  595 (2050)
T 3cmu_A          561 VVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFY  595 (2050)
T ss_dssp             EEEEEEEEEEEEESSSCSCCEEEEEEETTTEECHH
T ss_pred             ccCcEEEEEEEecCCCCCCceEEEEEEeCCCcccc
Confidence            11135789999999999998766666555444333

>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=99.87  E-value=4.8e-21  Score=192.22  Aligned_cols=206  Identities=16%  Similarity=0.113  Sum_probs=144.6

Q ss_pred             CCccccccCchhhhhhh--c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCC
Q 009230          276 GDEFGISTGWRALNELY--N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKK  352 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~--~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~  352 (539)
                      ....++|||++.||.++  | |++|++++|+|+||+|||+|+++++.+++.+ |.+|+||++|++.....    +...|+
T Consensus        39 ~~~~~i~TG~~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~la~~~~~~-g~~vlyid~E~s~~~~~----a~~~g~  113 (356)
T 1u94_A           39 MDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE-GKTCAFIDAEHALDPIY----ARKLGV  113 (356)
T ss_dssp             CCCCEECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEESSCCCCHHH----HHHTTC
T ss_pred             ccCCcccCCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHC-CCeEEEEeCCCCccHHH----HHHcCC
Confidence            34678999999999999  4 9999999999999999999999999999885 89999999999876542    222343


Q ss_pred             CccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCC---CC-
Q 009230          353 PFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQR---PV-  428 (539)
Q Consensus       353 ~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~---~~-  428 (539)
                      +..                         .++++     ...+.+++.+.++.++...++++||||++..+....   .. 
T Consensus       114 ~~~-------------------------~l~i~-----~~~~~e~~~~~~~~l~~~~~~~lVVIDsl~~l~~~~e~~~~~  163 (356)
T 1u94_A          114 DID-------------------------NLLCS-----QPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEI  163 (356)
T ss_dssp             CGG-------------------------GCEEE-----CCSSHHHHHHHHHHHHHHTCCSEEEEECGGGCCCHHHHTTC-
T ss_pred             Chh-------------------------heeee-----CCCCHHHHHHHHHHHHhccCCCEEEEcCHHHhcchhhhcccc
Confidence            321                         12222     223567788888888888899999999777665311   00 


Q ss_pred             CC----CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC---CCC
Q 009230          429 SQ----TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD---PEA  500 (539)
Q Consensus       429 ~~----~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~---~~~  500 (539)
                      +.    .....+.++++.|+.+++++||+||+++| +++...+.+ .|.  .-.|+..+++.||+++.|+|.+.   .+.
T Consensus       164 g~~~~~~q~r~~~~~l~~L~~~a~~~~~~VI~~nq~~~~~~~~fg-~~~--~~~gG~~l~~~advrl~l~r~~~~k~g~~  240 (356)
T 1u94_A          164 GDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKIGVMFG-NPE--TTTGGNALKFYASVRLDIRRIGAVKEGEN  240 (356)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHHHHTCEEEEEEC-----------------CTTCSHHHHHCSEEEEEEEEEEEESSSS
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHhCCEEEEEeccccccCcccC-CCc--ccCCCcceeeeccEEEEEEEeeeeccCcc
Confidence            01    11235678899999999999999999999 665433211 111  12345689999999999998652   111


Q ss_pred             CCCCcEEEEEEEeeCCCcc
Q 009230          501 GPIDRVQVCVRKVRNKVVG  519 (539)
Q Consensus       501 ~~~~~~~l~i~K~R~g~~G  519 (539)
                      ...+.+.+.|.|+|+++..
T Consensus       241 ~~g~~~~~~i~K~r~~p~~  259 (356)
T 1u94_A          241 VVGSETRVKVVKNKIAAPF  259 (356)
T ss_dssp             EEEEEEEEEEEEESSBCSC
T ss_pred             ccCcEEEEEECCCccCCCC
Confidence            0124688999999999844

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=99.87  E-value=2.1e-21  Score=224.99  Aligned_cols=212  Identities=16%  Similarity=0.123  Sum_probs=159.2

Q ss_pred             CccccccCchhhhhhh--c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          277 DEFGISTGWRALNELY--N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~--~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      ...++|||++.||.++  | |++|++++|+|+||+|||+|++|++.+++.+ |.+|+|||+||+..++.    +...|++
T Consensus       360 ~~~~isTGi~~LD~lLg~GGl~~G~lilI~G~pGsGKTtLaLq~a~~~~~~-G~~vlyis~E~s~~~~~----a~~lGvd  434 (1706)
T 3cmw_A          360 DVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE-GKTCAFIDAEHALDPIY----ARKLGVD  434 (1706)
T ss_dssp             SCCEECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEECTTSCCCHHH----HHHTTCC
T ss_pred             cCceeccCcHHHHHHhccCCcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh-CCCeEEEEccCchHHHH----HHHcCCC
Confidence            4578999999999999  4 9999999999999999999999999999985 99999999999988763    3334554


Q ss_pred             ccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCC----CCC
Q 009230          354 FFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQR----PVS  429 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~----~~~  429 (539)
                      ...                         ++++     ...+.+++.+.++.++.+.++++||||++..+....    ..+
T Consensus       435 ~~~-------------------------L~i~-----~~~~~e~~l~~l~~lv~~~~~~lVVIDSL~al~~~~e~e~~~g  484 (1706)
T 3cmw_A          435 IDN-------------------------LLCS-----QPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIG  484 (1706)
T ss_dssp             GGG-------------------------CEEE-----CCSSHHHHHHHHHHHHHHTCCSEEEESCSTTCCCHHHHHSCTT
T ss_pred             HHH-------------------------eEEc-----CCCCHHHHHHHHHHHHHhcCCCEEEECCHHHhhcccccccccc
Confidence            321                         1222     123578888888888888999999999777765310    001


Q ss_pred             C----CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC---CCCC
Q 009230          430 Q----TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD---PEAG  501 (539)
Q Consensus       430 ~----~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~---~~~~  501 (539)
                      .    .....+.++++.|+.+|+++||+||+++| +++...+.+. +  ..-.|+..+++.||++|.|+|.+.   .+..
T Consensus       485 ~~~~~~q~r~~s~~Lr~L~~~ak~~~v~VI~inQl~~~vg~~fg~-~--~~p~gg~ale~~ADv~L~L~R~~~~~~g~~~  561 (1706)
T 3cmw_A          485 DSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKIGVMFGN-P--ETTTGGNALKFYASVRLDIRRIGAVKEGENV  561 (1706)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHHHHHHTCEEEEEECEEECTTCCSSC-C--EEESSCSHHHHHEEEEEEEEEEEEEEETTEE
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHcCCEEEEEeecccccccccCC-C--ccCCCCcceeeeCCEEEEEEeccccccCccc
Confidence            1    23345788999999999999999999999 7765433111 1  112478899999999999999752   1111


Q ss_pred             CCCcEEEEEEEeeCCCcceeeeEEE
Q 009230          502 PIDRVQVCVRKVRNKVVGTIGEAFL  526 (539)
Q Consensus       502 ~~~~~~l~i~K~R~g~~G~~~~~~l  526 (539)
                      ..+.+++.|.|||+++.+....+.+
T Consensus       562 ~~~~~~l~V~KnR~gp~~~~~~F~I  586 (1706)
T 3cmw_A          562 VGSETRVKVVKNKIAAPFKQAEFQI  586 (1706)
T ss_dssp             EEEEEEEEEEEESSSCSCCEEEEEE
T ss_pred             cCcEEEEEEEecCCCCCCCeEEEEE
Confidence            1235789999999999988655544

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=99.85  E-value=9.4e-21  Score=192.70  Aligned_cols=242  Identities=14%  Similarity=0.138  Sum_probs=152.9

Q ss_pred             chHHHHHHhccccCccccccccchHHHHHHHhhccCCCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHH
Q 009230          240 GALKEVVENAELYPIMGLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDAL  317 (539)
Q Consensus       240 ~~~~~~~~~A~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~l  317 (539)
                      ..+.+++..|..+...+..+..++.+.-        ....+++||++.||++++  +++|+++.|+|+||+|||||++++
T Consensus       127 ~~~~~i~~~a~~~~~~~~~ta~~l~~~~--------~~~~~i~TG~~~LD~lLgGGI~~Gei~~I~G~sGsGKTTLl~~l  198 (400)
T 3lda_A          127 AKADKLLNEAARLVPMGFVTAADFHMRR--------SELICLTTGSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTL  198 (400)
T ss_dssp             HHHHHHHHHHHHHSCCSCCCHHHHHHHH--------HTSCEECCSCHHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccCCCHHHHHhhh--------ccCCccccCChhHHHHhcCCcCCCcEEEEEcCCCCChHHHHHHH
Confidence            4566667766655445555544443211        345689999999999994  999999999999999999999999


Q ss_pred             HHHHHHh-----cCCeEEEEeCCCC--HHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCC
Q 009230          318 ICNINEH-----AGWKFVLCSMENK--VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCEND  390 (539)
Q Consensus       318 a~~~a~~-----~g~~vl~~s~E~~--~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~  390 (539)
                      +.+.+..     .+.+++||+.|++  ..++..  ++...++.              .+.   +   + +...+...  .
T Consensus       199 a~~~~~p~~~Gg~~~~viyid~E~~~~~~rl~~--~a~~~gl~--------------~~~---v---l-eni~~~~~--~  253 (400)
T 3lda_A          199 AVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLVS--IAQRFGLD--------------PDD---A---L-NNVAYARA--Y  253 (400)
T ss_dssp             HHHTTSCGGGTCCSSEEEEEESSSCCCHHHHHH--HHHHTTCC--------------HHH---H---H-HTEEEEEC--C
T ss_pred             HHHhccCcccCCCCCcEEEEeCCCccCHHHHHH--HHHHcCCC--------------hHh---H---h-hcEEEecc--C
Confidence            9887652     2578999999986  444433  23333332              111   1   1 12233211  1


Q ss_pred             CCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCC----CCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCC
Q 009230          391 SLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVS----QTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHN  465 (539)
Q Consensus       391 ~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~----~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~  465 (539)
                      ......+++..+..++...++++||||++..+....-.+    ..+...+.+++..|+.+++++|++||+++| .+..+.
T Consensus       254 ~~~~~~~~l~~~~~~l~~~~~~llVIDs~t~~~~~~~sg~g~l~~Rq~~l~~il~~L~~lake~gitVIlv~Hv~~~~~g  333 (400)
T 3lda_A          254 NADHQLRLLDAAAQMMSESRFSLIVVDSVMALYRTDFSGRGELSARQMHLAKFMRALQRLADQFGVAVVVTNQVVAQVDG  333 (400)
T ss_dssp             SHHHHHHHHHHHHHHHHHSCEEEEEEETGGGGCC------CCHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEC------
T ss_pred             ChHHHHHHHHHHHHHHHhcCCceEEecchhhhCchhhcCccchHHHHHHHHHHHHHHHHHHHHcCCEEEEEEeecccCCc
Confidence            111122344455556667789999999888876532111    112334578999999999999999999999 433322


Q ss_pred             CCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCCCcce
Q 009230          466 WVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGT  520 (539)
Q Consensus       466 ~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~G~  520 (539)
                      ...-........|+..+++.+|++|.|++.+.      ....+.+.|+|+++.++
T Consensus       334 ~~~~~g~~~~p~gg~~l~~~ad~vl~L~~~~g------~~R~l~v~K~R~~p~~e  382 (400)
T 3lda_A          334 GMAFNPDPKKPIGGNIMAYSSTTRLGFKKGKG------CQRLCKVVDSPCLPEAE  382 (400)
T ss_dssp             --------------CHHHHHCSEEEEEEECST------TEEEEEEEECSSSCSCE
T ss_pred             cccccCCCccCCchhHHHHhcceEEEEEecCC------CcEEEEEEcCCCCCCCc
Confidence            10000011123467889999999999998642      24789999999999887

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=99.84  E-value=5.8e-20  Score=179.80  Aligned_cols=232  Identities=14%  Similarity=0.128  Sum_probs=143.7

Q ss_pred             cccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh---------cCCeEEEEeCCCCHHHHHHHHHHH
Q 009230          279 FGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEH---------AGWKFVLCSMENKVREHARKLLEK  348 (539)
Q Consensus       279 ~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~---------~g~~vl~~s~E~~~~~~~~r~~~~  348 (539)
                      ..++||++.||.+++ +++|++++|.|++|+|||||+++++..++..         .+.+|+|+++|++..++..|+.+.
T Consensus        11 ~~i~tg~~~ld~~lggl~~G~i~~i~G~~GsGKTtl~~~l~~~~~~g~~~~g~~~~~~~~v~~~~~e~~~~~~~~r~~~~   90 (279)
T 1nlf_A           11 EAFAAAPPPLDYVLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHAL   90 (279)
T ss_dssp             HHHHSCCCCCCEEETTEETTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSSCHHHHHHHHHHH
T ss_pred             HHhcCCCCChheeECCccCCCEEEEEcCCCCCHHHHHHHHHHHHhcCCCcCCCccCCCccEEEEECCCCHHHHHHHHHHH
Confidence            458899999999998 9999999999999999999999999876541         136899999999998887776543


Q ss_pred             hhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeec--CCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCC
Q 009230          349 HIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCE--NDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQR  426 (539)
Q Consensus       349 ~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~--~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~  426 (539)
                      .  ..            +.......+.+.+    .+....  .....+... ...++.++  .++++||||+...+....
T Consensus        91 g--~~------------~~~~~~~~~~~~l----~l~~~~~~~~~~ls~g~-~~~i~~l~--~~~~livlDe~~~~~~~d  149 (279)
T 1nlf_A           91 G--AH------------LSAEERQAVADGL----LIQPLIGSLPNIMAPEW-FDGLKRAA--EGRRLMVLDTLRRFHIEE  149 (279)
T ss_dssp             H--TT------------SCHHHHHHHHHHE----EECCCTTSCCCTTSHHH-HHHHHHHH--TTCSEEEEECGGGGCCSC
T ss_pred             H--hh------------cChhhhhhccCce----EEeecCCCCcccCCHHH-HHHHHHhc--CCCCEEEECCHHHhcCCC
Confidence            2  21            2222222222222    111000  011112222 33444433  369999999888765432


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCC--------
Q 009230          427 PVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDP--------  498 (539)
Q Consensus       427 ~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~--------  498 (539)
                         .+....+.++++.|+.++++.|++||+++|..+.....+..+..++.+||+.+...+..+..+.+..+.        
T Consensus       150 ---~~~~~~~~~~~~~L~~l~~~~g~tvi~i~H~~~~~~~~g~~~~~~~~~g~~~l~d~v~~~~~~~~~~~~~~~~~gi~  226 (279)
T 1nlf_A          150 ---ENASGPMAQVIGRMEAIAADTGCSIVFLHHASKGAAMMGAGDQQQASRGSSVLVDNIRWQSYLSSMTSAEAEEWGVD  226 (279)
T ss_dssp             ---TTCHHHHHHHHHHHHHHHHHHCCEEEEEEEC--------------------CTGGGCSCEEEEEECCHHHHHHTTCC
T ss_pred             ---cCchHHHHHHHHHHHHHHHHcCCEEEEEecCCCcccccCCchhhhhccchhhhccchhhhhhccCCCHHHHHHhCCC
Confidence               233456788999999999999999999999333322223345567789999998766666666665421        


Q ss_pred             CCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCCCceecc
Q 009230          499 EAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRVTGEYMD  537 (539)
Q Consensus       499 ~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~~~rf~~  537 (539)
                      +......+++.+.|+|+++.|...  .+.++ ++|.|..
T Consensus       227 ~~~~~~~~~~~v~K~~~~~~~~~~--~~~~~-~~G~l~~  262 (279)
T 1nlf_A          227 DDQRRFFVRFGVSKANYGAPFADR--WFRRH-DGGVLKP  262 (279)
T ss_dssp             TTSGGGEEEEEEEECSSSSCCCCE--EEEEC-GGGCEEE
T ss_pred             hhhcCcEEEeeeccccCCCCCCce--EEEEc-CCeeEec
Confidence            111123578999999999998752  45554 6777754

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=99.84  E-value=6.4e-20  Score=183.10  Aligned_cols=214  Identities=14%  Similarity=0.095  Sum_probs=156.0

Q ss_pred             ccccccCchhhhhhhc---cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCc
Q 009230          278 EFGISTGWRALNELYN---VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPF  354 (539)
Q Consensus       278 ~~gi~tg~~~LD~~~~---l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~  354 (539)
                      ...+|||++.||.+++   +++|++++|+|+||+|||||+++++..++.. |.+|+|++.|++.....    +...+++.
T Consensus        39 ~~~i~TG~~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~~~~~-gg~VlyId~E~s~~~~r----a~rlgv~~  113 (356)
T 3hr8_A           39 VEVIPTGSLAIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAEAQKM-GGVAAFIDAEHALDPVY----AKNLGVDL  113 (356)
T ss_dssp             CCEECCSCHHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHHHHHT-TCCEEEEESSCCCCHHH----HHHHTCCG
T ss_pred             CceecCCCHHHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHHHHhc-CCeEEEEecccccchHH----HHHcCCch
Confidence            6789999999999984   9999999999999999999999999998875 88999999998866542    22224332


Q ss_pred             cccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcccccccc-C--CC-CCC
Q 009230          355 FEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDH-Q--RP-VSQ  430 (539)
Q Consensus       355 ~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~-~--~~-~~~  430 (539)
                      .                         ..++.     ...+.+++...++.++...++++||||++..+.. .  .+ .++
T Consensus       114 ~-------------------------~l~i~-----~~~~~e~~l~~~~~l~~~~~~dlvVIDSi~~l~~~~el~g~~G~  163 (356)
T 3hr8_A          114 K-------------------------SLLIS-----QPDHGEQALEIVDELVRSGVVDLIVVDSVAALVPRAEIEGAMGD  163 (356)
T ss_dssp             G-------------------------GCEEE-----CCSSHHHHHHHHHHHHHTSCCSEEEEECTTTCCCHHHHTTCCCS
T ss_pred             h-------------------------hhhhh-----hccCHHHHHHHHHHHhhhcCCCeEEehHhhhhcChhhhcccchh
Confidence            1                         12222     2345777888888777778899999999888764 1  11 011


Q ss_pred             ----CHHHHHHHHHHHHHHHHHHhCcEEEEEecCC-CCCCCCCCCCCcccccccccchhccceEEEEEeCCC---CCCCC
Q 009230          431 ----TETEYVSQMLTMVKRFAQHHACHVWFVAHPR-QLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD---PEAGP  502 (539)
Q Consensus       431 ----~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r-~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~---~~~~~  502 (539)
                          .....+.++++.|+.+|++++++||+++|.+ +...-.   .+.....|+..++..+|++|.|.+.+.   .+...
T Consensus       164 ~q~~~qar~la~~L~~L~~lak~~~~tVI~inqv~~k~g~~f---g~p~~~~GG~~l~h~~~~rl~l~k~~~~k~g~~~~  240 (356)
T 3hr8_A          164 MQVGLQARLMSQALRKIAGSVNKSKAVVIFTNQIRMKIGVMF---GSPETTTGGLALKFYATMRMEVRRGEPIKEGKDVI  240 (356)
T ss_dssp             SCSSHHHHHHHHHHHHHHHHHHTSSCEEEEEEESSSCSSSSS---CSCSSCTHHHHHHHHCSEEEEEEEEEEEEETTEEE
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEeeeeecccccc---CCcccCCCcchhhhhCcEEEEEEeccccccCCccc
Confidence                1234577889999999999999999999953 332211   122356789999999999999998531   11001


Q ss_pred             CCcEEEEEEEeeCCCcceeeeEEEEEe
Q 009230          503 IDRVQVCVRKVRNKVVGTIGEAFLSYN  529 (539)
Q Consensus       503 ~~~~~l~i~K~R~g~~G~~~~~~l~fd  529 (539)
                      .+.+.+.+.|||.++.+..+.+.+.|+
T Consensus       241 g~~~~vkvvKnr~~~~~~~~~f~i~~~  267 (356)
T 3hr8_A          241 GNVISVKIVKNKVAPPFKTAQTYIIYG  267 (356)
T ss_dssp             EEEEEEEEEEESSSCCCCEEEEEEETT
T ss_pred             ccEEEEEEEeCCCCCCCceEEEEEeeC
Confidence            235788999999998888665555443

>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=99.84  E-value=1.5e-19  Score=181.30  Aligned_cols=206  Identities=16%  Similarity=0.108  Sum_probs=145.5

Q ss_pred             CCccccccCchhhhhhhc---cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCC
Q 009230          276 GDEFGISTGWRALNELYN---VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKK  352 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~---l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~  352 (539)
                      ....+++||++.||.+++   +++|++++|+|+||+|||||+++++.+++.. |.+|+|+++|++.....    +...|+
T Consensus        37 ~~~~~i~TG~~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~~~~~-g~~vlyi~~E~~~~~~~----a~~lG~  111 (349)
T 2zr9_A           37 QPISVIPTGSISLDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAA-GGIAAFIDAEHALDPEY----AKKLGV  111 (349)
T ss_dssp             CCCCEECCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT-TCCEEEEESSCCCCHHH----HHHTTC
T ss_pred             ccCCccccCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhC-CCeEEEEECCCCcCHHH----HHHcCC
Confidence            345789999999999984   9999999999999999999999999999885 89999999999866542    223344


Q ss_pred             CccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccC-C--CC-
Q 009230          353 PFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQ-R--PV-  428 (539)
Q Consensus       353 ~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~-~--~~-  428 (539)
                      +..                         .++++     ...+.+++.+.++.++...++++||||++..+... .  +. 
T Consensus       112 ~~~-------------------------~l~i~-----~~~~~e~~l~~~~~l~~~~~~~lIVIDsl~~l~~~~e~~~~~  161 (349)
T 2zr9_A          112 DTD-------------------------SLLVS-----QPDTGEQALEIADMLVRSGALDIIVIDSVAALVPRAEIEGEM  161 (349)
T ss_dssp             CGG-------------------------GCEEE-----CCSSHHHHHHHHHHHHTTTCCSEEEEECGGGCCCHHHHTTC-
T ss_pred             CHH-------------------------HeEEe-----cCCCHHHHHHHHHHHHhcCCCCEEEEcChHhhcchhhhcccc
Confidence            321                         12222     23357777777877777788999999988887621 0  00 


Q ss_pred             CC----CHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC---CCC
Q 009230          429 SQ----TETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD---PEA  500 (539)
Q Consensus       429 ~~----~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~---~~~  500 (539)
                      ++    .....+.+++..|+.+++++|++||+++| +++.....+ .|  ..-.|+..+++.||.++.++|.+.   .+.
T Consensus       162 gd~~~~~q~r~~~~~l~~L~~~a~~~~~tVI~inh~~~~~~~~~~-~p--~~~~gg~~l~~~ad~~l~lrr~~~~k~g~~  238 (349)
T 2zr9_A          162 GDSHVGLQARLMSQALRKMTGALNNSGTTAIFINELREKIGVMFG-SP--ETTTGGKALKFYASVRLDVRRIETLKDGTD  238 (349)
T ss_dssp             ---CCCHHHHHHHHHHHHHHHHHHHHTCEEEEEEECC--------------CCSSHHHHHHHCSEEEEEEEEEEECSSSS
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHhCCEEEEEeccccccCcccC-CC--cccCCchHhhhccceEEEEEEeeeeecCcc
Confidence            01    11225678889999999999999999999 554432111 11  112467889999999999998642   111


Q ss_pred             CCCCcEEEEEEEeeCCCcc
Q 009230          501 GPIDRVQVCVRKVRNKVVG  519 (539)
Q Consensus       501 ~~~~~~~l~i~K~R~g~~G  519 (539)
                      ...+.+.+.|.|+|.++..
T Consensus       239 ~~g~~~~~~i~K~~~~p~~  257 (349)
T 2zr9_A          239 AVGNRTRVKVVKNKVSPPF  257 (349)
T ss_dssp             CCEEEEEEEEEEESSSCCC
T ss_pred             ccCCEEEEEeCCCccCCCC
Confidence            1124678999999999844

>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=99.83  E-value=1.8e-19  Score=172.47  Aligned_cols=209  Identities=14%  Similarity=0.107  Sum_probs=132.5

Q ss_pred             ccccccCchhhhhhh-c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc-----CCeEEEEeCCCC--HHHHHHHHHHH
Q 009230          278 EFGISTGWRALNELY-N-VLPGELTIVTGVPNSGKSEWIDALICNINEHA-----GWKFVLCSMENK--VREHARKLLEK  348 (539)
Q Consensus       278 ~~gi~tg~~~LD~~~-~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~-----g~~vl~~s~E~~--~~~~~~r~~~~  348 (539)
                      ..+++||++.||+++ | +++|++++|.|+||+|||||+.+++.+++...     +.+++|++.|++  +.++..++.. 
T Consensus         3 ~~~i~tG~~~LD~~l~ggi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~~~~~~-   81 (243)
T 1n0w_A            3 IIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAER-   81 (243)
T ss_dssp             CCEECCSCHHHHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHHHHHHH-
T ss_pred             ceEecCCChHHHHhhcCCCcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHHHHHHH-
Confidence            357999999999999 4 99999999999999999999999998765421     679999999994  6655544322 


Q ss_pred             hhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHH---HHHHHHHHHHHcCCcEEEEccccccccC
Q 009230          349 HIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKW---VLDLAKAAVLRHGVRGLVIDPYNELDHQ  425 (539)
Q Consensus       349 ~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~---i~~~i~~~~~~~~~~~vvID~~~~l~~~  425 (539)
                       .++              ..++   +   + +...++.     ..+.++   +...+..+....++++||||++..+...
T Consensus        82 -~g~--------------~~~~---~---~-~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~lliiD~~~~~~~~  134 (243)
T 1n0w_A           82 -YGL--------------SGSD---V---L-DNVAYAR-----AFNTDHQTQLLYQASAMMVESRYALLIVDSATALYRT  134 (243)
T ss_dssp             -TTC--------------CHHH---H---H-HTEEEEE-----CCSHHHHHHHHHHHHHHHHHSCEEEEEEETSSGGGC-
T ss_pred             -cCC--------------CHHH---H---h-hCeEEEe-----cCCHHHHHHHHHHHHHHHhcCCceEEEEeCchHHHHH
Confidence             222              1211   1   1 2223321     123333   3344555666678999999988887643


Q ss_pred             CCCC-C--C-HHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCC
Q 009230          426 RPVS-Q--T-ETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEA  500 (539)
Q Consensus       426 ~~~~-~--~-~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~  500 (539)
                      .-++ .  . +...+.+++..|+.+++++|++||+++| ++....+..-..+...-.|+..+++.||.++.|++.+.   
T Consensus       135 ~~~~~~~~~~r~~~~~~~~~~l~~~~~~~~~tvi~~~h~~~~~~~~~~~~~~~~~~~g~~~~~~~~d~vi~l~~~~~---  211 (243)
T 1n0w_A          135 DYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQVDGAAMFAADPKKPIGGNIIAHASTTRLYLRKGRG---  211 (243)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHHHHCCEEEEEC-------------------------CCTTCEEEEEEECST---
T ss_pred             HhcCCccHHHHHHHHHHHHHHHHHHHHHcCCEEEEEeeeeecCCCccccCCCcccCCccChhhhcCcEEEEEEEcCC---
Confidence            2111 0  1 1224778999999999999999999999 55443210000000112566789999999999998532   


Q ss_pred             CCCCcEEEEEEEeeCCCcce
Q 009230          501 GPIDRVQVCVRKVRNKVVGT  520 (539)
Q Consensus       501 ~~~~~~~l~i~K~R~g~~G~  520 (539)
                         ....+.+.|+|+++.+.
T Consensus       212 ---~~r~l~v~K~r~~~~~~  228 (243)
T 1n0w_A          212 ---ETRICKIYDSPCLPEAE  228 (243)
T ss_dssp             ---TEEEEEECCBTTBSCEE
T ss_pred             ---CeEEEEEEECCCCCCCe
Confidence               25689999999988764

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=99.81  E-value=2.3e-18  Score=163.53  Aligned_cols=207  Identities=14%  Similarity=0.087  Sum_probs=144.5

Q ss_pred             cccccCchhhhhhh-c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccc
Q 009230          279 FGISTGWRALNELY-N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFE  356 (539)
Q Consensus       279 ~gi~tg~~~LD~~~-~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~  356 (539)
                      .+++||++.||+++ | +++|++++|.|+||+|||||+.+++...+.. +.+|+|++.|++..++..++.  ..+.....
T Consensus         3 ~~i~tg~~~Ld~~~~ggi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~-~~~v~~~~~~~~~~~~~~~~~--~~~~~~~~   79 (235)
T 2w0m_A            3 SRLSTGILDFDKLIQGGIPQGFFIALTGEPGTGKTIFSLHFIAKGLRD-GDPCIYVTTEESRDSIIRQAK--QFNWDFEE   79 (235)
T ss_dssp             CEECCSCHHHHGGGTTSEETTCEEEEECSTTSSHHHHHHHHHHHHHHH-TCCEEEEESSSCHHHHHHHHH--HTTCCCGG
T ss_pred             ccccCCchHHHHHhcCCCcCCCEEEEEcCCCCCHHHHHHHHHHHHHHC-CCeEEEEEcccCHHHHHHHHH--HhcchHHH
Confidence            47899999999999 4 9999999999999999999999999888875 889999999999988877764  34544433


Q ss_pred             cccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCc--EEEEccccccccCCCCCCCHHH
Q 009230          357 ANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVR--GLVIDPYNELDHQRPVSQTETE  434 (539)
Q Consensus       357 i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~--~vvID~~~~l~~~~~~~~~~~~  434 (539)
                      +...    .+..  +......+.  ..++    ....+.+++...+..+....+++  +||||+.+.+....      ..
T Consensus        80 ~~~~----~~~~--~~~~~~~~~--~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~llilDe~~~~~~~d------~~  141 (235)
T 2w0m_A           80 YIEK----KLII--IDALMKEKE--DQWS----LVNLTPEELVNKVIEAKQKLGYGKARLVIDSVSALFLDK------PA  141 (235)
T ss_dssp             GBTT----TEEE--EECCC------CTTB----CSSCCHHHHHHHHHHHHHHHCSSCEEEEEETGGGGSSSC------GG
T ss_pred             HhhC----CEEE--EeccccccC--ceee----ecCCCHHHHHHHHHHHHHhhCCCceEEEEECchHhhcCC------HH
Confidence            2210    0000  000000000  1111    12337788887787777778999  99999887765321      12


Q ss_pred             HHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEe
Q 009230          435 YVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKV  513 (539)
Q Consensus       435 ~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~  513 (539)
                      ...+++..|+.+++++|++||+++| .+....    ..     .  ..+++.||.++.|++.+...   .....+.|.|+
T Consensus       142 ~~~~~~~~l~~~~~~~~~~vi~~~h~~~~~~~----~~-----~--~~~~~~~d~vi~l~~~~~~~---~~~r~l~v~K~  207 (235)
T 2w0m_A          142 MARKISYYLKRVLNKWNFTIYATSQYAITTSQ----AF-----G--FGVEHVADGIIRFRRMIRNG---ELHRYILIEKM  207 (235)
T ss_dssp             GHHHHHHHHHHHHHHTTEEEEEEEC----------------------CHHHHCSEEEEEEEEEETT---EEEEEEEEEEE
T ss_pred             HHHHHHHHHHHHHHhCCCeEEEEeccCccccc----cc-----c--cchheeeeEEEEEEEEecCC---cEEEEEEEEec
Confidence            3567889999999999999999999 542211    11     1  35889999999999876422   13578999999


Q ss_pred             eCCCcce
Q 009230          514 RNKVVGT  520 (539)
Q Consensus       514 R~g~~G~  520 (539)
                      |+++.+.
T Consensus       208 r~~~~~~  214 (235)
T 2w0m_A          208 RQTDHDK  214 (235)
T ss_dssp             TTCCCCC
T ss_pred             cCCcccc
Confidence            9987653

>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=99.76  E-value=1.4e-17  Score=160.67  Aligned_cols=212  Identities=12%  Similarity=0.069  Sum_probs=132.9

Q ss_pred             ccccccCchhhhhhh-----c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-cCCeEEEEeCCCCHHHHHHHHHHHhh
Q 009230          278 EFGISTGWRALNELY-----N-VLPGELTIVTGVPNSGKSEWIDALICNINEH-AGWKFVLCSMENKVREHARKLLEKHI  350 (539)
Q Consensus       278 ~~gi~tg~~~LD~~~-----~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-~g~~vl~~s~E~~~~~~~~r~~~~~~  350 (539)
                      ...++||++.||.++     | +++| +++|+|+||+|||||++|++.+++.+ .|.+|+|++.|.+....  |  +...
T Consensus         4 ~~risTGi~~LD~~LGg~~~GGl~~G-iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~--r--a~~l   78 (333)
T 3io5_A            4 MDVVRTKIPMMNIALSGEITGGMQSG-LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPA--Y--LRSM   78 (333)
T ss_dssp             --CBCCSCHHHHHHHHSSTTCCBCSE-EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHH--H--HHHT
T ss_pred             CCEecCCCHHHHHHhCCCCCCCCcCC-eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHH--H--HHHh
Confidence            357999999999988     5 9999 99999999999999999999998874 27899999999886543  2  2223


Q ss_pred             CCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHH-HHHHHHH--HHHcCCcEEEEccccccccC-C
Q 009230          351 KKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWV-LDLAKAA--VLRHGVRGLVIDPYNELDHQ-R  426 (539)
Q Consensus       351 ~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i-~~~i~~~--~~~~~~~~vvID~~~~l~~~-~  426 (539)
                      |++..                         ..++.     ...+.+++ ...++.+  ++...+++|||||+..+... .
T Consensus        79 Gvd~d-------------------------~llv~-----~~~~~E~~~l~i~~~l~~i~~~~~~lvVIDSI~aL~~~~e  128 (333)
T 3io5_A           79 GVDPE-------------------------RVIHT-----PVQSLEQLRIDMVNQLDAIERGEKVVVFIDSLGNLASKKE  128 (333)
T ss_dssp             TCCGG-------------------------GEEEE-----ECSBHHHHHHHHHHHHHTCCTTCCEEEEEECSTTCBCC--
T ss_pred             CCCHH-------------------------HeEEE-----cCCCHHHHHHHHHHHHHHhhccCceEEEEecccccccchh
Confidence            54332                         12222     22356666 5555554  45567999999999998742 1


Q ss_pred             -CCC--C------CHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC
Q 009230          427 -PVS--Q------TETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD  497 (539)
Q Consensus       427 -~~~--~------~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~  497 (539)
                       .+.  .      .....+.+.++.|..+|+++|++||++.|.++...-. ..|.  - .|+..+ ..|.+-|.|.+.+.
T Consensus       129 ieg~~gd~~~gsv~qaR~~s~~LrkL~~~ak~~~i~vi~tNQV~k~G~~f-g~p~--~-~GG~~l-~~ss~Rl~lrk~~~  203 (333)
T 3io5_A          129 TEDALNEKVVSDMTRAKTMKSLFRIVTPYFSTKNIPCIAINHTYETQEMF-SKTV--M-GGGTGP-MYSADTVFIIGKRQ  203 (333)
T ss_dssp             ------------CTHHHHHHHHHHHHHHHHHHTTCEEEEEEEC-------------------CCG-GGGSSEEEEEEEC-
T ss_pred             ccCccccccccHHHHHHHHHHHHHHHHHHHHHhCCEEEEECCeeecCccc-CCCC--C-CCccee-eeeeEEEEEEeccc
Confidence             111  1      2334566777888889999999999999965532211 2232  2 566667 88888888876442


Q ss_pred             ---CCCCCCCcEEEEEEEeeCCCcceeeeEEEEEe
Q 009230          498 ---PEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYN  529 (539)
Q Consensus       498 ---~~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd  529 (539)
                         .+.-..+.+.+.+.|+|--.......+.+.|+
T Consensus       204 ik~~~~~~G~~~~v~~~k~kv~k~k~~~~~~i~~~  238 (333)
T 3io5_A          204 IKDGSDLQGYQFVLNVEKSRTVKEKSKFFIDVKFD  238 (333)
T ss_dssp             ---------CEEEEEEEECSSBCTTCEEEEEBCTT
T ss_pred             cccCCccEEeEEEEeEEEEEEccCCcCCcEEEEec
Confidence               11112345677778877644433323334333

>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=99.74  E-value=2.5e-17  Score=156.12  Aligned_cols=199  Identities=13%  Similarity=0.134  Sum_probs=126.5

Q ss_pred             CccccccCchhhhhhh-c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-----cCCeEEEEeCCCC--HHHHHHHHHH
Q 009230          277 DEFGISTGWRALNELY-N-VLPGELTIVTGVPNSGKSEWIDALICNINEH-----AGWKFVLCSMENK--VREHARKLLE  347 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~-~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-----~g~~vl~~s~E~~--~~~~~~r~~~  347 (539)
                      ....++||++.||.++ | +++|+++.|.|++|+|||||+..++......     .+..++|++.|..  .+++....  
T Consensus         3 ~~~~i~tG~~~LD~~l~ggi~~G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~~i~~~~--   80 (231)
T 4a74_A            3 TIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREIA--   80 (231)
T ss_dssp             CCCEECCSCHHHHHHTTSSEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHH--
T ss_pred             cCCccCCCChhHHhHhcCCCCCCcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHHHHHHHH--
Confidence            4568999999999999 4 9999999999999999999999998765541     1567999999875  44332221  


Q ss_pred             HhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHH-----HcCCcEEEEcccccc
Q 009230          348 KHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVL-----RHGVRGLVIDPYNEL  422 (539)
Q Consensus       348 ~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~-----~~~~~~vvID~~~~l  422 (539)
                      ...+              +..+   .+    .+...+...  ............+..+..     ..++++|++|+....
T Consensus        81 ~~~~--------------~~~~---~~----~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~llilDe~~~~  137 (231)
T 4a74_A           81 QNRG--------------LDPD---EV----LKHIYVARA--FNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSH  137 (231)
T ss_dssp             HHTT--------------SCHH---HH----HHTEEEEEC--CSHHHHHHHHHHHHHHHHHHTTSSSCEEEEEEETSSHH
T ss_pred             HHcC--------------CCHH---HH----hhcEEEEec--CChHHHHHHHHHHHHHHHHhcccCCceeEEEECChHHH
Confidence            1122              2222   11    122222211  111111222334444444     568999999988776


Q ss_pred             ccCCCCCCC----HHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC
Q 009230          423 DHQRPVSQT----ETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD  497 (539)
Q Consensus       423 ~~~~~~~~~----~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~  497 (539)
                      .....++..    +...+.+++..|+.++++.|++||+++| .+.               ++..+++.||.++.|.+...
T Consensus       138 l~~~~~~~~~~~~r~~~~~~~~~~l~~~~~~~g~tvi~vtH~~~~---------------~g~~~~~~~d~~l~l~~~~~  202 (231)
T 4a74_A          138 FRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQVQAN---------------GGHILAHSATLRVYLRKGKG  202 (231)
T ss_dssp             HHHHSCSTTHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECC------------------------CCSEEEEEEECTT
T ss_pred             hccccCCCcchhHHHHHHHHHHHHHHHHHHHCCCeEEEEeecccC---------------cchhhHhhceEEEEEEecCC
Confidence            543211111    1122568999999999999999999999 433               34568899999999998442


Q ss_pred             CCCCCCCcEEEEEEEeeCCCccee
Q 009230          498 PEAGPIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       498 ~~~~~~~~~~l~i~K~R~g~~G~~  521 (539)
                            ....+.+.|+|+++.|.+
T Consensus       203 ------~~r~l~~~K~r~~~~~~~  220 (231)
T 4a74_A          203 ------GKRIARLIDAPHLPEGEA  220 (231)
T ss_dssp             ------SCEEEEEESCC--CCSCE
T ss_pred             ------CeEEEEEEeCCCCCCceE
Confidence                  356789999999988874

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=99.72  E-value=4.3e-17  Score=190.95  Aligned_cols=182  Identities=16%  Similarity=0.154  Sum_probs=140.4

Q ss_pred             CCccccccCchhhhhhh--c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCC
Q 009230          276 GDEFGISTGWRALNELY--N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKK  352 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~--~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~  352 (539)
                      ....++|||+++||+++  | +++|++++|+|+||+|||+|++|++.+++.+ +.+|+|||+||+..++.    +...|+
T Consensus       708 ~~~~~i~TG~~eLD~llggGGl~~G~lilIaG~PG~GKTtLalqlA~~~a~~-g~~VlyiS~Ees~~ql~----A~rlG~  782 (2050)
T 3cmu_A          708 MDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE-GKTCAFIDAEHALDPIY----ARKLGV  782 (2050)
T ss_dssp             TSCCEECCSCHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTT-TCCEEEECTTSCCCHHH----HHHTTC
T ss_pred             cccceeecCChHHHHHhccCCcCCCcEEEEEcCCCCCHHHHHHHHHHHHHhc-CCcEEEEECCCcHHHHH----HHHcCC
Confidence            45678999999999999  3 9999999999999999999999999999885 88999999999999885    222232


Q ss_pred             CccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcccccccc-C----C-
Q 009230          353 PFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDH-Q----R-  426 (539)
Q Consensus       353 ~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~-~----~-  426 (539)
                      +.                          ..+++    .+..+++++.+.++.+..+.++++||||++..+.. .    . 
T Consensus       783 ~~--------------------------~~l~i----~~~~~i~~i~~~~r~l~~~~~~~LVIIDsLq~i~~~~~~~~~~  832 (2050)
T 3cmu_A          783 DI--------------------------DNLLC----SQPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEI  832 (2050)
T ss_dssp             CT--------------------------TTCEE----ECCSSHHHHHHHHHHHHHHTCCSEEEESCGGGCCCHHHHHSCT
T ss_pred             Cc--------------------------cceEE----ecCCCHHHHHHHHHHHhhccCCCEEEEcchhhhcccccccCCC
Confidence            11                          12444    24578999999999988888999999995555443 1    1 


Q ss_pred             CCCCC--HHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          427 PVSQT--ETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       427 ~~~~~--~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                      ++...  ....+.++++.|+.+|+++||+||+++| +|..+.-.+ .|  ..-.|+..+...+++.+.|.|.
T Consensus       833 Gs~~q~La~Reis~ilr~Lk~lAke~~v~VI~l~Qv~r~~e~~fg-dp--~~p~GG~~l~h~a~~Rl~Lrr~  901 (2050)
T 3cmu_A          833 GDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKIGVMFG-NP--ETTTGGNALKFYASVRLDIRRI  901 (2050)
T ss_dssp             TCCCTTHHHHHHHHHHHHHHHHHHTTTCEEEEEECCEECTTCCSS-CC--EECSSHHHHHHHEEEEEEEEEE
T ss_pred             CchhhHHHHHHHHHHHHHHHHHHHHhCCEEEEeccccccchhhcC-CC--ccccCCceeeeeeeEEEEEEee
Confidence            11111  1224788999999999999999999999 887764211 12  2335778999999999999875

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=99.71  E-value=1.6e-16  Score=159.59  Aligned_cols=239  Identities=13%  Similarity=0.158  Sum_probs=150.4

Q ss_pred             chHHHHHHhccccCcc-ccccccchHHHHHHHhhccCCCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHH
Q 009230          240 GALKEVVENAELYPIM-GLFNFRDYFDEIDAYYHRTSGDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDA  316 (539)
Q Consensus       240 ~~~~~~~~~A~~~~~~-~~~~~~~~~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~  316 (539)
                      ..+..+++.|...... +..+..++++..        .....++||++.||.+++  +++|+++.|.|+||+|||||+++
T Consensus        79 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~--------~~~~~isTG~~~LD~lL~ggi~~G~i~~I~G~~GsGKTTL~~~  150 (349)
T 1pzn_A           79 GTALKIIQAARKAANLGTFMRADEYLKKR--------ATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHT  150 (349)
T ss_dssp             HHHHHHHHHHHHHCSTTSCEEHHHHHHHH--------HTCCEECCSCHHHHHHHTSSEESSEEEEEEESTTSSHHHHHHH
T ss_pred             HHHHHHHHHHhhhccccCCccHHHHHhhh--------ccCCeecCCCHHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHH
Confidence            4566666666543222 555555554331        234689999999999985  99999999999999999999999


Q ss_pred             HHHHHHHh--c---CCeEEEEeCCCC--HHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecC
Q 009230          317 LICNINEH--A---GWKFVLCSMENK--VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCEN  389 (539)
Q Consensus       317 la~~~a~~--~---g~~vl~~s~E~~--~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~  389 (539)
                      ++...+..  .   +.+|+|++.|..  ++++..  +....+              +..+       .+.+...+...  
T Consensus       151 l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i~~--i~q~~~--------------~~~~-------~v~~ni~~~~~--  205 (349)
T 1pzn_A          151 LAVMVQLPPEEGGLNGSVIWIDTENTFRPERIRE--IAQNRG--------------LDPD-------EVLKHIYVARA--  205 (349)
T ss_dssp             HHHHTTSCGGGTSCSCEEEEEESSSCCCHHHHHH--HHHTTT--------------CCHH-------HHGGGEEEEEC--
T ss_pred             HHHHhccchhcCCCCCeEEEEeCCCCCCHHHHHH--HHHHcC--------------CCHH-------HHhhCEEEEec--
Confidence            99876421  2   368999999986  333322  122111              2221       12223333321  


Q ss_pred             CCCCCHHHHHHHHHHHHHH-----cCCcEEEEccccccccCCCCC-C---CHHHHHHHHHHHHHHHHHHhCcEEEEEec-
Q 009230          390 DSLPSIKWVLDLAKAAVLR-----HGVRGLVIDPYNELDHQRPVS-Q---TETEYVSQMLTMVKRFAQHHACHVWFVAH-  459 (539)
Q Consensus       390 ~~~~~~~~i~~~i~~~~~~-----~~~~~vvID~~~~l~~~~~~~-~---~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-  459 (539)
                      ........+...++.++..     .++++||||+.+.++.....+ .   .+...+.+++..|+.+++++|++||+++| 
T Consensus       206 ~~~~~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~ta~ld~~~~~~~~~~~r~~~~~~~l~~L~~la~~~~~tvii~~h~  285 (349)
T 1pzn_A          206 FNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQV  285 (349)
T ss_dssp             CSHHHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTTHHHHCCSTTTHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEC
T ss_pred             CChHHHHHHHHHHHHHHHHhccccCCCCEEEEeCchHhhhhhhcccccHHHHHHHHHHHHHHHHHHHHHcCcEEEEEccc
Confidence            1111233455566666666     689999999999876432111 1   12234778999999999999999999999 


Q ss_pred             CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeCCCcce
Q 009230          460 PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGT  520 (539)
Q Consensus       460 ~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~g~~G~  520 (539)
                      ........+.   ..-..|+..+++.+|..|.+.+...      ....+.+.|+|+++.|.
T Consensus       286 ~~~~~~~~~~---~~~~~~G~~l~~~~~~rL~l~~~~~------~~Ri~k~~ks~~~~~~~  337 (349)
T 1pzn_A          286 QARPDAFFGD---PTRPIGGHILAHSATLRVYLRKGKG------GKRIARLIDAPHLPEGE  337 (349)
T ss_dssp             C------------------CCCCCTTCSEEEEEEECTT------SEEEEEESCSSSSCCSE
T ss_pred             ccccccccCC---ccccCCcceEeecCcEEEEEEEcCC------CeEEEEEEeCCCCCCeE
Confidence            4433211011   1123567788999999999998642      24567778888877765

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=99.62  E-value=1.6e-14  Score=153.61  Aligned_cols=202  Identities=17%  Similarity=0.203  Sum_probs=139.0

Q ss_pred             CccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCc
Q 009230          277 DEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPF  354 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~  354 (539)
                      ....+++|++.||.+++  +.+|++++|.|++|+|||||+.+++...+.. |.+++|+++|.+..++..++..  .+   
T Consensus       259 ~~~~l~~g~~~ld~vL~g~i~~G~i~~i~G~~GsGKSTLl~~l~g~~~~~-G~~vi~~~~ee~~~~l~~~~~~--~g---  332 (525)
T 1tf7_A          259 SNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACAN-KERAILFAYEESRAQLLRNAYS--WG---  332 (525)
T ss_dssp             CCCEECCSCHHHHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTT-TCCEEEEESSSCHHHHHHHHHT--TS---
T ss_pred             ccceeecChHHHHHHhCCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHhC-CCCEEEEEEeCCHHHHHHHHHH--cC---
Confidence            44678999999999985  9999999999999999999999999887764 8899999999998887766521  12   


Q ss_pred             cccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHH
Q 009230          355 FEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETE  434 (539)
Q Consensus       355 ~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~  434 (539)
                                 ++.+++.      ....+.+........+..+....+...+...+++++||||...|....    ...+
T Consensus       333 -----------~~~~~~~------~~g~~~~~~~~p~~LS~g~~q~~~~a~~l~~~p~llilDp~~~Ld~~~----~~~~  391 (525)
T 1tf7_A          333 -----------MDFEEME------RQNLLKIVCAYPESAGLEDHLQIIKSEINDFKPARIAIDSLSALARGV----SNNA  391 (525)
T ss_dssp             -----------CCHHHHH------HTTSEEECCCCGGGSCHHHHHHHHHHHHHTTCCSEEEEECHHHHTSSS----CHHH
T ss_pred             -----------CCHHHHH------hCCCEEEEEeccccCCHHHHHHHHHHHHHhhCCCEEEEcChHHHHhhC----ChHH
Confidence                       2222211      111122211112334566666666666667899999999888876532    1222


Q ss_pred             HHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCccccccc-ccchhccceEEEEEeCCCCCCCCCCcEEEEEEE
Q 009230          435 YVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGS-AHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRK  512 (539)
Q Consensus       435 ~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs-~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K  512 (539)
                       ..+.+..|-..+++.|++||+++| ..+..          .+.++ ..++..||.|+.|+..+...   .....+.+.|
T Consensus       392 -~~~~i~~ll~~l~~~g~tvilvsh~~~~~~----------~~~~~~~~l~~~~D~vi~L~~ge~~~---~~~R~l~v~K  457 (525)
T 1tf7_A          392 -FRQFVIGVTGYAKQEEITGLFTNTSDQFMG----------AHSITDSHISTITDTIILLQYVEIRG---EMSRAINVFK  457 (525)
T ss_dssp             -HHHHHHHHHHHHHHTTCEEEEEEECSSSSC----------CCSSCSSCCTTTCSEEEEEEEEEETT---EEEEEEEEEE
T ss_pred             -HHHHHHHHHHHHHhCCCEEEEEECcccccC----------cccccCcccceeeeEEEEEEEEEeCC---EEEEEEEEEE
Confidence             334444444455678999999999 43332          13343 55788999999998765321   2357889999


Q ss_pred             eeCCCcc
Q 009230          513 VRNKVVG  519 (539)
Q Consensus       513 ~R~g~~G  519 (539)
                      +|.++..
T Consensus       458 ~R~~~~~  464 (525)
T 1tf7_A          458 MRGSWHD  464 (525)
T ss_dssp             ESSSCCC
T ss_pred             CCCCCCC
Confidence            9999873

>3bs4_A Uncharacterized protein PH0321; structural genomics, unknown function, PSI-2, protein struct initiative; 1.60A {Pyrococcus horikoshii}

Probab=99.61  E-value=9.4e-15  Score=138.99  Aligned_cols=222  Identities=8%  Similarity=-0.093  Sum_probs=131.6

Q ss_pred             ccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCcccc
Q 009230          280 GISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEA  357 (539)
Q Consensus       280 gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i  357 (539)
                      .++||+++||++++  +++|.+++|.|.||+|||+|++|++.+.+.+ |.+++||++|+++.++..++.+  .|+++...
T Consensus         2 ~i~tGi~~LD~~l~GGl~~gs~~li~g~p~~~~~~l~~qfl~~g~~~-Ge~~~~~~~~e~~~~l~~~~~~--~G~dl~~~   78 (260)
T 3bs4_A            2 SLSWEIEELDREIGKIKKHSLILIHEEDASSRGKDILFYILSRKLKS-DNLVGMFSISYPLQLIIRILSR--FGVDVIKY   78 (260)
T ss_dssp             CBCCSSHHHHHHHCCBCTTCEEEEEECSGGGCHHHHHHHHHHHHHHT-TCEEEEEECSSCHHHHHHHHHH--TTCCHHHH
T ss_pred             cCccCcHHHHHHhCCCCCCCcEEEEEeCCCccHHHHHHHHHHHHHHC-CCcEEEEEEeCCHHHHHHHHHH--cCCCHHHH
Confidence            47899999999996  9999999999999999999999999999986 9999999999999999988854  56665543


Q ss_pred             ccCCCCCCCCHHHHHHHHHHhhc---cceeEeecCCCCCCHHHHHHHHHHHHHH----------cC-Cc-EEEEcccccc
Q 009230          358 NYGGSAERMTVEEFEQGKAWLSN---TFSLIRCENDSLPSIKWVLDLAKAAVLR----------HG-VR-GLVIDPYNEL  422 (539)
Q Consensus       358 ~~~~~~~~l~~~~~~~~~~~l~~---~~~~i~~~~~~~~~~~~i~~~i~~~~~~----------~~-~~-~vvID~~~~l  422 (539)
                      ...+...-++.  ..   ..+..   ...++  .+....+++++...++.++..          .+ .+ ++|||++..+
T Consensus        79 ~~~g~l~i~d~--~~---~~~~~~~~~~~v~--~~~~e~d~~~l~~~i~~iv~~~~~~~~i~~~~~~~rvv~vidsldsl  151 (260)
T 3bs4_A           79 LENHRLAIVDT--FG---SFHGIKATMPGVW--YLEGMLSSETLPIKYAKAVEDHKKVWMDLNLFEGRELYGFAISMSGY  151 (260)
T ss_dssp             HHTTSEEEECH--HH---HHHTC---CTTEE--CCCSCCCTTTHHHHHHHHHHHHHHHHHHTTCSTTCCEEEEEETGGGG
T ss_pred             hhCCcEEEEEc--cc---cccccccccccee--cccccCCHHHHHHHHHHHHHhhccccchhhccCCceEEEEEeecchH
Confidence            21100000111  00   01110   11111  111134555554444444433          24 45 3577766665


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHH-----HHHH-hCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          423 DHQRPVSQTETEYVSQMLTMVKR-----FAQH-HACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       423 ~~~~~~~~~~~~~~~~~~~~Lk~-----lA~~-~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      ....    .....+..+...+..     +.++ .+++++++.+ .....           .....+...||.||.|...+
T Consensus       152 ~~~~----~~~~~~~~~~~ll~~~~~~~~~~~~~~~ttil~~~-~~~~~-----------~~~~~l~~laD~VI~lr~~e  215 (260)
T 3bs4_A          152 LEVF----TPEETLRYLETSAEVRYGHPAYKKYPRGTNFWLWE-GVKDK-----------RVLLSVYRRADYVLKTRSSL  215 (260)
T ss_dssp             GGTS----CHHHHHHHHHHHHHHHHHCHHHHSSCCCEEEEEEE-SCSCH-----------HHHHHHHHHCSEEEEEEEEE
T ss_pred             HHHh----ChhhHHHHHHHHHHhhhhHHHHhccCCcEEEEEEC-CCccc-----------ccccceEEEeeEEEEEEEEe
Confidence            5432    222222223333222     3344 6777777765 11110           11245678899999998765


Q ss_pred             CCCCCCCCcEEEEEEEeeCCCcceeeeEEEEEeCC
Q 009230          497 DPEAGPIDRVQVCVRKVRNKVVGTIGEAFLSYNRV  531 (539)
Q Consensus       497 ~~~~~~~~~~~l~i~K~R~g~~G~~~~~~l~fd~~  531 (539)
                      ...   .-...|.|.|.|.+..-. +.-++.|...
T Consensus       216 ~~g---~~rR~L~V~K~Rg~~~~~-~~re~~i~~~  246 (260)
T 3bs4_A          216 GEN---GIKRELLVIKTPKPIEEL-VRFEYEFKGN  246 (260)
T ss_dssp             ETT---EEEEEEEEEECCC------CEEEEEEETT
T ss_pred             cCC---ceEEEEEEEECCCCCcCC-ceEEEEEecC
Confidence            321   124789999999865432 2224566554

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=99.16  E-value=7.2e-11  Score=114.67  Aligned_cols=124  Identities=20%  Similarity=0.156  Sum_probs=89.0

Q ss_pred             ccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC--CCHHHHHHHHHHHhhCCCccc
Q 009230          280 GISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME--NKVREHARKLLEKHIKKPFFE  356 (539)
Q Consensus       280 gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E--~~~~~~~~r~~~~~~~~~~~~  356 (539)
                      -++||++.||++++ +++|.+++|.|+||+|||+|+++++.+   . |.+|+|+++|  ++              ++.  
T Consensus       105 ~i~TGi~~LD~lLGGi~~gsviLI~GpPGsGKTtLAlqlA~~---~-G~~VlyIs~~~eE~--------------v~~--  164 (331)
T 2vhj_A          105 ELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEA---L-GGKDKYATVRFGEP--------------LSG--  164 (331)
T ss_dssp             TCCSBCCEEEEETTEEEESEEEEEECSCSSSHHHHHHHHHHH---H-HTTSCCEEEEBSCS--------------STT--
T ss_pred             ccccCcHHHHHHhCCCCCCcEEEEEcCCCCCHHHHHHHHHHh---C-CCCEEEEEecchhh--------------hhh--
Confidence            36799999999998 999999999999999999999999876   3 7899999993  32              000  


Q ss_pred             cccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCC---CCCHH
Q 009230          357 ANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPV---SQTET  433 (539)
Q Consensus       357 i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~---~~~~~  433 (539)
                               +.                         .+++.+...+.....+.+  +||||++..+......   .....
T Consensus       165 ---------~~-------------------------~~le~~l~~i~~~l~~~~--LLVIDsI~aL~~~~~~~s~~G~v~  208 (331)
T 2vhj_A          165 ---------YN-------------------------TDFNVFVDDIARAMLQHR--VIVIDSLKNVIGAAGGNTTSGGIS  208 (331)
T ss_dssp             ---------CB-------------------------CCHHHHHHHHHHHHHHCS--EEEEECCTTTC-----------CC
T ss_pred             ---------hh-------------------------cCHHHHHHHHHHHHhhCC--EEEEecccccccccccccccchHH
Confidence                     00                         123444544544445555  9999998887532210   00012


Q ss_pred             HHHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          434 EYVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       434 ~~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                      +.+.+++..|..++++.+++++++.+
T Consensus       209 ~~lrqlL~~L~~~~k~~gvtVIlttn  234 (331)
T 2vhj_A          209 RGAFDLLSDIGAMAASRGCVVIASLN  234 (331)
T ss_dssp             HHHHHHHHHHHHHHHHHTCEEEEECC
T ss_pred             HHHHHHHHHHHHHHhhCCCEEEEEeC
Confidence            45778999999999999999888766

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=99.09  E-value=1.1e-08  Score=108.58  Aligned_cols=202  Identities=12%  Similarity=0.107  Sum_probs=123.6

Q ss_pred             CccccccCchhhhhhh-c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCc
Q 009230          277 DEFGISTGWRALNELY-N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPF  354 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~-~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~  354 (539)
                      ....+++|.+.||++. | +++|++++|.|++|+|||||+.+++...+...+..++|++.+.+..++..+.  ...|+.+
T Consensus        17 ~~~~~~~g~~~Ld~i~~G~i~~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~~~~~g~i~v~g~~~~~~~~~~~--~~~g~~~   94 (525)
T 1tf7_A           17 AIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNA--RSFGWDL   94 (525)
T ss_dssp             SCCEECCCCTTHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESSSCHHHHHHHH--GGGTCCH
T ss_pred             ccccccCCchhHHHhcCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEeCCHHHHHHHH--HHcCCCh
Confidence            3467889999999986 5 9999999999999999999999986555554477899999998766554332  2233322


Q ss_pred             cccccCCCCCCCCHHHHHHHHHHhhccceeEeecC-------CCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCC
Q 009230          355 FEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCEN-------DSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRP  427 (539)
Q Consensus       355 ~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~-------~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~  427 (539)
                      ..              ..     ....+.++....       -....++.+...+.......++++|+||+.+.+...  
T Consensus        95 q~--------------~~-----~~~~l~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~LS~g~~~~lilDe~t~~~~~--  153 (525)
T 1tf7_A           95 AK--------------LV-----DEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQ--  153 (525)
T ss_dssp             HH--------------HH-----HTTSEEEEECCCCSSCCSCCSSHHHHHHHHHHHHHHHHHTCSEEEEECSTTTSTT--
T ss_pred             HH--------------hh-----ccCcEEEEecCcccchhhhhcccCHHHHHHHHHHHHHHcCCCEEEECCHHHHHHh--
Confidence            21              11     001111111100       012234444444444444567999999988765532  


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcE
Q 009230          428 VSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRV  506 (539)
Q Consensus       428 ~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~  506 (539)
                       ...+......+.+.++.+.+ .|++||+++| ......          .......+..||.|+.|......  + ....
T Consensus       154 -~~lD~~~~~~l~~ll~~l~~-~g~tvl~itH~~~~~~~----------~~~~~i~~~laD~vi~L~~~~~~--G-~~~r  218 (525)
T 1tf7_A          154 -YDASSVVRRELFRLVARLKQ-IGATTVMTTERIEEYGP----------IARYGVEEFVSDNVVILRNVLEG--E-RRRR  218 (525)
T ss_dssp             -TCCHHHHHHHHHHHHHHHHH-HTCEEEEEEECSSSSSC----------SSTTSCHHHHCSEEEEEEEECST--T-CCEE
T ss_pred             -cCCHHHHHHHHHHHHHHHHH-CCCEEEEEecCCCCccc----------cccccceeeeeeEEEEEEEEccC--C-ceeE
Confidence             12233444566666666655 6999999999 432211          01111125669999999875431  1 1245


Q ss_pred             EEEEEEeeCC
Q 009230          507 QVCVRKVRNK  516 (539)
Q Consensus       507 ~l~i~K~R~g  516 (539)
                      .+.+.|.|..
T Consensus       219 ~l~~~k~r~~  228 (525)
T 1tf7_A          219 TLEILKLRGT  228 (525)
T ss_dssp             EEEEEEETTS
T ss_pred             EEEEEECCCC
Confidence            6778887753

>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=98.75  E-value=8e-09  Score=96.11  Aligned_cols=145  Identities=11%  Similarity=0.097  Sum_probs=90.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQ  373 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~  373 (539)
                      -.+|.+++++|++|+||||.+++++.+++.+ |.+|++++.+.+..  ....++...|+...                  
T Consensus         9 ~~~G~i~litG~mGsGKTT~ll~~~~r~~~~-g~kVli~~~~~d~r--~~~~i~srlG~~~~------------------   67 (223)
T 2b8t_A            9 KKIGWIEFITGPMFAGKTAELIRRLHRLEYA-DVKYLVFKPKIDTR--SIRNIQSRTGTSLP------------------   67 (223)
T ss_dssp             --CCEEEEEECSTTSCHHHHHHHHHHHHHHT-TCCEEEEEECCCGG--GCSSCCCCCCCSSC------------------
T ss_pred             cCCcEEEEEECCCCCcHHHHHHHHHHHHHhc-CCEEEEEEeccCch--HHHHHHHhcCCCcc------------------
Confidence            4678999999999999999999999998875 99999998887543  11111111111100                  


Q ss_pred             HHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcE
Q 009230          374 GKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACH  453 (539)
Q Consensus       374 ~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~  453 (539)
                              .+.+       ...+++.+.++.......+++|+||....+.             .++++.|+.++. .+++
T Consensus        68 --------~~~~-------~~~~~i~~~i~~~~~~~~~dvViIDEaQ~l~-------------~~~ve~l~~L~~-~gi~  118 (223)
T 2b8t_A           68 --------SVEV-------ESAPEILNYIMSNSFNDETKVIGIDEVQFFD-------------DRICEVANILAE-NGFV  118 (223)
T ss_dssp             --------CEEE-------SSTHHHHHHHHSTTSCTTCCEEEECSGGGSC-------------THHHHHHHHHHH-TTCE
T ss_pred             --------cccc-------CCHHHHHHHHHHHhhCCCCCEEEEecCccCc-------------HHHHHHHHHHHh-CCCe
Confidence                    0111       1224455544433223458999999775432             124455566666 4999


Q ss_pred             EEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          454 VWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       454 vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      ||++-|...-.+        .-+.++..+...||.|.-|..-.
T Consensus       119 Vil~Gl~~df~~--------~~F~~~~~Ll~lAD~V~el~~ic  153 (223)
T 2b8t_A          119 VIISGLDKNFKG--------EPFGPIAKLFTYADKITKLTAIC  153 (223)
T ss_dssp             EEEECCSBCTTS--------SBCTTHHHHHHHCSEEEECCEEC
T ss_pred             EEEEeccccccC--------CcCCCcHHHHHHhheEeecceec
Confidence            999988322211        12445677888999999876544

>1t6t_1 Putative protein; structural genomics, PSI, protein structur initiative, midwest center for structural genomics, MCSG, U function; 1.80A {Aquifex aeolicus} SCOP: c.136.1.1

Probab=98.54  E-value=1.2e-07  Score=77.39  Aligned_cols=72  Identities=19%  Similarity=0.314  Sum_probs=57.1

Q ss_pred             CcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCE-EEEEecCCccchHHHH
Q 009230          124 SDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASR-IILATDGDPPGQALAE  202 (539)
Q Consensus       124 ~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~-ivl~~DnD~~G~~~~~  202 (539)
                      +.++||||-.|..+++++|+.++++. +|++       ++            .+...+.+.++ |++++|+|.+|++++.
T Consensus        21 ~~vIvVEGk~D~~~L~~~g~~~iI~t-~Gta-------l~------------~~i~~l~~~~~~VIIltD~D~aGe~ir~   80 (118)
T 1t6t_1           21 EAVILVEGKNDKKALSKFSIKNVIDL-SGKR-------YA------------DVVDMLEGKWEKVILLFDLDTHGERINQ   80 (118)
T ss_dssp             TSEEEESSHHHHHHHHTTTCCCEEEC-TTSC-------HH------------HHHHHHTTTCSEEEECCCSSHHHHHHHH
T ss_pred             CcEEEEEChHHHHHHHHhCcCcEEEE-CCCc-------HH------------HHHHHHHhCCCEEEEEECCChhHHHHHH
Confidence            67999999999999999999988875 4553       11            12345665565 9999999999999999


Q ss_pred             HHHHHhcCCceEE
Q 009230          203 ELARRVGRERCWR  215 (539)
Q Consensus       203 ~~~~~l~~~~~~~  215 (539)
                      ++.+.|+...+++
T Consensus        81 ~i~~~l~~~~~~v   93 (118)
T 1t6t_1           81 KMKELLSSQGFLV   93 (118)
T ss_dssp             HHHHHHHHTTCEE
T ss_pred             HHHHhcCccCcee
Confidence            9999997655544

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=97.97  E-value=3.4e-05  Score=74.12  Aligned_cols=61  Identities=15%  Similarity=0.226  Sum_probs=42.7

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|--+       ++.+ ......+++.|++++++.|.+||+++|.-..                  +.+.||
T Consensus       159 ~~~P~lLlLDEPt-------s~LD-~~~~~~i~~~l~~l~~~~g~tvi~vtHdl~~------------------~~~~~d  212 (275)
T 3gfo_A          159 VMEPKVLILDEPT-------AGLD-PMGVSEIMKLLVEMQKELGITIIIATHDIDI------------------VPLYCD  212 (275)
T ss_dssp             TTCCSEEEEECTT-------TTCC-HHHHHHHHHHHHHHHHHHCCEEEEEESCCSS------------------GGGGCS
T ss_pred             HcCCCEEEEECcc-------ccCC-HHHHHHHHHHHHHHHhhCCCEEEEEecCHHH------------------HHHhCC
Confidence            3689999999222       2233 3445678888888885559999999993221                  346789


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .+++|..
T Consensus       213 rv~~l~~  219 (275)
T 3gfo_A          213 NVFVMKE  219 (275)
T ss_dssp             EEEEEET
T ss_pred             EEEEEEC
Confidence            9998874

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.90  E-value=4.9e-05  Score=68.07  Aligned_cols=42  Identities=21%  Similarity=0.217  Sum_probs=35.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      +.+|+.++|.|+||+|||+++..++..+....|..++|++.+
T Consensus        35 ~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~~~   76 (180)
T 3ec2_A           35 PEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTK   76 (180)
T ss_dssp             GGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEEHH
T ss_pred             ccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEEHH
Confidence            556899999999999999999999988874458888887643

>2fcj_A Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A*

Probab=97.88  E-value=7.6e-05  Score=60.98  Aligned_cols=101  Identities=19%  Similarity=0.224  Sum_probs=66.6

Q ss_pred             CCcEEEEechhhHHHHHHhC--CCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCccchHH
Q 009230          123 ESDIIIVEGEMDKLSMEEAG--FLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQAL  200 (539)
Q Consensus       123 ~~~v~i~EG~~Dalsl~~~g--~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~~G~~~  200 (539)
                      -+.++||||..|..++.+++  ..+++++ +|+-+        ..    ....    +..+.+.+.|+++.|+|.+|++-
T Consensus         4 i~~vIVVEGk~D~~~L~~~~~~~~~iI~t-~Gsi~--------~~----~l~~----I~~~~~~r~VIi~TD~D~~GekI   66 (119)
T 2fcj_A            4 VEKVIIVEGRSDKQKVAAVLNEPVVIVCT-NGTIS--------DA----RLEE----LADELEGYDVYLLADADEAGEKL   66 (119)
T ss_dssp             CCEEEEESSHHHHHHHHHHBSSCCEEEEC-CSCCC--------HH----HHHH----HHHHTTTSEEEEECCSSHHHHHH
T ss_pred             cCeEEEEechHHHHHHHHhcCCCCCEEEe-CCccC--------HH----HHHH----HHHHhcCCCEEEEECCCccHHHH
Confidence            35799999999999999998  3455664 45411        00    0011    22334578999999999999999


Q ss_pred             HHHHHHHhcCCceEEEecCCCCCCCCCCChHHHHHhcCcchHHHHHHhccc
Q 009230          201 AEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAEL  251 (539)
Q Consensus       201 ~~~~~~~l~~~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~~~~~~~A~~  251 (539)
                      .+.+.+.++..  ...-+|.     ....++++    ..+.+.+++.++..
T Consensus        67 Rk~i~~~lp~~--~hafi~r-----~~~gVE~a----~~~~I~~aL~~~~~  106 (119)
T 2fcj_A           67 RRQFRRMFPEA--EHLYIDR-----AYREVAAA----PIWHLAQVLLRARF  106 (119)
T ss_dssp             HHHHHHHCTTS--EEECCCT-----TTCSTTTS----CHHHHHHHHHHTTC
T ss_pred             HHHHHHHCCCC--cEEeccC-----CccCcccC----CHHHHHHHHHhccc
Confidence            99999999764  3444452     22233332    34667777777654

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=97.86  E-value=1.1e-05  Score=72.67  Aligned_cols=134  Identities=12%  Similarity=0.099  Sum_probs=84.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHH---HHHHHHHHhhCCCccccccCCCCCCCCHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVRE---HARKLLEKHIKKPFFEANYGGSAERMTVEE  370 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~---~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~  370 (539)
                      -..|.|.+|+|+.|+|||+.+++.+.+...+ +.+|+|++.+.+.+.   +..|+     |.                  
T Consensus        17 ~~~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~-~~kvl~~kp~~D~R~~~~i~S~~-----g~------------------   72 (195)
T 1w4r_A           17 KTRGQIQVILGPMFSGKSTELMRRVRRFQIA-QYKCLVIKYAKDTRYSSSFCTHD-----RN------------------   72 (195)
T ss_dssp             --CCEEEEEEECTTSCHHHHHHHHHHHHHHT-TCCEEEEEETTCCCGGGSCCHHH-----HH------------------
T ss_pred             CCceEEEEEECCCCCcHHHHHHHHHHHHHHc-CCeEEEEccccCccchhhhhhcc-----CC------------------
Confidence            3468999999999999999999999998875 999999998855431   11111     00                  


Q ss_pred             HHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHh
Q 009230          371 FEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHH  450 (539)
Q Consensus       371 ~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~  450 (539)
                            .. +. ..+       .+.+++.+.      ...+++|+||....+ .      +       +...+..++ +.
T Consensus        73 ------~~-~A-~~~-------~~~~d~~~~------~~~~DvIlIDEaQFf-k------~-------~ve~~~~L~-~~  116 (195)
T 1w4r_A           73 ------TM-EA-LPA-------CLLRDVAQE------ALGVAVIGIDEGQFF-P------D-------IVEFCEAMA-NA  116 (195)
T ss_dssp             ------HS-EE-EEE-------SSGGGGHHH------HHTCSEEEESSGGGC-T------T-------HHHHHHHHH-HT
T ss_pred             ------cc-cc-eec-------CCHHHHHHh------ccCCCEEEEEchhhh-H------H-------HHHHHHHHH-HC
Confidence                  00 00 111       112233332      235899999966554 1      1       223335666 78


Q ss_pred             CcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          451 ACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       451 ~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                      |++||+......-.+        .-+.++..+-..||.|.-|..-
T Consensus       117 gk~VI~~GL~~DF~~--------~~F~~~~~Ll~~Ad~v~kl~ai  153 (195)
T 1w4r_A          117 GKTVIVAALDGTFQR--------KPFGAILNLVPLAESVVKLTAV  153 (195)
T ss_dssp             TCEEEEEEESBCTTS--------SBCTTGGGGGGGCSEEEECCEE
T ss_pred             CCeEEEEeccccccc--------ccchhHHHHHHhcCeEEEeeeE
Confidence            999999877322221        1256778888999999877654

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=97.80  E-value=5.7e-05  Score=69.02  Aligned_cols=141  Identities=11%  Similarity=0.093  Sum_probs=81.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQ  373 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~  373 (539)
                      -.+|.+.+++|+.|+||||.+++++.++..+ |.+|++|....+.+.-...+.+ ..|.....+.               
T Consensus        25 ~~~G~l~vitG~MgsGKTT~lL~~a~r~~~~-g~kVli~k~~~d~R~ge~~i~s-~~g~~~~a~~---------------   87 (214)
T 2j9r_A           25 NQNGWIEVICGSMFSGKSEELIRRVRRTQFA-KQHAIVFKPCIDNRYSEEDVVS-HNGLKVKAVP---------------   87 (214)
T ss_dssp             CCSCEEEEEECSTTSCHHHHHHHHHHHHHHT-TCCEEEEECC------------------CCEEE---------------
T ss_pred             CCCCEEEEEECCCCCcHHHHHHHHHHHHHHC-CCEEEEEEeccCCcchHHHHHh-hcCCeeEEee---------------
Confidence            5678999999999999999999999998875 9999999866543311111111 1122211110               


Q ss_pred             HHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcE
Q 009230          374 GKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACH  453 (539)
Q Consensus       374 ~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~  453 (539)
                                 +    ..   .+++.+.+.     ..+++|+||-...+. .            +.+..|+.++. .+++
T Consensus        88 -----------~----~~---~~~~~~~~~-----~~~dvViIDEaQF~~-~------------~~V~~l~~l~~-~~~~  130 (214)
T 2j9r_A           88 -----------V----SA---SKDIFKHIT-----EEMDVIAIDEVQFFD-G------------DIVEVVQVLAN-RGYR  130 (214)
T ss_dssp             -----------C----SS---GGGGGGGCC-----SSCCEEEECCGGGSC-T------------THHHHHHHHHH-TTCE
T ss_pred             -----------c----CC---HHHHHHHHh-----cCCCEEEEECcccCC-H------------HHHHHHHHHhh-CCCE
Confidence                       0    00   011111111     147999999554421 1            12355666665 4999


Q ss_pred             EEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          454 VWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       454 vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      ||+......-.+        .-+.++..+-..||.|.-|..-.
T Consensus       131 Vi~~Gl~~DF~~--------~~F~~~~~Ll~~AD~Vtel~aiC  165 (214)
T 2j9r_A          131 VIVAGLDQDFRG--------LPFGQVPQLMAIAEHVTKLQAVC  165 (214)
T ss_dssp             EEEEECSBCTTS--------CBCTTHHHHHHHCSEEEECCCBC
T ss_pred             EEEEeccccccc--------CccccHHHHHHhcccEEeeeeEe
Confidence            999876222211        23567788889999999887554

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.79  E-value=1.2e-05  Score=72.68  Aligned_cols=140  Identities=16%  Similarity=0.100  Sum_probs=81.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQ  373 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~  373 (539)
                      ..+|.+.+++|+.|+||||.+++++.+...+ |.+|+++....+.+     .     +.  ..+...     +.      
T Consensus         5 ~~~g~i~v~~G~mgsGKTT~ll~~a~r~~~~-g~kV~v~k~~~d~r-----~-----~~--~~i~s~-----~g------   60 (191)
T 1xx6_A            5 KDHGWVEVIVGPMYSGKSEELIRRIRRAKIA-KQKIQVFKPEIDNR-----Y-----SK--EDVVSH-----MG------   60 (191)
T ss_dssp             TTCCEEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEEEC-------------------CEEECT-----TS------
T ss_pred             CCCCEEEEEECCCCCcHHHHHHHHHHHHHHC-CCEEEEEEeccCcc-----c-----hH--HHHHhh-----cC------
Confidence            3568899999999999999999999998775 99999997553321     1     00  011100     00      


Q ss_pred             HHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcE
Q 009230          374 GKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACH  453 (539)
Q Consensus       374 ~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~  453 (539)
                          +.-....+    ...   +++.+.+.     ...++|+||-...+.        +     +.+..|+.++.. +++
T Consensus        61 ----~~~~a~~~----~~~---~~i~~~~~-----~~~dvViIDEaqfl~--------~-----~~v~~l~~l~~~-~~~  110 (191)
T 1xx6_A           61 ----EKEQAVAI----KNS---REILKYFE-----EDTEVIAIDEVQFFD--------D-----EIVEIVNKIAES-GRR  110 (191)
T ss_dssp             ----CEEECEEE----SSS---THHHHHCC-----TTCSEEEECSGGGSC--------T-----HHHHHHHHHHHT-TCE
T ss_pred             ----CceeeEee----CCH---HHHHHHHh-----ccCCEEEEECCCCCC--------H-----HHHHHHHHHHhC-CCE
Confidence                00000111    111   23333221     247999999544321        1     234566777765 999


Q ss_pred             EEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          454 VWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       454 vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                      ||+......-.+        .-+.++..+...||.|.-+..-
T Consensus       111 Vi~~Gl~~df~~--------~~F~~~~~L~~~AD~V~el~~i  144 (191)
T 1xx6_A          111 VICAGLDMDFRG--------KPFGPIPELMAIAEFVDKIQAI  144 (191)
T ss_dssp             EEEEECSBCTTS--------CBCTTHHHHHHHCSEEEECCEE
T ss_pred             EEEEeccccccc--------CcCccHHHHHHHcccEEeeeeE
Confidence            999766222111        1245678888999999776543

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=97.78  E-value=0.00017  Score=71.79  Aligned_cols=60  Identities=15%  Similarity=0.226  Sum_probs=43.6

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+++++++|--+       ++.+ ......+++.|+++.++.|++||+++|.-.                  .+.+.||.
T Consensus       180 ~~P~lLLlDEPT-------s~LD-~~~~~~i~~lL~~l~~~~g~Tii~vTHdl~------------------~~~~~aDr  233 (366)
T 3tui_C          180 SNPKVLLCDQAT-------SALD-PATTRSILELLKDINRRLGLTILLITHEMD------------------VVKRICDC  233 (366)
T ss_dssp             TCCSEEEEESTT-------TTSC-HHHHHHHHHHHHHHHHHSCCEEEEEESCHH------------------HHHHHCSE
T ss_pred             cCCCEEEEECCC-------ccCC-HHHHHHHHHHHHHHHHhCCCEEEEEecCHH------------------HHHHhCCE
Confidence            579999999222       2233 344567889999999999999999999321                  24567888


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      |++|..
T Consensus       234 v~vl~~  239 (366)
T 3tui_C          234 VAVISN  239 (366)
T ss_dssp             EEEEET
T ss_pred             EEEEEC
Confidence            888865

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=97.78  E-value=0.00016  Score=72.44  Aligned_cols=54  Identities=13%  Similarity=0.144  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          397 WVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       397 ~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      +-...++.++  .+++++++|-=+       ++.+ .....++...|+++.++.|+++|+++|.
T Consensus       140 QRVaiArAL~--~~P~lLLLDEPt-------s~LD-~~~~~~l~~~l~~l~~~~g~tii~vTHd  193 (381)
T 3rlf_A          140 QRVAIGRTLV--AEPSVFLLDEPL-------SNLD-AALRVQMRIEISRLHKRLGRTMIYVTHD  193 (381)
T ss_dssp             HHHHHHHHHH--HCCSEEEEESTT-------TTSC-HHHHHHHHHHHHHHHHHHCCEEEEECSC
T ss_pred             HHHHHHHHHH--cCCCEEEEECCC-------cCCC-HHHHHHHHHHHHHHHHhCCCEEEEEECC
Confidence            3344444443  478999999222       2233 3344678888999999999999999993

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=97.76  E-value=4.2e-05  Score=73.22  Aligned_cols=60  Identities=13%  Similarity=0.128  Sum_probs=43.5

Q ss_pred             CCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceE
Q 009230          410 GVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNG  489 (539)
Q Consensus       410 ~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~v  489 (539)
                      +++++++|-       +.++.+ ......+++.|++++++.+++||+++|.-.                  .+.+.||.+
T Consensus       165 ~p~lLllDE-------Pts~LD-~~~~~~i~~~l~~l~~~~~~tvi~vtHdl~------------------~~~~~~d~v  218 (266)
T 4g1u_C          165 TPRWLFLDE-------PTSALD-LYHQQHTLRLLRQLTRQEPLAVCCVLHDLN------------------LAALYADRI  218 (266)
T ss_dssp             CCEEEEECC-------CCSSCC-HHHHHHHHHHHHHHHHHSSEEEEEECSCHH------------------HHHHHCSEE
T ss_pred             CCCEEEEeC-------ccccCC-HHHHHHHHHHHHHHHHcCCCEEEEEEcCHH------------------HHHHhCCEE
Confidence            799999992       212333 344567888899999888899999999311                  245688999


Q ss_pred             EEEEeC
Q 009230          490 IVIHRN  495 (539)
Q Consensus       490 l~l~r~  495 (539)
                      ++|+.-
T Consensus       219 ~vl~~G  224 (266)
T 4g1u_C          219 MLLAQG  224 (266)
T ss_dssp             EEEETT
T ss_pred             EEEECC
Confidence            988753

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=97.76  E-value=0.00014  Score=68.15  Aligned_cols=60  Identities=10%  Similarity=0.115  Sum_probs=43.3

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|--+       ++.+ ......+++.|++++++.+.+||+++|.-.                   +...||
T Consensus       161 ~~~p~llllDEPt-------s~LD-~~~~~~i~~~l~~l~~~~g~tvi~vtHd~~-------------------~~~~~d  213 (235)
T 3tif_A          161 ANNPPIILADQPT-------WALD-SKTGEKIMQLLKKLNEEDGKTVVVVTHDIN-------------------VARFGE  213 (235)
T ss_dssp             TTCCSEEEEESTT-------TTSC-HHHHHHHHHHHHHHHHHHCCEEEEECSCHH-------------------HHTTSS
T ss_pred             HcCCCEEEEeCCc-------ccCC-HHHHHHHHHHHHHHHHHcCCEEEEEcCCHH-------------------HHHhCC
Confidence            3579999999222       2233 344567888899999888999999999311                   224789


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|+.
T Consensus       214 ~i~~l~~  220 (235)
T 3tif_A          214 RIIYLKD  220 (235)
T ss_dssp             EEEEEET
T ss_pred             EEEEEEC
Confidence            9999974

>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=97.73  E-value=0.00067  Score=69.16  Aligned_cols=41  Identities=17%  Similarity=0.325  Sum_probs=36.3

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      ++.+++++|++|+||||++..+|..++.+ |.+|++++.+.-
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~~~-G~kVllv~~D~~  139 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQKR-GYKVGVVCSDTW  139 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTT-TCCEEEEECCCS
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHHHC-CCeEEEEeCCCc
Confidence            35799999999999999999999988875 999999998843

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=97.72  E-value=8.7e-05  Score=70.67  Aligned_cols=60  Identities=12%  Similarity=0.166  Sum_probs=41.7

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+++++++|-=+       ++.+ ......+++.|++++++ +.+||+++|.-..                  +...||
T Consensus       169 ~~~p~lllLDEPt-------s~LD-~~~~~~l~~~l~~l~~~-g~tvi~vtHd~~~------------------~~~~~d  221 (257)
T 1g6h_A          169 MTNPKMIVMDEPI-------AGVA-PGLAHDIFNHVLELKAK-GITFLIIEHRLDI------------------VLNYID  221 (257)
T ss_dssp             HTCCSEEEEESTT-------TTCC-HHHHHHHHHHHHHHHHT-TCEEEEECSCCST------------------TGGGCS
T ss_pred             HcCCCEEEEeCCc-------cCCC-HHHHHHHHHHHHHHHHC-CCEEEEEecCHHH------------------HHHhCC
Confidence            3679999999222       2223 34456788888888765 9999999994221                  346889


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       222 ~v~~l~~  228 (257)
T 1g6h_A          222 HLYVMFN  228 (257)
T ss_dssp             EEEEEET
T ss_pred             EEEEEEC
Confidence            9998863

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=97.69  E-value=0.00028  Score=70.03  Aligned_cols=45  Identities=18%  Similarity=0.189  Sum_probs=33.2

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      -.+++++++|-=+       ++.+ .....++...|+++.++.+++||+++|.
T Consensus       161 ~~~P~lLLLDEP~-------s~LD-~~~r~~l~~~l~~l~~~~g~tvi~vTHd  205 (355)
T 1z47_A          161 APRPQVLLFDEPF-------AAID-TQIRRELRTFVRQVHDEMGVTSVFVTHD  205 (355)
T ss_dssp             TTCCSEEEEESTT-------CCSS-HHHHHHHHHHHHHHHHHHTCEEEEECSC
T ss_pred             HcCCCEEEEeCCc-------ccCC-HHHHHHHHHHHHHHHHhcCCEEEEECCC
Confidence            3579999999222       2223 3445678888899999999999999993

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=97.69  E-value=0.00054  Score=63.07  Aligned_cols=41  Identities=17%  Similarity=0.201  Sum_probs=36.1

Q ss_pred             CCCcE-EEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          295 LPGEL-TIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       295 ~~G~l-~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      .+|.+ +++.|++|+|||+++++++..++.+ |.+|+++..+.
T Consensus         3 ~~g~l~I~~~~kgGvGKTt~a~~la~~l~~~-G~~V~v~d~D~   44 (228)
T 2r8r_A            3 ARGRLKVFLGAAPGVGKTYAMLQAAHAQLRQ-GVRVMAGVVET   44 (228)
T ss_dssp             CCCCEEEEEESSTTSSHHHHHHHHHHHHHHT-TCCEEEEECCC
T ss_pred             CCceEEEEEECCCCCcHHHHHHHHHHHHHHC-CCCEEEEEeCC
Confidence            35776 6678999999999999999999986 99999999886

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=97.66  E-value=6.2e-05  Score=68.61  Aligned_cols=141  Identities=13%  Similarity=0.062  Sum_probs=84.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQ  373 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~  373 (539)
                      -..|.+.+|+|+-|+||||.+++.+.+...+ |.+|++|....+...-.. .++...|.....+                
T Consensus        25 ~~~G~I~vitG~M~sGKTT~Llr~~~r~~~~-g~kvli~kp~~D~R~~~~-~I~Sr~G~~~~a~----------------   86 (219)
T 3e2i_A           25 YHSGWIECITGSMFSGKSEELIRRLRRGIYA-KQKVVVFKPAIDDRYHKE-KVVSHNGNAIEAI----------------   86 (219)
T ss_dssp             --CCEEEEEEECTTSCHHHHHHHHHHHHHHT-TCCEEEEEEC------------CBTTBCCEEE----------------
T ss_pred             cCCceEEEEECCCCCCHHHHHHHHHHHHHHc-CCceEEEEeccCCcchhh-hHHHhcCCceeeE----------------
Confidence            5679999999999999999999988887764 999999988765442222 2222233222111                


Q ss_pred             HHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcE
Q 009230          374 GKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACH  453 (539)
Q Consensus       374 ~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~  453 (539)
                                .+    ..   .++|.+.+     ..++++|+||-. |.+.            .+++..|..+| +.|++
T Consensus        87 ----------~v----~~---~~di~~~i-----~~~~dvV~IDEa-QFf~------------~~~v~~l~~la-~~gi~  130 (219)
T 3e2i_A           87 ----------NI----SK---ASEIMTHD-----LTNVDVIGIDEV-QFFD------------DEIVSIVEKLS-ADGHR  130 (219)
T ss_dssp             ----------EE----SS---GGGGGGSC-----CTTCSEEEECCG-GGSC------------THHHHHHHHHH-HTTCE
T ss_pred             ----------Ee----CC---HHHHHHHH-----hcCCCEEEEech-hcCC------------HHHHHHHHHHH-HCCCE
Confidence                      11    00   11222111     136889999933 3331            14667778888 79999


Q ss_pred             EEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          454 VWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       454 vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      |++..=...-.        ..-+.++..+-..||.|.-|..--
T Consensus       131 Vi~~GLd~DF~--------~~~F~~~~~Ll~~Ad~v~kl~aiC  165 (219)
T 3e2i_A          131 VIVAGLDMDFR--------GEPFEPMPKLMAVSEQVTKLQAVC  165 (219)
T ss_dssp             EEEEEESBCTT--------SCBCTTHHHHHHHCSEEEEECEEC
T ss_pred             EEEeecccccc--------cCCCccHHHHHHhcceEEEeeeEc
Confidence            99865421111        123567888999999999887543

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=97.62  E-value=0.00011  Score=67.65  Aligned_cols=137  Identities=12%  Similarity=0.085  Sum_probs=80.7

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQG  374 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~  374 (539)
                      ..|.+.+++|+.|+||||.+++.+.+...+ |.+|++|....+.+.- ..+.+. .|.....                  
T Consensus        17 ~~g~l~v~~G~MgsGKTT~lL~~~~r~~~~-g~kvli~kp~~D~Ryg-~~i~sr-~G~~~~a------------------   75 (234)
T 2orv_A           17 TRGQIQVILGPMFSGKSTELMRRVRRFQIA-QYKCLVIKYAKDTRYS-SSFCTH-DRNTMEA------------------   75 (234)
T ss_dssp             -CCEEEEEECCTTSCHHHHHHHHHHHHHTT-TCCEEEEEETTCCCC-------------CEE------------------
T ss_pred             CceEEEEEECCCCCcHHHHHHHHHHHHHHC-CCeEEEEeecCCccch-HHHHhh-cCCeeEE------------------
Confidence            468999999999999999999999998764 9999999866543211 122111 1221110                  


Q ss_pred             HHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEE
Q 009230          375 KAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHV  454 (539)
Q Consensus       375 ~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~v  454 (539)
                              +-+    ...   +++.+.+      ..+++|+||-...+.       .    +.++++.|    .+.+++|
T Consensus        76 --------~~i----~~~---~di~~~~------~~~dvViIDEaQF~~-------~----v~el~~~l----~~~gi~V  119 (234)
T 2orv_A           76 --------LPA----CLL---RDVAQEA------LGVAVIGIDEGQFFP-------D----IVEFCEAM----ANAGKTV  119 (234)
T ss_dssp             --------EEE----SSG---GGGHHHH------TTCSEEEESSGGGCT-------T----HHHHHHHH----HHTTCEE
T ss_pred             --------Eec----CCH---HHHHHHh------ccCCEEEEEchhhhh-------h----HHHHHHHH----HhCCCEE
Confidence                    111    111   2233222      458999999554431       1    33333333    3489999


Q ss_pred             EEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          455 WFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       455 i~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      |+......-.+        .-+.++..+-..||.|.-|..-.
T Consensus       120 I~~GL~~DF~~--------~~F~~~~~Ll~~AD~VtelkaIC  153 (234)
T 2orv_A          120 IVAALDGTFQR--------KPFGAILNLVPLAESVVKLTAVC  153 (234)
T ss_dssp             EEECCSBCTTS--------SBCTTGGGGGGGCSEEEECCEEC
T ss_pred             EEEeccccccc--------CCcccHHHHHHhcccEEeeeeEe
Confidence            99876322221        12556777888999988775533

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=97.62  E-value=0.00032  Score=66.53  Aligned_cols=32  Identities=19%  Similarity=0.253  Sum_probs=26.3

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++
T Consensus        30 vl~~vsl~i~~Gei~~l~G~NGsGKSTLlk~l~   62 (256)
T 1vpl_A           30 ILKGISFEIEEGEIFGLIGPNGAGKTTTLRIIS   62 (256)
T ss_dssp             EEEEEEEEECTTCEEEEECCTTSSHHHHHHHHT
T ss_pred             EEEeeEEEEcCCcEEEEECCCCCCHHHHHHHHh
Confidence            3554444 9999999999999999999987665

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=97.60  E-value=8.5e-05  Score=74.38  Aligned_cols=53  Identities=19%  Similarity=0.199  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          398 VLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       398 i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      -...++.++  .+++++++|-=+       ++.+ .....++...|+++.++.+++||+++|.
T Consensus       149 RvalArAL~--~~P~lLLLDEP~-------s~LD-~~~r~~l~~~l~~l~~~~g~tvi~vTHd  201 (372)
T 1v43_A          149 RVAVARAIV--VEPDVLLMDEPL-------SNLD-AKLRVAMRAEIKKLQQKLKVTTIYVTHD  201 (372)
T ss_dssp             HHHHHHHHT--TCCSEEEEESTT-------TTSC-HHHHHHHHHHHHHHHHHHTCEEEEEESC
T ss_pred             HHHHHHHHh--cCCCEEEEcCCC-------ccCC-HHHHHHHHHHHHHHHHhCCCEEEEEeCC
Confidence            334444333  579999999222       2223 3345678888899999999999999993

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=97.60  E-value=0.00044  Score=69.24  Aligned_cols=45  Identities=11%  Similarity=0.155  Sum_probs=33.1

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      -.+++++++|-=+       ++.+ .....++...|+++.++.+++||+++|.
T Consensus       155 ~~~P~lLLLDEP~-------s~LD-~~~r~~l~~~l~~l~~~~g~tvi~vTHd  199 (372)
T 1g29_1          155 VRKPQVFLMDEPL-------SNLD-AKLRVRMRAELKKLQRQLGVTTIYVTHD  199 (372)
T ss_dssp             HTCCSEEEEECTT-------TTSC-HHHHHHHHHHHHHHHHHHTCEEEEEESC
T ss_pred             hcCCCEEEECCCC-------ccCC-HHHHHHHHHHHHHHHHhcCCEEEEECCC
Confidence            3579999999222       2223 3345678888899988999999999993

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=97.58  E-value=0.00028  Score=67.24  Aligned_cols=60  Identities=15%  Similarity=0.185  Sum_probs=42.1

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+++++++|--+       .+.+ ......+.+.|++++++ +.+||+++|.-.                  .+.+.||
T Consensus       175 ~~~p~lllLDEPt-------s~LD-~~~~~~~~~~l~~l~~~-g~tvi~vtHd~~------------------~~~~~~d  227 (263)
T 2olj_A          175 AMEPKIMLFDEPT-------SALD-PEMVGEVLSVMKQLANE-GMTMVVVTHEMG------------------FAREVGD  227 (263)
T ss_dssp             TTCCSEEEEESTT-------TTSC-HHHHHHHHHHHHHHHHT-TCEEEEECSCHH------------------HHHHHCS
T ss_pred             HCCCCEEEEeCCc-------ccCC-HHHHHHHHHHHHHHHhC-CCEEEEEcCCHH------------------HHHHhCC
Confidence            3579999999222       2233 34456788888888776 999999999311                  2456899


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       228 ~v~~l~~  234 (263)
T 2olj_A          228 RVLFMDG  234 (263)
T ss_dssp             EEEEEET
T ss_pred             EEEEEEC
Confidence            9999863

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=97.58  E-value=0.0004  Score=66.35  Aligned_cols=60  Identities=22%  Similarity=0.311  Sum_probs=41.1

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+++++++|--+       .+.+ ......+++.|++++++ +.+||+++|.-..                  +...||
T Consensus       154 ~~~p~lllLDEPt-------s~LD-~~~~~~l~~~l~~l~~~-g~tii~vtHd~~~------------------~~~~~d  206 (266)
T 2yz2_A          154 VHEPDILILDEPL-------VGLD-REGKTDLLRIVEKWKTL-GKTVILISHDIET------------------VINHVD  206 (266)
T ss_dssp             TTCCSEEEEESTT-------TTCC-HHHHHHHHHHHHHHHHT-TCEEEEECSCCTT------------------TGGGCS
T ss_pred             HcCCCEEEEcCcc-------ccCC-HHHHHHHHHHHHHHHHc-CCEEEEEeCCHHH------------------HHHhCC
Confidence            4689999999222       2223 34456788888888776 9999999994221                  335688


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       207 ~v~~l~~  213 (266)
T 2yz2_A          207 RVVVLEK  213 (266)
T ss_dssp             EEEEEET
T ss_pred             EEEEEEC
Confidence            8888863

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=97.57  E-value=0.00041  Score=69.16  Aligned_cols=45  Identities=13%  Similarity=0.114  Sum_probs=33.1

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      -.+++++++|-=+.       +.+ .....++...|+++.++.+++||+++|.
T Consensus       149 ~~~P~lLLLDEP~s-------~LD-~~~r~~l~~~l~~l~~~~g~tvi~vTHd  193 (362)
T 2it1_A          149 VKEPEVLLLDEPLS-------NLD-ALLRLEVRAELKRLQKELGITTVYVTHD  193 (362)
T ss_dssp             TTCCSEEEEESGGG-------GSC-HHHHHHHHHHHHHHHHHHTCEEEEEESC
T ss_pred             HcCCCEEEEECccc-------cCC-HHHHHHHHHHHHHHHHhCCCEEEEECCC
Confidence            35799999993332       222 2344678888899988999999999993

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=97.57  E-value=0.0003  Score=66.71  Aligned_cols=167  Identities=16%  Similarity=0.186  Sum_probs=84.3

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-----CeEEEEeCC------CCHHHHHHHHHHHhhCCCcc
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAG-----WKFVLCSME------NKVREHARKLLEKHIKKPFF  355 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-----~~vl~~s~E------~~~~~~~~r~~~~~~~~~~~  355 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++--.--..|     ..+.|+.-+      ++..+.   +. ... ....
T Consensus        21 l~~isl~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~I~~~~~i~~v~q~~~~~~~~tv~en---l~-~~~-~~~~   95 (253)
T 2nq2_C           21 FQQLNFDLNKGDILAVLGQNGCGKSTLLDLLLGIHRPIQGKIEVYQSIGFVPQFFSSPFAYSVLDI---VL-MGR-STHI   95 (253)
T ss_dssp             EEEEEEEEETTCEEEEECCSSSSHHHHHHHHTTSSCCSEEEEEECSCEEEECSCCCCSSCCBHHHH---HH-GGG-GGGS
T ss_pred             EEEEEEEECCCCEEEEECCCCCCHHHHHHHHhCCCCCCCcEEEEeccEEEEcCCCccCCCCCHHHH---HH-Hhh-hhhc
Confidence            454444 999999999999999999997766532211112     235555432      223222   21 100 0000


Q ss_pred             ccccCCCCCCCCHHH---HHHHHHHhhccceeEeecCCCCCCHHH--HHHHHHHHHHHcCCcEEEEccccccccCCCCCC
Q 009230          356 EANYGGSAERMTVEE---FEQGKAWLSNTFSLIRCENDSLPSIKW--VLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQ  430 (539)
Q Consensus       356 ~i~~~~~~~~l~~~~---~~~~~~~l~~~~~~i~~~~~~~~~~~~--i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~  430 (539)
                      .+.     .....+.   ..++.+.+.-. .+.. ......+-.+  -...++.  --.+++++++|--+       .+.
T Consensus        96 ~~~-----~~~~~~~~~~~~~~l~~~~l~-~~~~-~~~~~LSgGq~qrv~lAra--L~~~p~lllLDEPt-------s~L  159 (253)
T 2nq2_C           96 NTF-----AKPKSHDYQVAMQALDYLNLT-HLAK-REFTSLSGGQRQLILIARA--IASECKLILLDEPT-------SAL  159 (253)
T ss_dssp             CTT-----CCCCHHHHHHHHHHHHHTTCG-GGTT-SBGGGSCHHHHHHHHHHHH--HHTTCSEEEESSSS-------TTS
T ss_pred             ccc-----cCCCHHHHHHHHHHHHHcCCh-HHhc-CChhhCCHHHHHHHHHHHH--HHcCCCEEEEeCCc-------ccC
Confidence            000     0011221   22233322100 0000 0012223332  2333333  33579999999222       222


Q ss_pred             CHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          431 TETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       431 ~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      + ......+++.|+.++++.+.+||+++|.-.                  .+...||.++.|..
T Consensus       160 D-~~~~~~l~~~l~~l~~~~g~tvi~vtHd~~------------------~~~~~~d~v~~l~~  204 (253)
T 2nq2_C          160 D-LANQDIVLSLLIDLAQSQNMTVVFTTHQPN------------------QVVAIANKTLLLNK  204 (253)
T ss_dssp             C-HHHHHHHHHHHHHHHHTSCCEEEEEESCHH------------------HHHHHCSEEEEEET
T ss_pred             C-HHHHHHHHHHHHHHHHhcCCEEEEEecCHH------------------HHHHhCCEEEEEeC
Confidence            3 344567788888887777999999999321                  13456777777764

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=97.56  E-value=0.00017  Score=71.66  Aligned_cols=33  Identities=27%  Similarity=0.520  Sum_probs=26.9

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|+++.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        19 ~L~~vsl~i~~Ge~~~llGpsGsGKSTLLr~iaG   52 (359)
T 3fvq_A           19 VLNDISLSLDPGEILFIIGASGCGKTTLLRCLAG   52 (359)
T ss_dssp             EEEEEEEEECTTCEEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEeeEEEEcCCCEEEEECCCCchHHHHHHHHhc
Confidence            4555544 99999999999999999999876653

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=97.55  E-value=0.00028  Score=67.26  Aligned_cols=60  Identities=17%  Similarity=0.212  Sum_probs=41.9

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+++++++|--+       ++.+ ......+.+.|+.++++ +.+||+++|.-.                  .+...||
T Consensus       169 ~~~p~lllLDEPt-------s~LD-~~~~~~~~~~l~~l~~~-g~tvi~vtHd~~------------------~~~~~~d  221 (262)
T 1b0u_A          169 AMEPDVLLFDEPT-------SALD-PELVGEVLRIMQQLAEE-GKTMVVVTHEMG------------------FARHVSS  221 (262)
T ss_dssp             HTCCSEEEEESTT-------TTSC-HHHHHHHHHHHHHHHHT-TCCEEEECSCHH------------------HHHHHCS
T ss_pred             hcCCCEEEEeCCC-------ccCC-HHHHHHHHHHHHHHHhC-CCEEEEEeCCHH------------------HHHHhCC
Confidence            3679999999222       2233 34456778888888766 999999999311                  2456889


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       222 ~v~~l~~  228 (262)
T 1b0u_A          222 HVIFLHQ  228 (262)
T ss_dssp             EEEEEET
T ss_pred             EEEEEEC
Confidence            9998863

>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=97.54  E-value=0.0011  Score=67.69  Aligned_cols=59  Identities=19%  Similarity=0.215  Sum_probs=43.9

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHH--HHHHhhCCCcc
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARK--LLEKHIKKPFF  355 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r--~~~~~~~~~~~  355 (539)
                      ++.+++++|++|+||||++..++..++.+ |.+|++++.+.........  ..+...+++..
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~~~-G~kVllv~~D~~r~~a~eqL~~~~~~~gv~~~  156 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYKKR-GYKVGLVAADVYRPAAYDQLLQLGNQIGVQVY  156 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHHHT-TCCEEEEEECCSCHHHHHHHHHHHHTTTCCEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEEecCccchhHHHHHHHHHHhcCCcee
Confidence            46899999999999999999999998875 9999999988542222222  23444566554

>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=97.52  E-value=0.0036  Score=60.92  Aligned_cols=43  Identities=23%  Similarity=0.263  Sum_probs=38.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      ..+|++++|.|++|+||||++..+|..++.. |.+|+++..+..
T Consensus       101 ~~~~~vi~ivG~~GsGKTTl~~~LA~~l~~~-g~kV~lv~~D~~  143 (306)
T 1vma_A          101 PEPPFVIMVVGVNGTGKTTSCGKLAKMFVDE-GKSVVLAAADTF  143 (306)
T ss_dssp             SSSCEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEEECTT
T ss_pred             CCCCeEEEEEcCCCChHHHHHHHHHHHHHhc-CCEEEEEccccc
Confidence            4678999999999999999999999888875 899999998864

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=97.46  E-value=0.0002  Score=68.89  Aligned_cols=32  Identities=22%  Similarity=0.379  Sum_probs=26.2

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++
T Consensus        36 vL~~isl~i~~Ge~~~liG~NGsGKSTLlk~l~   68 (279)
T 2ihy_A           36 ILKKISWQIAKGDKWILYGLNGAGKTTLLNILN   68 (279)
T ss_dssp             EEEEEEEEEETTCEEEEECCTTSSHHHHHHHHT
T ss_pred             EEEeeeEEEcCCCEEEEECCCCCcHHHHHHHHh
Confidence            3454444 9999999999999999999977655

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=97.46  E-value=0.0013  Score=64.69  Aligned_cols=143  Identities=14%  Similarity=0.119  Sum_probs=78.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC---HHHHHHHHHHHhhCCCccccccCCCCCCCCHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK---VREHARKLLEKHIKKPFFEANYGGSAERMTVEE  370 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~---~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~  370 (539)
                      -.+|+++.|.|++|+||||++..++...... +..|++...+..   +.+... ..+...|+++..-..     .+.+..
T Consensus       126 ~~~g~vi~lvG~nGaGKTTll~~Lag~l~~~-~g~V~l~g~D~~r~~a~eql~-~~~~~~gv~~v~q~~-----~~~p~~  198 (328)
T 3e70_C          126 AEKPYVIMFVGFNGSGKTTTIAKLANWLKNH-GFSVVIAASDTFRAGAIEQLE-EHAKRIGVKVIKHSY-----GADPAA  198 (328)
T ss_dssp             SCSSEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEEECCSSTTHHHHHH-HHHHHTTCEEECCCT-----TCCHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHhc-CCEEEEEeecccccchHHHHH-HHHHHcCceEEeccc-----cCCHHH
Confidence            4789999999999999999999999877664 889999987753   222222 223445554332111     233221


Q ss_pred             -HHH-HHHHhh-c-cceeEeecCCCCCC-HHHHHHHHHHHHHH--cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHH
Q 009230          371 -FEQ-GKAWLS-N-TFSLIRCENDSLPS-IKWVLDLAKAAVLR--HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMV  443 (539)
Q Consensus       371 -~~~-~~~~l~-~-~~~~i~~~~~~~~~-~~~i~~~i~~~~~~--~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~L  443 (539)
                       ..+ +..... . ...++..  .+... -..+...+..+.+.  ....++++|....               .+++..+
T Consensus       199 ~v~e~l~~~~~~~~d~vliDt--aG~~~~~~~l~~eL~~i~ral~~de~llvLDa~t~---------------~~~~~~~  261 (328)
T 3e70_C          199 VAYDAIQHAKARGIDVVLIDT--AGRSETNRNLMDEMKKIARVTKPNLVIFVGDALAG---------------NAIVEQA  261 (328)
T ss_dssp             HHHHHHHHHHHHTCSEEEEEE--CCSCCTTTCHHHHHHHHHHHHCCSEEEEEEEGGGT---------------THHHHHH
T ss_pred             HHHHHHHHHHhccchhhHHhh--ccchhHHHHHHHHHHHHHHHhcCCCCEEEEecHHH---------------HHHHHHH
Confidence             111 111111 1 1223321  22211 11223333322222  2345678882221               1455667


Q ss_pred             HHHHHHhCcEEEEEecC
Q 009230          444 KRFAQHHACHVWFVAHP  460 (539)
Q Consensus       444 k~lA~~~~i~vi~~~q~  460 (539)
                      +.|.+..++++++++|.
T Consensus       262 ~~~~~~~~it~iilTKl  278 (328)
T 3e70_C          262 RQFNEAVKIDGIILTKL  278 (328)
T ss_dssp             HHHHHHSCCCEEEEECG
T ss_pred             HHHHHhcCCCEEEEeCc
Confidence            78888899999999993

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=97.44  E-value=0.00015  Score=72.19  Aligned_cols=45  Identities=16%  Similarity=0.114  Sum_probs=33.2

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      -.+++++++|-=+       ++.+ ......+...|+++.++.+++||+++|.
T Consensus       149 ~~~P~lLLLDEP~-------s~LD-~~~r~~l~~~l~~l~~~~g~tvi~vTHd  193 (359)
T 2yyz_A          149 VKQPKVLLFDEPL-------SNLD-ANLRMIMRAEIKHLQQELGITSVYVTHD  193 (359)
T ss_dssp             TTCCSEEEEESTT-------TTSC-HHHHHHHHHHHHHHHHHHCCEEEEEESC
T ss_pred             HcCCCEEEEECCc-------ccCC-HHHHHHHHHHHHHHHHhcCCEEEEEcCC
Confidence            3579999999222       2223 3345678888899988999999999993

>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=97.43  E-value=0.0013  Score=66.33  Aligned_cols=49  Identities=14%  Similarity=0.149  Sum_probs=35.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC--CCHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME--NKVREHARKLLE  347 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E--~~~~~~~~r~~~  347 (539)
                      .++|.|+||+|||+++..++.......+.+++|+++.  .++..+...++.
T Consensus        46 ~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~   96 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIAR   96 (389)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccCCCHHHHHHHHHH
Confidence            8999999999999999988866543215788988843  334555555543

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=97.43  E-value=0.0002  Score=67.42  Aligned_cols=60  Identities=13%  Similarity=0.232  Sum_probs=41.4

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|-=+       .+.+ ......+++.|+++++ .+.+||+++|...                  .+...||
T Consensus       155 ~~~p~lllLDEPt-------s~LD-~~~~~~l~~~l~~~~~-~g~tvi~vtHd~~------------------~~~~~~d  207 (240)
T 1ji0_A          155 MSRPKLLMMDEPS-------LGLA-PILVSEVFEVIQKINQ-EGTTILLVEQNAL------------------GALKVAH  207 (240)
T ss_dssp             TTCCSEEEEECTT-------TTCC-HHHHHHHHHHHHHHHH-TTCCEEEEESCHH------------------HHHHHCS
T ss_pred             HcCCCEEEEcCCc-------ccCC-HHHHHHHHHHHHHHHH-CCCEEEEEecCHH------------------HHHHhCC
Confidence            3689999999222       2233 3445667788888876 6899999999321                  2456889


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       208 ~v~~l~~  214 (240)
T 1ji0_A          208 YGYVLET  214 (240)
T ss_dssp             EEEEEET
T ss_pred             EEEEEEC
Confidence            9998863

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=97.42  E-value=0.0032  Score=61.02  Aligned_cols=40  Identities=20%  Similarity=0.279  Sum_probs=36.6

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.++++.|++|+||||++.+++..++.. |.+|++++.+..
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~-g~~v~l~~~D~~  137 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKK-GFKVGLVGADVY  137 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHT-TCCEEEEECCCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHC-CCeEEEEecCCC
Confidence            7899999999999999999999998875 999999999853

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=97.42  E-value=0.00012  Score=65.00  Aligned_cols=23  Identities=26%  Similarity=0.404  Sum_probs=21.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDA  316 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~  316 (539)
                      +.+|+++.|.|++|+|||||+..
T Consensus         6 i~~gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            6 IPELSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             EESSEEEEEECCTTSCHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHH
Confidence            78999999999999999999886

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=97.40  E-value=0.00054  Score=67.93  Aligned_cols=44  Identities=11%  Similarity=0.114  Sum_probs=32.8

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      .+++++++|-=+       ++.+ ......+...|+++.++.+++||+++|.
T Consensus       144 ~~P~lLLLDEP~-------s~LD-~~~~~~l~~~l~~l~~~~g~tii~vTHd  187 (348)
T 3d31_A          144 TNPKILLLDEPL-------SALD-PRTQENAREMLSVLHKKNKLTVLHITHD  187 (348)
T ss_dssp             SCCSEEEEESSS-------TTSC-HHHHHHHHHHHHHHHHHTTCEEEEEESC
T ss_pred             cCCCEEEEECcc-------ccCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            579999999222       2223 3345678888899988999999999993

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=97.40  E-value=0.0006  Score=64.37  Aligned_cols=32  Identities=25%  Similarity=0.340  Sum_probs=26.3

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        25 l~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~l~G   57 (247)
T 2ff7_A           25 LDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQR   57 (247)
T ss_dssp             EEEEEEEEETTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            554444 99999999999999999999776553

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=97.38  E-value=0.00018  Score=67.98  Aligned_cols=32  Identities=28%  Similarity=0.408  Sum_probs=26.2

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++
T Consensus        15 vl~~vsl~i~~Ge~~~liG~NGsGKSTLlk~l~   47 (249)
T 2qi9_C           15 RLGPLSGEVRAGEILHLVGPNGAGKSTLLARMA   47 (249)
T ss_dssp             TEEEEEEEEETTCEEEEECCTTSSHHHHHHHHT
T ss_pred             EEeeeEEEEcCCCEEEEECCCCCcHHHHHHHHh
Confidence            3454444 9999999999999999999977655

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=97.36  E-value=0.00022  Score=70.92  Aligned_cols=45  Identities=13%  Similarity=0.083  Sum_probs=32.1

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      -.+++++++|-=+.-       .+. ....++...|+++.++.+++||+++|.
T Consensus       156 ~~~P~lLLLDEP~s~-------LD~-~~r~~l~~~l~~l~~~~g~tvi~vTHd  200 (353)
T 1oxx_K          156 VKDPSLLLLDEPFSN-------LDA-RMRDSARALVKEVQSRLGVTLLVVSHD  200 (353)
T ss_dssp             TTCCSEEEEESTTTT-------SCG-GGHHHHHHHHHHHHHHHCCEEEEEESC
T ss_pred             HhCCCEEEEECCccc-------CCH-HHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            357999999933222       221 234567788888888899999999993

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=97.35  E-value=0.00047  Score=64.07  Aligned_cols=58  Identities=9%  Similarity=0.105  Sum_probs=40.3

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+++++++|--+       .+.+ ......+.+.|+.++++ +.+||+++|.-.                  .+ ..||
T Consensus       156 ~~~p~lllLDEPt-------~~LD-~~~~~~~~~~l~~l~~~-g~tvi~vtHd~~------------------~~-~~~d  207 (224)
T 2pcj_A          156 ANEPILLFADEPT-------GNLD-SANTKRVMDIFLKINEG-GTSIVMVTHERE------------------LA-ELTH  207 (224)
T ss_dssp             TTCCSEEEEESTT-------TTCC-HHHHHHHHHHHHHHHHT-TCEEEEECSCHH------------------HH-TTSS
T ss_pred             HcCCCEEEEeCCC-------CCCC-HHHHHHHHHHHHHHHHC-CCEEEEEcCCHH------------------HH-HhCC
Confidence            3579999999222       2223 34456788888888777 999999999311                  12 4789


Q ss_pred             eEEEEE
Q 009230          488 NGIVIH  493 (539)
Q Consensus       488 ~vl~l~  493 (539)
                      .++.|.
T Consensus       208 ~v~~l~  213 (224)
T 2pcj_A          208 RTLEMK  213 (224)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            988886

>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=97.34  E-value=0.0006  Score=68.71  Aligned_cols=55  Identities=15%  Similarity=0.083  Sum_probs=40.7

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhc-------CCeEEEEeCCC---CHHHHHHHHHHHhhC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHA-------GWKFVLCSMEN---KVREHARKLLEKHIK  351 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~-------g~~vl~~s~E~---~~~~~~~r~~~~~~~  351 (539)
                      +..++|.|+||+|||+++..++..+....       +.+++++++..   ++..++..++....+
T Consensus        45 ~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~  109 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKLTG  109 (384)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHHHHHHHHHHHC
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHHHHHHHHHhcC
Confidence            34899999999999999999987765531       78899988543   566666666554433

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=97.34  E-value=0.0017  Score=63.76  Aligned_cols=43  Identities=16%  Similarity=0.277  Sum_probs=38.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      ..+|++++|.|++|+||||++..+|..++.. |.+|+++..+..
T Consensus       102 ~~~~~vI~ivG~~G~GKTT~~~~LA~~l~~~-g~kVllid~D~~  144 (320)
T 1zu4_A          102 ENRLNIFMLVGVNGTGKTTSLAKMANYYAEL-GYKVLIAAADTF  144 (320)
T ss_dssp             TTSCEEEEEESSTTSSHHHHHHHHHHHHHHT-TCCEEEEECCCS
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHHC-CCeEEEEeCCCc
Confidence            5678999999999999999999999988875 999999998864

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=97.34  E-value=0.0047  Score=60.00  Aligned_cols=43  Identities=16%  Similarity=0.303  Sum_probs=37.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.+|+++.|.|++|+||||++..++...... +..|.+...+..
T Consensus        97 ~~~g~vi~lvG~nGsGKTTll~~Lag~l~~~-~g~V~l~g~d~~  139 (302)
T 3b9q_A           97 FRKPAVIMIVGVNGGGKTTSLGKLAHRLKNE-GTKVLMAAGDTF  139 (302)
T ss_dssp             SSSCEEEEEECCTTSCHHHHHHHHHHHHHHT-TCCEEEECCCCS
T ss_pred             cCCCcEEEEEcCCCCCHHHHHHHHHHHHHHc-CCeEEEEeeccc
Confidence            6789999999999999999999999877654 889998887753

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=97.30  E-value=0.0011  Score=70.09  Aligned_cols=61  Identities=10%  Similarity=0.034  Sum_probs=44.0

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|-=+       .+.+ ......+++.|++++++.+.+||+++|...                  .+...||
T Consensus       417 ~~~p~lLlLDEPt-------~~LD-~~~~~~i~~~l~~l~~~~g~tvi~vsHd~~------------------~~~~~~d  470 (538)
T 1yqt_A          417 LRDADIYLLDEPS-------AYLD-VEQRLAVSRAIRHLMEKNEKTALVVEHDVL------------------MIDYVSD  470 (538)
T ss_dssp             TSCCSEEEEECTT-------TTCC-HHHHHHHHHHHHHHHHHHTCEEEEECSCHH------------------HHHHHCS
T ss_pred             HhCCCEEEEeCCc-------ccCC-HHHHHHHHHHHHHHHHhCCCEEEEEeCCHH------------------HHHHhCC
Confidence            3579999999222       2223 345667888899999889999999999322                  2456788


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       471 rv~vl~~  477 (538)
T 1yqt_A          471 RLMVFEG  477 (538)
T ss_dssp             EEEEEEE
T ss_pred             EEEEEeC
Confidence            8888863

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=97.30  E-value=0.0005  Score=72.46  Aligned_cols=61  Identities=15%  Similarity=0.098  Sum_probs=44.5

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+++++++|-       +.++.+ .....++++.|++++++.+.+||+++|.-.                  .+.+.||
T Consensus       401 ~~~p~lLlLDE-------PT~gLD-~~~~~~i~~~l~~l~~~~g~tvi~vsHdl~------------------~~~~~aD  454 (538)
T 3ozx_A          401 AKEADLYVLDQ-------PSSYLD-VEERYIVAKAIKRVTRERKAVTFIIDHDLS------------------IHDYIAD  454 (538)
T ss_dssp             HSCCSEEEEES-------TTTTCC-HHHHHHHHHHHHHHHHHTTCEEEEECSCHH------------------HHHHHCS
T ss_pred             HcCCCEEEEeC-------CccCCC-HHHHHHHHHHHHHHHHhCCCEEEEEeCCHH------------------HHHHhCC
Confidence            46899999992       222333 344567889999999999999999999321                  2456789


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .|+.|..
T Consensus       455 ri~vl~~  461 (538)
T 3ozx_A          455 RIIVFKG  461 (538)
T ss_dssp             EEEEEEE
T ss_pred             EEEEEeC
Confidence            9888875

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=97.28  E-value=0.0023  Score=63.28  Aligned_cols=134  Identities=13%  Similarity=0.100  Sum_probs=72.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC--------CHHHHHHHHHHHhhCCCccccccCCCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN--------KVREHARKLLEKHIKKPFFEANYGGSAER  365 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~--------~~~~~~~r~~~~~~~~~~~~i~~~~~~~~  365 (539)
                      +..|.+++|.|++|+|||+++.+++...    +  ++|+++..        +...+...+......              
T Consensus        28 l~~~~~v~i~G~~G~GKT~Ll~~~~~~~----~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~--------------   87 (350)
T 2qen_A           28 LENYPLTLLLGIRRVGKSSLLRAFLNER----P--GILIDCRELYAERGHITREELIKELQSTISP--------------   87 (350)
T ss_dssp             HHHCSEEEEECCTTSSHHHHHHHHHHHS----S--EEEEEHHHHHHTTTCBCHHHHHHHHHHHSCS--------------
T ss_pred             HhcCCeEEEECCCcCCHHHHHHHHHHHc----C--cEEEEeecccccccCCCHHHHHHHHHHHHHH--------------
Confidence            4445799999999999999998887542    3  88888753        344444444322110              


Q ss_pred             CCHHHHHHHHHHhhccceeEe-ec-CCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHH
Q 009230          366 MTVEEFEQGKAWLSNTFSLIR-CE-NDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMV  443 (539)
Q Consensus       366 l~~~~~~~~~~~l~~~~~~i~-~~-~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~L  443 (539)
                      .  +.+.   +.+.-. +-+. .. +....+++.+...+..+....++-+||||++..+..... ..+     ..+...|
T Consensus        88 ~--~~~~---~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~-~~~-----~~~~~~L  155 (350)
T 2qen_A           88 F--QKFQ---SKFKIS-LNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGS-RGG-----KELLALF  155 (350)
T ss_dssp             H--HHHH---HHHTCC-CCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTT-TTT-----HHHHHHH
T ss_pred             H--HhHh---hhceeE-EEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCc-cch-----hhHHHHH
Confidence            0  0011   111000 0000 00 001235666776666655555577999998887754110 001     2344555


Q ss_pred             HHHHHH-hCcEEEEEec
Q 009230          444 KRFAQH-HACHVWFVAH  459 (539)
Q Consensus       444 k~lA~~-~~i~vi~~~q  459 (539)
                      +.+... .++.+|++..
T Consensus       156 ~~~~~~~~~~~~il~g~  172 (350)
T 2qen_A          156 AYAYDSLPNLKIILTGS  172 (350)
T ss_dssp             HHHHHHCTTEEEEEEES
T ss_pred             HHHHHhcCCeEEEEECC
Confidence            555554 4788888765

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=97.28  E-value=0.0082  Score=59.63  Aligned_cols=43  Identities=16%  Similarity=0.303  Sum_probs=37.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.+|+++.|.|++|+||||++..++...... +..|++...+..
T Consensus       154 ~~~g~vi~lvG~nGsGKTTll~~Lag~l~~~-~G~V~l~g~D~~  196 (359)
T 2og2_A          154 FRKPAVIMIVGVNGGGKTTSLGKLAHRLKNE-GTKVLMAAGDTF  196 (359)
T ss_dssp             SSSSEEEEEECCTTSCHHHHHHHHHHHHHHT-TCCEEEECCCCS
T ss_pred             cCCCeEEEEEcCCCChHHHHHHHHHhhcccc-CCEEEEeccccc
Confidence            6789999999999999999999999877654 889999887753

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=97.28  E-value=0.0066  Score=59.01  Aligned_cols=40  Identities=28%  Similarity=0.427  Sum_probs=34.9

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      +|+++.|.|++|+||||++..++...... +.+|++...+.
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~~~-~g~V~l~g~D~  140 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQNL-GKKVMFCAGDT  140 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHTT-TCCEEEECCCC
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhc-CCEEEEEeecC
Confidence            68999999999999999999999777654 78999988775

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.26  E-value=0.00032  Score=63.07  Aligned_cols=41  Identities=22%  Similarity=0.205  Sum_probs=35.5

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +|.+.+++|++|+||||++++++.+...+ |.+|+++..+.+
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~~~~~~~~~-g~~v~~~~~~~d   42 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLSFVEIYKLG-KKKVAVFKPKID   42 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHHT-TCEEEEEEEC--
T ss_pred             ccEEEEEECCCCCCHHHHHHHHHHHHHHC-CCeEEEEeeccc
Confidence            47899999999999999999999988775 899999987754

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=97.24  E-value=0.0015  Score=69.70  Aligned_cols=158  Identities=16%  Similarity=0.072  Sum_probs=82.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-----CeEEEEeCC------CCHHHHHHHHHHHhhCCCccccccCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAG-----WKFVLCSME------NKVREHARKLLEKHIKKPFFEANYGGS  362 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-----~~vl~~s~E------~~~~~~~~r~~~~~~~~~~~~i~~~~~  362 (539)
                      +.+|+++.|.|++|+|||||+.-++--..-..|     ..+.|+.-+      .+..+.+.   ....+        .  
T Consensus       375 ~~~GEiv~iiG~NGsGKSTLlk~l~Gl~~p~~G~~~~~~~i~~~~q~~~~~~~~tv~e~~~---~~~~~--------~--  441 (608)
T 3j16_B          375 FSDSEILVMMGENGTGKTTLIKLLAGALKPDEGQDIPKLNVSMKPQKIAPKFPGTVRQLFF---KKIRG--------Q--  441 (608)
T ss_dssp             CCTTCEEEEESCTTSSHHHHHHHHHTSSCCSBCCCCCSCCEEEECSSCCCCCCSBHHHHHH---HHCSS--------T--
T ss_pred             cccceEEEEECCCCCcHHHHHHHHhcCCCCCCCcCccCCcEEEecccccccCCccHHHHHH---HHhhc--------c--
Confidence            566689999999999999998766532211123     235555433      22333221   11000        0  


Q ss_pred             CCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHH
Q 009230          363 AERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTM  442 (539)
Q Consensus       363 ~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~  442 (539)
                        ........++.+.+.-..+ . .......+=.+--..+-..+...+++++++|-       +..+.+ ......+++.
T Consensus       442 --~~~~~~~~~~l~~l~l~~~-~-~~~~~~LSGGqkQRv~iAraL~~~p~lLlLDE-------PT~gLD-~~~~~~i~~l  509 (608)
T 3j16_B          442 --FLNPQFQTDVVKPLRIDDI-I-DQEVQHLSGGELQRVAIVLALGIPADIYLIDE-------PSAYLD-SEQRIICSKV  509 (608)
T ss_dssp             --TTSHHHHHHTHHHHTSTTT-S-SSBSSSCCHHHHHHHHHHHHTTSCCSEEEECC-------TTTTCC-HHHHHHHHHH
T ss_pred             --cccHHHHHHHHHHcCChhh-h-cCChhhCCHHHHHHHHHHHHHHhCCCEEEEEC-------CCCCCC-HHHHHHHHHH
Confidence              1122222223333221100 0 00012223222211111112235799999992       222333 3455678888


Q ss_pred             HHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          443 VKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       443 Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      |++++++.+.+||+++|.-.                  .+...||.++.+..
T Consensus       510 l~~l~~~~g~tviivtHdl~------------------~~~~~aDrvivl~~  543 (608)
T 3j16_B          510 IRRFILHNKKTAFIVEHDFI------------------MATYLADKVIVFEG  543 (608)
T ss_dssp             HHHHHHHHTCEEEEECSCHH------------------HHHHHCSEEEECEE
T ss_pred             HHHHHHhCCCEEEEEeCCHH------------------HHHHhCCEEEEEeC
Confidence            99999889999999999321                  24567888888864

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=97.24  E-value=0.0093  Score=61.41  Aligned_cols=42  Identities=19%  Similarity=0.253  Sum_probs=36.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      +.+|++++|.|++|+||||++..|+..+... +..|++...+.
T Consensus       290 i~~GeVI~LVGpNGSGKTTLl~~LAgll~~~-~G~V~l~g~D~  331 (503)
T 2yhs_A          290 GKAPFVILMVGVNGVGKTTTIGKLARQFEQQ-GKSVMLAAGDT  331 (503)
T ss_dssp             SCTTEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEECCCT
T ss_pred             ccCCeEEEEECCCcccHHHHHHHHHHHhhhc-CCeEEEecCcc
Confidence            7789999999999999999999998776654 78898887664

>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=97.24  E-value=0.0012  Score=66.39  Aligned_cols=40  Identities=13%  Similarity=0.296  Sum_probs=32.2

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhc--CCeEEEEeCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHA--GWKFVLCSME  335 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~--g~~vl~~s~E  335 (539)
                      .+..++|.|++|+|||+++..++.......  +.+++|+++.
T Consensus        44 ~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~   85 (386)
T 2qby_A           44 KPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTR   85 (386)
T ss_dssp             CCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECC
Confidence            356899999999999999999887765532  6788888753

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=97.23  E-value=0.00014  Score=69.83  Aligned_cols=33  Identities=33%  Similarity=0.398  Sum_probs=26.9

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        34 vl~~vsl~i~~Ge~~~i~G~nGsGKSTLlk~l~G   67 (271)
T 2ixe_A           34 VLQGLTFTLYPGKVTALVGPNGSGKSTVAALLQN   67 (271)
T ss_dssp             CEEEEEEEECTTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             eeEeeEEEECCCCEEEEECCCCCCHHHHHHHHhc
Confidence            3555544 99999999999999999999876653

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=97.23  E-value=0.0023  Score=64.26  Aligned_cols=52  Identities=13%  Similarity=0.154  Sum_probs=37.7

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhc-----CCeEEEEeCCC--CHHHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHA-----GWKFVLCSMEN--KVREHARKLLE  347 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~-----g~~vl~~s~E~--~~~~~~~r~~~  347 (539)
                      .+..++|.|+||+|||+++..++.......     +.+++|+++..  +...+...++.
T Consensus        43 ~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~  101 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASAIAE  101 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHHHHHH
Confidence            456789999999999999999988775532     67888887653  34455555443

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=97.21  E-value=0.0018  Score=69.15  Aligned_cols=158  Identities=16%  Similarity=0.032  Sum_probs=83.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-----CeEEEEeCC------CCHHHHHHHHHHHhhCCCccccccCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAG-----WKFVLCSME------NKVREHARKLLEKHIKKPFFEANYGGS  362 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-----~~vl~~s~E------~~~~~~~~r~~~~~~~~~~~~i~~~~~  362 (539)
                      +.+|+++.|.|++|+|||||+.-++--..-..|     ..+.|+.-+      ++..+.+........       .    
T Consensus       379 v~~Gei~~i~G~NGsGKSTLlk~l~Gl~~p~~G~I~~~~~i~~v~Q~~~~~~~~tv~e~~~~~~~~~~-------~----  447 (607)
T 3bk7_A          379 IRKGEVIGIVGPNGIGKTTFVKMLAGVEEPTEGKVEWDLTVAYKPQYIKAEYEGTVYELLSKIDSSKL-------N----  447 (607)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHHTSSCCSBSCCCCCCCEEEECSSCCCCCSSBHHHHHHHHHHHHH-------H----
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHhcCCCCCceEEEEeeEEEEEecCccCCCCCcHHHHHHhhhccCC-------C----
Confidence            579999999999999999998876642211112     245555432      334333221100000       0    


Q ss_pred             CCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHH
Q 009230          363 AERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTM  442 (539)
Q Consensus       363 ~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~  442 (539)
                          ..+...++.+.+.-... . .......+-.+-....-..+...+++++++|-=+       .+.+ ......+++.
T Consensus       448 ----~~~~~~~~l~~~~l~~~-~-~~~~~~LSGGe~QRv~iAraL~~~p~lLlLDEPt-------~~LD-~~~~~~l~~~  513 (607)
T 3bk7_A          448 ----SNFYKTELLKPLGIIDL-Y-DRNVEDLSGGELQRVAIAATLLRDADIYLLDEPS-------AYLD-VEQRLAVSRA  513 (607)
T ss_dssp             ----CHHHHHHTHHHHTCTTT-T-TSBGGGCCHHHHHHHHHHHHHTSCCSEEEEECTT-------TTCC-HHHHHHHHHH
T ss_pred             ----HHHHHHHHHHHcCCchH-h-cCChhhCCHHHHHHHHHHHHHHhCCCEEEEeCCc-------cCCC-HHHHHHHHHH
Confidence                01112222222211000 0 0001122222222211122234679999999222       2233 3455678888


Q ss_pred             HHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          443 VKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       443 Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                      |++++++.+.+||+++|...                  .+...||.++.|..
T Consensus       514 l~~l~~~~g~tvi~vsHd~~------------------~~~~~adrv~vl~~  547 (607)
T 3bk7_A          514 IRHLMEKNEKTALVVEHDVL------------------MIDYVSDRLIVFEG  547 (607)
T ss_dssp             HHHHHHHTTCEEEEECSCHH------------------HHHHHCSEEEEEEE
T ss_pred             HHHHHHhCCCEEEEEeCCHH------------------HHHHhCCEEEEEcC
Confidence            99999889999999999321                  24567888888863

>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=97.21  E-value=0.0029  Score=61.27  Aligned_cols=43  Identities=12%  Similarity=0.148  Sum_probs=37.8

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .+|++++|.|++|+||||++..++..++...|.+|++++.+..
T Consensus       103 ~~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D~~  145 (296)
T 2px0_A          103 IHSKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTDTY  145 (296)
T ss_dssp             CCSSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECCCS
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecCcc
Confidence            4688999999999999999999999888645899999998853

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=97.20  E-value=0.0046  Score=59.92  Aligned_cols=42  Identities=19%  Similarity=0.260  Sum_probs=37.8

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV  338 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~  338 (539)
                      +|+++.|.|++|+||||++..++...+.. |.+|+++..+...
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~-~~~v~l~~~d~~~  138 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGK-GRRPLLVAADTQR  138 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHT-TCCEEEEECCSSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEecCCccc
Confidence            78899999999999999999999988875 8999999988653

>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=97.15  E-value=0.0088  Score=60.75  Aligned_cols=141  Identities=15%  Similarity=0.176  Sum_probs=77.6

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHH--HHHHHhhCCCccccccCCCCCCCCHHHH-H
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHAR--KLLEKHIKKPFFEANYGGSAERMTVEEF-E  372 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~--r~~~~~~~~~~~~i~~~~~~~~l~~~~~-~  372 (539)
                      ++.+++++|++|+||||++..++..++.. |.+|+++..+...-....  +..+...+++......     ..++.++ .
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~-g~~Vllvd~D~~r~aa~~qL~~~~~~~gv~v~~~~~-----~~~p~~i~~  170 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGK-GRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMD-----GESPESIRR  170 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTT-TCCEEEEECCSSCHHHHHHHHHHHHHHTCCEEECCT-----TCCHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEeeccccCchhHHHHHHhcccCCccEEecCC-----CCCHHHHHH
Confidence            67899999999999999999999998875 999999998854221111  2233445665432211     1344444 3


Q ss_pred             HHHHHhh-cc--ceeEeecCCCCCCH-HHHHHHHHHHHHHcCC--cEEEEccccccccCCCCCCCHHHHHHHHHHHHHHH
Q 009230          373 QGKAWLS-NT--FSLIRCENDSLPSI-KWVLDLAKAAVLRHGV--RGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRF  446 (539)
Q Consensus       373 ~~~~~l~-~~--~~~i~~~~~~~~~~-~~i~~~i~~~~~~~~~--~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~l  446 (539)
                      ++.+.+. ..  .++|  |..+.... ..+...+..+.....+  -++|+|. .   .    + .      ..+..++.|
T Consensus       171 ~~l~~~~~~~~DvVII--DTaG~l~~d~~l~~el~~i~~~~~pd~vlLVvDa-~---t----g-q------~av~~a~~f  233 (425)
T 2ffh_A          171 RVEEKARLEARDLILV--DTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDA-M---T----G-Q------EALSVARAF  233 (425)
T ss_dssp             HHHHHHHHTTCSEEEE--ECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEG-G---G----T-T------HHHHHHHHH
T ss_pred             HHHHHHHHCCCCEEEE--cCCCcccccHHHHHHHHHhhhccCCceEEEEEec-c---c----h-H------HHHHHHHHH
Confidence            4444442 22  2334  32222222 2233333333222233  3566772 1   1    1 1      122334556


Q ss_pred             HHHhCcEEEEEec
Q 009230          447 AQHHACHVWFVAH  459 (539)
Q Consensus       447 A~~~~i~vi~~~q  459 (539)
                      ....++..+++++
T Consensus       234 ~~~l~i~GVIlTK  246 (425)
T 2ffh_A          234 DEKVGVTGLVLTK  246 (425)
T ss_dssp             HHHTCCCEEEEES
T ss_pred             HhcCCceEEEEeC
Confidence            6677888888877

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=97.13  E-value=0.0028  Score=56.37  Aligned_cols=38  Identities=21%  Similarity=0.368  Sum_probs=29.4

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHh------cCCeEEEEeC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEH------AGWKFVLCSM  334 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~------~g~~vl~~s~  334 (539)
                      +..++|.|+||+|||+++..++..+...      .+.+++++++
T Consensus        43 ~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDM   86 (195)
T ss_dssp             SCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECH
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeH
Confidence            3568899999999999999998877552      1567776654

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=97.13  E-value=9.5e-05  Score=69.55  Aligned_cols=61  Identities=11%  Similarity=0.034  Sum_probs=43.5

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+++++++|--+       .+.+ ......+++.|+.++++.+.+||+++|.-.                  .+...||
T Consensus       142 ~~~p~lllLDEPt-------s~LD-~~~~~~~~~~l~~l~~~~g~tvi~vtHd~~------------------~~~~~~d  195 (240)
T 2onk_A          142 VIQPRLLLLDEPL-------SAVD-LKTKGVLMEELRFVQREFDVPILHVTHDLI------------------EAAMLAD  195 (240)
T ss_dssp             TTCCSSBEEESTT-------SSCC-HHHHHHHHHHHHHHHHHHTCCEEEEESCHH------------------HHHHHCS
T ss_pred             HcCCCEEEEeCCc-------ccCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHhCC
Confidence            3679999999222       2223 344567888888888888999999999311                  2456889


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .++.|..
T Consensus       196 ~i~~l~~  202 (240)
T 2onk_A          196 EVAVMLN  202 (240)
T ss_dssp             EEEEEET
T ss_pred             EEEEEEC
Confidence            9998874

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=97.09  E-value=0.00083  Score=65.34  Aligned_cols=32  Identities=28%  Similarity=0.505  Sum_probs=26.2

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++
T Consensus        69 vL~~isl~i~~Ge~vaivG~sGsGKSTLl~ll~  101 (306)
T 3nh6_A           69 TLQDVSFTVMPGQTLALVGPSGAGKSTILRLLF  101 (306)
T ss_dssp             EEEEEEEEECTTCEEEEESSSCHHHHHHHHHHT
T ss_pred             eeeeeeEEEcCCCEEEEECCCCchHHHHHHHHH
Confidence            3555544 9999999999999999999976554

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.09  E-value=0.0039  Score=62.54  Aligned_cols=32  Identities=28%  Similarity=0.348  Sum_probs=25.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      =+++.||||+|||.++..+|..    .+.+.+.++.
T Consensus       184 GvLL~GPPGTGKTllAkAiA~e----~~~~f~~v~~  215 (405)
T 4b4t_J          184 GVILYGPPGTGKTLLARAVAHH----TDCKFIRVSG  215 (405)
T ss_dssp             CEEEESCSSSSHHHHHHHHHHH----HTCEEEEEEG
T ss_pred             ceEEeCCCCCCHHHHHHHHHHh----hCCCceEEEh
Confidence            3789999999999998877655    4778777654

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=97.05  E-value=0.0045  Score=62.78  Aligned_cols=52  Identities=13%  Similarity=0.050  Sum_probs=38.8

Q ss_pred             CCcEEEE--EcCCCCChhHHHHHHHHHHHHhc-----CCeEEEEeCC--CCHHHHHHHHHH
Q 009230          296 PGELTIV--TGVPNSGKSEWIDALICNINEHA-----GWKFVLCSME--NKVREHARKLLE  347 (539)
Q Consensus       296 ~G~l~~i--~G~~G~GKT~~~~~la~~~a~~~-----g~~vl~~s~E--~~~~~~~~r~~~  347 (539)
                      .+..++|  .|++|+|||+++..++.......     +.+++|+++.  .++..+...++.
T Consensus        49 ~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  109 (412)
T 1w5s_A           49 SDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVR  109 (412)
T ss_dssp             CCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHH
T ss_pred             CCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHHHHHHHHHH
Confidence            4568888  99999999999999987765421     5788999853  456666666554

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.04  E-value=0.0062  Score=62.02  Aligned_cols=38  Identities=21%  Similarity=0.422  Sum_probs=28.5

Q ss_pred             ccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          293 NVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       293 ~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      |+.+-.=+++.||||+|||+++..+|..    .|.++++++.
T Consensus       211 g~~~prGvLL~GPPGtGKTllAkAiA~e----~~~~~~~v~~  248 (437)
T 4b4t_L          211 GIKPPKGVLLYGPPGTGKTLLAKAVAAT----IGANFIFSPA  248 (437)
T ss_dssp             CCCCCCEEEEESCTTSSHHHHHHHHHHH----HTCEEEEEEG
T ss_pred             CCCCCCeEEEECCCCCcHHHHHHHHHHH----hCCCEEEEeh
Confidence            4444345889999999999998877755    3788777763

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=97.04  E-value=0.0086  Score=56.84  Aligned_cols=33  Identities=30%  Similarity=0.397  Sum_probs=26.4

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |+.+.- +. |+++.|.|++|+|||||+.-++--.
T Consensus        21 l~~vsl~i~-Ge~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           21 LENINLEVN-GEKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             EEEEEEEEC-SSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEeeeEEEC-CEEEEEECCCCCCHHHHHHHHhCCC
Confidence            444433 89 9999999999999999988776443

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.01  E-value=0.0046  Score=62.86  Aligned_cols=113  Identities=16%  Similarity=0.178  Sum_probs=64.4

Q ss_pred             ccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHH
Q 009230          293 NVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFE  372 (539)
Q Consensus       293 ~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~  372 (539)
                      |+.+-.=+++.||||+|||+++..+|..    .+.+++.+++-.                    +...    .+.+.   
T Consensus       202 g~~~prGiLL~GPPGtGKT~lakAiA~~----~~~~~~~v~~~~--------------------l~~~----~~Ge~---  250 (428)
T 4b4t_K          202 GIDPPRGVLLYGPPGTGKTMLVKAVANS----TKAAFIRVNGSE--------------------FVHK----YLGEG---  250 (428)
T ss_dssp             CCCCCCEEEEESCTTTTHHHHHHHHHHH----HTCEEEEEEGGG--------------------TCCS----SCSHH---
T ss_pred             CCCCCceEEEECCCCCCHHHHHHHHHHH----hCCCeEEEecch--------------------hhcc----ccchh---
Confidence            4333334889999999999998887755    377877775421                    0000    01110   


Q ss_pred             HHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCC---C-CCCH-HHHHHHHHHHHHHHH
Q 009230          373 QGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRP---V-SQTE-TEYVSQMLTMVKRFA  447 (539)
Q Consensus       373 ~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~---~-~~~~-~~~~~~~~~~Lk~lA  447 (539)
                                            ...+ ..+-..++...+-+|+||.+..+.....   . +... ...+.+++..+..+.
T Consensus       251 ----------------------e~~i-r~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~  307 (428)
T 4b4t_K          251 ----------------------PRMV-RDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFD  307 (428)
T ss_dssp             ----------------------HHHH-HHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSC
T ss_pred             ----------------------HHHH-HHHHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCC
Confidence                                  1111 1122234556788999998877765431   1 1122 234556666666666


Q ss_pred             HHhCcEEEEEec
Q 009230          448 QHHACHVWFVAH  459 (539)
Q Consensus       448 ~~~~i~vi~~~q  459 (539)
                      ...++.||+++.
T Consensus       308 ~~~~v~vI~aTN  319 (428)
T 4b4t_K          308 QSTNVKVIMATN  319 (428)
T ss_dssp             SSCSEEEEEEES
T ss_pred             CCCCEEEEEecC
Confidence            666776666665

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=96.99  E-value=0.0047  Score=56.75  Aligned_cols=32  Identities=16%  Similarity=0.293  Sum_probs=26.2

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++
T Consensus        24 il~~vsl~i~~Ge~~~iiG~NGsGKSTLlk~l~   56 (214)
T 1sgw_A           24 VLERITMTIEKGNVVNFHGPNGIGKTTLLKTIS   56 (214)
T ss_dssp             EEEEEEEEEETTCCEEEECCTTSSHHHHHHHHT
T ss_pred             EEeeeEEEEcCCCEEEEECCCCCCHHHHHHHHh
Confidence            3554444 9999999999999999999977655

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=96.98  E-value=0.0028  Score=67.69  Aligned_cols=33  Identities=21%  Similarity=0.246  Sum_probs=26.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |+.+.- +++|+.+.|.|++|+||||++.-++--
T Consensus       359 l~~i~l~i~~G~~~~ivG~sGsGKSTll~~l~g~  392 (582)
T 3b5x_A          359 LSHVSFSIPQGKTVALVGRSGSGKSTIANLFTRF  392 (582)
T ss_pred             cccceEEECCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            444433 899999999999999999998776643

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=96.97  E-value=0.00047  Score=61.32  Aligned_cols=43  Identities=28%  Similarity=0.335  Sum_probs=31.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLL  346 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~  346 (539)
                      +++|.|++|||||+|+.+++..     +.+++|+.++.. ..+...|+.
T Consensus         1 ~ilV~Gg~~SGKS~~A~~la~~-----~~~~~yiaT~~~~d~e~~~rI~   44 (180)
T 1c9k_A            1 MILVTGGARSGKSRHAEALIGD-----APQVLYIATSQILDDEMAARIQ   44 (180)
T ss_dssp             CEEEEECTTSSHHHHHHHHHCS-----CSSEEEEECCCC------CHHH
T ss_pred             CEEEECCCCCcHHHHHHHHHhc-----CCCeEEEecCCCCCHHHHHHHH
Confidence            4789999999999999988743     678999999875 344555543

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=96.94  E-value=0.0055  Score=58.84  Aligned_cols=38  Identities=18%  Similarity=0.283  Sum_probs=29.3

Q ss_pred             ccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          293 NVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       293 ~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ++.++.-++|.|+||+|||+++..++..    .+.++++++.
T Consensus        47 ~~~~~~~~ll~G~~GtGKT~la~~la~~----~~~~~~~v~~   84 (285)
T 3h4m_A           47 GIEPPKGILLYGPPGTGKTLLAKAVATE----TNATFIRVVG   84 (285)
T ss_dssp             CCCCCSEEEEESSSSSSHHHHHHHHHHH----TTCEEEEEEG
T ss_pred             CCCCCCeEEEECCCCCcHHHHHHHHHHH----hCCCEEEEeh
Confidence            4555667899999999999998887654    3677777654

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.90  E-value=0.013  Score=59.01  Aligned_cols=38  Identities=21%  Similarity=0.288  Sum_probs=28.2

Q ss_pred             ccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          293 NVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       293 ~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      |+++-.=+++.||||+|||.++..+|..    .+.+++.++.
T Consensus       212 Gi~~prGvLLyGPPGTGKTlLAkAiA~e----~~~~fi~v~~  249 (437)
T 4b4t_I          212 GIKPPKGVILYGAPGTGKTLLAKAVANQ----TSATFLRIVG  249 (437)
T ss_dssp             TCCCCSEEEEESSTTTTHHHHHHHHHHH----HTCEEEEEES
T ss_pred             CCCCCCCCceECCCCchHHHHHHHHHHH----hCCCEEEEEH
Confidence            4333345889999999999998877755    3778777664

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.90  E-value=0.041  Score=56.15  Aligned_cols=40  Identities=18%  Similarity=0.252  Sum_probs=35.5

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      ..+++++|.+|+||||++.++|..++.+.|.+|+.++++.
T Consensus       100 ~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~  139 (433)
T 2xxa_A          100 PAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADV  139 (433)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCC
Confidence            3578888999999999999999999874499999999995

>3pih_A Uvrabc system protein A; hydrolase, ABC ATPase, DNA repair, nucleotide excision repai hydrolase-DNA complex; HET: DNA; 2.90A {Thermotoga maritima}

Probab=96.82  E-value=0.0078  Score=66.98  Aligned_cols=32  Identities=31%  Similarity=0.408  Sum_probs=25.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +++|+++.|.|++|+|||||+.....
T Consensus       600 Lk~Vsl~I~~Geiv~I~G~SGSGKSTLl~~~l~  632 (916)
T 3pih_A          600 LKNIDVEIPLGVFVCVTGVSGSGKSSLVMETLY  632 (916)
T ss_dssp             CCSEEEEEESSSEEEEECSTTSSHHHHHHHTHH
T ss_pred             ccccceEEcCCcEEEEEccCCCChhhhHHHHHH
Confidence            444433 89999999999999999999865443

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=96.80  E-value=0.0062  Score=62.60  Aligned_cols=40  Identities=10%  Similarity=0.145  Sum_probs=32.5

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhc-CCeEEEEeCCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHA-GWKFVLCSMEN  336 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~-g~~vl~~s~E~  336 (539)
                      +.-++|.|+||+|||+++..++..+.... +.+++|++.+.
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~~  170 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEK  170 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHH
Confidence            35788999999999999999988776542 78899988653

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=96.76  E-value=0.034  Score=57.73  Aligned_cols=39  Identities=23%  Similarity=0.435  Sum_probs=34.5

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      ...++|+|++|+||||++..++..++.+ |.+|++++.+.
T Consensus       101 ~~vI~ivG~~GvGKTTl~~kLA~~l~~~-G~kVllVd~D~  139 (504)
T 2j37_W          101 QNVIMFVGLQGSGKTTTCSKLAYYYQRK-GWKTCLICADT  139 (504)
T ss_dssp             -EEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC-CCeEEEEeccc
Confidence            3578899999999999999999998875 99999999874

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.76  E-value=0.0013  Score=58.85  Aligned_cols=46  Identities=22%  Similarity=0.335  Sum_probs=35.3

Q ss_pred             hhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          288 LNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       288 LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ||.-....+|.+++|.|.+|+||||++..++..+... |.++.+++.
T Consensus         4 ~~~~~~~~~~~~i~l~G~~GsGKsT~~~~L~~~l~~~-~~~~~~~~~   49 (186)
T 2yvu_A            4 LTTYKCIEKGIVVWLTGLPGSGKTTIATRLADLLQKE-GYRVEVLDG   49 (186)
T ss_dssp             ----CCCSCCEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEEH
T ss_pred             cccccccCCCcEEEEEcCCCCCHHHHHHHHHHHHHhc-CCeEEEeeH
Confidence            4543236688999999999999999999999887764 888888763

>3b60_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; HET: ANP; 3.70A {Salmonella typhimurium} SCOP: c.37.1.12 f.37.1.1 PDB: 3b5y_A* 3b5z_A* 3b5w_A

Probab=96.75  E-value=0.0036  Score=66.89  Aligned_cols=26  Identities=23%  Similarity=0.319  Sum_probs=23.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +++|+.+.|.|++|+||||++.-++.
T Consensus       366 i~~G~~~~ivG~sGsGKSTLl~~l~g  391 (582)
T 3b60_A          366 IPAGKTVALVGRSGSGKSTIASLITR  391 (582)
T ss_dssp             ECTTCEEEEEECTTSSHHHHHHHHTT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhh
Confidence            89999999999999999999876654

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.74  E-value=0.0016  Score=56.29  Aligned_cols=40  Identities=25%  Similarity=0.300  Sum_probs=34.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      + +|+.+.|.|++|+|||+++..++..+.. .|.+++|++.+
T Consensus        34 ~-~g~~~~l~G~~G~GKTtL~~~i~~~~~~-~g~~~~~~~~~   73 (149)
T 2kjq_A           34 K-HGQFIYVWGEEGAGKSHLLQAWVAQALE-AGKNAAYIDAA   73 (149)
T ss_dssp             C-CCSEEEEESSSTTTTCHHHHHHHHHHHT-TTCCEEEEETT
T ss_pred             c-CCCEEEEECCCCCCHHHHHHHHHHHHHh-cCCcEEEEcHH
Confidence            5 8999999999999999999998877665 48888888765

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=96.70  E-value=0.0068  Score=63.91  Aligned_cols=26  Identities=27%  Similarity=0.308  Sum_probs=23.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +.+|+++.|.|++|+|||||+.-++-
T Consensus        44 i~~Ge~~~LvG~NGaGKSTLlk~l~G   69 (538)
T 1yqt_A           44 VKEGMVVGIVGPNGTGKSTAVKILAG   69 (538)
T ss_dssp             CCTTSEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999876653

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=96.70  E-value=0.0062  Score=59.79  Aligned_cols=36  Identities=28%  Similarity=0.317  Sum_probs=27.8

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      .+..-++|.|+||+|||+++..++..    .+.++++++.
T Consensus        49 ~~~~~vLl~GppGtGKT~la~aia~~----~~~~~~~v~~   84 (322)
T 3eie_A           49 KPTSGILLYGPPGTGKSYLAKAVATE----ANSTFFSVSS   84 (322)
T ss_dssp             CCCCEEEEECSSSSCHHHHHHHHHHH----HTCEEEEEEH
T ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHH----HCCCEEEEch
Confidence            34456899999999999998887654    3678777754

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.68  E-value=0.011  Score=60.12  Aligned_cols=39  Identities=18%  Similarity=0.231  Sum_probs=28.8

Q ss_pred             hccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          292 YNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       292 ~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +|+.+-.=+++.||||+|||+++..+|..    .+.+++.++.
T Consensus       238 ~Gi~pprGILLyGPPGTGKTlLAkAiA~e----~~~~fi~vs~  276 (467)
T 4b4t_H          238 LGIDPPKGILLYGPPGTGKTLCARAVANR----TDATFIRVIG  276 (467)
T ss_dssp             HTCCCCSEEEECSCTTSSHHHHHHHHHHH----HTCEEEEEEG
T ss_pred             CCCCCCCceEeeCCCCCcHHHHHHHHHhc----cCCCeEEEEh
Confidence            34444456889999999999998877755    3777776654

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=96.68  E-value=0.011  Score=64.74  Aligned_cols=114  Identities=22%  Similarity=0.214  Sum_probs=65.8

Q ss_pred             hccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHHH
Q 009230          292 YNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEF  371 (539)
Q Consensus       292 ~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~  371 (539)
                      +++.+-.=++|.||||+|||+++..+|..    .|.++++++.    .++.    +.                ...+.+ 
T Consensus       233 ~g~~~p~GILL~GPPGTGKT~LAraiA~e----lg~~~~~v~~----~~l~----sk----------------~~gese-  283 (806)
T 3cf2_A          233 IGVKPPRGILLYGPPGTGKTLIARAVANE----TGAFFFLING----PEIM----SK----------------LAGESE-  283 (806)
T ss_dssp             CCCCCCCEEEEECCTTSCHHHHHHHHHTT----TTCEEEEEEH----HHHH----SS----------------CTTHHH-
T ss_pred             cCCCCCCeEEEECCCCCCHHHHHHHHHHH----hCCeEEEEEh----HHhh----cc----------------cchHHH-
Confidence            34333345889999999999998776643    4777776653    2221    10                000000 


Q ss_pred             HHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCC--CCCHHHHHHHHHHHHHHHHHH
Q 009230          372 EQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPV--SQTETEYVSQMLTMVKRFAQH  449 (539)
Q Consensus       372 ~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~--~~~~~~~~~~~~~~Lk~lA~~  449 (539)
                                              ..+. .+-..+..+.+-+|+||.+-.+......  +......+.+++..+..+..+
T Consensus       284 ------------------------~~lr-~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~  338 (806)
T 3cf2_A          284 ------------------------SNLR-KAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQR  338 (806)
T ss_dssp             ------------------------HHHH-HHHHHHTTSCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGG
T ss_pred             ------------------------HHHH-HHHHHHHHcCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhccccc
Confidence                                    0111 1112234567889999988888754322  233444556666666666666


Q ss_pred             hCcEEEEEec
Q 009230          450 HACHVWFVAH  459 (539)
Q Consensus       450 ~~i~vi~~~q  459 (539)
                      .++.||..+.
T Consensus       339 ~~V~VIaaTN  348 (806)
T 3cf2_A          339 AHVIVMAATN  348 (806)
T ss_dssp             GCEEEEEECS
T ss_pred             CCEEEEEecC
Confidence            6777776655

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=96.66  E-value=0.008  Score=58.39  Aligned_cols=37  Identities=19%  Similarity=0.309  Sum_probs=29.0

Q ss_pred             ccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          293 NVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       293 ~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      ++.++.-++|.|+||+|||+++..++..    .+.+.++++
T Consensus        45 ~~~~~~~vLL~Gp~GtGKT~la~ala~~----~~~~~i~v~   81 (301)
T 3cf0_A           45 GMTPSKGVLFYGPPGCGKTLLAKAIANE----CQANFISIK   81 (301)
T ss_dssp             CCCCCSEEEEECSSSSSHHHHHHHHHHH----TTCEEEEEC
T ss_pred             CCCCCceEEEECCCCcCHHHHHHHHHHH----hCCCEEEEE
Confidence            3677888999999999999998887754    356666554

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=96.65  E-value=0.0032  Score=62.51  Aligned_cols=65  Identities=12%  Similarity=0.167  Sum_probs=54.7

Q ss_pred             cccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc-CCeEEEEeCCCCHHHHHH
Q 009230          279 FGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHA-GWKFVLCSMENKVREHAR  343 (539)
Q Consensus       279 ~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~-g~~vl~~s~E~~~~~~~~  343 (539)
                      ..+.||+..+|-++.+.+|+-+.|.|++|+|||+++.+++..+..++ +..++|+...+..+++..
T Consensus       156 ~~~~tGiraID~~~pi~rGQr~~IvG~sG~GKTtLl~~Iar~i~~~~~~v~~I~~lIGER~~Ev~~  221 (422)
T 3ice_A          156 STEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTE  221 (422)
T ss_dssp             CTTHHHHHHHHHHSCCBTTCEEEEECCSSSSHHHHHHHHHHHHHHHCTTSEEEEEEESSCHHHHHH
T ss_pred             CcccccceeeeeeeeecCCcEEEEecCCCCChhHHHHHHHHHHhhcCCCeeEEEEEecCChHHHHH
Confidence            45778999999888899999999999999999999999998887753 446778888888876643

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.62  E-value=0.014  Score=59.43  Aligned_cols=38  Identities=16%  Similarity=0.224  Sum_probs=28.3

Q ss_pred             ccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          293 NVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       293 ~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      |+++-.=+++.||||+|||.++..+|..    .|.+++.++.
T Consensus       211 g~~~prGvLLyGPPGTGKTllAkAiA~e----~~~~f~~v~~  248 (434)
T 4b4t_M          211 GIRAPKGALMYGPPGTGKTLLARACAAQ----TNATFLKLAA  248 (434)
T ss_dssp             CCCCCCEEEEESCTTSSHHHHHHHHHHH----HTCEEEEEEG
T ss_pred             CCCCCCeeEEECcCCCCHHHHHHHHHHH----hCCCEEEEeh
Confidence            3333345889999999999998877655    4778777764

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=96.61  E-value=0.0044  Score=63.39  Aligned_cols=65  Identities=25%  Similarity=0.282  Sum_probs=52.2

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVRE  340 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~  340 (539)
                      .....+.||+..+|.+..+.+|+-.+|.|++|+|||+++..++.+.+.+++.-++|...-....+
T Consensus       130 ~~~e~l~TGir~ID~L~pi~kGq~~~i~G~sGvGKTtL~~~l~~~~~~~~~~i~V~~~iGertte  194 (473)
T 1sky_E          130 TEVEILETGIKVVDLLAPYIKGGKIGLFGGAGVGKTVLIQELIHNIAQEHGGISVFAGVGERTRE  194 (473)
T ss_dssp             CSCCEECCSCHHHHHHSCEETTCEEEEECCSSSCHHHHHHHHHHHHHHHTCCCEEEEEESSCHHH
T ss_pred             ccCccccccchHHHHHhhhccCCEEEEECCCCCCccHHHHHHHhhhhhccCcEEEEeeeccCchH
Confidence            34456889999999998777899999999999999999999999988765555566655555443

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=96.60  E-value=0.0035  Score=65.15  Aligned_cols=57  Identities=19%  Similarity=0.195  Sum_probs=38.5

Q ss_pred             ccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc---CCeEEEEeCCC
Q 009230          280 GISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHA---GWKFVLCSMEN  336 (539)
Q Consensus       280 gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~---g~~vl~~s~E~  336 (539)
                      .++.|...-..-+.  +..+.-.+|+|.||+|||+++..++..++..+   ..++..+.+.+
T Consensus       148 ~v~lG~d~~G~pv~ldL~~~pHlLIaG~TGSGKSt~L~~li~sLl~~~~p~~v~l~liDpK~  209 (512)
T 2ius_A          148 TVVLGKDIAGEPVVADLAKMPHLLVAGTTGSGASVGVNAMILSMLYKAQPEDVRFIMIDPKM  209 (512)
T ss_dssp             EEEEEEETTSCEEEEEGGGSCSEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECCSS
T ss_pred             eEEEEEcCCCCEEEEEcccCceEEEECCCCCCHHHHHHHHHHHHHHhCCCceEEEEEECCch
Confidence            45556433222222  77788899999999999999999998877642   23455555444

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=96.57  E-value=0.0038  Score=66.66  Aligned_cols=26  Identities=27%  Similarity=0.335  Sum_probs=23.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +.+|+++.|.|++|+|||||+.-++-
T Consensus       100 ~~~Gei~~LvGpNGaGKSTLLkiL~G  125 (608)
T 3j16_B          100 PRPGQVLGLVGTNGIGKSTALKILAG  125 (608)
T ss_dssp             CCTTSEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCCCCEEEEECCCCChHHHHHHHHhc
Confidence            78999999999999999999776553

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=96.56  E-value=0.02  Score=56.07  Aligned_cols=39  Identities=23%  Similarity=0.220  Sum_probs=29.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ..+..-++|.|+||+|||+++..++...   .+.++++++..
T Consensus        42 ~~~~~~iLL~GppGtGKT~la~ala~~~---~~~~~~~i~~~   80 (322)
T 1xwi_A           42 RTPWRGILLFGPPGTGKSYLAKAVATEA---NNSTFFSISSS   80 (322)
T ss_dssp             CCCCSEEEEESSSSSCHHHHHHHHHHHT---TSCEEEEEECC
T ss_pred             CCCCceEEEECCCCccHHHHHHHHHHHc---CCCcEEEEEhH
Confidence            4445678899999999999998887653   26677666653

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=96.55  E-value=0.006  Score=63.93  Aligned_cols=148  Identities=14%  Similarity=0.162  Sum_probs=81.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc---CCeEEEEeCCCCHHHHHHHHHHHhhCCCccccccCCCCCCCCHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHA---GWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEE  370 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~---g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~  370 (539)
                      |..+--.+|+|.||+|||+++..++..++..+   ..+++.+.+-+  .++     +...+++--.  ..   -.-+.++
T Consensus       211 L~k~pHlLIaG~TGSGKS~~L~tlI~sLl~~~sP~ev~lilIDpKg--~eL-----s~~~~lPHl~--~~---Vvtd~~~  278 (574)
T 2iut_A          211 LAKMPHLLVAGTTGSGKSVGVNAMLLSILFKSTPSEARLIMIDPKM--LEL-----SIYEGIPHLL--CP---VVTDMKE  278 (574)
T ss_dssp             GGGSCCEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECSSS--HHH-----HTTTTCTTBS--SS---CBCCHHH
T ss_pred             hhhCCeeEEECCCCCCHHHHHHHHHHHHHHhCCCcceEEEEeCCCh--hhh-----HhhcCCCccc--ce---eeCCHHH
Confidence            55555688999999999999999999988642   24566676665  222     2233332110  00   0112333


Q ss_pred             HHHHHHHh----hccceeEeecCCCCCCHHHHHHHHHHHHHH---------------------cC--CcEEEEccccccc
Q 009230          371 FEQGKAWL----SNTFSLIRCENDSLPSIKWVLDLAKAAVLR---------------------HG--VRGLVIDPYNELD  423 (539)
Q Consensus       371 ~~~~~~~l----~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~---------------------~~--~~~vvID~~~~l~  423 (539)
                      ...+..|+    ..+.-.+.  ..+-.++......+......                     ..  .-+||||.+..++
T Consensus       279 a~~~L~~lv~EMerR~~ll~--~~gvrni~~Yn~~~~~~~~~G~~~~dp~~~~~~~~~~~~~~~~lP~ivvVIDE~~~L~  356 (574)
T 2iut_A          279 AANALRWSVAEMERRYRLMA--AMGVRNLAGFNRKVKDAEEAGTPLTDPLFRRESPDDEPPQLSTLPTIVVVVDEFADMM  356 (574)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH--HHTCSSHHHHHHHHHHHHHTTCCCBCTTCCCCSTTCCCCBCCCCCEEEEEESCCTTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH--HcCCccHHHHHHHHHHHhhcccccccccccccccccccccccCCCcEEEEEeCHHHHh
Confidence            33332222    22111110  01222344333322221110                     01  2389999998887


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CC
Q 009230          424 HQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PR  461 (539)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r  461 (539)
                      ....      ..+...+..|.+.++.+||++|+.+| +.
T Consensus       357 ~~~~------~~~~~~L~~Iar~GRa~GIhLIlaTQRPs  389 (574)
T 2iut_A          357 MIVG------KKVEELIARIAQKARAAGIHLILATQRPS  389 (574)
T ss_dssp             HHTC------HHHHHHHHHHHHHCTTTTEEEEEEESCCC
T ss_pred             hhhh------HHHHHHHHHHHHHHhhCCeEEEEEecCcc
Confidence            5321      24556777888888899999999999 54

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=96.52  E-value=0.0025  Score=61.80  Aligned_cols=34  Identities=18%  Similarity=0.134  Sum_probs=27.5

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      -..++|.|+||+|||+++..+|..+    |.+++++++
T Consensus        36 p~~lLl~GppGtGKT~la~aiA~~l----~~~~i~v~~   69 (293)
T 3t15_A           36 PLILGIWGGKGQGKSFQCELVFRKM----GINPIMMSA   69 (293)
T ss_dssp             CSEEEEEECTTSCHHHHHHHHHHHH----TCCCEEEEH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh----CCCEEEEeH
Confidence            3467889999999999988887654    778887774

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=96.52  E-value=0.0028  Score=58.95  Aligned_cols=39  Identities=18%  Similarity=0.156  Sum_probs=34.2

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .+..++|.|+||+|||+++..++..+... +.++.|++.+
T Consensus        51 ~~~~~ll~G~~G~GKT~la~~l~~~~~~~-~~~~~~~~~~   89 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLIHAACARANEL-ERRSFYIPLG   89 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEEGG
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEEEHH
Confidence            46789999999999999999999888775 8999999874

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=96.45  E-value=0.037  Score=53.29  Aligned_cols=35  Identities=23%  Similarity=0.323  Sum_probs=27.0

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ++.-++|.|+||+|||+++..++..    .+.+.++++.
T Consensus        53 ~~~~vll~Gp~GtGKT~la~~la~~----~~~~~~~i~~   87 (297)
T 3b9p_A           53 PAKGLLLFGPPGNGKTLLARAVATE----CSATFLNISA   87 (297)
T ss_dssp             CCSEEEEESSSSSCHHHHHHHHHHH----TTCEEEEEES
T ss_pred             CCCeEEEECcCCCCHHHHHHHHHHH----hCCCeEEeeH
Confidence            4567899999999999998877654    3666666654

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=96.44  E-value=0.0034  Score=73.42  Aligned_cols=170  Identities=18%  Similarity=0.197  Sum_probs=87.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHhhCCCc---cc----cccCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---ENKVREHARKLLEKHIKKPF---FE----ANYGGSA  363 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---E~~~~~~~~r~~~~~~~~~~---~~----i~~~~~~  363 (539)
                      +++|+.+.|.|++|+||||++.-+..-. .-....+.+=..   +.+...+..++ +....-+.   ..    |.+|.+.
T Consensus      1102 I~~Ge~vaIVG~SGsGKSTL~~lL~rl~-~p~~G~I~iDG~di~~i~~~~lR~~i-~~V~Qdp~LF~gTIreNI~~gld~ 1179 (1321)
T 4f4c_A         1102 VEPGQTLALVGPSGCGKSTVVALLERFY-DTLGGEIFIDGSEIKTLNPEHTRSQI-AIVSQEPTLFDCSIAENIIYGLDP 1179 (1321)
T ss_dssp             ECTTCEEEEECSTTSSTTSHHHHHTTSS-CCSSSEEEETTEETTTBCHHHHHTTE-EEECSSCCCCSEEHHHHHSSSSCT
T ss_pred             ECCCCEEEEECCCCChHHHHHHHHhcCc-cCCCCEEEECCEEhhhCCHHHHHhhe-EEECCCCEeeCccHHHHHhccCCC
Confidence            8999999999999999999976554322 111234433221   24455554443 21111110   11    2222222


Q ss_pred             CCCCHHHHHHHH------HHhhcc---ceeEeecCCCCCCH--HHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCH
Q 009230          364 ERMTVEEFEQGK------AWLSNT---FSLIRCENDSLPSI--KWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTE  432 (539)
Q Consensus       364 ~~l~~~~~~~~~------~~l~~~---~~~i~~~~~~~~~~--~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~  432 (539)
                      ...+++++.++.      +.+...   .....-+.....+-  .+.+..+|.+.  .+++++++|--+.-++      .+
T Consensus      1180 ~~~sd~ei~~Al~~a~l~~~I~~Lp~GldT~vge~G~~LSgGQrQriaiARAll--r~~~ILiLDEaTSaLD------~~ 1251 (1321)
T 4f4c_A         1180 SSVTMAQVEEAARLANIHNFIAELPEGFETRVGDRGTQLSGGQKQRIAIARALV--RNPKILLLDEATSALD------TE 1251 (1321)
T ss_dssp             TTSCHHHHHHHHHHTTCHHHHHTSTTTTCSEETTTSCSSCHHHHHHHHHHHHHH--SCCSEEEEESCCCSTT------SH
T ss_pred             CCCCHHHHHHHHHHhCChHHHHcCcCCCCCEecCCCcccCHHHHHHHHHHHHHH--hCCCEEEEeCccccCC------HH
Confidence            356777776653      223221   11110011112232  34555555544  4789999995443331      22


Q ss_pred             HHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          433 TEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       433 ~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      ++  ..+.+.|+++.  -+++||+++|.-..                   -..||.|++|..-+
T Consensus      1252 tE--~~Iq~~l~~~~--~~~TvI~IAHRLsT-------------------i~~aD~I~Vld~G~ 1292 (1321)
T 4f4c_A         1252 SE--KVVQEALDRAR--EGRTCIVIAHRLNT-------------------VMNADCIAVVSNGT 1292 (1321)
T ss_dssp             HH--HHHHHHHTTTS--SSSEEEEECSSSST-------------------TTTCSEEEEESSSS
T ss_pred             HH--HHHHHHHHHHc--CCCEEEEeccCHHH-------------------HHhCCEEEEEECCE
Confidence            22  23444444433  48999999992111                   24689999997543

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=96.43  E-value=0.014  Score=68.41  Aligned_cols=146  Identities=19%  Similarity=0.219  Sum_probs=73.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC----CCCHHHHHHHHHHHhhCCCc-------cccccCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM----ENKVREHARKLLEKHIKKPF-------FEANYGGS  362 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~----E~~~~~~~~r~~~~~~~~~~-------~~i~~~~~  362 (539)
                      +++|+++.|.|++|+||||++.-+....--. ...+. +..    +.+...+..++ +....-+.       ..|..|  
T Consensus       441 i~~G~~vaivG~sGsGKSTll~ll~~~~~~~-~G~I~-idG~~i~~~~~~~lr~~i-~~v~Q~~~Lf~~TI~eNI~~g--  515 (1321)
T 4f4c_A          441 VNAGQTVALVGSSGCGKSTIISLLLRYYDVL-KGKIT-IDGVDVRDINLEFLRKNV-AVVSQEPALFNCTIEENISLG--  515 (1321)
T ss_dssp             ECTTCEEEEEECSSSCHHHHHHHHTTSSCCS-EEEEE-ETTEETTTSCHHHHHHHE-EEECSSCCCCSEEHHHHHHTT--
T ss_pred             ecCCcEEEEEecCCCcHHHHHHHhccccccc-cCccc-CCCccchhccHHHHhhcc-cccCCcceeeCCchhHHHhhh--
Confidence            8999999999999999999976554322111 12222 221    23444443332 21111110       011122  


Q ss_pred             CCCCCHHHHHHHHH------Hhhc---cce-eEeecCCCCC--C--HHHHHHHHHHHHHHcCCcEEEEccccccccCCCC
Q 009230          363 AERMTVEEFEQGKA------WLSN---TFS-LIRCENDSLP--S--IKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPV  428 (539)
Q Consensus       363 ~~~l~~~~~~~~~~------~l~~---~~~-~i~~~~~~~~--~--~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~  428 (539)
                      .+..+++++.++.+      .+..   ... .+  . +...  +  ..+-++.+|.+.  .+++++++|.-+.-++.   
T Consensus       516 ~~~~~~~~v~~a~~~a~l~~~i~~lp~G~~T~v--G-e~G~~LSGGQkQRiaiARAl~--~~~~IliLDE~tSaLD~---  587 (1321)
T 4f4c_A          516 KEGITREEMVAACKMANAEKFIKTLPNGYNTLV--G-DRGTQLSGGQKQRIAIARALV--RNPKILLLDEATSALDA---  587 (1321)
T ss_dssp             CTTCCHHHHHHHHHHTTCHHHHHHSTTTTSSEE--S-SSSCCCCHHHHHHHHHHHHHT--TCCSEEEEESTTTTSCT---
T ss_pred             cccchHHHHHHHHHHccchhHHHcCCCCCccEe--c-CCCCCCCHHHHHHHHHHHHHc--cCCCEEEEecccccCCH---
Confidence            12356777665532      2222   111 12  1 1112  2  233344444332  47899999966655432   


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          429 SQTETEYVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       429 ~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                       .++.    .+.+.|..+.  .|.++|+++|
T Consensus       588 -~te~----~i~~~l~~~~--~~~T~iiiaH  611 (1321)
T 4f4c_A          588 -ESEG----IVQQALDKAA--KGRTTIIIAH  611 (1321)
T ss_dssp             -TTHH----HHHHHHHHHH--TTSEEEEECS
T ss_pred             -HHHH----HHHHHHHHHh--CCCEEEEEcc
Confidence             2332    3444444444  3789999999

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.42  E-value=0.0037  Score=57.15  Aligned_cols=41  Identities=24%  Similarity=0.401  Sum_probs=33.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ..+|+++.|.|++|+|||||+..++...-.. |..+.+++.+
T Consensus        19 ~~~g~~v~I~G~sGsGKSTl~~~l~~~~~~~-g~~~g~v~~d   59 (208)
T 3c8u_A           19 QPGRQLVALSGAPGSGKSTLSNPLAAALSAQ-GLPAEVVPMD   59 (208)
T ss_dssp             CCSCEEEEEECCTTSCTHHHHHHHHHHHHHT-TCCEEEEESG
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHhhc-CCceEEEecC
Confidence            4679999999999999999999887665543 5567788765

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=96.41  E-value=0.009  Score=53.61  Aligned_cols=41  Identities=17%  Similarity=0.081  Sum_probs=33.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      -.+| +++|.+++|.||||.++-++..++.+ |.+|+++.+--
T Consensus        26 ~~~g-~i~v~tG~GkGKTTaA~GlalRA~g~-G~rV~~vQF~K   66 (196)
T 1g5t_A           26 EERG-IIIVFTGNGKGKTTAAFGTAARAVGH-GKNVGVVQFIK   66 (196)
T ss_dssp             -CCC-CEEEEESSSSCHHHHHHHHHHHHHHT-TCCEEEEESSC
T ss_pred             ccCc-eEEEECCCCCCHHHHHHHHHHHHHHC-CCeEEEEEeeC
Confidence            3444 77788888999999999999999984 99999997653

>3qxc_A Dethiobiotin synthetase; DTBS, structural genomics, ATP BIND biology, protein structure initiative, midwest center for S genomics, MCSG; HET: ATP; 1.34A {Helicobacter pylori} PDB: 3mle_A* 3qxh_A* 3qxj_A* 3qxs_A* 3qxx_A* 3qy0_A* 2qmo_A

Probab=96.40  E-value=0.082  Score=49.29  Aligned_cols=136  Identities=10%  Similarity=0.005  Sum_probs=73.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe-----CCC------CHHHHHHHHHHHhh-CCCccccccCCCCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS-----MEN------KVREHARKLLEKHI-KKPFFEANYGGSAERM  366 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s-----~E~------~~~~~~~r~~~~~~-~~~~~~i~~~~~~~~l  366 (539)
                      +.+.+-.+|+|||++++.++..+.++ |.+|.||-     .+.      +...+++ -.+..+ +.+...+..-.....+
T Consensus        24 i~ItgT~t~vGKT~vs~gL~~~L~~~-G~~V~~fKPv~~g~~~~~~~~~D~~~~~~-~~~~~~~g~~~~~~~p~~~~~p~  101 (242)
T 3qxc_A           24 LFISATNTNAGKTTCARLLAQYCNAC-GVKTILLKPIETGVNDAINHSSDAHLFLQ-DNRLLDRSLTLKDISFYRYHKVS  101 (242)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHT-TCCEEEECCEECSCCTTTCCCSHHHHHHH-HHHTTCTTCCHHHHCCEECSSSS
T ss_pred             EEEEeCCCCCcHHHHHHHHHHHHHhC-CCceEEEeeeecCCcccCCCCchHHHHHH-HHHHHhCCCChHHeeeEEECCCC
Confidence            55555569999999999999998886 99999994     221      1121111 112222 4432211000000011


Q ss_pred             CHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHH
Q 009230          367 TVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRF  446 (539)
Q Consensus       367 ~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~l  446 (539)
                      ++.--    ..+...        .....++.|.+.++.+.  .+.++||||.-..+..+..  ..         .....+
T Consensus       102 sp~~a----a~~~g~--------~~~i~~~~I~~~~~~l~--~~~D~vlIEGagGl~~pl~--~~---------~~~adl  156 (242)
T 3qxc_A          102 APLIA----QQEEDP--------NAPIDTDNLTQRLHNFT--KTYDLVIVEGAGGLCVPIT--LE---------ENMLDF  156 (242)
T ss_dssp             CHHHH----HHHHCT--------TCCCCHHHHHHHHHHGG--GTCSEEEEECCSCTTCBSS--SS---------CBHHHH
T ss_pred             ChHHH----HHHcCC--------CCcCCHHHHHHHHHHHH--hcCCEEEEECCCCcccccc--cc---------chHHHH
Confidence            11110    011110        00335667776666543  4678999997776664321  11         112346


Q ss_pred             HHHhCcEEEEEecCC
Q 009230          447 AQHHACHVWFVAHPR  461 (539)
Q Consensus       447 A~~~~i~vi~~~q~r  461 (539)
                      |+.++.|||+|+..+
T Consensus       157 A~~l~~pVILV~~~~  171 (242)
T 3qxc_A          157 ALKLKAKMLLISHDN  171 (242)
T ss_dssp             HHHHTCEEEEEECCS
T ss_pred             HHHcCCCEEEEEcCC
Confidence            788999999999844

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=96.39  E-value=0.004  Score=56.51  Aligned_cols=40  Identities=28%  Similarity=0.181  Sum_probs=33.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ..+|+++.|.|++|+||||++..++..+-. .|..+.|+..
T Consensus        22 ~~~g~~i~l~G~sGsGKSTl~~~La~~l~~-~G~~~~~~d~   61 (200)
T 3uie_A           22 DQKGCVIWVTGLSGSGKSTLACALNQMLYQ-KGKLCYILDG   61 (200)
T ss_dssp             TSCCEEEEEECSTTSSHHHHHHHHHHHHHH-TTCCEEEEEH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHh-cCceEEEecC
Confidence            678999999999999999999999887764 3766666663

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=96.36  E-value=0.019  Score=57.17  Aligned_cols=57  Identities=18%  Similarity=0.292  Sum_probs=40.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEE------eCCCCHHHHHHHHHHHhhCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLC------SMENKVREHARKLLEKHIKK  352 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~------s~E~~~~~~~~r~~~~~~~~  352 (539)
                      ..+|..++|.|+||+|||+++..++..+..  ..+...+      +.+++..+...+.+....+.
T Consensus        67 ~~~~~~vLl~GppGtGKT~la~~la~~l~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (368)
T 3uk6_A           67 KIAGRAVLIAGQPGTGKTAIAMGMAQALGP--DTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGV  129 (368)
T ss_dssp             CCTTCEEEEEESTTSSHHHHHHHHHHHHCS--SCCEEEEEGGGGSCSSSCHHHHHHHHHHHSBEE
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHhcc--cCCcccccchhhhhcccchhHHHHHHHHHHHHH
Confidence            445678999999999999999998877532  2344433      45677777777766554443

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=96.35  E-value=0.019  Score=61.34  Aligned_cols=26  Identities=23%  Similarity=0.297  Sum_probs=23.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +.+|+++.|.|++|+|||||+.-++-
T Consensus       114 i~~Ge~~~LiG~NGsGKSTLlkiL~G  139 (607)
T 3bk7_A          114 VKDGMVVGIVGPNGTGKTTAVKILAG  139 (607)
T ss_dssp             CCTTSEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCCCEEEEECCCCChHHHHHHHHhC
Confidence            78999999999999999999876653

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.35  E-value=0.037  Score=53.86  Aligned_cols=57  Identities=11%  Similarity=0.118  Sum_probs=41.0

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhc------CCeEEEEeCC--CCHHHHHHHHHHHhhCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHA------GWKFVLCSME--NKVREHARKLLEKHIKK  352 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~------g~~vl~~s~E--~~~~~~~~r~~~~~~~~  352 (539)
                      ++..++|.|+||+|||+++..++..+-...      ...++++.+-  .++..++..+...+.|.
T Consensus        44 ~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~~L~g~  108 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISKE  108 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHHHHSCC
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHHHhcCC
Confidence            445778999999999999999988875421      3467788754  45667777777776664

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=96.32  E-value=0.0032  Score=67.43  Aligned_cols=31  Identities=26%  Similarity=0.523  Sum_probs=25.1

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      |+++.- +++|+.+.|.|++|+||||++.-++
T Consensus       371 l~~isl~i~~G~~~~ivG~sGsGKSTll~~l~  402 (598)
T 3qf4_B          371 LKDITFHIKPGQKVALVGPTGSGKTTIVNLLM  402 (598)
T ss_dssp             CCSEEEECCTTCEEEEECCTTSSTTHHHHHHT
T ss_pred             ccceEEEEcCCCEEEEECCCCCcHHHHHHHHh
Confidence            444333 8999999999999999999976554

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=96.29  E-value=0.0064  Score=62.06  Aligned_cols=65  Identities=23%  Similarity=0.236  Sum_probs=55.5

Q ss_pred             CccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHH
Q 009230          277 DEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREH  341 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~  341 (539)
                      ....+.||+..+|-++-+.+|.=..|.|++|+|||+++.+++.+++.+++.-++|....+..+++
T Consensus       133 ~~e~l~TGir~ID~l~pigkGQr~~Ifgg~G~GKT~L~~~i~~~~~~~~~~v~V~~~iGER~rEv  197 (482)
T 2ck3_D          133 EQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREG  197 (482)
T ss_dssp             CCCEECCSCHHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHTTTTCSSEEEEEEESCCHHHH
T ss_pred             cCcCCccceEEEecccccccCCeeeeecCCCCChHHHHHHHHHhhHhhCCCEEEEEECCCcchHH
Confidence            44578999999999988999999999999999999999999999877555567777777777654

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=96.26  E-value=0.036  Score=55.81  Aligned_cols=36  Identities=22%  Similarity=0.321  Sum_probs=28.3

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ++.-++|.|+||+|||+++..++..    .+.+++++++.
T Consensus       147 ~~~~vLL~GppGtGKT~la~aia~~----~~~~~~~v~~~  182 (389)
T 3vfd_A          147 PARGLLLFGPPGNGKTMLAKAVAAE----SNATFFNISAA  182 (389)
T ss_dssp             CCSEEEEESSTTSCHHHHHHHHHHH----TTCEEEEECSC
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHh----hcCcEEEeeHH
Confidence            3457899999999999998877543    47888877763

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=96.25  E-value=0.028  Score=55.98  Aligned_cols=35  Identities=23%  Similarity=0.330  Sum_probs=27.8

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +..-++|.|+||+|||+++..++..    .+.++++++.
T Consensus       116 ~~~~vLl~GppGtGKT~la~aia~~----~~~~~~~i~~  150 (357)
T 3d8b_A          116 PPKGILLFGPPGTGKTLIGKCIASQ----SGATFFSISA  150 (357)
T ss_dssp             CCSEEEEESSTTSSHHHHHHHHHHH----TTCEEEEEEG
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHH----cCCeEEEEeh
Confidence            3456889999999999999887654    3778887765

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.23  E-value=0.036  Score=53.65  Aligned_cols=37  Identities=22%  Similarity=0.316  Sum_probs=28.7

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCC----eEEEEe
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGW----KFVLCS  333 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~----~vl~~s  333 (539)
                      ++.-++|.|+||+|||+++..++..+... +.    ++++++
T Consensus        66 ~~~~vll~G~~GtGKT~la~~la~~l~~~-~~~~~~~~~~~~  106 (309)
T 3syl_A           66 PTLHMSFTGNPGTGKTTVALKMAGLLHRL-GYVRKGHLVSVT  106 (309)
T ss_dssp             CCCEEEEEECTTSSHHHHHHHHHHHHHHT-TSSSSCCEEEEC
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHHhc-CCcCCCcEEEEc
Confidence            34468999999999999999998877653 33    666665

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.21  E-value=0.0053  Score=55.75  Aligned_cols=42  Identities=19%  Similarity=0.309  Sum_probs=34.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      ..+|.++.|+|++|+||||++..++..+... +.+|.+++.+.
T Consensus        19 ~~~~~~i~i~G~~GsGKstl~~~l~~~~~~~-~~~v~~~~~d~   60 (201)
T 1rz3_A           19 TAGRLVLGIDGLSRSGKTTLANQLSQTLREQ-GISVCVFHMDD   60 (201)
T ss_dssp             CSSSEEEEEEECTTSSHHHHHHHHHHHHHHT-TCCEEEEEGGG
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHHHhhc-CCeEEEeccCc
Confidence            5678999999999999999999888766543 78888886653

>4aby_A DNA repair protein RECN; hydrolase, double strand break repair, ATPase, nucleotide binding domain; HET: DNA; 3.00A {Deinococcus radiodurans}

Probab=96.21  E-value=0.013  Score=59.72  Aligned_cols=34  Identities=29%  Similarity=0.317  Sum_probs=27.3

Q ss_pred             Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          284 GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       284 g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      +|..|+.+.- +.+| +++|.|++|+||||++.-+.
T Consensus        47 nf~~l~~v~l~~~~G-~~~lvG~NGaGKStLl~aI~   81 (415)
T 4aby_A           47 NLATITQLELELGGG-FCAFTGETGAGKSIIVDALG   81 (415)
T ss_dssp             EETTEEEEEEECCSS-EEEEEESHHHHHHHHTHHHH
T ss_pred             cccceeeEEEecCCC-cEEEECCCCCCHHHHHHHHH
Confidence            4555665544 9999 99999999999999987654

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=96.20  E-value=0.041  Score=56.74  Aligned_cols=35  Identities=26%  Similarity=0.335  Sum_probs=26.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +++|  ++|.|+||+|||+++..++..    .+.++++++.
T Consensus        48 ~p~g--vLL~GppGtGKT~Laraia~~----~~~~f~~is~   82 (476)
T 2ce7_A           48 MPKG--ILLVGPPGTGKTLLARAVAGE----ANVPFFHISG   82 (476)
T ss_dssp             CCSE--EEEECCTTSSHHHHHHHHHHH----HTCCEEEEEG
T ss_pred             CCCe--EEEECCCCCCHHHHHHHHHHH----cCCCeeeCCH
Confidence            4555  789999999999998887753    3677776653

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=96.19  E-value=0.0026  Score=57.05  Aligned_cols=39  Identities=31%  Similarity=0.400  Sum_probs=29.7

Q ss_pred             ccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          293 NVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       293 ~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .+.+|++++|.|+||+||||++..++..    .+...++++.+
T Consensus         5 ~i~~g~~i~l~G~~GsGKSTl~~~La~~----~~~g~i~i~~d   43 (191)
T 1zp6_A            5 DDLGGNILLLSGHPGSGKSTIAEALANL----PGVPKVHFHSD   43 (191)
T ss_dssp             -CCTTEEEEEEECTTSCHHHHHHHHHTC----SSSCEEEECTT
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHhc----cCCCeEEEccc
Confidence            3788999999999999999998887643    24455566543

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=96.18  E-value=0.019  Score=61.25  Aligned_cols=25  Identities=40%  Similarity=0.578  Sum_probs=22.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      +++|+.+.|.|++|+||||++.-++
T Consensus       366 i~~Ge~~~ivG~sGsGKSTll~~l~  390 (587)
T 3qf4_A          366 VKPGSLVAVLGETGSGKSTLMNLIP  390 (587)
T ss_dssp             ECTTCEEEEECSSSSSHHHHHHTTT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHh
Confidence            8999999999999999999976554

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.18  E-value=0.0036  Score=56.75  Aligned_cols=37  Identities=11%  Similarity=0.134  Sum_probs=31.8

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .-++|.|+||+|||+++..++..+... +.+++|++..
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~-~~~~~~~~~~   91 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKR-NVSSLIVYVP   91 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTT-TCCEEEEEHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEEEhH
Confidence            578899999999999999999887764 8899998754

>3igf_A ALL4481 protein; two-domained protein consisting of the N-terminal alpha-beta the C-terminal all beta domain., structural genomics; 2.00A {Nostoc SP}

Probab=96.13  E-value=0.0075  Score=60.24  Aligned_cols=36  Identities=11%  Similarity=0.141  Sum_probs=33.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      .+++++|..|+||||++.++|..++.. |.+|+++++
T Consensus         3 ~i~~~~gkGG~GKTt~a~~la~~la~~-g~~vllvd~   38 (374)
T 3igf_A            3 LILTFLGKSGVARTKIAIAAAKLLASQ-GKRVLLAGL   38 (374)
T ss_dssp             EEEEEECSBHHHHHHHHHHHHHHHHHT-TCCEEEEEC
T ss_pred             EEEEEeCCCCCcHHHHHHHHHHHHHHC-CCCeEEEeC
Confidence            367889999999999999999999986 999999999

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=96.13  E-value=0.0064  Score=53.92  Aligned_cols=38  Identities=21%  Similarity=0.150  Sum_probs=31.4

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      .+|.+++|.|++|+||||++..++..+.. .|.+++++.
T Consensus         3 ~~g~~i~l~G~~GsGKST~~~~L~~~l~~-~g~~~i~~d   40 (179)
T 2pez_A            3 MRGCTVWLTGLSGAGKTTVSMALEEYLVC-HGIPCYTLD   40 (179)
T ss_dssp             -CCEEEEEECCTTSSHHHHHHHHHHHHHH-TTCCEEEEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHhh-CCCcEEEEC
Confidence            36889999999999999999998877654 488888765

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=96.13  E-value=0.051  Score=53.96  Aligned_cols=35  Identities=26%  Similarity=0.309  Sum_probs=26.5

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      .+..-++|.|+||+|||+++..++..+    +.++++++
T Consensus        82 ~~~~~iLL~GppGtGKT~la~ala~~~----~~~~~~v~  116 (355)
T 2qp9_X           82 KPTSGILLYGPPGTGKSYLAKAVATEA----NSTFFSVS  116 (355)
T ss_dssp             CCCCCEEEECSTTSCHHHHHHHHHHHH----TCEEEEEE
T ss_pred             CCCceEEEECCCCCcHHHHHHHHHHHh----CCCEEEee
Confidence            333457889999999999998887653    66777665

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=96.12  E-value=0.005  Score=58.45  Aligned_cols=38  Identities=24%  Similarity=0.331  Sum_probs=31.7

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ++.+++|+|.||+||||++..++..+.. .|.++++++.
T Consensus         3 ~~~lIvl~G~pGSGKSTla~~La~~L~~-~g~~~i~~~~   40 (260)
T 3a4m_A            3 DIMLIILTGLPGVGKSTFSKNLAKILSK-NNIDVIVLGS   40 (260)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHH-TTCCEEEECT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHHHh-CCCEEEEECc
Confidence            4568999999999999999999887665 3888887765

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=96.11  E-value=0.0071  Score=53.15  Aligned_cols=38  Identities=18%  Similarity=0.379  Sum_probs=32.7

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      ++.|+|++|+||||++..++..+..+ |.+|..+..+..
T Consensus         6 ~i~i~G~sGsGKTTl~~~L~~~l~~~-g~~v~~ik~~~~   43 (169)
T 1xjc_A            6 VWQVVGYKHSGKTTLMEKWVAAAVRE-GWRVGTVKHHGH   43 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEECCC-
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhHhc-CCeeeEEEeCCC
Confidence            68899999999999999999887764 899999987653

>2vf7_A UVRA2, excinuclease ABC, subunit A.; DNA-binding protein, nucleotide-binding, zinc-binding domain, SOS response, metal-binding; HET: ADP; 2.30A {Deinococcus radiodurans} PDB: 2vf8_A*

Probab=96.10  E-value=0.021  Score=63.00  Aligned_cols=23  Identities=43%  Similarity=0.540  Sum_probs=22.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDA  316 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~  316 (539)
                      +++|+++.|+|++|+|||||+..
T Consensus       520 i~~Geiv~I~G~nGSGKSTLl~~  542 (842)
T 2vf7_A          520 FPLGVMTSVTGVSGSGKSTLVSQ  542 (842)
T ss_dssp             EESSSEEEEECCTTSSHHHHCCC
T ss_pred             EcCCCEEEEEcCCCcCHHHHHHH
Confidence            99999999999999999999986

>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A {Geobacillus}

Probab=96.10  E-value=0.014  Score=63.35  Aligned_cols=31  Identities=32%  Similarity=0.534  Sum_probs=25.2

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      |+.+.- +++|+++.|.|++|+|||||+.-++
T Consensus       338 L~~vsl~I~~Ge~vaIiGpnGsGKSTLl~~i~  369 (670)
T 3ux8_A          338 LKNVSVKIPLGTFVAVTGVSGSGKSTLVNEVL  369 (670)
T ss_dssp             CCSEEEEEETTSEEEEECSTTSSHHHHHTTTH
T ss_pred             cccceeEecCCCEEEEEeeCCCCHHHHHHHHH
Confidence            444433 8999999999999999999986543

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=96.08  E-value=0.0061  Score=62.48  Aligned_cols=66  Identities=26%  Similarity=0.191  Sum_probs=53.9

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREH  341 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~  341 (539)
                      .....+.||+..+|-++-+.+|.=..|.|++|+|||+++.+++.+++.+++.-++|...-+..++.
T Consensus       144 ~~~e~l~TGirvID~l~pigkGqr~gIfgg~GvGKT~L~~~l~~~~a~~~~~v~V~~~iGER~rEv  209 (498)
T 1fx0_B          144 TKLSIFETGIKVVNLLAPYRRGGKIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGGVGERTREG  209 (498)
T ss_dssp             CCCCCCCCSCTTHHHHSCCCTTCCEEEEECSSSSHHHHHHHHHHHTTTTCSSCEEEEEESCCSHHH
T ss_pred             ccccccccceeEeeeecccccCCeEEeecCCCCCchHHHHHHHHHHHhhCCCEEEEEEcccCcHHH
Confidence            345578999999999988999999999999999999999999999887555566666666655443

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=96.08  E-value=0.0093  Score=66.64  Aligned_cols=28  Identities=25%  Similarity=0.217  Sum_probs=24.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +.+|++++|.||+|+||||++.+++...
T Consensus       659 ~~~g~i~~ItGpNGsGKSTlLr~ial~~  686 (934)
T 3thx_A          659 KDKQMFHIITGPNMGGKSTYIRQTGVIV  686 (934)
T ss_dssp             TTTBCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            5679999999999999999999986543

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=96.07  E-value=0.022  Score=53.69  Aligned_cols=38  Identities=18%  Similarity=0.195  Sum_probs=28.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      +.+..-++|.|+||+|||+++..++..    .+.++++++..
T Consensus        36 ~~~~~~vll~G~~GtGKT~la~~la~~----~~~~~~~~~~~   73 (262)
T 2qz4_A           36 AKVPKGALLLGPPGCGKTLLAKAVATE----AQVPFLAMAGA   73 (262)
T ss_dssp             CCCCCEEEEESCTTSSHHHHHHHHHHH----HTCCEEEEETT
T ss_pred             CCCCceEEEECCCCCCHHHHHHHHHHH----hCCCEEEechH
Confidence            344456889999999999999888764    26677777654

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=96.06  E-value=0.0068  Score=55.45  Aligned_cols=40  Identities=20%  Similarity=0.084  Sum_probs=34.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +.+|.+++|.|++|+||||++..++..+-...|.++.+++
T Consensus        22 ~~~~~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~   61 (211)
T 1m7g_A           22 NQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   61 (211)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEEC
Confidence            7789999999999999999999998877623488888886

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=96.04  E-value=0.0029  Score=58.38  Aligned_cols=35  Identities=14%  Similarity=0.057  Sum_probs=23.3

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .|+.+.- +.+|+++.|.|++|+||||++..++-..
T Consensus        12 ~l~~isl~i~~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           12 SGLVPRGSMNNIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             ----------CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             cccCCceecCCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3555544 8999999999999999999988877543

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=96.01  E-value=0.0088  Score=58.78  Aligned_cols=39  Identities=18%  Similarity=0.191  Sum_probs=36.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .+.+++|..|+||||++.++|..+|.. |.+|+.++++..
T Consensus        15 ~i~v~sgKGGvGKTTvA~~LA~~lA~~-G~rVLlvD~D~~   53 (324)
T 3zq6_A           15 TFVFIGGKGGVGKTTISAATALWMARS-GKKTLVISTDPA   53 (324)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHT-TCCEEEEECCSS
T ss_pred             EEEEEeCCCCchHHHHHHHHHHHHHHC-CCcEEEEeCCCC
Confidence            688899999999999999999999986 999999999974

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.97  E-value=0.011  Score=56.14  Aligned_cols=45  Identities=31%  Similarity=0.350  Sum_probs=33.4

Q ss_pred             hhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEE
Q 009230          287 ALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLC  332 (539)
Q Consensus       287 ~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~  332 (539)
                      .|+.+. +.+|++++|.|++|+||||++.-++..........+.+.
T Consensus        16 vl~~i~-i~~g~~v~i~Gp~GsGKSTll~~l~g~~~~~~~G~I~~~   60 (261)
T 2eyu_A           16 KVLELC-HRKMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITI   60 (261)
T ss_dssp             HHHHGG-GCSSEEEEEECSTTCSHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             HHHHHh-hCCCCEEEEECCCCccHHHHHHHHHHhCCCCCCCEEEEc
Confidence            344444 899999999999999999999888766543214566554

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=95.97  E-value=0.061  Score=58.85  Aligned_cols=137  Identities=18%  Similarity=0.165  Sum_probs=74.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC-CHHHHHHHHHHHh--hCCCccccccCCCCCCCCHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN-KVREHARKLLEKH--IKKPFFEANYGGSAERMTVEE  370 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~-~~~~~~~r~~~~~--~~~~~~~i~~~~~~~~l~~~~  370 (539)
                      +..|+-++|+|+||+|||+.+...+.+.....|.+++|+..-- -..+...++ ...  .|+...... |    .....+
T Consensus        43 ~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~P~r~La~q~~~~~-~~~~~~g~~v~~~~-G----~~~~~~  116 (715)
T 2va8_A           43 LLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRALTNEKYLTF-KDWELIGFKVAMTS-G----DYDTDD  116 (715)
T ss_dssp             TTTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEECSCHHHHHHHHHHH-GGGGGGTCCEEECC-S----CSSSCC
T ss_pred             hcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEeCcHHHHHHHHHHH-HHhhcCCCEEEEEe-C----CCCCch
Confidence            5668899999999999999998877766554588999997542 133444444 111  233332221 1    111000


Q ss_pred             HHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHH-HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009230          371 FEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVL-RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQH  449 (539)
Q Consensus       371 ~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~-~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~  449 (539)
                           .++....++|       .|++.+...++.-.. -.++++||||-...+..     ......+..++..++     
T Consensus       117 -----~~~~~~~Iiv-------~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~-----~~~~~~l~~i~~~~~-----  174 (715)
T 2va8_A          117 -----AWLKNYDIII-------TTYEKLDSLWRHRPEWLNEVNYFVLDELHYLND-----PERGPVVESVTIRAK-----  174 (715)
T ss_dssp             -----GGGGGCSEEE-------ECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGC-----TTTHHHHHHHHHHHH-----
T ss_pred             -----hhcCCCCEEE-------EcHHHHHHHHhCChhHhhccCEEEEechhhcCC-----cccchHHHHHHHhcc-----
Confidence                 1222333433       145555444433111 23578999997665432     122334444554443     


Q ss_pred             hCcEEEEEec
Q 009230          450 HACHVWFVAH  459 (539)
Q Consensus       450 ~~i~vi~~~q  459 (539)
                       ++.+|+++-
T Consensus       175 -~~~ii~lSA  183 (715)
T 2va8_A          175 -RRNLLALSA  183 (715)
T ss_dssp             -TSEEEEEES
T ss_pred             -cCcEEEEcC
Confidence             677777776

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=95.96  E-value=0.012  Score=58.25  Aligned_cols=63  Identities=13%  Similarity=0.161  Sum_probs=53.7

Q ss_pred             cccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc-CCeEEEEeCCCCHHHH
Q 009230          279 FGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHA-GWKFVLCSMENKVREH  341 (539)
Q Consensus       279 ~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~-g~~vl~~s~E~~~~~~  341 (539)
                      ..+.||+..+|-++-+.+|+=..|.|++|+|||+++.+|+.+++.++ +..++|....+..+++
T Consensus       157 e~~~tGiraID~l~PigrGQR~lIfg~~g~GKT~Ll~~Ia~~i~~~~~dv~~V~~lIGER~~EV  220 (427)
T 3l0o_A          157 DPKIYSTRLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIANGIAENHPDTIRIILLIDERPEEV  220 (427)
T ss_dssp             STTCHHHHHHHHHSCCBTTCEEEEEECTTCCHHHHHHHHHHHHHHHCTTSEEEEEECSCCHHHH
T ss_pred             cchhccchhhhhcccccCCceEEEecCCCCChhHHHHHHHHHHhhcCCCeEEEEEEeccCcchH
Confidence            35789999999888899999999999999999999999998887753 4567788888887765

>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=95.93  E-value=0.0055  Score=60.17  Aligned_cols=39  Identities=15%  Similarity=0.320  Sum_probs=33.3

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      +..++|.|+||+|||+++..++..+... +.+++|++.+.
T Consensus        37 ~~~lll~G~~GtGKT~la~~i~~~~~~~-~~~~~~i~~~~   75 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQAAGNEAKKR-GYRVIYSSADD   75 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHHHHHHHHHHT-TCCEEEEEHHH
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHC-CCEEEEEEHHH
Confidence            4568899999999999999999887765 89999998653

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.92  E-value=0.0079  Score=58.62  Aligned_cols=38  Identities=18%  Similarity=0.173  Sum_probs=33.2

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHH-HhcCCeEEEEeCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNIN-EHAGWKFVLCSME  335 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a-~~~g~~vl~~s~E  335 (539)
                      +.-++|.|+||+|||+++..++..+. .. |.+|+|++..
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~~~~~~-g~~v~~~~~~  190 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHELSEKK-GVSTTLLHFP  190 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHHHHS-CCCEEEEEHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHhc-CCcEEEEEHH
Confidence            46788999999999999999999888 64 9999998753

>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B* 3thy_B* 3thz_B*

Probab=95.92  E-value=0.0015  Score=72.85  Aligned_cols=28  Identities=25%  Similarity=0.284  Sum_probs=24.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +.+|++++|.||+|+||||++.+++...
T Consensus       670 ~~~g~i~~ItGPNGaGKSTlLr~i~~i~  697 (918)
T 3thx_B          670 EDSERVMIITGPNMGGKSSYIKQVALIT  697 (918)
T ss_dssp             TTSCCEEEEESCCCHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCchHHHHHHHHHHH
Confidence            5689999999999999999999987543

>2woj_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; HET: ADP; 1.99A {Saccharomyces cerevisiae} PDB: 3h84_A 3zs8_A 3zs9_A* 3sja_A 3sjb_A 3sjc_A 3sjd_A* 3idq_A 3a36_A 3a37_A*

Probab=95.92  E-value=0.0076  Score=59.99  Aligned_cols=49  Identities=18%  Similarity=0.236  Sum_probs=39.8

Q ss_pred             hhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHH--HhcCCeEEEEeCCCC
Q 009230          288 LNELYNVLPGELTIVTGVPNSGKSEWIDALICNIN--EHAGWKFVLCSMENK  337 (539)
Q Consensus       288 LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a--~~~g~~vl~~s~E~~  337 (539)
                      |+.++.-..-.+++.+|..|+||||++.++|..+|  . .|.+|+.++++..
T Consensus         9 l~~l~~~~~~~i~v~sgKGGvGKTTvaanLA~~lA~~~-~G~rVLLvD~D~~   59 (354)
T 2woj_A            9 LHSLITSTTHKWIFVGGKGGVGKTTSSCSIAIQMALSQ-PNKQFLLISTDPA   59 (354)
T ss_dssp             CHHHHTCSSCCEEEEEESTTSSHHHHHHHHHHHHHHHC-TTSCEEEEECCSS
T ss_pred             HHHHhcCCCcEEEEEeCCCCCcHHHHHHHHHHHHHHhc-CCCeEEEEECCCC
Confidence            44444322235888999999999999999999999  6 4999999999985

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.91  E-value=0.0045  Score=55.12  Aligned_cols=26  Identities=15%  Similarity=0.240  Sum_probs=22.8

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .+|++++|.|+||+||||++..++..
T Consensus         3 ~~g~~i~i~GpsGsGKSTL~~~L~~~   28 (180)
T 1kgd_A            3 HMRKTLVLLGAHGVGRRHIKNTLITK   28 (180)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            46899999999999999999887754

>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein biosynthesis, nucleotide-binding, phosphorylation, RNA- binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A

Probab=95.89  E-value=0.045  Score=61.15  Aligned_cols=25  Identities=20%  Similarity=0.214  Sum_probs=23.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      +.+|+.+.|.|++|+|||||+.-++
T Consensus       458 I~~Ge~v~LiGpNGsGKSTLLk~La  482 (986)
T 2iw3_A          458 LKRARRYGICGPNGCGKSTLMRAIA  482 (986)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHh
Confidence            8999999999999999999988877

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=95.89  E-value=0.0054  Score=55.53  Aligned_cols=28  Identities=18%  Similarity=0.115  Sum_probs=23.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +.+|..++|.|+||+||||++..++..+
T Consensus        22 ~~~~~~i~l~G~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           22 SNAMVRIFLTGYMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCCCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            7889999999999999999998887553

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=95.89  E-value=0.008  Score=56.84  Aligned_cols=41  Identities=12%  Similarity=0.298  Sum_probs=36.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      ..+.-++++.|.+|+||||++.+++..++ . |.+|+.++++.
T Consensus        11 ~~~~~i~~~~GkgGvGKTTl~~~La~~l~-~-g~~v~vvd~D~   51 (262)
T 1yrb_A           11 GMASMIVVFVGTAGSGKTTLTGEFGRYLE-D-NYKVAYVNLDT   51 (262)
T ss_dssp             TCCCEEEEEECSTTSSHHHHHHHHHHHHT-T-TSCEEEEECCS
T ss_pred             CcceEEEEEeCCCCCCHHHHHHHHHHHHH-C-CCeEEEEeCCC
Confidence            44556899999999999999999999988 5 99999999885

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.81  E-value=0.0053  Score=55.72  Aligned_cols=27  Identities=19%  Similarity=0.256  Sum_probs=23.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|++++|.|++|+||||++..++..
T Consensus         3 i~~g~~i~l~G~~GsGKSTl~~~L~~~   29 (207)
T 2j41_A            3 NEKGLLIVLSGPSGVGKGTVRKRIFED   29 (207)
T ss_dssp             -CCCCEEEEECSTTSCHHHHHHHHHHC
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHh
Confidence            568999999999999999998877644

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.80  E-value=0.0054  Score=55.62  Aligned_cols=27  Identities=22%  Similarity=0.377  Sum_probs=22.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+++.|.|++|+||||++..++..
T Consensus         4 m~~g~ii~l~Gp~GsGKSTl~~~L~~~   30 (205)
T 3tr0_A            4 MNKANLFIISAPSGAGKTSLVRALVKA   30 (205)
T ss_dssp             -CCCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCCcEEEEECcCCCCHHHHHHHHHhh
Confidence            457999999999999999998877644

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=95.78  E-value=0.18  Score=46.51  Aligned_cols=42  Identities=17%  Similarity=0.101  Sum_probs=28.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHH------hcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINE------HAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~------~~g~~vl~~s~E  335 (539)
                      +..|.-+++.+++|+|||...+-.+.+...      ..+.+++++..-
T Consensus        59 ~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt  106 (236)
T 2pl3_A           59 ALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPT  106 (236)
T ss_dssp             HHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSS
T ss_pred             HhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCC
Confidence            455667889999999999865554444332      236778888743

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=95.78  E-value=0.0068  Score=60.05  Aligned_cols=42  Identities=19%  Similarity=0.154  Sum_probs=35.7

Q ss_pred             cccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          279 FGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       279 ~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ..+.||...||.++.+.+|+.+.|.|++|+||||++..++..
T Consensus        53 ~~~~tg~~ald~ll~i~~Gq~~gIiG~nGaGKTTLl~~I~g~   94 (347)
T 2obl_A           53 QPFILGVRAIDGLLTCGIGQRIGIFAGSGVGKSTLLGMICNG   94 (347)
T ss_dssp             SEECCSCHHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             eecCCCCEEEEeeeeecCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            345678899999966999999999999999999997766654

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=95.77  E-value=0.012  Score=58.15  Aligned_cols=48  Identities=29%  Similarity=0.349  Sum_probs=38.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      |+.+.- +.+|+++.|.|+||+|||||+..++..... .+..|.+++.+.
T Consensus        45 l~~i~~~~~~g~~v~i~G~~GaGKSTLl~~l~g~~~~-~~g~v~i~~~d~   93 (337)
T 2qm8_A           45 IDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTA-AGHKVAVLAVDP   93 (337)
T ss_dssp             HHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHHHH-TTCCEEEEEECG
T ss_pred             HHhCCcccCCCeEEEEECCCCCCHHHHHHHHHHhhhh-CCCEEEEEEEcC
Confidence            444444 889999999999999999999998866655 378899888664

>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A {Geobacillus}

Probab=95.74  E-value=0.013  Score=63.69  Aligned_cols=28  Identities=32%  Similarity=0.529  Sum_probs=24.0

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWI  314 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~  314 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+
T Consensus        33 ~L~~vsl~i~~Ge~~~liGpNGaGKSTLl   61 (670)
T 3ux8_A           33 NLKNIDVEIPRGKLVVLTGLSGSGKSSLA   61 (670)
T ss_dssp             TCCSEEEEEETTSEEEEECSTTSSHHHHH
T ss_pred             ceeccEEEECCCCEEEEECCCCCCHHHHh
Confidence            4555544 999999999999999999996

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=95.73  E-value=0.0066  Score=62.00  Aligned_cols=38  Identities=24%  Similarity=0.379  Sum_probs=34.7

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      ..++|+|++|+||||++..++..++.+ |.+|++++++.
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~l~~~-G~kVllv~~D~  137 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARYIQKR-GLKPALIAADT  137 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHHHHHH-HCCEEEECCSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEEeccc
Confidence            478899999999999999999999886 99999999884

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=95.72  E-value=0.0059  Score=55.69  Aligned_cols=27  Identities=22%  Similarity=0.343  Sum_probs=22.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+++.|.|++|+||||++.-++--
T Consensus        17 i~~Gei~~l~GpnGsGKSTLl~~l~gl   43 (207)
T 1znw_A           17 AAVGRVVVLSGPSAVGKSTVVRCLRER   43 (207)
T ss_dssp             --CCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            899999999999999999998877644

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=95.70  E-value=0.031  Score=59.61  Aligned_cols=49  Identities=14%  Similarity=0.059  Sum_probs=33.8

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHH---HhcCCeEEEEeCCCC-HHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNIN---EHAGWKFVLCSMENK-VREHARKL  345 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a---~~~g~~vl~~s~E~~-~~~~~~r~  345 (539)
                      ..+++|.|++|+|||+++.+++....   ......++|+++... ...+...+
T Consensus       147 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~~~~~~~~~l  199 (591)
T 1z6t_A          147 PGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKL  199 (591)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESCCHHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCCchHHHHHHH
Confidence            46999999999999999999886542   221235888887644 33344433

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=95.68  E-value=0.0092  Score=53.34  Aligned_cols=34  Identities=26%  Similarity=0.420  Sum_probs=28.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +++|.|+||+||||++..++..+-. .|.++.+++
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~~-~g~~~~~~~   36 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILDN-QGINNKIIN   36 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHT-TTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHh-cCceEEEEE
Confidence            6899999999999999999887654 377788884

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=95.66  E-value=0.0065  Score=55.49  Aligned_cols=26  Identities=23%  Similarity=0.346  Sum_probs=22.8

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .+|++++|.||+|+||||++..++..
T Consensus         6 ~~g~~i~l~GpsGsGKsTl~~~L~~~   31 (208)
T 3tau_A            6 ERGLLIVLSGPSGVGKGTVREAVFKD   31 (208)
T ss_dssp             CCCCEEEEECCTTSCHHHHHHHHHHS
T ss_pred             CCCcEEEEECcCCCCHHHHHHHHHhh
Confidence            57899999999999999998877644

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=95.65  E-value=0.0095  Score=60.98  Aligned_cols=42  Identities=26%  Similarity=0.242  Sum_probs=35.1

Q ss_pred             cccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          279 FGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       279 ~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ..+.+|...||.++.+.+|+.+.|.|++|+|||||+..++..
T Consensus       139 ~~~~tg~~vld~vl~i~~Gq~~~IvG~sGsGKSTLl~~Iag~  180 (438)
T 2dpy_A          139 HVLDTGVRAINALLTVGRGQRMGLFAGSGVGKSVLLGMMARY  180 (438)
T ss_dssp             SBCCCSCHHHHHHSCCBTTCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             eecCCCceEEeeeEEecCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            345567889999955999999999999999999997666654

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=95.65  E-value=0.01  Score=57.82  Aligned_cols=42  Identities=17%  Similarity=0.022  Sum_probs=32.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-CeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAG-WKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-~~vl~~s~E  335 (539)
                      ..+|+++.|.|++|+|||||+..++.-.....| ..+.|++.+
T Consensus        87 ~~~g~ivgI~G~sGsGKSTL~~~L~gll~~~~G~~~v~~v~qd  129 (312)
T 3aez_A           87 RPVPFIIGVAGSVAVGKSTTARVLQALLARWDHHPRVDLVTTD  129 (312)
T ss_dssp             SCCCEEEEEECCTTSCHHHHHHHHHHHHHTSTTCCCEEEEEGG
T ss_pred             CCCCEEEEEECCCCchHHHHHHHHHhhccccCCCCeEEEEecC
Confidence            678999999999999999999887755432223 468888776

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=95.64  E-value=0.0078  Score=54.53  Aligned_cols=28  Identities=25%  Similarity=0.304  Sum_probs=23.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      ..+|++++|.|++|+||||++..++...
T Consensus        26 ~~~g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           26 GEPTRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            5679999999999999999998887553

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=95.64  E-value=0.0073  Score=52.56  Aligned_cols=28  Identities=14%  Similarity=0.233  Sum_probs=25.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +.+|+++.|.|+.|+|||||+.-++...
T Consensus        30 i~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           30 TEKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             CSSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            8999999999999999999988877554

>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein, targeting factor, ATP-bindi TRC40, ARSA, nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus jannaschii} PDB: 3ug6_A*

Probab=95.63  E-value=0.012  Score=58.55  Aligned_cols=41  Identities=22%  Similarity=0.250  Sum_probs=37.2

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      ...+.+++|..|+||||++.++|..+|.. |.+|+.++++..
T Consensus        25 ~~~i~v~sgKGGvGKTTvA~~LA~~lA~~-G~rVLlvD~D~~   65 (349)
T 3ug7_A           25 GTKYIMFGGKGGVGKTTMSAATGVYLAEK-GLKVVIVSTDPA   65 (349)
T ss_dssp             SCEEEEEECSSSTTHHHHHHHHHHHHHHS-SCCEEEEECCTT
T ss_pred             CCEEEEEeCCCCccHHHHHHHHHHHHHHC-CCeEEEEeCCCC
Confidence            34688899999999999999999999986 999999999984

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=95.63  E-value=0.012  Score=58.29  Aligned_cols=50  Identities=16%  Similarity=0.183  Sum_probs=40.1

Q ss_pred             hhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHH-hcCCeEEEEeCCC
Q 009230          287 ALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINE-HAGWKFVLCSMEN  336 (539)
Q Consensus       287 ~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~-~~g~~vl~~s~E~  336 (539)
                      .|+.++.-..-.+++++|..|+||||++.++|..+|. +.|.+|+.++++.
T Consensus         8 ~L~~~l~~~~~~i~~~~gkGGvGKTt~a~~lA~~la~~~~g~~vllid~D~   58 (348)
T 3io3_A            8 TLESIVQHDSLKWIFVGGKGGVGKTTTSSSVAVQLALAQPNEQFLLISTDP   58 (348)
T ss_dssp             SSHHHHTCTTCSEEEEECSTTSSHHHHHHHHHHHHHHHCTTSCEEEEECCS
T ss_pred             hHHHHhcCCCcEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCeEEEEECCC
Confidence            3455554223369999999999999999999999993 3599999999993

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=95.61  E-value=0.0071  Score=58.59  Aligned_cols=35  Identities=29%  Similarity=0.344  Sum_probs=29.5

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .|+.+.- +++|+++.|.|++|+|||||+.-++.-.
T Consensus       115 vL~~vsl~i~~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          115 ALKLWLKGIPKKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             HHHHHHHTCTTCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             hhccceEEecCCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            4555544 9999999999999999999999887665

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=95.60  E-value=0.0069  Score=55.85  Aligned_cols=27  Identities=37%  Similarity=0.514  Sum_probs=22.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++|++++|.||+|+|||||+..++-.
T Consensus        13 ~~~G~ii~l~GpsGsGKSTLlk~L~g~   39 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSLIQALLKT   39 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHhcc
Confidence            889999999999999999998876643

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=95.59  E-value=0.01  Score=58.49  Aligned_cols=39  Identities=18%  Similarity=0.159  Sum_probs=35.8

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .+++++|..|+||||++.++|..++.. |.+|+.++++-.
T Consensus        17 ~i~~~sgkGGvGKTt~a~~lA~~la~~-g~~vllid~D~~   55 (334)
T 3iqw_A           17 RWIFVGGKGGVGKTTTSCSLAIQLAKV-RRSVLLLSTDPA   55 (334)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHTTS-SSCEEEEECCSS
T ss_pred             EEEEEeCCCCccHHHHHHHHHHHHHhC-CCcEEEEECCCC
Confidence            588999999999999999999999985 999999999943

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=95.58  E-value=0.014  Score=51.61  Aligned_cols=38  Identities=18%  Similarity=0.222  Sum_probs=32.0

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      .+++|+|++|+|||||+..++..+... |.+|..+..+.
T Consensus         7 ~~i~i~G~sGsGKTTl~~~l~~~l~~~-g~~v~~i~~~~   44 (174)
T 1np6_A            7 PLLAFAAWSGTGKTTLLKKLIPALCAR-GIRPGLIKHTH   44 (174)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHT-TCCEEEEEECC
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhcccc-CCceeEEeeCC
Confidence            578999999999999999998877654 88888887654

>3bfv_A CAPA1, CAPB2, membrane protein CAPA1, protein tyrosine kinase; chimerical protein, P-loop protein, capsule biogenesis/degradation; HET: ADP; 1.80A {Staphylococcus aureus} PDB: 2ved_A*

Probab=95.57  E-value=0.017  Score=55.19  Aligned_cols=40  Identities=20%  Similarity=0.355  Sum_probs=34.1

Q ss_pred             cEEEEE-cCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH
Q 009230          298 ELTIVT-GVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV  338 (539)
Q Consensus       298 ~l~~i~-G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~  338 (539)
                      .+++|+ +.+|+||||++.++|..+++. |.+|+++.+++..
T Consensus        83 kvI~vts~kgG~GKTt~a~nLA~~lA~~-G~rVLLID~D~~~  123 (271)
T 3bfv_A           83 QSIVITSEAPGAGKSTIAANLAVAYAQA-GYKTLIVDGDMRK  123 (271)
T ss_dssp             CEEEEECSSTTSSHHHHHHHHHHHHHHT-TCCEEEEECCSSS
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHhC-CCeEEEEeCCCCC
Confidence            466666 458999999999999999985 9999999999753

>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase, ATP binding site, hydro; HET: ADP; 2.15A {Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A* 1ii9_A*

Probab=95.57  E-value=0.014  Score=62.50  Aligned_cols=41  Identities=22%  Similarity=0.217  Sum_probs=37.4

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +..+++++|.+|+||||++.++|..++.. |.+|++++++..
T Consensus         7 ~~~i~~~sgkGGvGKTT~a~~lA~~lA~~-G~rVLlvd~D~~   47 (589)
T 1ihu_A            7 IPPYLFFTGKGGVGKTSISCATAIRLAEQ-GKRVLLVSTDPA   47 (589)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEECCTT
T ss_pred             CCEEEEEeCCCcCHHHHHHHHHHHHHHHC-CCcEEEEECCCC
Confidence            34689999999999999999999999986 999999999974

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=95.56  E-value=0.012  Score=63.73  Aligned_cols=53  Identities=26%  Similarity=0.428  Sum_probs=43.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLLE  347 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~~  347 (539)
                      +....+++|.||||+|||+.+.+++.++..+ |.+||.++.--. ...+..|+..
T Consensus       202 l~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~-~~~ILv~a~TN~AvD~i~erL~~  255 (646)
T 4b3f_X          202 LSQKELAIIHGPPGTGKTTTVVEIILQAVKQ-GLKVLCCAPSNIAVDNLVERLAL  255 (646)
T ss_dssp             HHCSSEEEEECCTTSCHHHHHHHHHHHHHHT-TCCEEEEESSHHHHHHHHHHHHH
T ss_pred             hcCCCceEEECCCCCCHHHHHHHHHHHHHhC-CCeEEEEcCchHHHHHHHHHHHh
Confidence            5555799999999999999999999998885 999999997744 4567777743

>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic hypermutat protein-DNA complex, DNA mispair, cancer; HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B* 2o8e_B* 2o8f_B*

Probab=95.52  E-value=0.0084  Score=67.86  Aligned_cols=45  Identities=16%  Similarity=0.236  Sum_probs=31.3

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                      ..++++|++|-..       .+.+.......+...|+.++++.++.+|+++|
T Consensus       866 a~~~sLlLLDEp~-------~Gtd~~dg~~~~~~il~~L~~~~g~~vl~~TH  910 (1022)
T 2o8b_B          866 ATAHSLVLVDELG-------RGTATFDGTAIANAVVKELAETIKCRTLFSTH  910 (1022)
T ss_dssp             CCTTCEEEEECTT-------TTSCHHHHHHHHHHHHHHHHHTSCCEEEEECC
T ss_pred             CCCCcEEEEECCC-------CCCChHHHHHHHHHHHHHHHhcCCCEEEEEeC
Confidence            3578999999322       23344443444667777787777999999999

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=95.49  E-value=0.012  Score=53.29  Aligned_cols=38  Identities=11%  Similarity=0.305  Sum_probs=32.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.+..+..|+||||++.++|..++.+ |.+|+++.++..
T Consensus         4 i~v~s~kgG~GKTt~a~~la~~la~~-g~~vlliD~D~~   41 (206)
T 4dzz_A            4 ISFLNPKGGSGKTTAVINIATALSRS-GYNIAVVDTDPQ   41 (206)
T ss_dssp             EEECCSSTTSSHHHHHHHHHHHHHHT-TCCEEEEECCTT
T ss_pred             EEEEeCCCCccHHHHHHHHHHHHHHC-CCeEEEEECCCC
Confidence            34555889999999999999999985 999999998843

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=95.49  E-value=0.011  Score=52.73  Aligned_cols=36  Identities=25%  Similarity=0.481  Sum_probs=27.7

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      |.+++|.|+||+||||++..++...-.+ |.+..+++
T Consensus         3 ~~~I~i~G~~GsGKsT~~~~L~~~l~~~-g~~~~~i~   38 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQLAMDNLRKE-GVNYKMVS   38 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHTT-TCCCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc-CcceEEEe
Confidence            5689999999999999999998776442 54344555

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=95.48  E-value=0.0076  Score=54.43  Aligned_cols=28  Identities=25%  Similarity=0.232  Sum_probs=23.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +++..-++|.||||+|||++++.++..+
T Consensus        55 iPkkn~ili~GPPGtGKTt~a~ala~~l   82 (212)
T 1tue_A           55 TPKKNCLVFCGPANTGKSYFGMSFIHFI   82 (212)
T ss_dssp             CTTCSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             CCcccEEEEECCCCCCHHHHHHHHHHHh
Confidence            5556678999999999999998887653

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=95.48  E-value=0.008  Score=54.65  Aligned_cols=28  Identities=18%  Similarity=0.259  Sum_probs=24.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      ..+|.+++|+|+||+||||++..++...
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             cccCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            6789999999999999999998887653

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}

Probab=95.46  E-value=0.017  Score=56.04  Aligned_cols=40  Identities=23%  Similarity=0.384  Sum_probs=34.1

Q ss_pred             CcEEEEEc-CCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          297 GELTIVTG-VPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       297 G~l~~i~G-~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      ..+++|++ .+|+||||++.++|..++.. |.+|+++.+++.
T Consensus       104 ~kvI~vts~kgG~GKTtva~nLA~~lA~~-G~rVLLID~D~r  144 (299)
T 3cio_A          104 NNILMITGATPDSGKTFVSSTLAAVIAQS-DQKVLFIDADLR  144 (299)
T ss_dssp             CCEEEEEESSSSSCHHHHHHHHHHHHHHT-TCCEEEEECCTT
T ss_pred             CeEEEEECCCCCCChHHHHHHHHHHHHhC-CCcEEEEECCCC
Confidence            34666665 58999999999999999985 999999999984

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=95.43  E-value=0.027  Score=57.86  Aligned_cols=67  Identities=18%  Similarity=0.201  Sum_probs=53.9

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-------cCCeEEEEeCCCCHHHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEH-------AGWKFVLCSMENKVREHA  342 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-------~g~~vl~~s~E~~~~~~~  342 (539)
                      .....+.||+..+|-++-+.+|+=..|.|++|+|||++++.+..+.+..       ++..++|....+..+++.
T Consensus       141 ~v~epl~TGiraID~l~PigrGQR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~  214 (510)
T 2ck3_A          141 SVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVA  214 (510)
T ss_dssp             CCCSBCCCSCHHHHHHSCCBTTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHH
T ss_pred             ccCccccccceeeccccccccCCEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHH
Confidence            3445688999999999889999999999999999999988766666652       355678888887777653

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=95.41  E-value=0.016  Score=57.65  Aligned_cols=42  Identities=29%  Similarity=0.403  Sum_probs=34.1

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR  339 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~  339 (539)
                      .-.++|+|.||+|||||+.+++..++.. |.+|+.++.+....
T Consensus        79 ~~~I~i~G~~G~GKSTl~~~L~~~l~~~-g~kV~vi~~Dp~~~  120 (355)
T 3p32_A           79 AHRVGITGVPGVGKSTAIEALGMHLIER-GHRVAVLAVDPSST  120 (355)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTT-TCCEEEEEEC----
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHhC-CCceEEEecCCCCC
Confidence            3478899999999999999999988775 99999999885443

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=95.40  E-value=0.011  Score=52.06  Aligned_cols=26  Identities=23%  Similarity=0.311  Sum_probs=22.7

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .+|++++|.|++|+||||++..++..
T Consensus         6 ~~g~~i~l~G~~GsGKSTl~~~l~~~   31 (175)
T 1knq_A            6 HDHHIYVLMGVSGSGKSAVASEVAHQ   31 (175)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHh
Confidence            56899999999999999998887654

>1g3q_A MIND ATPase, cell division inhibitor; alpha-beta-alpha layered, protein-ADP complex, cell cycle, hydrolase; HET: ADP; 2.00A {Pyrococcus furiosus} SCOP: c.37.1.10 PDB: 1g3r_A* 1ion_A*

Probab=95.38  E-value=0.017  Score=53.68  Aligned_cols=38  Identities=21%  Similarity=0.351  Sum_probs=33.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.+.++..|+||||++.++|..++.+ |.+|+++.++..
T Consensus         5 i~v~s~kgGvGKTt~a~~LA~~la~~-g~~VlliD~D~~   42 (237)
T 1g3q_A            5 ISIVSGKGGTGKTTVTANLSVALGDR-GRKVLAVDGDLT   42 (237)
T ss_dssp             EEEECSSTTSSHHHHHHHHHHHHHHT-TCCEEEEECCTT
T ss_pred             EEEecCCCCCCHHHHHHHHHHHHHhc-CCeEEEEeCCCC
Confidence            45556789999999999999999986 999999999863

>1hyq_A MIND, cell division inhibitor (MIND-1); MINC, FTSZ, bacterial cell division, cell cycle; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.10

Probab=95.37  E-value=0.018  Score=54.43  Aligned_cols=38  Identities=16%  Similarity=0.299  Sum_probs=33.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.+.++..|+||||++.++|..++.. |.+|+++.++..
T Consensus         5 I~v~s~kgGvGKTt~a~~LA~~la~~-g~~VlliD~D~~   42 (263)
T 1hyq_A            5 ITVASGKGGTGKTTITANLGVALAQL-GHDVTIVDADIT   42 (263)
T ss_dssp             EEEEESSSCSCHHHHHHHHHHHHHHT-TCCEEEEECCCS
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHhC-CCcEEEEECCCC
Confidence            55667899999999999999999986 999999999863

>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; 3.01A {Schizosaccharomyces pombe}

Probab=95.35  E-value=0.015  Score=57.25  Aligned_cols=39  Identities=18%  Similarity=0.162  Sum_probs=36.3

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .+.+++|..|+||||++.++|..++.. |.+|++++++..
T Consensus        20 ~i~v~sgkGGvGKTTva~~LA~~lA~~-G~rVllvD~D~~   58 (329)
T 2woo_A           20 KWIFVGGKGGVGKTTTSCSLAIQMSKV-RSSVLLISTDPA   58 (329)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHHHHTS-SSCEEEEECCTT
T ss_pred             EEEEEeCCCCCcHHHHHHHHHHHHHHC-CCeEEEEECCCC
Confidence            588899999999999999999999985 999999999976

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=95.35  E-value=0.012  Score=52.07  Aligned_cols=37  Identities=27%  Similarity=0.389  Sum_probs=28.6

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHh------cCCeEEEEe
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEH------AGWKFVLCS  333 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~------~g~~vl~~s  333 (539)
                      +..++|.|+||+|||+++..++..+...      .+.++++++
T Consensus        43 ~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~~~   85 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLD   85 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEEEC
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEEEe
Confidence            3467999999999999999998876542      156676664

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=95.31  E-value=0.011  Score=52.06  Aligned_cols=34  Identities=18%  Similarity=0.236  Sum_probs=25.7

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +.+++|+|+||+||||++..++..    .+.+.+.++.
T Consensus         3 ~~~i~l~G~~GsGKST~a~~La~~----l~~~~~~~~~   36 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCLQSV----LPEPWLAFGV   36 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH----SSSCEEEEEH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh----cCCCeEEecc
Confidence            568999999999999998877654    3555554443

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.30  E-value=0.01  Score=55.74  Aligned_cols=35  Identities=26%  Similarity=0.257  Sum_probs=24.1

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .|+.+.- +.+|+++.|.|++|+||||++..++...
T Consensus        14 ~l~~isl~i~~g~iigI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           14 GTENLYFQSMRPFLIGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             ---------CCSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eecceeccCCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            4555544 8999999999999999999998776543

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=95.29  E-value=0.017  Score=56.30  Aligned_cols=42  Identities=17%  Similarity=0.136  Sum_probs=36.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      +..-.++.|+|--|+||||.+.+++..+|.. |++|+.+.++-
T Consensus        45 i~~aKVIAIaGKGGVGKTTtavNLA~aLA~~-GkkVllID~Dp   86 (314)
T 3fwy_A           45 ITGAKVFAVYGKGGIGKSTTSSNLSAAFSIL-GKRVLQIGCDP   86 (314)
T ss_dssp             --CCEEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEEESS
T ss_pred             CCCceEEEEECCCccCHHHHHHHHHHHHHHC-CCeEEEEecCC
Confidence            4445799999999999999999999999996 99999999983

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=95.26  E-value=0.02  Score=52.12  Aligned_cols=38  Identities=26%  Similarity=0.350  Sum_probs=31.1

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      .+|-+++|.|++|+||||++..++..+-.. +..|..+.
T Consensus         7 ~~~~~I~l~G~~GsGKsT~~~~L~~~l~~~-~~~v~~~~   44 (215)
T 1nn5_A            7 RRGALIVLEGVDRAGKSTQSRKLVEALCAA-GHRAELLR   44 (215)
T ss_dssp             CCCCEEEEEESTTSSHHHHHHHHHHHHHHT-TCCEEEEE
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHHc-CCcEEEee
Confidence            357799999999999999999999887654 78875443

>2ph1_A Nucleotide-binding protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; 2.70A {Archaeoglobus fulgidus dsm 4304} PDB: 3kb1_A*

Probab=95.24  E-value=0.019  Score=54.35  Aligned_cols=39  Identities=18%  Similarity=0.198  Sum_probs=34.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV  338 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~  338 (539)
                      +.+..+..|+||||++.++|..++.. |.+|+++.++...
T Consensus        21 I~v~s~kGGvGKTT~a~nLA~~la~~-G~~VlliD~D~~~   59 (262)
T 2ph1_A           21 IAVMSGKGGVGKSTVTALLAVHYARQ-GKKVGILDADFLG   59 (262)
T ss_dssp             EEEECSSSCTTHHHHHHHHHHHHHHT-TCCEEEEECCSSC
T ss_pred             EEEEcCCCCCCHHHHHHHHHHHHHHC-CCeEEEEeCCCCC
Confidence            55667889999999999999999986 9999999988654

>3q9l_A Septum site-determining protein MIND; ATPase, bacterial cell division inhibitor, MINC, MINE, cell hydrolase; HET: ATP; 2.34A {Escherichia coli} PDB: 3r9i_A* 3r9j_A*

Probab=95.23  E-value=0.019  Score=54.04  Aligned_cols=37  Identities=19%  Similarity=0.294  Sum_probs=32.9

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      +.+.++..|+||||++.++|..++.+ |.+|+++.++.
T Consensus         5 i~v~s~kgGvGKTt~a~~LA~~la~~-g~~VlliD~D~   41 (260)
T 3q9l_A            5 IVVTSGKGGVGKTTSSAAIATGLAQK-GKKTVVIDFAI   41 (260)
T ss_dssp             EEEECSSTTSSHHHHHHHHHHHHHHT-TCCEEEEECCC
T ss_pred             EEEECCCCCCcHHHHHHHHHHHHHhC-CCcEEEEECCC
Confidence            45557889999999999999999985 99999999986

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=95.21  E-value=0.013  Score=52.34  Aligned_cols=26  Identities=38%  Similarity=0.497  Sum_probs=22.5

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++.+++|.|+||+||||++..++..
T Consensus         3 ~~~~~I~l~G~~GsGKST~~~~L~~~   28 (193)
T 2rhm_A            3 QTPALIIVTGHPATGKTTLSQALATG   28 (193)
T ss_dssp             SCCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45679999999999999999888755

>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=95.21  E-value=0.13  Score=52.77  Aligned_cols=56  Identities=18%  Similarity=0.201  Sum_probs=41.3

Q ss_pred             cCCCcEEEEEcCCCCChhH-HHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          294 VLPGELTIVTGVPNSGKSE-WIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~-~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      +..++++++.|+||+|||. +++.++.++... |.+++|++   |-..++..+.....|.+
T Consensus        16 l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~-~~~~lvl~---Ptr~La~Q~~~~l~g~~   72 (451)
T 2jlq_A           16 FRKKRLTIMDLHPGAGKTKRILPSIVREALLR-RLRTLILA---PTRVVAAEMEEALRGLP   72 (451)
T ss_dssp             GSTTCEEEECCCTTSSCCTTHHHHHHHHHHHT-TCCEEEEE---SSHHHHHHHHHHTTTSC
T ss_pred             HhcCCeEEEECCCCCCHhhHHHHHHHHHHHhc-CCcEEEEC---CCHHHHHHHHHHhcCce
Confidence            6667899999999999999 688877776664 88999998   33456655555444443

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=95.20  E-value=0.019  Score=67.03  Aligned_cols=31  Identities=29%  Similarity=0.327  Sum_probs=25.4

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      |+.+.- +++|+.+.|.|++|+||||++.-++
T Consensus      1049 l~~vsl~i~~Ge~v~ivG~sGsGKSTl~~~l~ 1080 (1284)
T 3g5u_A         1049 LQGLSLEVKKGQTLALVGSSGCGKSTVVQLLE 1080 (1284)
T ss_dssp             BSSCCEEECSSSEEEEECSSSTTHHHHHHHHT
T ss_pred             ecceeEEEcCCCEEEEECCCCCCHHHHHHHHh
Confidence            444433 9999999999999999999977655

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=95.20  E-value=0.025  Score=55.87  Aligned_cols=45  Identities=22%  Similarity=0.260  Sum_probs=37.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR  339 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~  339 (539)
                      ..+|..+.|.|+||+||||++..++...... |.+|.+++.+....
T Consensus        53 ~~~~~~i~i~G~~g~GKSTl~~~l~~~~~~~-~~~v~v~~~d~~~~   97 (341)
T 2p67_A           53 CGNTLRLGVTGTPGAGKSTFLEAFGMLLIRE-GLKVAVIAVDPSSP   97 (341)
T ss_dssp             CSCSEEEEEEECTTSCHHHHHHHHHHHHHHT-TCCEEEEEECCC--
T ss_pred             cCCCEEEEEEcCCCCCHHHHHHHHHHHHHhc-CCeEEEEeecCCcC
Confidence            6778899999999999999999999887764 89999999886543

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=95.19  E-value=0.0096  Score=55.63  Aligned_cols=32  Identities=34%  Similarity=0.487  Sum_probs=26.4

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++
T Consensus        20 vl~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~l~   52 (237)
T 2cbz_A           20 TLNGITFSIPEGALVAVVGQVGCGKSSLLSALL   52 (237)
T ss_dssp             SEEEEEEEECTTCEEEEECSTTSSHHHHHHHHT
T ss_pred             eeeeeEEEECCCCEEEEECCCCCCHHHHHHHHh
Confidence            3555444 9999999999999999999987665

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.18  E-value=0.0087  Score=54.17  Aligned_cols=27  Identities=19%  Similarity=0.276  Sum_probs=21.3

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .+|++++|.|++|+||||++..++...
T Consensus         2 ~~g~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            2 AGPRPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             ---CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            478999999999999999998877543

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=95.17  E-value=0.023  Score=56.36  Aligned_cols=42  Identities=29%  Similarity=0.428  Sum_probs=31.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      ..+|++++|+|++|+||||++..++..+....+..++  +.|.+
T Consensus       120 ~~~~g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~--t~ed~  161 (356)
T 3jvv_A          120 DVPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHIL--TIEDP  161 (356)
T ss_dssp             HCSSEEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEE--EEESS
T ss_pred             hCCCCEEEEECCCCCCHHHHHHHHHhcccCCCCcEEE--EccCc
Confidence            5678899999999999999999887766553355554  44544

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=95.16  E-value=0.17  Score=52.41  Aligned_cols=38  Identities=26%  Similarity=0.316  Sum_probs=28.9

Q ss_pred             ccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          293 NVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       293 ~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +..+..-++|.|+||+|||+++..++..    .+.+++++++
T Consensus       234 g~~~~~~vLL~GppGtGKT~lAraia~~----~~~~fv~vn~  271 (489)
T 3hu3_A          234 GVKPPRGILLYGPPGTGKTLIARAVANE----TGAFFFLING  271 (489)
T ss_dssp             TCCCCCEEEEECSTTSSHHHHHHHHHHH----CSSEEEEEEH
T ss_pred             CCCCCCcEEEECcCCCCHHHHHHHHHHH----hCCCEEEEEc
Confidence            4444456889999999999998877543    4788888773

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=95.13  E-value=0.014  Score=52.66  Aligned_cols=27  Identities=19%  Similarity=0.316  Sum_probs=23.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .-+|++++|.||+|+||||++..++..
T Consensus        16 ~~~g~~ivl~GPSGaGKsTL~~~L~~~   42 (197)
T 3ney_A           16 FQGRKTLVLIGASGVGRSHIKNALLSQ   42 (197)
T ss_dssp             CCSCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCCEEEEECcCCCCHHHHHHHHHhh
Confidence            346899999999999999998887754

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=95.12  E-value=0.02  Score=55.01  Aligned_cols=38  Identities=24%  Similarity=0.317  Sum_probs=33.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .+.|+|..|+||||++.++|..++.. |.+|+.+.++..
T Consensus         4 vIavs~KGGvGKTT~a~nLA~~La~~-G~rVlliD~D~q   41 (289)
T 2afh_E            4 QCAIYGKGGIGKSTTTQNLVAALAEM-GKKVMIVGCDPK   41 (289)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHT-TCCEEEEEECSS
T ss_pred             EEEEeCCCcCcHHHHHHHHHHHHHHC-CCeEEEEecCCC
Confidence            44557999999999999999999986 999999999854

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=95.11  E-value=0.06  Score=54.55  Aligned_cols=115  Identities=16%  Similarity=0.121  Sum_probs=65.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHHHHh-hCCCccccccCCCCCCCCHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLLEKH-IKKPFFEANYGGSAERMTVEEF  371 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~~~~-~~~~~~~i~~~~~~~~l~~~~~  371 (539)
                      +..|.-+++.++||+|||.+.+-.+..... .+..++|+..--. ..++..++.... .++....+.     +..+..+.
T Consensus        33 i~~~~~~lv~apTGsGKT~~~l~~~~~~~~-~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~-----g~~~~~~~  106 (414)
T 3oiy_A           33 IVQGKSFTMVAPTGVGKTTFGMMTALWLAR-KGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFY-----SSMKKEEK  106 (414)
T ss_dssp             HTTTCCEECCSCSSSSHHHHHHHHHHHHHT-TTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECC-----TTSCHHHH
T ss_pred             HhcCCCEEEEeCCCCCHHHHHHHHHHHHhc-CCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEE-----CCCChhhH
Confidence            445667889999999999966666566554 4788999886533 344544543321 233332222     23455444


Q ss_pred             HHHHHHhhc--cceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcccccc
Q 009230          372 EQGKAWLSN--TFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNEL  422 (539)
Q Consensus       372 ~~~~~~l~~--~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l  422 (539)
                      ......+..  ..++|       .|++.+...+.. .....+++||||-...+
T Consensus       107 ~~~~~~l~~~~~~Iiv-------~Tp~~l~~~l~~-~~~~~~~~iViDEaH~~  151 (414)
T 3oiy_A          107 EKFEKSFEEDDYHILV-------FSTQFVSKNREK-LSQKRFDFVFVDDVDAV  151 (414)
T ss_dssp             HHHHHHHHHTCCSEEE-------EEHHHHHHCHHH-HTTCCCSEEEESCHHHH
T ss_pred             HHHHHHhhcCCCCEEE-------ECHHHHHHHHHH-hccccccEEEEeChHhh
Confidence            333334433  22333       145555554443 33457999999966544

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=95.11  E-value=0.0077  Score=55.91  Aligned_cols=25  Identities=16%  Similarity=0.307  Sum_probs=19.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      +.+|+++.|.|++|+||||++..++
T Consensus        24 v~~G~ii~l~Gp~GsGKSTl~~~L~   48 (231)
T 3lnc_A           24 KSVGVILVLSSPSGCGKTTVANKLL   48 (231)
T ss_dssp             EECCCEEEEECSCC----CHHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHH
Confidence            7899999999999999999988776

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=95.08  E-value=0.14  Score=53.44  Aligned_cols=39  Identities=18%  Similarity=0.239  Sum_probs=32.3

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      ..+++++|.||+||||++..++..+-.. +..+..|+.+.
T Consensus        35 ~~lIvlvGlpGSGKSTia~~La~~L~~~-~~d~~v~s~D~   73 (520)
T 2axn_A           35 PTVIVMVGLPARGKTYISKKLTRYLNWI-GVPTKVFNVGE   73 (520)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEEHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhc-CCCeEEecccH
Confidence            3689999999999999999999877654 77888887553

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*

Probab=95.08  E-value=0.044  Score=60.34  Aligned_cols=27  Identities=22%  Similarity=0.260  Sum_probs=24.3

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .+|++++|.|++|+|||||+.+++.-.
T Consensus       605 ~~g~i~~ItGpNGsGKSTlLr~iagl~  631 (800)
T 1wb9_A          605 PQRRMLIITGPNMGGKSTYMRQTALIA  631 (800)
T ss_dssp             SSSCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCChHHHHHHHHHHH
Confidence            478999999999999999999998754

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=95.08  E-value=0.018  Score=54.63  Aligned_cols=38  Identities=18%  Similarity=0.246  Sum_probs=33.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      ++.|+|..|+||||++.++|..++.. |.+|+++.++..
T Consensus         3 vI~vs~KGGvGKTT~a~nLA~~la~~-G~~VlliD~D~q   40 (269)
T 1cp2_A            3 QVAIYGKGGIGKSTTTQNLTSGLHAM-GKTIMVVGCDPK   40 (269)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTT-TCCEEEEEECTT
T ss_pred             EEEEecCCCCcHHHHHHHHHHHHHHC-CCcEEEEcCCCC
Confidence            34557999999999999999999975 999999998853

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.08  E-value=0.047  Score=53.96  Aligned_cols=23  Identities=26%  Similarity=0.281  Sum_probs=20.3

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      ++|.|++|+||||++..++..+.
T Consensus        39 ~ll~Gp~G~GKTtl~~~la~~l~   61 (354)
T 1sxj_E           39 LLLYGPNGTGKKTRCMALLESIF   61 (354)
T ss_dssp             EEEECSTTSSHHHHHHTHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Confidence            88999999999999998887653

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}

Probab=95.07  E-value=0.021  Score=57.22  Aligned_cols=36  Identities=17%  Similarity=0.121  Sum_probs=32.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      +.+.+|..|+||||++.++|..++.. |.+|+++.++
T Consensus       146 Iav~s~KGGvGKTT~a~nLA~~La~~-g~rVlliD~D  181 (373)
T 3fkq_A          146 VIFTSPCGGVGTSTVAAACAIAHANM-GKKVFYLNIE  181 (373)
T ss_dssp             EEEECSSTTSSHHHHHHHHHHHHHHH-TCCEEEEECC
T ss_pred             EEEECCCCCChHHHHHHHHHHHHHhC-CCCEEEEECC
Confidence            44455799999999999999999996 9999999999

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=95.07  E-value=0.01  Score=55.57  Aligned_cols=36  Identities=19%  Similarity=0.105  Sum_probs=32.7

Q ss_pred             EEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          301 IVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       301 ~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .|+|..|+||||++.++|..++.. |.+|+.+.++..
T Consensus         4 ~vs~kGGvGKTt~a~~LA~~la~~-g~~VlliD~D~~   39 (254)
T 3kjh_A            4 AVAGKGGVGKTTVAAGLIKIMASD-YDKIYAVDGDPD   39 (254)
T ss_dssp             EEECSSSHHHHHHHHHHHHHHTTT-CSCEEEEEECTT
T ss_pred             EEecCCCCCHHHHHHHHHHHHHHC-CCeEEEEeCCCC
Confidence            448999999999999999999986 999999999874

>3la6_A Tyrosine-protein kinase WZC; P-loop protein, nucleotide binding domain, walker A motif, B protein kinase, oligomerization; HET: ADP; 3.20A {Escherichia coli}

Probab=95.07  E-value=0.022  Score=54.75  Aligned_cols=39  Identities=15%  Similarity=0.164  Sum_probs=33.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV  338 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~  338 (539)
                      +.+.++.+|+||||++.++|..+|.. |.+|+++.+++..
T Consensus        95 I~vts~kgG~GKTtva~nLA~~lA~~-G~rVLLID~D~~~  133 (286)
T 3la6_A           95 LMMTGVSPSIGMTFVCANLAAVISQT-NKRVLLIDCDMRK  133 (286)
T ss_dssp             EEEEESSSSSSHHHHHHHHHHHHHTT-TCCEEEEECCTTT
T ss_pred             EEEECCCCCCcHHHHHHHHHHHHHhC-CCCEEEEeccCCC
Confidence            55555679999999999999999985 9999999999863

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=95.06  E-value=0.017  Score=50.46  Aligned_cols=27  Identities=41%  Similarity=0.742  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      +++|.|+||+||||++..+     ...|.+++
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-----~~~g~~~i   29 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-----KERGAKVI   29 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-----HHTTCEEE
T ss_pred             EEEEECCCCCCHHHHHHHH-----HHCCCcEE
Confidence            7899999999999998877     22477754

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=95.06  E-value=0.15  Score=53.88  Aligned_cols=52  Identities=13%  Similarity=0.008  Sum_probs=36.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHH---HHHHhcCCeEEEEeCCCC----HHHHHHHHHHHh
Q 009230          298 ELTIVTGVPNSGKSEWIDALIC---NINEHAGWKFVLCSMENK----VREHARKLLEKH  349 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~---~~a~~~g~~vl~~s~E~~----~~~~~~r~~~~~  349 (539)
                      .++.|.|.+|+||||+|.+++.   .....+-..++|++....    ...+...++...
T Consensus       153 ~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~l  211 (549)
T 2a5y_B          153 FFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLML  211 (549)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHHH
Confidence            6899999999999999998885   122222356788877653    566666665543

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=95.06  E-value=0.012  Score=53.30  Aligned_cols=38  Identities=26%  Similarity=0.488  Sum_probs=27.2

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHH----hcC-CeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINE----HAG-WKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~----~~g-~~vl~~s~E  335 (539)
                      -+++++|+||+|||+++..++...+.    ..| .++.|..++
T Consensus         6 mi~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~~   48 (199)
T 2r2a_A            6 EICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIK   48 (199)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECCT
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecCC
Confidence            37899999999999999887766541    236 555555443

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=95.05  E-value=0.014  Score=51.97  Aligned_cols=25  Identities=28%  Similarity=0.404  Sum_probs=22.0

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +|.+++|.|+||+||||++..++..
T Consensus         3 ~g~~I~l~G~~GsGKST~~~~La~~   27 (186)
T 3cm0_A            3 VGQAVIFLGPPGAGKGTQASRLAQE   27 (186)
T ss_dssp             CEEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            5778999999999999998888754

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=95.02  E-value=0.013  Score=53.19  Aligned_cols=37  Identities=22%  Similarity=0.175  Sum_probs=28.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      +.+|.++.|+|++|+||||++..++...     ..+.+++.+
T Consensus        18 ~~~~~~i~i~G~~GsGKSTl~~~L~~~~-----~~~~~i~~D   54 (207)
T 2qt1_A           18 GSKTFIIGISGVTNSGKTTLAKNLQKHL-----PNCSVISQD   54 (207)
T ss_dssp             SCCCEEEEEEESTTSSHHHHHHHHHTTS-----TTEEEEEGG
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHhc-----CCcEEEeCC
Confidence            7889999999999999999987665321     046666655

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=95.00  E-value=0.011  Score=55.36  Aligned_cols=32  Identities=22%  Similarity=0.305  Sum_probs=26.4

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        18 l~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~l~G   50 (243)
T 1mv5_A           18 LRDISFEAQPNSIIAFAGPSGGGKSTIFSLLER   50 (243)
T ss_dssp             EEEEEEEECTTEEEEEECCTTSSHHHHHHHHTT
T ss_pred             EEEeEEEEcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            444444 99999999999999999999876653

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=94.98  E-value=0.012  Score=52.66  Aligned_cols=23  Identities=35%  Similarity=0.396  Sum_probs=20.8

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |++++|.|++|+||||++..++.
T Consensus         2 g~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            2 KKLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHhc
Confidence            67899999999999999998864

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=94.97  E-value=0.021  Score=53.25  Aligned_cols=39  Identities=8%  Similarity=0.103  Sum_probs=33.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.+..+..|+||||++.++|..++...|.+|+++.++..
T Consensus         7 I~v~s~kGGvGKTt~a~~LA~~la~~~g~~VlliD~D~~   45 (245)
T 3ea0_A            7 FGFVSAKGGDGGSCIAANFAFALSQEPDIHVLAVDISLP   45 (245)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHTTSTTCCEEEEECCTT
T ss_pred             EEEECCCCCcchHHHHHHHHHHHHhCcCCCEEEEECCCC
Confidence            445567899999999999999998744999999999865

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=94.97  E-value=0.016  Score=50.73  Aligned_cols=22  Identities=27%  Similarity=0.120  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCChhHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +++|.|+||+||||++..++..
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~   24 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKE   24 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            7899999999999998887654

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=94.97  E-value=0.029  Score=56.17  Aligned_cols=39  Identities=31%  Similarity=0.356  Sum_probs=31.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEE
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLC  332 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~  332 (539)
                      +.+|++++|.|++|+||||++..++..+.......++++
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll~~l~~~~~~~~~g~I~~~  171 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITI  171 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHHHHHHHHHHHHSCCEEEEE
T ss_pred             hcCCCEEEEECCCCCCHHHHHHHHHhhcCcCCCcEEEEe
Confidence            788999999999999999999998876654313566554

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.96  E-value=0.0086  Score=54.72  Aligned_cols=27  Identities=19%  Similarity=0.134  Sum_probs=24.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+|+++.|.|++|+|||||+.-++--
T Consensus        19 i~~Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           19 IDTNTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             HHHCSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             ccCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            788999999999999999999888755

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=94.94  E-value=0.011  Score=54.82  Aligned_cols=32  Identities=22%  Similarity=0.438  Sum_probs=26.5

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++
T Consensus        23 il~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~l~   55 (229)
T 2pze_A           23 VLKDINFKIERGQLLAVAGSTGAGKTSLLMMIM   55 (229)
T ss_dssp             SEEEEEEEEETTCEEEEECCTTSSHHHHHHHHT
T ss_pred             eeeeeEEEEcCCCEEEEECCCCCCHHHHHHHHh
Confidence            3555544 9999999999999999999987665

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=94.93  E-value=0.011  Score=56.29  Aligned_cols=33  Identities=36%  Similarity=0.422  Sum_probs=26.8

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        35 vl~~vsl~i~~Ge~~~l~G~NGsGKSTLlk~l~G   68 (267)
T 2zu0_C           35 ILRGLSLDVHPGEVHAIMGPNGSGKSTLSATLAG   68 (267)
T ss_dssp             EEEEEEEEECTTCEEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEeeEEEEcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            3454444 99999999999999999999876653

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=94.93  E-value=0.028  Score=51.04  Aligned_cols=39  Identities=18%  Similarity=0.218  Sum_probs=31.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      ..+|-+++|.|++|+||||++..++..+-.. +..+..+.
T Consensus         7 ~~~~~~I~l~G~~GsGKST~~~~L~~~l~~~-~~~~~~~~   45 (212)
T 2wwf_A            7 KKKGKFIVFEGLDRSGKSTQSKLLVEYLKNN-NVEVKHLY   45 (212)
T ss_dssp             CBCSCEEEEEESTTSSHHHHHHHHHHHHHHT-TCCEEEEE
T ss_pred             hhcCCEEEEEcCCCCCHHHHHHHHHHHHHHc-CCcEEEEe
Confidence            3457799999999999999999999877654 77775444

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=94.92  E-value=0.027  Score=50.26  Aligned_cols=34  Identities=24%  Similarity=0.360  Sum_probs=27.7

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +++|.|++|+||||++..++..+... |.+++...
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~~-g~~~i~~d   35 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQK-GYFVSLYR   35 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHT-TCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-CCeEEEEe
Confidence            67899999999999999998876543 88877553

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=94.91  E-value=0.019  Score=55.84  Aligned_cols=41  Identities=15%  Similarity=0.099  Sum_probs=31.2

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHH-hcCCeEEEEeCC
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINE-HAGWKFVLCSME  335 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~-~~g~~vl~~s~E  335 (539)
                      .+|+++.|.|++|+|||||+..++...-. ..+..+.+++.+
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~l~~~~~~G~i~vi~~d  119 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTD  119 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHhhCCCCCeEEEEecC
Confidence            78899999999999999999877754420 124567777665

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=94.91  E-value=0.014  Score=53.18  Aligned_cols=37  Identities=24%  Similarity=0.269  Sum_probs=26.9

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .+|+++.|.|++|+||||++..++...    +..+.|++.+
T Consensus         4 ~~~~~i~i~G~~GsGKSTl~~~l~~~~----~~~i~~v~~d   40 (211)
T 3asz_A            4 PKPFVIGIAGGTASGKTTLAQALARTL----GERVALLPMD   40 (211)
T ss_dssp             -CCEEEEEEESTTSSHHHHHHHHHHHH----GGGEEEEEGG
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHh----CCCeEEEecC
Confidence            578999999999999999988776542    2135666543

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=94.91  E-value=0.01  Score=55.88  Aligned_cols=32  Identities=28%  Similarity=0.283  Sum_probs=26.3

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        19 l~~vsl~i~~Ge~~~l~G~nGsGKSTLlk~l~G   51 (250)
T 2d2e_A           19 LKGVNLVVPKGEVHALMGPNGAGKSTLGKILAG   51 (250)
T ss_dssp             EEEEEEEEETTCEEEEECSTTSSHHHHHHHHHT
T ss_pred             EeceEEEEcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            444433 99999999999999999999876653

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=94.91  E-value=0.13  Score=52.58  Aligned_cols=54  Identities=22%  Similarity=0.296  Sum_probs=36.1

Q ss_pred             CCcEEEEEcCCCCChhHHH-HHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          296 PGELTIVTGVPNSGKSEWI-DALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~-~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      +|+.+++.|++|+|||..+ +.++..+.. .|.+++|+..-   ..++..+.....+.+
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~-~g~~~lvl~Pt---~~La~Q~~~~~~~~~   55 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK-KRLRTVILAPT---RVVASEMYEALRGEP   55 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH-TTCCEEEEESS---HHHHHHHHHHTTTSC
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh-CCCCEEEECcH---HHHHHHHHHHhCCCe
Confidence            3678999999999999875 555545555 48899999843   445555444433443

>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=94.90  E-value=0.11  Score=56.99  Aligned_cols=139  Identities=15%  Similarity=0.149  Sum_probs=76.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC-CCHHHHHHHHHH-HhhCCCccccccCCCCCCCCHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME-NKVREHARKLLE-KHIKKPFFEANYGGSAERMTVEEF  371 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E-~~~~~~~~r~~~-~~~~~~~~~i~~~~~~~~l~~~~~  371 (539)
                      +..|+-++++|+||+|||+.+...+.+.....|.+++|+..- .-..++..++.. ...|+....+. |    ..+.++ 
T Consensus        36 ~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~~l~i~P~raLa~q~~~~~~~l~~~g~~v~~~~-G----~~~~~~-  109 (720)
T 2zj8_A           36 ILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEFQDWEKIGLRVAMAT-G----DYDSKD-  109 (720)
T ss_dssp             GGGTCEEEEECCGGGCHHHHHHHHHHHHHHHHCSEEEEECSSGGGHHHHHHHTGGGGGGTCCEEEEC-S----CSSCCC-
T ss_pred             hcCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCCEEEEEcCcHHHHHHHHHHHHHHHhcCCEEEEec-C----CCCccc-
Confidence            455889999999999999988665555444348899999865 335566666521 11244333222 1    111100 


Q ss_pred             HHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHH-HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHh
Q 009230          372 EQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVL-RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHH  450 (539)
Q Consensus       372 ~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~-~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~  450 (539)
                          .++....+++       .|++.+...++.-.. -.++++||||-...+..     ..+...+..++..++.     
T Consensus       110 ----~~~~~~~Iiv-------~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~-----~~r~~~~~~ll~~l~~-----  168 (720)
T 2zj8_A          110 ----EWLGKYDIII-------ATAEKFDSLLRHGSSWIKDVKILVADEIHLIGS-----RDRGATLEVILAHMLG-----  168 (720)
T ss_dssp             ----GGGGGCSEEE-------ECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGC-----TTTHHHHHHHHHHHBT-----
T ss_pred             ----cccCCCCEEE-------ECHHHHHHHHHcChhhhhcCCEEEEECCcccCC-----CcccHHHHHHHHHhhc-----
Confidence                1122333443       145555444433111 13578999996665532     1233445556665551     


Q ss_pred             CcEEEEEec
Q 009230          451 ACHVWFVAH  459 (539)
Q Consensus       451 ~i~vi~~~q  459 (539)
                      ++.+|+++-
T Consensus       169 ~~~ii~lSA  177 (720)
T 2zj8_A          169 KAQIIGLSA  177 (720)
T ss_dssp             TBEEEEEEC
T ss_pred             CCeEEEEcC
Confidence            677777776

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=94.89  E-value=0.022  Score=58.42  Aligned_cols=66  Identities=18%  Similarity=0.241  Sum_probs=53.3

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA  342 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~  342 (539)
                      .....+.||+..+|-++-+.+|+=..|.|++|+|||++++++..+.+. ++..++|....+..+++.
T Consensus       154 ~v~epl~TGiraID~l~PigrGQR~~I~g~~g~GKT~Lal~~I~~~~~-~dv~~V~~~IGeR~~Ev~  219 (515)
T 2r9v_A          154 PVDTPLQTGIKAIDSMIPIGRGQRELIIGDRQTGKTAIAIDTIINQKG-QGVYCIYVAIGQKKSAIA  219 (515)
T ss_dssp             CCCSEECCSCHHHHHHSCEETTCBEEEEEETTSSHHHHHHHHHHTTTT-TTEEEEEEEESCCHHHHH
T ss_pred             CCCcchhcCccccccccccccCCEEEEEcCCCCCccHHHHHHHHHhhc-CCcEEEEEEcCCCcHHHH
Confidence            445678999999999988999999999999999999998876666553 355667888777777653

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=94.89  E-value=0.014  Score=51.43  Aligned_cols=32  Identities=28%  Similarity=0.522  Sum_probs=24.1

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      .+++|.|+||+||||++..++..     .....+++.
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~~-----~~~~~~i~~   34 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIAK-----NPGFYNINR   34 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH-----STTEEEECH
T ss_pred             eEEEEecCCCCCHHHHHHHHHhh-----cCCcEEecH
Confidence            47899999999999998887752     233456664

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=94.88  E-value=0.013  Score=51.52  Aligned_cols=25  Identities=20%  Similarity=0.116  Sum_probs=21.0

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|.+++|.|++|+||||++..++..
T Consensus         3 ~~~~i~l~G~~GsGKSTl~~~La~~   27 (173)
T 1kag_A            3 EKRNIFLVGPMGAGKSTIGRQLAQQ   27 (173)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHH
Confidence            3678999999999999998877644

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=94.86  E-value=0.024  Score=51.75  Aligned_cols=37  Identities=16%  Similarity=0.148  Sum_probs=32.7

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.+..+..|+||||++.++|..++.. | +|+++.++..
T Consensus         3 I~v~s~KGGvGKTT~a~~LA~~la~~-g-~VlliD~D~q   39 (209)
T 3cwq_A            3 ITVASFKGGVGKTTTAVHLSAYLALQ-G-ETLLIDGDPN   39 (209)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHTT-S-CEEEEEECTT
T ss_pred             EEEEcCCCCCcHHHHHHHHHHHHHhc-C-CEEEEECCCC
Confidence            45667899999999999999999986 9 9999998865

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=94.85  E-value=0.024  Score=58.16  Aligned_cols=66  Identities=17%  Similarity=0.199  Sum_probs=52.9

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA  342 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~  342 (539)
                      .....+.||+..+|-++-+.+|+=..|.|++|+|||++++++..+.+. ++..++|....+..+++.
T Consensus       141 ~v~epl~TGiraID~l~PigrGQR~~Ifg~~g~GKT~Lal~~I~~~~~-~dv~~V~~~iGeR~~Ev~  206 (502)
T 2qe7_A          141 SVHEPLQTGIKAIDSMIPIGRGQRELIIGDRQTGKTTIAIDTIINQKG-QDVICIYVAIGQKQSTVA  206 (502)
T ss_dssp             CCCSBCCCSCHHHHHSSCCBTTCBCEEEECSSSCHHHHHHHHHHGGGS-CSEEEEEEEESCCHHHHH
T ss_pred             CCCCccccceeecccccccccCCEEEEECCCCCCchHHHHHHHHHhhc-CCcEEEEEECCCcchHHH
Confidence            344578899999999988999999999999999999998876666553 355667887777776553

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.83  E-value=0.014  Score=55.36  Aligned_cols=32  Identities=25%  Similarity=0.285  Sum_probs=26.6

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++-
T Consensus        36 l~~vsl~i~~Ge~~~i~G~nGsGKSTLl~~l~G   68 (260)
T 2ghi_A           36 LKSINFFIPSGTTCALVGHTGSGKSTIAKLLYR   68 (260)
T ss_dssp             EEEEEEEECTTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             eEeeEEEECCCCEEEEECCCCCCHHHHHHHHhc
Confidence            554444 99999999999999999999887654

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=94.79  E-value=0.036  Score=60.76  Aligned_cols=36  Identities=19%  Similarity=0.316  Sum_probs=24.4

Q ss_pred             ccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEE
Q 009230          293 NVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLC  332 (539)
Q Consensus       293 ~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~  332 (539)
                      ++.+..=+++.||||+|||.++..+|..    .+.+.+.+
T Consensus       507 g~~~~~gvLl~GPPGtGKT~lAkaiA~e----~~~~f~~v  542 (806)
T 3cf2_A          507 GMTPSKGVLFYGPPGCGKTLLAKAIANE----CQANFISI  542 (806)
T ss_dssp             CCCCCSCCEEESSTTSSHHHHHHHHHHT----TTCEEEEC
T ss_pred             CCCCCceEEEecCCCCCchHHHHHHHHH----hCCceEEe
Confidence            4333344789999999999987666544    46665533

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=94.79  E-value=0.018  Score=55.51  Aligned_cols=37  Identities=19%  Similarity=0.228  Sum_probs=27.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ...+.+++|+|+||+||||++..++...    +...+++|.
T Consensus        30 ~~~~~livl~G~sGsGKSTla~~L~~~~----~~~~~~Is~   66 (287)
T 1gvn_B           30 VESPTAFLLGGQPGSGKTSLRSAIFEET----QGNVIVIDN   66 (287)
T ss_dssp             CSSCEEEEEECCTTSCTHHHHHHHHHHT----TTCCEEECT
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHh----CCCeEEEec
Confidence            3456799999999999999988876542    234566665

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=94.78  E-value=0.018  Score=54.35  Aligned_cols=23  Identities=22%  Similarity=0.276  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .+++|+|+||+||||++..++..
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~   24 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQE   24 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHhc
Confidence            37899999999999999988765

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=94.71  E-value=0.029  Score=57.43  Aligned_cols=66  Identities=18%  Similarity=0.336  Sum_probs=52.7

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA  342 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~  342 (539)
                      .....+.||+..+|-++-+.+|+=..|.|++|+|||+++++...+... .+..++|...-+...++.
T Consensus       141 ~v~epl~TGikaID~l~PigrGQR~~Ifg~~g~GKT~l~l~~I~n~~~-~dv~~V~~~IGeR~~ev~  206 (513)
T 3oaa_A          141 SVDQPVQTGYKAVDSMIPIGRGQRELIIGDRQTGKTALAIDAIINQRD-SGIKCIYVAIGQKASTIS  206 (513)
T ss_dssp             CCCCBCCCSCHHHHHHSCCBTTCBCEEEESSSSSHHHHHHHHHHTTSS-SSCEEEEEEESCCHHHHH
T ss_pred             CcCcccccceeeeccccccccCCEEEeecCCCCCcchHHHHHHHhhcc-CCceEEEEEecCChHHHH
Confidence            445678899999999988999999999999999999998776666433 355677888887776543

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=94.71  E-value=0.021  Score=51.81  Aligned_cols=35  Identities=29%  Similarity=0.246  Sum_probs=27.1

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEE
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLC  332 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~  332 (539)
                      +|-+++|.|+||+||||++..++..+-.. | .++..
T Consensus         3 ~~~~I~i~G~~GsGKsT~~~~L~~~l~~~-g-~~~~~   37 (213)
T 2plr_A            3 KGVLIAFEGIDGSGKSSQATLLKDWIELK-R-DVYLT   37 (213)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHTTT-S-CEEEE
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHhhc-C-CEEEe
Confidence            36689999999999999999998775432 4 56443

>1byi_A Dethiobiotin synthase; biotin synthesis, cyclo-ligase, ligase; 0.97A {Escherichia coli} SCOP: c.37.1.10 PDB: 1bs1_A* 1a82_A 1dad_A* 1dae_A* 1daf_A* 1dag_A* 1dah_A* 1dai_A* 1dak_A* 1dam_A* 1dbs_A 1dts_A

Probab=94.69  E-value=0.033  Score=51.17  Aligned_cols=34  Identities=15%  Similarity=0.089  Sum_probs=29.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +.+....+|+||||++.++|..++++ |.+|+++.
T Consensus         4 I~v~s~kgGvGKTt~a~nLa~~la~~-G~rVll~d   37 (224)
T 1byi_A            4 YFVTGTDTEVGKTVASCALLQAAKAA-GYRTAGYK   37 (224)
T ss_dssp             EEEEESSTTSCHHHHHHHHHHHHHHT-TCCEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-CCCEEEEc
Confidence            44555679999999999999999986 99999975

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=94.68  E-value=0.039  Score=50.80  Aligned_cols=42  Identities=21%  Similarity=0.171  Sum_probs=34.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHH-hcCCeEEEEeCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINE-HAGWKFVLCSMEN  336 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~-~~g~~vl~~s~E~  336 (539)
                      -.+|-+++|.|.+|+||||++..++..+.. . |.+|.+++-|-
T Consensus        18 ~~~~~~i~~~G~~g~GKst~~~~l~~~l~~~~-g~~v~~~treP   60 (223)
T 3ld9_A           18 GPGSMFITFEGIDGSGKTTQSHLLAEYLSEIY-GVNNVVLTREP   60 (223)
T ss_dssp             -CCCEEEEEECSTTSSHHHHHHHHHHHHHHHH-CGGGEEEEESS
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHhhcc-CceeeEeeeCC
Confidence            346789999999999999999999988766 5 88888755553

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=94.65  E-value=0.025  Score=58.11  Aligned_cols=66  Identities=20%  Similarity=0.190  Sum_probs=53.7

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA  342 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~  342 (539)
                      .....+.||+..+|-++-+.+|.=..|.|++|+|||++++++..+.+. ++..++|....+..+++.
T Consensus       142 ~v~epl~TGiraID~l~PigrGQR~~Ifg~~g~GKT~Lal~~I~~~~~-~dv~~V~~~iGeR~~Ev~  207 (507)
T 1fx0_A          142 SVYEPLQTGLIAIDAMIPVGRGQRELIIGDRQTGKTAVATDTILNQQG-QNVICVYVAIGQKASSVA  207 (507)
T ss_dssp             CCCSBCCCSCTTTTTTSCCBTTCBCBEEESSSSSHHHHHHHHHHTCCT-TTCEEEEEEESCCHHHHH
T ss_pred             ccCCcccccceecccccccccCCEEEEecCCCCCccHHHHHHHHHhhc-CCcEEEEEEcCCCchHHH
Confidence            344568899999999988999999999999999999998876666554 366778888888777653

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=94.63  E-value=0.022  Score=50.52  Aligned_cols=36  Identities=28%  Similarity=0.458  Sum_probs=27.1

Q ss_pred             Cchhh--hhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          284 GWRAL--NELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       284 g~~~L--D~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +|..+  +.+.- |.+| +++|.|++|+||||++..+..-
T Consensus        11 nf~~~~~~~~~~~~~~g-~~~i~G~NGsGKStll~ai~~~   49 (182)
T 3kta_A           11 GFKSYGNKKVVIPFSKG-FTAIVGANGSGKSNIGDAILFV   49 (182)
T ss_dssp             SBGGGCSSCEEEECCSS-EEEEEECTTSSHHHHHHHHHHH
T ss_pred             CeEeecCccEEEecCCC-cEEEECCCCCCHHHHHHHHHHH
Confidence            44555  44333 8888 9999999999999998876543

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=94.62  E-value=0.041  Score=54.56  Aligned_cols=43  Identities=21%  Similarity=0.285  Sum_probs=34.2

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR  339 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~  339 (539)
                      .+..+.|.|+||+|||||+..++...... +.+|.+++.+....
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~~~~~~-~~~v~V~~~dp~~~  115 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGKMLTER-GHKLSVLAVDPSSC  115 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEECCC---
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHhhhc-CCeEEEEeecCCCC
Confidence            36789999999999999999998776554 88999998876543

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=94.57  E-value=0.024  Score=50.27  Aligned_cols=24  Identities=17%  Similarity=0.030  Sum_probs=20.9

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +..++|.|+||+||||++..++..
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~   28 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKL   28 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            468899999999999998888754

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=94.55  E-value=0.026  Score=54.40  Aligned_cols=41  Identities=20%  Similarity=0.020  Sum_probs=30.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC--CeEEEE-eCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAG--WKFVLC-SME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g--~~vl~~-s~E  335 (539)
                      -.++.++.|+|++|+|||||+..++..+... |  .+++.+ +.+
T Consensus        28 ~~~~~ii~I~G~sGsGKSTla~~L~~~l~~~-g~~~~~~~iv~~D   71 (290)
T 1odf_A           28 NKCPLFIFFSGPQGSGKSFTSIQIYNHLMEK-YGGEKSIGYASID   71 (290)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHHHHHHH-HGGGSCEEEEEGG
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHhhhc-CCCCceEEEeccc
Confidence            3456799999999999999999888776543 3  334444 776

>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH, niaid, borellia burgdorferi, plasmid partition protein, iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A

Probab=94.53  E-value=0.022  Score=54.09  Aligned_cols=38  Identities=24%  Similarity=0.213  Sum_probs=32.9

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV  338 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~  338 (539)
                      +.+..+..|+||||++.++|..++ + |.+|+++.++...
T Consensus        30 I~v~s~kGGvGKTT~a~~LA~~la-~-g~~VlliD~D~~~   67 (267)
T 3k9g_A           30 ITIASIKGGVGKSTSAIILATLLS-K-NNKVLLIDMDTQA   67 (267)
T ss_dssp             EEECCSSSSSCHHHHHHHHHHHHT-T-TSCEEEEEECTTC
T ss_pred             EEEEeCCCCchHHHHHHHHHHHHH-C-CCCEEEEECCCCC
Confidence            445578899999999999999999 6 9999999999654

>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase, ATP binding site, hydro; HET: ADP; 2.15A {Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A* 1ii9_A*

Probab=94.53  E-value=0.038  Score=59.00  Aligned_cols=52  Identities=17%  Similarity=0.303  Sum_probs=43.8

Q ss_pred             chhhhhhhc-c--CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          285 WRALNELYN-V--LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       285 ~~~LD~~~~-l--~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .+.||.+++ +  ..+.++++.|.+|+||||++.++|..++.. |.+|++++++..
T Consensus       312 ~~~l~~~~~~~~~~~~~~~~~~~~~g~Gktt~a~~lA~~l~~~-g~~vllvD~Dp~  366 (589)
T 1ihu_A          312 IPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADM-GFDVHLTTSDPA  366 (589)
T ss_dssp             CCCHHHHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEESCCC
T ss_pred             cchhhhhhhhhhccCCeEEEEecCCCCChhhHHHHHHHHHHHC-CCcEEEEeCCCc
Confidence            467777776 3  344678889999999999999999999986 999999999965

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=94.52  E-value=0.024  Score=50.59  Aligned_cols=24  Identities=21%  Similarity=0.307  Sum_probs=20.7

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+++|.|+||+||||++..++..
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~   26 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEK   26 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999998887754

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.47  E-value=0.03  Score=53.91  Aligned_cols=39  Identities=21%  Similarity=0.141  Sum_probs=28.3

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      +-++.|+|++|+||||++..++..+-.. +..+.+++++.
T Consensus         5 ~~iIgItG~sGSGKSTva~~L~~~lg~~-~~~~~vI~~D~   43 (290)
T 1a7j_A            5 HPIISVTGSSGAGTSTVKHTFDQIFRRE-GVKAVSIEGDA   43 (290)
T ss_dssp             SCEEEEESCC---CCTHHHHHHHHHHHH-TCCEEEEEGGG
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHhhc-CCCeeEeecch
Confidence            3489999999999999999988765443 67788888763

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=94.46  E-value=0.025  Score=50.04  Aligned_cols=27  Identities=22%  Similarity=0.290  Sum_probs=22.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ...+.+++|.|+||+||||++..++..
T Consensus         8 ~~~~~~i~i~G~~GsGKst~~~~l~~~   34 (180)
T 3iij_A            8 FMLLPNILLTGTPGVGKTTLGKELASK   34 (180)
T ss_dssp             TCCCCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             cccCCeEEEEeCCCCCHHHHHHHHHHH
Confidence            345678999999999999998887755

>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=94.44  E-value=0.069  Score=49.52  Aligned_cols=57  Identities=14%  Similarity=0.244  Sum_probs=37.8

Q ss_pred             hhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCC----eEEEEeCCC-CHHHHHHHH
Q 009230          289 NELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGW----KFVLCSMEN-KVREHARKL  345 (539)
Q Consensus       289 D~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~----~vl~~s~E~-~~~~~~~r~  345 (539)
                      ..++. +..|+.+++.|++|+|||+++..++.......+.    .+++....- ...++..++
T Consensus        67 ~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~  129 (235)
T 3llm_A           67 SEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERV  129 (235)
T ss_dssp             HHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHH
Confidence            34445 7778999999999999998877777665543343    677665442 233444444

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=94.44  E-value=0.029  Score=49.96  Aligned_cols=27  Identities=22%  Similarity=0.439  Sum_probs=22.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ..+|..++|+|+||+||||++..++..
T Consensus         7 ~~~~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A            7 QPKGINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             CCSSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHh
Confidence            345778999999999999998877643

>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=94.43  E-value=0.088  Score=57.45  Aligned_cols=140  Identities=16%  Similarity=0.142  Sum_probs=75.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC-CHHHHHHHHHHHh--hCCCccccccCCCCCCCCHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN-KVREHARKLLEKH--IKKPFFEANYGGSAERMTVEE  370 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~-~~~~~~~r~~~~~--~~~~~~~i~~~~~~~~l~~~~  370 (539)
                      +..|+-++++|+||+|||+.+...+.+...+ +.+++|+..-- -..+...++ ...  .|+....+. |. ... ..  
T Consensus        37 i~~~~~~lv~apTGsGKT~~~~l~il~~~~~-~~~~l~i~P~r~La~q~~~~~-~~~~~~g~~v~~~~-G~-~~~-~~--  109 (702)
T 2p6r_A           37 VFSGKNLLLAMPTAAGKTLLAEMAMVREAIK-GGKSLYVVPLRALAGEKYESF-KKWEKIGLRIGIST-GD-YES-RD--  109 (702)
T ss_dssp             HTTCSCEEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEEESSHHHHHHHHHHH-TTTTTTTCCEEEEC-SS-CBC-CS--
T ss_pred             HhCCCcEEEEcCCccHHHHHHHHHHHHHHHh-CCcEEEEeCcHHHHHHHHHHH-HHHHhcCCEEEEEe-CC-CCc-ch--
Confidence            4557889999999999999888777776664 78899887432 133344444 111  122222211 10 000 00  


Q ss_pred             HHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHH-HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009230          371 FEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVL-RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQH  449 (539)
Q Consensus       371 ~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~-~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~  449 (539)
                           ..+....++|.       |++.+...++.-.. -.++++||||-...+..     ..+...+..++..++.+  .
T Consensus       110 -----~~~~~~~Iiv~-------Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~-----~~r~~~~~~ll~~l~~~--~  170 (702)
T 2p6r_A          110 -----EHLGDCDIIVT-------TSEKADSLIRNRASWIKAVSCLVVDEIHLLDS-----EKRGATLEILVTKMRRM--N  170 (702)
T ss_dssp             -----SCSTTCSEEEE-------EHHHHHHHHHTTCSGGGGCCEEEETTGGGGGC-----TTTHHHHHHHHHHHHHH--C
T ss_pred             -----hhccCCCEEEE-------CHHHHHHHHHcChhHHhhcCEEEEeeeeecCC-----CCcccHHHHHHHHHHhc--C
Confidence                 01122223331       34544444332111 23578999996665542     12334556666666643  2


Q ss_pred             hCcEEEEEec
Q 009230          450 HACHVWFVAH  459 (539)
Q Consensus       450 ~~i~vi~~~q  459 (539)
                      .++.+|+++-
T Consensus       171 ~~~~ii~lSA  180 (702)
T 2p6r_A          171 KALRVIGLSA  180 (702)
T ss_dssp             TTCEEEEEEC
T ss_pred             cCceEEEECC
Confidence            3677888776

>2oze_A ORF delta'; para, walker type atpases, DNA segregation, PSM19035, plasmid, DNA binding protein; HET: AGS EPE; 1.83A {Streptococcus pyogenes}

Probab=94.42  E-value=0.032  Score=53.80  Aligned_cols=40  Identities=13%  Similarity=0.111  Sum_probs=33.4

Q ss_pred             cEEEEE---cCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH
Q 009230          298 ELTIVT---GVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV  338 (539)
Q Consensus       298 ~l~~i~---G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~  338 (539)
                      ..++|+   +..|+||||++.++|..++.. |.+|+.+.++...
T Consensus        35 ~~i~v~~~s~KGGvGKTT~a~nLA~~la~~-G~rVlliD~D~q~   77 (298)
T 2oze_A           35 EAIVILNNYFKGGVGKSKLSTMFAYLTDKL-NLKVLMIDKDLQA   77 (298)
T ss_dssp             SCEEEEECCSSSSSSHHHHHHHHHHHHHHT-TCCEEEEEECTTC
T ss_pred             cEEEEEeccCCCCchHHHHHHHHHHHHHhC-CCeEEEEeCCCCC
Confidence            344455   599999999999999999985 9999999988653

>1wcv_1 SOJ, segregation protein; ATPase, bacterial, chromosome segregation; 1.6A {Thermus thermophilus} PDB: 2bej_A* 2bek_A*

Probab=94.41  E-value=0.023  Score=53.66  Aligned_cols=39  Identities=13%  Similarity=0.161  Sum_probs=33.4

Q ss_pred             cEEEE-EcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          298 ELTIV-TGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       298 ~l~~i-~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .++.| .+..|+||||++.++|..++.. |.+|+++.++..
T Consensus         7 ~vI~v~s~kGGvGKTt~a~~LA~~la~~-g~~VlliD~D~~   46 (257)
T 1wcv_1            7 RRIALANQKGGVGKTTTAINLAAYLARL-GKRVLLVDLDPQ   46 (257)
T ss_dssp             CEEEECCSSCCHHHHHHHHHHHHHHHHT-TCCEEEEECCTT
T ss_pred             EEEEEEeCCCCchHHHHHHHHHHHHHHC-CCCEEEEECCCC
Confidence            44555 5788999999999999999986 999999999864

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=94.37  E-value=0.026  Score=57.27  Aligned_cols=38  Identities=26%  Similarity=0.301  Sum_probs=29.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEE
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLC  332 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~  332 (539)
                      ..+|++++|+|++|+||||++..++..+... ...+.++
T Consensus       164 ~~~ggii~I~GpnGSGKTTlL~allg~l~~~-~g~I~~~  201 (418)
T 1p9r_A          164 KRPHGIILVTGPTGSGKSTTLYAGLQELNSS-ERNILTV  201 (418)
T ss_dssp             TSSSEEEEEECSTTSCHHHHHHHHHHHHCCT-TSCEEEE
T ss_pred             HhcCCeEEEECCCCCCHHHHHHHHHhhcCCC-CCEEEEe
Confidence            3688999999999999999998887655332 4566655

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=94.36  E-value=0.029  Score=50.18  Aligned_cols=26  Identities=23%  Similarity=0.387  Sum_probs=22.2

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++.+++|.|+||+||||++..++..
T Consensus         7 ~~~~~I~l~G~~GsGKsT~~~~La~~   32 (196)
T 2c95_A            7 KKTNIIFVVGGPGSGKGTQCEKIVQK   32 (196)
T ss_dssp             TTSCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            35679999999999999998888754

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=94.34  E-value=0.093  Score=58.62  Aligned_cols=36  Identities=25%  Similarity=0.394  Sum_probs=28.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhc------CCeEEEEeC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHA------GWKFVLCSM  334 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~------g~~vl~~s~  334 (539)
                      -++|.|+||+|||+++..++..+....      +.+++++++
T Consensus       193 ~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~  234 (854)
T 1qvr_A          193 NPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQM  234 (854)
T ss_dssp             CCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC
T ss_pred             ceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeeh
Confidence            468999999999999999998876521      567776654

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=94.34  E-value=0.024  Score=51.16  Aligned_cols=35  Identities=20%  Similarity=0.276  Sum_probs=27.7

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +|-+++|.|++|+||||++..++..+  . |.+++.+.
T Consensus         3 ~~~~I~l~G~~GsGKsT~~~~L~~~l--~-g~~~~~~~   37 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQCMNIMESI--P-ANTIKYLN   37 (204)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHTS--C-GGGEEEEE
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH--C-CCceEEEe
Confidence            57789999999999999988877654  1 56776655

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=94.33  E-value=0.054  Score=50.35  Aligned_cols=43  Identities=16%  Similarity=0.380  Sum_probs=32.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      --+|.+++|.|++|+||||.+..++..+... |.+++.++-|..
T Consensus        24 ~~~~~~i~~eG~~GsGKsT~~~~l~~~l~~~-~~~~~~~~rep~   66 (236)
T 3lv8_A           24 AMNAKFIVIEGLEGAGKSTAIQVVVETLQQN-GIDHITRTREPG   66 (236)
T ss_dssp             --CCCEEEEEESTTSCHHHHHHHHHHHHHHT-TCCCEEEEESSC
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHhc-CCCeeeeecCCC
Confidence            3457899999999999999999999887764 888333444533

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=94.33  E-value=0.025  Score=50.82  Aligned_cols=26  Identities=31%  Similarity=0.300  Sum_probs=22.1

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ..|..++|+|+||+|||++++.++..
T Consensus        32 ~~g~~ilI~GpsGsGKStLA~~La~~   57 (205)
T 2qmh_A           32 IYGLGVLITGDSGVGKSETALELVQR   57 (205)
T ss_dssp             ETTEEEEEECCCTTTTHHHHHHHHTT
T ss_pred             ECCEEEEEECCCCCCHHHHHHHHHHh
Confidence            45678999999999999998887754

>2xj4_A MIPZ; replication, cell division, ATPase, WACA; 1.60A {Caulobacter vibrioides} PDB: 2xj9_A* 2xit_A

Probab=94.32  E-value=0.036  Score=53.26  Aligned_cols=37  Identities=16%  Similarity=0.166  Sum_probs=32.7

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      +.+..+..|+||||++.++|..++.. |.+|+++.++.
T Consensus         7 I~v~s~KGGvGKTT~a~nLA~~La~~-G~~VlliD~D~   43 (286)
T 2xj4_A            7 IVVGNEKGGAGKSTIAVHLVTALLYG-GAKVAVIDLDL   43 (286)
T ss_dssp             EEECCSSSCTTHHHHHHHHHHHHHHT-TCCEEEEECCT
T ss_pred             EEEEcCCCCCCHHHHHHHHHHHHHHC-CCcEEEEECCC
Confidence            44556789999999999999999986 99999999987

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=94.32  E-value=0.026  Score=56.38  Aligned_cols=28  Identities=25%  Similarity=0.264  Sum_probs=25.2

Q ss_pred             ccCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          293 NVLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       293 ~l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++++|++++|.|+||+||||++..++..
T Consensus       165 ~i~~~~~i~l~G~~GsGKSTl~~~l~~~  192 (377)
T 1svm_A          165 NIPKKRYWLFKGPIDSGKTTLAAALLEL  192 (377)
T ss_dssp             CCTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            3899999999999999999999988753

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=94.23  E-value=0.045  Score=50.06  Aligned_cols=37  Identities=27%  Similarity=0.334  Sum_probs=30.8

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +|-+++|.|++|+||||.+..++..+... |.+|....
T Consensus         5 ~g~~i~~eG~~gsGKsT~~~~l~~~l~~~-~~~v~~~~   41 (213)
T 4edh_A            5 TGLFVTLEGPEGAGKSTNRDYLAERLRER-GIEVQLTR   41 (213)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHTT-TCCEEEEE
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHHHHc-CCCccccc
Confidence            57899999999999999999998877654 88886443

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=94.20  E-value=0.029  Score=50.66  Aligned_cols=25  Identities=32%  Similarity=0.290  Sum_probs=21.2

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      ..+++|.|++|+||||++..++...
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3589999999999999988877653

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=94.16  E-value=0.042  Score=50.89  Aligned_cols=36  Identities=14%  Similarity=0.277  Sum_probs=29.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEE
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVL  331 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~  331 (539)
                      ..+|.+++|.|++|+||||++..++..+..  |..|+.
T Consensus        23 ~~~g~~i~i~G~~GsGKsT~~~~l~~~l~~--~~~~~~   58 (229)
T 4eaq_A           23 NAMSAFITFEGPEGSGKTTVINEVYHRLVK--DYDVIM   58 (229)
T ss_dssp             CCCCEEEEEECCTTSCHHHHHHHHHHHHTT--TSCEEE
T ss_pred             cCCCeEEEEEcCCCCCHHHHHHHHHHHHhc--CCCcee
Confidence            668999999999999999999888876543  566653

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=94.14  E-value=0.021  Score=57.37  Aligned_cols=33  Identities=27%  Similarity=0.408  Sum_probs=27.5

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|+.+.- +.+|+++.|.|++|+||||++.-++-
T Consensus        36 ~L~~vsl~i~~Ge~~~llGpsGsGKSTLLr~iaG   69 (390)
T 3gd7_A           36 ILENISFSISPGQRVGLLGRTGSGKSTLLSAFLR   69 (390)
T ss_dssp             SEEEEEEEECTTCEEEEEESTTSSHHHHHHHHHT
T ss_pred             EeeceeEEEcCCCEEEEECCCCChHHHHHHHHhC
Confidence            4555544 99999999999999999999877663

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=94.14  E-value=0.035  Score=50.95  Aligned_cols=25  Identities=20%  Similarity=0.236  Sum_probs=21.7

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +|-+++|.|+||+||||++..++..
T Consensus         3 ~~~~I~l~G~~GsGKsT~a~~La~~   27 (220)
T 1aky_A            3 ESIRMVLIGPPGAGKGTQAPNLQER   27 (220)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4668999999999999998888754

>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=94.11  E-value=0.26  Score=44.36  Aligned_cols=40  Identities=15%  Similarity=0.071  Sum_probs=30.2

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhc-----CCeEEEEeCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHA-----GWKFVLCSME  335 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~-----g~~vl~~s~E  335 (539)
                      .|.-++|.+++|+|||..+...+.......     +.+++++..-
T Consensus        47 ~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~   91 (216)
T 3b6e_A           47 EGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNK   91 (216)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESS
T ss_pred             cCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECH
Confidence            345688999999999999888877665431     5688888643

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=94.10  E-value=0.026  Score=49.92  Aligned_cols=31  Identities=19%  Similarity=0.159  Sum_probs=19.9

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      ++.+++|.|.||+||||++..++..    .|.+++
T Consensus         4 ~~~~I~l~G~~GsGKST~a~~La~~----l~~~~i   34 (183)
T 2vli_A            4 RSPIIWINGPFGVGKTHTAHTLHER----LPGSFV   34 (183)
T ss_dssp             -CCEEEEECCC----CHHHHHHHHH----STTCEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHh----cCCCEE
Confidence            3568999999999999998877644    366654

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=94.10  E-value=0.023  Score=54.64  Aligned_cols=31  Identities=23%  Similarity=0.451  Sum_probs=25.7

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      |+.+.- +.+|+++.|.|++|+|||||+.-++
T Consensus        54 l~~isl~i~~Ge~~~i~G~NGsGKSTLlk~l~   85 (290)
T 2bbs_A           54 LKDINFKIERGQLLAVAGSTGAGKTSLLMMIM   85 (290)
T ss_dssp             EEEEEEEECTTCEEEEEESTTSSHHHHHHHHT
T ss_pred             EEeeEEEEcCCCEEEEECCCCCcHHHHHHHHh
Confidence            444443 9999999999999999999977655

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=94.08  E-value=0.035  Score=51.91  Aligned_cols=26  Identities=23%  Similarity=0.239  Sum_probs=22.0

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++++++|.|++|+||||++..++..
T Consensus        25 ~~~~~i~l~G~~GsGKSTl~k~La~~   50 (246)
T 2bbw_A           25 SKLLRAVILGPPGSGKGTVCQRIAQN   50 (246)
T ss_dssp             -CCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            34689999999999999999888754

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=94.02  E-value=0.039  Score=53.83  Aligned_cols=38  Identities=13%  Similarity=0.087  Sum_probs=28.9

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHH-hcCCeEEEEeCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINE-HAGWKFVLCSMEN  336 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~-~~g~~vl~~s~E~  336 (539)
                      ++.|+|++|+|||||+..++..... ..+..|.+++.+.
T Consensus        94 iigI~GpsGSGKSTl~~~L~~ll~~~~~~~~v~~i~~D~  132 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTSRVLKALLSRWPDHPNVEVITTDG  132 (321)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcccCCCCeEEEEeecc
Confidence            8999999999999999877654431 1245788888874

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=94.00  E-value=0.046  Score=51.29  Aligned_cols=34  Identities=24%  Similarity=0.412  Sum_probs=25.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +++|  ++|.|+||+|||+++..++...    +.+.++++
T Consensus        48 ~~~g--~ll~G~~G~GKTtl~~~i~~~~----~~~~i~~~   81 (254)
T 1ixz_A           48 IPKG--VLLVGPPGVGKTHLARAVAGEA----RVPFITAS   81 (254)
T ss_dssp             CCSE--EEEECCTTSSHHHHHHHHHHHT----TCCEEEEE
T ss_pred             CCCe--EEEECCCCCCHHHHHHHHHHHh----CCCEEEee
Confidence            6677  8899999999999988777542    34555554

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=93.98  E-value=0.038  Score=53.50  Aligned_cols=38  Identities=16%  Similarity=0.157  Sum_probs=30.7

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ...++|.|+||+|||+++..++...... +.+++++.+.
T Consensus        47 ~~~~ll~G~~GtGKt~la~~la~~~~~~-~~~~~~~~~~   84 (311)
T 4fcw_A           47 IGSFLFLGPTGVGKTELAKTLAATLFDT-EEAMIRIDMT   84 (311)
T ss_dssp             SEEEEEESCSSSSHHHHHHHHHHHHHSC-GGGEEEEEGG
T ss_pred             ceEEEEECCCCcCHHHHHHHHHHHHcCC-CcceEEeecc
Confidence            4578999999999999999988876553 6677777664

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=93.98  E-value=0.037  Score=64.59  Aligned_cols=31  Identities=26%  Similarity=0.332  Sum_probs=25.3

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      |+++.- +++|+.+.|.|++|+||||++.-++
T Consensus       406 L~~isl~i~~G~~~~ivG~sGsGKSTl~~ll~  437 (1284)
T 3g5u_A          406 LKGLNLKVKSGQTVALVGNSGCGKSTTVQLMQ  437 (1284)
T ss_dssp             EEEEEEEECTTCEEEEECCSSSSHHHHHHHTT
T ss_pred             eecceEEEcCCCEEEEECCCCCCHHHHHHHHh
Confidence            444433 8999999999999999999976554

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=93.96  E-value=0.064  Score=51.12  Aligned_cols=35  Identities=23%  Similarity=0.431  Sum_probs=27.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +++|  ++|.|+||+|||+++..++..    .+.+.++++.
T Consensus        43 ~~~G--vlL~Gp~GtGKTtLakala~~----~~~~~i~i~g   77 (274)
T 2x8a_A           43 TPAG--VLLAGPPGCGKTLLAKAVANE----SGLNFISVKG   77 (274)
T ss_dssp             CCSE--EEEESSTTSCHHHHHHHHHHH----TTCEEEEEET
T ss_pred             CCCe--EEEECCCCCcHHHHHHHHHHH----cCCCEEEEEc
Confidence            6667  899999999999998877653    3556666664

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=93.94  E-value=0.016  Score=52.85  Aligned_cols=34  Identities=24%  Similarity=0.372  Sum_probs=27.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +++|.|++|+||||++..++..+-. .|.+|.++.
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~~-~g~~v~~~~   35 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFRA-AGRSVATLA   35 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHHE-EEEEEEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHh-cCCeEEEEe
Confidence            6889999999999999998877654 366776553

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=93.93  E-value=0.033  Score=53.99  Aligned_cols=32  Identities=31%  Similarity=0.512  Sum_probs=27.0

Q ss_pred             hhhhhhccCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          287 ALNELYNVLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       287 ~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|+++.+..|+++.|.|++|+|||||+..++
T Consensus       155 gi~~L~~~l~G~i~~l~G~sG~GKSTLln~l~  186 (302)
T 2yv5_A          155 GIDELVDYLEGFICILAGPSGVGKSSILSRLT  186 (302)
T ss_dssp             THHHHHHHTTTCEEEEECSTTSSHHHHHHHHH
T ss_pred             CHHHHHhhccCcEEEEECCCCCCHHHHHHHHH
Confidence            35666666678999999999999999998877

>3pg5_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 3.30A {Corynebacterium diphtheriae}

Probab=93.93  E-value=0.027  Score=56.10  Aligned_cols=38  Identities=8%  Similarity=0.167  Sum_probs=33.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.+..+..|+||||++.++|..+|.. |.+|+++.++..
T Consensus         4 Iav~s~KGGvGKTT~a~nLA~~LA~~-G~rVLlID~D~q   41 (361)
T 3pg5_A            4 ISFFNNKGGVGKTTLSTNVAHYFALQ-GKRVLYVDCDPQ   41 (361)
T ss_dssp             EEBCCSSCCHHHHHHHHHHHHHHHHT-TCCEEEEECCTT
T ss_pred             EEEEcCCCCCcHHHHHHHHHHHHHhC-CCcEEEEEcCCC
Confidence            45556899999999999999999985 999999999965

>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=93.89  E-value=0.066  Score=55.19  Aligned_cols=40  Identities=13%  Similarity=0.235  Sum_probs=33.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCC-eEEEEeCCCCHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGW-KFVLCSMENKVR  339 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~-~vl~~s~E~~~~  339 (539)
                      .++|.|+||+|||+++..++..+... |. +++.++.-..+.
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~l~~~-~~~~il~~a~T~~Aa   87 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEALIST-GETGIILAAPTHAAK   87 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHT-TCCCEEEEESSHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhc-CCceEEEecCcHHHH
Confidence            99999999999999999999888875 65 788887665443

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=93.87  E-value=0.036  Score=56.54  Aligned_cols=65  Identities=12%  Similarity=0.090  Sum_probs=51.4

Q ss_pred             CccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc---CCeEEEEeCCCCHHHH
Q 009230          277 DEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHA---GWKFVLCSMENKVREH  341 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~---g~~vl~~s~E~~~~~~  341 (539)
                      ....+.||+..+|-++-+.+|.=..|.|++|+|||+++.++|.+...++   +.-++|....+..+++
T Consensus       132 ~~e~l~TGir~ID~l~pigrGQr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev  199 (469)
T 2c61_A          132 PKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEA  199 (469)
T ss_dssp             CCSBCBCSCHHHHTTSCCBTTCBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHH
T ss_pred             cccccceeeEeeeeeeccccCCEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHH
Confidence            4457899999999998899998888999999999999998887764321   2457777777776654

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=93.84  E-value=0.044  Score=49.37  Aligned_cols=29  Identities=21%  Similarity=0.235  Sum_probs=23.2

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeE
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKF  329 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~v  329 (539)
                      +-+++|.|+||+||||++..++...    |.++
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~l----~~~~   48 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEKL----GIPQ   48 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH----TCCE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh----CCcE
Confidence            3589999999999999988877653    5554

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=93.84  E-value=0.021  Score=48.70  Aligned_cols=37  Identities=16%  Similarity=0.067  Sum_probs=26.5

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      .+.-++|.|+||+|||+++..++...... +.+++ +.+
T Consensus        23 ~~~~vll~G~~GtGKt~lA~~i~~~~~~~-~~~~v-~~~   59 (145)
T 3n70_A           23 TDIAVWLYGAPGTGRMTGARYLHQFGRNA-QGEFV-YRE   59 (145)
T ss_dssp             CCSCEEEESSTTSSHHHHHHHHHHSSTTT-TSCCE-EEE
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHhCCcc-CCCEE-EEC
Confidence            34457899999999999998877654443 55655 443

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=93.82  E-value=0.029  Score=52.79  Aligned_cols=38  Identities=11%  Similarity=0.037  Sum_probs=28.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ..++.+++|.|+||+||||++..++...    +..+.+++.+
T Consensus        29 ~~~~~~i~l~G~~GsGKSTla~~L~~~l----~~~~~~~~~D   66 (253)
T 2p5t_B           29 SKQPIAILLGGQSGAGKTTIHRIKQKEF----QGNIVIIDGD   66 (253)
T ss_dssp             CSSCEEEEEESCGGGTTHHHHHHHHHHT----TTCCEEECGG
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHhc----CCCcEEEecH
Confidence            4566899999999999999988877542    4445566655

>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=93.81  E-value=0.059  Score=54.27  Aligned_cols=48  Identities=21%  Similarity=0.228  Sum_probs=38.8

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARK  344 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r  344 (539)
                      .+.-++|.|++|+|||+++..++..... .|.+++++..+.....+.+.
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~~~-~~~~~~~~D~~~~~~~~~~~   81 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLREYM-QGSRVIIIDPEREYKEMCRK   81 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHHT-TTCCEEEEESSCCSHHHHHH
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHHHH-CCCEEEEEeCCcCHHHHHHH
Confidence            4567889999999999999999888765 48899999888766655444

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=93.80  E-value=0.036  Score=54.17  Aligned_cols=36  Identities=17%  Similarity=0.261  Sum_probs=26.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      -+++.+++|.|++|+|||+++..+|..      .+.-++|.+
T Consensus        37 ~~~~~lIvI~GPTgsGKTtLa~~LA~~------l~~eiIs~D   72 (339)
T 3a8t_A           37 HRKEKLLVLMGATGTGKSRLSIDLAAH------FPLEVINSD   72 (339)
T ss_dssp             -CCCEEEEEECSTTSSHHHHHHHHHTT------SCEEEEECC
T ss_pred             ccCCceEEEECCCCCCHHHHHHHHHHH------CCCcEEccc
Confidence            345679999999999999998877743      345566765

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=93.79  E-value=0.041  Score=49.33  Aligned_cols=27  Identities=22%  Similarity=0.383  Sum_probs=22.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.++.+++|.|+||+||||++..++..
T Consensus         9 ~~~~~~I~l~G~~GsGKsT~a~~L~~~   35 (199)
T 2bwj_A            9 LRKCKIIFIIGGPGSGKGTQCEKLVEK   35 (199)
T ss_dssp             HHHSCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            334568999999999999998887765

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=93.79  E-value=0.12  Score=53.68  Aligned_cols=65  Identities=17%  Similarity=0.152  Sum_probs=51.9

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHAR  343 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~  343 (539)
                      .....+.||+..+|-++-+.+|.-..|.|++|+|||+++.+++.+.   +..-++|...-+..+++..
T Consensus       211 ~~~epl~TGirvID~l~PigrGqr~~Ifgg~g~GKT~L~~~ia~~~---~~~v~V~~~iGER~~Ev~e  275 (600)
T 3vr4_A          211 NPDVPMITGQRVIDTFFPVTKGGAAAVPGPFGAGKTVVQHQIAKWS---DVDLVVYVGCGERGNEMTD  275 (600)
T ss_dssp             CCCSBCCCCCHHHHHHSCCBTTCEEEEECCTTSCHHHHHHHHHHHS---SCSEEEEEEEEECHHHHHH
T ss_pred             CCCceecccchhhhccCCccCCCEEeeecCCCccHHHHHHHHHhcc---CCCEEEEEEecccHHHHHH
Confidence            3446788999999999889999999999999999999999887552   2345677777777776543

>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=93.75  E-value=0.063  Score=56.92  Aligned_cols=43  Identities=28%  Similarity=0.371  Sum_probs=35.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +..+.+++|.|+||+|||+++..++..+... |.+|++.+.-..
T Consensus       201 ~~~~~~~~I~G~pGTGKTt~i~~l~~~l~~~-g~~Vl~~ApT~~  243 (574)
T 3e1s_A          201 LAGHRLVVLTGGPGTGKSTTTKAVADLAESL-GLEVGLCAPTGK  243 (574)
T ss_dssp             HTTCSEEEEECCTTSCHHHHHHHHHHHHHHT-TCCEEEEESSHH
T ss_pred             HHhCCEEEEEcCCCCCHHHHHHHHHHHHHhc-CCeEEEecCcHH
Confidence            3346799999999999999999998777664 999998876443

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=93.70  E-value=0.028  Score=52.80  Aligned_cols=34  Identities=24%  Similarity=0.286  Sum_probs=27.0

Q ss_pred             hhhhhhc-cCC---CcEEEEEcCCCCChhHHHHHHHHH
Q 009230          287 ALNELYN-VLP---GELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       287 ~LD~~~~-l~~---G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|+++.- +.+   |+.++|.|++|+||||++..++..
T Consensus        34 ~l~~~~~~i~~~l~g~~i~l~G~~GsGKSTl~~~La~~   71 (250)
T 3nwj_A           34 ILKKKAEEVKPYLNGRSMYLVGMMGSGKTTVGKIMARS   71 (250)
T ss_dssp             HHHHHHHTTHHHHTTCCEEEECSTTSCHHHHHHHHHHH
T ss_pred             hhhhhhhhhhhhcCCCEEEEECCCCCCHHHHHHHHHHh
Confidence            3454443 666   999999999999999998887754

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=93.66  E-value=0.025  Score=56.39  Aligned_cols=28  Identities=32%  Similarity=0.474  Sum_probs=24.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +.+|++++|.|++|+||||++.-++...
T Consensus       172 i~~G~~i~ivG~sGsGKSTll~~l~~~~  199 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLMKALMQEI  199 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHHHHHHTTS
T ss_pred             HhcCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            8999999999999999999988776543

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=93.64  E-value=0.041  Score=51.74  Aligned_cols=27  Identities=22%  Similarity=0.239  Sum_probs=23.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ..+|.++.|.|++|+||||++..++..
T Consensus        24 ~~~g~~I~I~G~~GsGKSTl~k~La~~   50 (252)
T 4e22_A           24 TAIAPVITVDGPSGAGKGTLCKALAES   50 (252)
T ss_dssp             TTTSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHh
Confidence            367899999999999999998877644

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=93.61  E-value=0.047  Score=48.90  Aligned_cols=29  Identities=24%  Similarity=0.386  Sum_probs=24.9

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAG  326 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g  326 (539)
                      |+.+.|.|++|+||||++.-++.... ..|
T Consensus         1 G~~i~i~G~nG~GKTTll~~l~g~~~-~~G   29 (189)
T 2i3b_A            1 ARHVFLTGPPGVGKTTLIHKASEVLK-SSG   29 (189)
T ss_dssp             CCCEEEESCCSSCHHHHHHHHHHHHH-HTT
T ss_pred             CCEEEEECCCCChHHHHHHHHHhhcc-cCC
Confidence            67899999999999999999887766 446

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=93.61  E-value=0.052  Score=49.73  Aligned_cols=27  Identities=26%  Similarity=0.416  Sum_probs=23.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +....+++|.|+||+||||.+..++..
T Consensus        26 ~~k~kiI~llGpPGsGKgTqa~~L~~~   52 (217)
T 3umf_A           26 LAKAKVIFVLGGPGSGKGTQCEKLVQK   52 (217)
T ss_dssp             TTSCEEEEEECCTTCCHHHHHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            666679999999999999998877754

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=93.59  E-value=0.043  Score=51.88  Aligned_cols=40  Identities=13%  Similarity=0.086  Sum_probs=30.8

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +.-++|.|+||+|||+++..++...... +.+++++++..-
T Consensus        29 ~~~vll~G~~GtGKt~la~~i~~~~~~~-~~~~~~v~~~~~   68 (265)
T 2bjv_A           29 DKPVLIIGERGTGKELIASRLHYLSSRW-QGPFISLNCAAL   68 (265)
T ss_dssp             CSCEEEECCTTSCHHHHHHHHHHTSTTT-TSCEEEEEGGGS
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHhcCcc-CCCeEEEecCCC
Confidence            3467899999999999998887665442 678888876543

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=93.57  E-value=0.043  Score=48.20  Aligned_cols=22  Identities=32%  Similarity=0.320  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++|.|+||+||||++..++..
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~   27 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKD   27 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            4789999999999998888754

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=93.55  E-value=0.039  Score=48.92  Aligned_cols=28  Identities=29%  Similarity=0.406  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeE
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKF  329 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~v  329 (539)
                      .+++|+|+||+||||++..++...    |.++
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l----g~~~   30 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKAL----GVGL   30 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH----TCCE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc----CCCE
Confidence            358899999999999988877542    6554

>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8

Probab=93.55  E-value=0.014  Score=56.57  Aligned_cols=32  Identities=22%  Similarity=0.370  Sum_probs=26.5

Q ss_pred             hhhhhccCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYNVLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++.++.+.+|+.+.|.|+||+|||||+..++-
T Consensus       164 ~~~L~~~~~G~~~~lvG~sG~GKSTLln~L~g  195 (307)
T 1t9h_A          164 LADIIPHFQDKTTVFAGQSGVGKSSLLNAISP  195 (307)
T ss_dssp             CTTTGGGGTTSEEEEEESHHHHHHHHHHHHCC
T ss_pred             HHHHHhhcCCCEEEEECCCCCCHHHHHHHhcc
Confidence            44555577899999999999999999887753

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=93.55  E-value=0.047  Score=49.12  Aligned_cols=23  Identities=17%  Similarity=0.198  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +++|.|++|+||||++..++..+
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l   24 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKL   24 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHhc
Confidence            57899999999999998887653

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=93.53  E-value=0.039  Score=55.84  Aligned_cols=32  Identities=25%  Similarity=0.261  Sum_probs=26.2

Q ss_pred             hhhhhc-cCCCcE--EEEEcCCCCChhHHHHHHHH
Q 009230          288 LNELYN-VLPGEL--TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       288 LD~~~~-l~~G~l--~~i~G~~G~GKT~~~~~la~  319 (539)
                      |+.+.- +.+|++  +.|.|++|+|||||+..++-
T Consensus        30 L~~vsl~i~~Gei~~vaLvG~nGaGKSTLln~L~G   64 (427)
T 2qag_B           30 DQLVNKSVSQGFCFNILCVGETGLGKSTLMDTLFN   64 (427)
T ss_dssp             HHHHHHSCC-CCEEEEEEECSTTSSSHHHHHHHHT
T ss_pred             cCCCceEecCCCeeEEEEECCCCCCHHHHHHHHhC
Confidence            665554 999999  99999999999999887653

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=93.51  E-value=0.047  Score=51.30  Aligned_cols=38  Identities=24%  Similarity=0.219  Sum_probs=27.6

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHh----cCCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEH----AGWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~----~g~~vl~~s~E  335 (539)
                      -++.|+|++|+||||++..++..+-..    .+..+++++++
T Consensus        23 ~iI~I~G~~GSGKST~a~~L~~~lg~~~~d~~~~~~~~i~~D   64 (252)
T 1uj2_A           23 FLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQD   64 (252)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTGGGSCGGGCSEEEEEGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhhhhcccccCCceEEEecC
Confidence            378999999999999998887653211    13457777766

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=93.50  E-value=0.036  Score=51.01  Aligned_cols=26  Identities=19%  Similarity=0.240  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINE  323 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~  323 (539)
                      ..++|.|++|+|||+++..++.....
T Consensus        46 ~~~ll~G~~G~GKT~l~~~~~~~~~~   71 (250)
T 1njg_A           46 HAYLFSGTRGVGKTSIARLLAKGLNC   71 (250)
T ss_dssp             SEEEEECSTTSCHHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            38899999999999999998876543

>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=93.49  E-value=1.3  Score=46.57  Aligned_cols=144  Identities=9%  Similarity=-0.011  Sum_probs=70.7

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcC------CeEEEEeCCCC-HHHHHHHHHHH---hhCCC---ccccccCCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAG------WKFVLCSMENK-VREHARKLLEK---HIKKP---FFEANYGGS  362 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g------~~vl~~s~E~~-~~~~~~r~~~~---~~~~~---~~~i~~~~~  362 (539)
                      .|.-+++.++||+|||...+-.+.+.+...+      .+++|++.--. ..++..++...   ..+..   ...+. +  
T Consensus       110 ~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~-g--  186 (563)
T 3i5x_A          110 EDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLV-G--  186 (563)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEEC-T--
T ss_pred             CCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEE-C--
Confidence            4678899999999999754443444333312      37888875422 23343333221   11111   11111 1  


Q ss_pred             CCCCCHHHHHHHHHHh-hcc-ceeEeecCCCCCCHHHHHHHHHHHH--HHcCCcEEEEccccccccCCCCCCCHHHHHHH
Q 009230          363 AERMTVEEFEQGKAWL-SNT-FSLIRCENDSLPSIKWVLDLAKAAV--LRHGVRGLVIDPYNELDHQRPVSQTETEYVSQ  438 (539)
Q Consensus       363 ~~~l~~~~~~~~~~~l-~~~-~~~i~~~~~~~~~~~~i~~~i~~~~--~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~  438 (539)
                        ..+.   ......+ ... .++|       .|++.+...+....  .-..+++||||-...+...     .-...+..
T Consensus       187 --~~~~---~~~~~~~~~~~~~Iiv-------~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~-----~f~~~~~~  249 (563)
T 3i5x_A          187 --GTDF---RAAMNKMNKLRPNIVI-------ATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEI-----GFRDDLET  249 (563)
T ss_dssp             --TSCH---HHHHHHHHHHCCSEEE-------ECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTST-----TTHHHHHH
T ss_pred             --CcCH---HHHHHHHhcCCCCEEE-------ECcHHHHHHHHhccccccccceEEEEeCHHHHhcc-----chHHHHHH
Confidence              1121   1111122 112 2333       14566665555432  2245899999966665532     12334445


Q ss_pred             HHHHHHHHHHH--hCcEEEEEec
Q 009230          439 MLTMVKRFAQH--HACHVWFVAH  459 (539)
Q Consensus       439 ~~~~Lk~lA~~--~~i~vi~~~q  459 (539)
                      ++..+......  .++.+++++-
T Consensus       250 i~~~l~~~~~~~~~~~~~l~~SA  272 (563)
T 3i5x_A          250 ISGILNEKNSKSADNIKTLLFSA  272 (563)
T ss_dssp             HHHHHHHHCSSCTTCCEEEEEES
T ss_pred             HHHhhhhccccCccCceEEEEEc
Confidence            55555433221  2677888876

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=93.48  E-value=0.044  Score=55.63  Aligned_cols=65  Identities=15%  Similarity=0.088  Sum_probs=50.2

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCC----eEEEEeCCCCHHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGW----KFVLCSMENKVREH  341 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~----~vl~~s~E~~~~~~  341 (539)
                      .....+.||+..+|-++-+.+|+=..|.|++|+|||+++.+|+.+... ++.    -++|...-+..+++
T Consensus       130 ~~~e~l~TGiraID~l~pigrGQr~~Ifgg~G~GKt~L~~~Ia~~~~~-~~d~~~~~~V~~~iGeR~~Ev  198 (465)
T 3vr4_D          130 YPDEFIQTGISAIDHLNTLVRGQKLPVFSGSGLPHKELAAQIARQATV-LDSSDDFAVVFAAIGITFEEA  198 (465)
T ss_dssp             CCCCBCBCSCHHHHTTSCCBTTCBCCEEECTTSCHHHHHHHHHHHCBC-SSCSSCEEEEEEEEEECHHHH
T ss_pred             CcccccccCceEEecccccccCCEEEEeCCCCcChHHHHHHHHHHHHh-ccCCCceEEEEEEecCCcHHH
Confidence            344568899999999988889988889999999999999887765432 122    67777777776655

>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=93.47  E-value=0.33  Score=58.07  Aligned_cols=143  Identities=11%  Similarity=0.046  Sum_probs=78.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHH-hcCCeEEEEeCCCC-HHHHHHHHHHHh---hCCCccccccCCCCCCCCH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINE-HAGWKFVLCSMENK-VREHARKLLEKH---IKKPFFEANYGGSAERMTV  368 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~-~~g~~vl~~s~E~~-~~~~~~r~~~~~---~~~~~~~i~~~~~~~~l~~  368 (539)
                      +..++-+++++|||+|||..+.-.+.+... ..+.+++|++.--. ..+....+....   .|+....+ .|    ..+.
T Consensus       939 ~~~~~nvlv~APTGSGKTliaelail~~l~~~~~~kavyi~P~raLa~q~~~~~~~~f~~~~g~~V~~l-tG----d~~~ 1013 (1724)
T 4f92_B          939 YNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLL-TG----ETST 1013 (1724)
T ss_dssp             HSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHHHTTTSCCCEEEC-CS----CHHH
T ss_pred             hcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCCCCEEEEEcChHHHHHHHHHHHHHHhchhcCCEEEEE-EC----CCCc
Confidence            456778999999999999866555544443 34678999976422 223333433322   22222211 11    1111


Q ss_pred             HHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHH---HHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHH
Q 009230          369 EEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAA---VLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKR  445 (539)
Q Consensus       369 ~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~---~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~  445 (539)
                       +    ...+....++|.       |++.+...++..   ..-.++++||||... ++..     .+...+..++..|+.
T Consensus      1014 -~----~~~~~~~~IiV~-------TPEkld~llr~~~~~~~l~~v~lvViDE~H-~l~d-----~rg~~le~il~rl~~ 1075 (1724)
T 4f92_B         1014 -D----LKLLGKGNIIIS-------TPEKWDILSRRWKQRKNVQNINLFVVDEVH-LIGG-----ENGPVLEVICSRMRY 1075 (1724)
T ss_dssp             -H----HHHHHHCSEEEE-------CHHHHHHHHTTTTTCHHHHSCSEEEECCGG-GGGS-----TTHHHHHHHHHHHHH
T ss_pred             -c----hhhcCCCCEEEE-------CHHHHHHHHhCcccccccceeeEEEeechh-hcCC-----CCCccHHHHHHHHHH
Confidence             1    112233334441       445443333321   112468999999665 4422     234556778888888


Q ss_pred             HHHHh--CcEEEEEec
Q 009230          446 FAQHH--ACHVWFVAH  459 (539)
Q Consensus       446 lA~~~--~i~vi~~~q  459 (539)
                      ++...  ++-+|++|-
T Consensus      1076 i~~~~~~~~riI~lSA 1091 (1724)
T 4f92_B         1076 ISSQIERPIRIVALSS 1091 (1724)
T ss_dssp             HHHTTSSCCEEEEEES
T ss_pred             HHhhcCCCceEEEEeC
Confidence            77654  677888876

>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=93.40  E-value=0.37  Score=45.31  Aligned_cols=52  Identities=15%  Similarity=0.070  Sum_probs=31.5

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHh------cCCeEEEEeCCCC-HHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEH------AGWKFVLCSMENK-VREHARKLL  346 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~------~g~~vl~~s~E~~-~~~~~~r~~  346 (539)
                      ..|.-+++.|++|+|||..++-.+...+..      .+..++|+..--. ..++..++.
T Consensus        89 ~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~  147 (262)
T 3ly5_A           89 LEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLK  147 (262)
T ss_dssp             HHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHH
T ss_pred             hCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHHHHHHHHH
Confidence            334557899999999997654444443332      3777888875322 334444443

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=93.34  E-value=0.051  Score=48.32  Aligned_cols=23  Identities=26%  Similarity=0.449  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .+++|.|+||+||||++..++..
T Consensus         7 ~~I~l~G~~GsGKsT~~~~L~~~   29 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999998877654

>3gqb_A V-type ATP synthase alpha chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_A* 3a5d_A 3j0j_A* 1um2_C

Probab=93.31  E-value=0.12  Score=53.53  Aligned_cols=65  Identities=23%  Similarity=0.160  Sum_probs=52.0

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHAR  343 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~  343 (539)
                      .....+.||+..+|-++-+.+|.-..|.|++|+|||+++.+++.+.   +..-++|...-+..+++..
T Consensus       200 ~~~epl~TGirvID~l~PigrGqr~~Ifg~~g~GKT~l~~~ia~~~---~~~v~V~~~iGER~~Ev~e  264 (578)
T 3gqb_A          200 DPNTPFLTGMRILDVLFPVAMGGTAAIPGPFGSGKSVTQQSLAKWS---NADVVVYVGSGERGNEMTD  264 (578)
T ss_dssp             CSCSEECCSCHHHHTTSCEETTCEEEECCCTTSCHHHHHHHHHHHS---SCSEEEEEEEEECHHHHHH
T ss_pred             cCCCcccccchhhhhcccccCCCEEeeeCCCCccHHHHHHHHHhcc---CCCEEEEEEecccHHHHHH
Confidence            3446788999999999889999999999999999999999887552   2445677777777776543

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=93.30  E-value=0.11  Score=47.30  Aligned_cols=38  Identities=13%  Similarity=0.355  Sum_probs=30.4

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCC-eEEEEeCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGW-KFVLCSME  335 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~-~vl~~s~E  335 (539)
                      +|-+++|.|++|+||||.+..++..+... |. .| .++-|
T Consensus         2 ~g~~i~~eG~~gsGKsT~~~~l~~~l~~~-~~~~v-~~~re   40 (213)
T 4tmk_A            2 RSKYIVIEGLEGAGKTTARNVVVETLEQL-GIRDM-VFTRE   40 (213)
T ss_dssp             CCCEEEEEECTTSCHHHHHHHHHHHHHHT-TCCCE-EEEES
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc-CCCcc-eeeeC
Confidence            47899999999999999999998877664 77 55 44445

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=93.28  E-value=0.047  Score=47.72  Aligned_cols=22  Identities=14%  Similarity=0.092  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +++|.|+||+||||++..++..
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~   25 (173)
T 1e6c_A            4 PIFMVGARGCGMTTVGRELARA   25 (173)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            6889999999999998887754

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=93.25  E-value=0.049  Score=56.03  Aligned_cols=37  Identities=14%  Similarity=0.194  Sum_probs=29.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-CeEE
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAG-WKFV  330 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-~~vl  330 (539)
                      +.+|+.+.|.|++|+|||||+.-++--.....| .++.
T Consensus       135 i~~Ge~v~IvGpnGsGKSTLlr~L~Gl~~p~~G~~pI~  172 (460)
T 2npi_A          135 NFEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLY  172 (460)
T ss_dssp             SSSCCCEEEEESTTSSHHHHHHHHHHTTHHHHCCCCEE
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhCcccccCCceeEE
Confidence            889999999999999999998887755444335 3344

>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=93.24  E-value=0.034  Score=50.45  Aligned_cols=24  Identities=25%  Similarity=0.350  Sum_probs=21.4

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICNINE  323 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~  323 (539)
                      ++|.|+||+|||+++..++..+..
T Consensus        41 ~ll~G~~G~GKT~l~~~l~~~~~~   64 (226)
T 2chg_A           41 LLFSGPPGTGKTATAIALARDLFG   64 (226)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHG
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhc
Confidence            899999999999999999877654

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=93.21  E-value=0.047  Score=55.36  Aligned_cols=66  Identities=15%  Similarity=0.130  Sum_probs=50.5

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHh----------cCCeEEEEeCCCCHHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEH----------AGWKFVLCSMENKVREH  341 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~----------~g~~vl~~s~E~~~~~~  341 (539)
                      .....+.||+..+|-++-+.+|+=..|.|++|+|||+++.+|+.+...+          .+.-++|...-+..+++
T Consensus       126 ~~~e~l~TGiraID~l~pigrGQr~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev  201 (464)
T 3gqb_B          126 KPEQFIQTGISTIDVMNTLVRGQKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQREL  201 (464)
T ss_dssp             CCCCBCBCSCHHHHTTSCCBTTCBCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHH
T ss_pred             CccccccCcceeeecccccccCCEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHH
Confidence            4456789999999999889999888899999999999998887654321          11267777777776655

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=93.19  E-value=0.083  Score=49.62  Aligned_cols=31  Identities=23%  Similarity=0.301  Sum_probs=24.5

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ++|.|+||+|||+++..++...    +.++++++.
T Consensus        48 vll~G~~GtGKT~la~~la~~~----~~~~~~i~~   78 (257)
T 1lv7_A           48 VLMVGPPGTGKTLLAKAIAGEA----KVPFFTISG   78 (257)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH----TCCEEEECS
T ss_pred             EEEECcCCCCHHHHHHHHHHHc----CCCEEEEeH
Confidence            8899999999999998887542    567766653

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=93.18  E-value=0.058  Score=49.15  Aligned_cols=22  Identities=23%  Similarity=0.484  Sum_probs=18.7

Q ss_pred             EEEEEcCCCCChhHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++|.|+||+||||++..++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEK   23 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3689999999999998887654

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=93.14  E-value=0.045  Score=57.61  Aligned_cols=41  Identities=27%  Similarity=0.268  Sum_probs=32.3

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +.+|+++.|.|++|+||||++..++..+-...|..+.++..
T Consensus       366 ~~~G~iI~LiG~sGSGKSTLar~La~~L~~~~G~~i~~lDg  406 (552)
T 3cr8_A          366 ERQGFTVFFTGLSGAGKSTLARALAARLMEMGGRCVTLLDG  406 (552)
T ss_dssp             GGSCEEEEEEESSCHHHHHHHHHHHHHHHTTCSSCEEEESS
T ss_pred             cccceEEEEECCCCChHHHHHHHHHHhhcccCCceEEEECC
Confidence            67899999999999999999998887765432346666654

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=93.10  E-value=0.092  Score=48.44  Aligned_cols=40  Identities=18%  Similarity=0.366  Sum_probs=29.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc---CCeEEEEe
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHA---GWKFVLCS  333 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~---g~~vl~~s  333 (539)
                      ..+|-+++|.|++|+||||.+..++..+...+   |.+|.+..
T Consensus        22 m~~g~~I~~eG~~GsGKsT~~~~l~~~l~~~~~~~g~~v~~~r   64 (227)
T 3v9p_A           22 MARGKFITFEGIDGAGKTTHLQWFCDRLQERLGPAGRHVVVTR   64 (227)
T ss_dssp             -CCCCEEEEECCC---CHHHHHHHHHHHHHHHGGGTCCEEEEE
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHhhccccceeeeeec
Confidence            56788999999999999999999987775532   78886543

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=93.09  E-value=0.044  Score=54.05  Aligned_cols=29  Identities=38%  Similarity=0.469  Sum_probs=24.4

Q ss_pred             cCCCcE--EEEEcCCCCChhHHHHHHHHHHH
Q 009230          294 VLPGEL--TIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       294 l~~G~l--~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      +..|++  +++.|+||+|||+++..++..+.
T Consensus        41 i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~   71 (340)
T 1sxj_C           41 VDEGKLPHLLFYGPPGTGKTSTIVALAREIY   71 (340)
T ss_dssp             HHTTCCCCEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Confidence            455666  89999999999999999987764

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=93.09  E-value=0.11  Score=57.22  Aligned_cols=52  Identities=19%  Similarity=0.374  Sum_probs=41.9

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH-HHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV-REHARKLLE  347 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~-~~~~~r~~~  347 (539)
                      .+.+++|.|+||+|||+.+..++..+....+.+|++++.-..+ .++..|+..
T Consensus       374 ~~~~~lI~GppGTGKT~~i~~~i~~l~~~~~~~ILv~a~tn~A~d~l~~rL~~  426 (802)
T 2xzl_A          374 QRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRD  426 (802)
T ss_dssp             TCSEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEESSHHHHHHHHHHHHH
T ss_pred             cCCCEEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEEcCcHHHHHHHHHHHHh
Confidence            3569999999999999999999888776448899999877554 567777754

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=93.08  E-value=0.057  Score=49.75  Aligned_cols=26  Identities=19%  Similarity=0.259  Sum_probs=20.7

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++-+++|.|+||+||||++..++..
T Consensus         5 ~~~~~I~l~G~~GsGKsT~a~~La~~   30 (227)
T 1zd8_A            5 ARLLRAVIMGAPGSGKGTVSSRITTH   30 (227)
T ss_dssp             --CCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             ccCcEEEEECCCCCCHHHHHHHHHHH
Confidence            34568999999999999998877654

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=93.08  E-value=0.16  Score=49.81  Aligned_cols=34  Identities=24%  Similarity=0.433  Sum_probs=28.3

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .+++|.|++|+|||+++.+++...    +.+++|+++.
T Consensus        31 ~~v~i~G~~G~GKT~L~~~~~~~~----~~~~~~~~~~   64 (357)
T 2fna_A           31 PITLVLGLRRTGKSSIIKIGINEL----NLPYIYLDLR   64 (357)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHH----TCCEEEEEGG
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhc----CCCEEEEEch
Confidence            489999999999999999887653    3457899876

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=93.06  E-value=0.33  Score=55.53  Aligned_cols=116  Identities=16%  Similarity=0.129  Sum_probs=66.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHHHHh-hCCCccccccCCCCCCCCHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLLEKH-IKKPFFEANYGGSAERMTVEEF  371 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~~~~-~~~~~~~i~~~~~~~~l~~~~~  371 (539)
                      +..|.-+++.|+||+|||.+.+-.+...+. .|..+++++.--. ..++..++.... .++....+. +    ..+..+.
T Consensus        90 il~g~dvlv~ApTGSGKTl~~l~~il~~~~-~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~-G----g~~~~er  163 (1104)
T 4ddu_A           90 IVQGKSFTMVAPTGVGKTTFGMMTALWLAR-KGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFY-S----SMKKEEK  163 (1104)
T ss_dssp             HTTTCCEEECCSTTCCHHHHHHHHHHHHHT-TTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEEC-T----TCCTTHH
T ss_pred             HHcCCCEEEEeCCCCcHHHHHHHHHHHHHh-cCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEe-C----CCCHHHH
Confidence            445667889999999999987777777665 4888999986633 344555543311 122222221 2    3333233


Q ss_pred             HHHHHHhhcc-c-eeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccc
Q 009230          372 EQGKAWLSNT-F-SLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELD  423 (539)
Q Consensus       372 ~~~~~~l~~~-~-~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~  423 (539)
                      ......+... . ++|       .|+..+.+.+.. ....++++||||-...+.
T Consensus       164 ~~~~~~l~~g~~~IlV-------~Tp~rL~~~l~~-l~~~~l~~lViDEaH~l~  209 (1104)
T 4ddu_A          164 EKFEKSFEEDDYHILV-------FSTQFVSKNREK-LSQKRFDFVFVDDVDAVL  209 (1104)
T ss_dssp             HHHHHHHHTSCCSEEE-------EEHHHHHHSHHH-HHTSCCSEEEESCHHHHT
T ss_pred             HHHHHHHhCCCCCEEE-------ECHHHHHHHHHh-hcccCcCEEEEeCCCccc
Confidence            3333344432 2 333       135555554443 344679999999665544

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=93.06  E-value=0.06  Score=47.34  Aligned_cols=37  Identities=19%  Similarity=0.374  Sum_probs=28.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      +.+.|.|++|+||||++.-++...... |.++..+...
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~~~-g~~~G~I~~d   39 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILRER-GLRVAVVKRH   39 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHHHT-TCCEEEEEC-
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhhc-CCceEEEEEc
Confidence            468899999999999999888776653 6666666554

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=93.04  E-value=0.069  Score=49.87  Aligned_cols=26  Identities=31%  Similarity=0.280  Sum_probs=21.8

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++-+++|.|+||+||||++..++..
T Consensus        27 ~~~~~I~l~G~~GsGKsT~a~~L~~~   52 (243)
T 3tlx_A           27 KPDGRYIFLGAPGSGKGTQSLNLKKS   52 (243)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            35568999999999999998887754

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=93.01  E-value=0.051  Score=48.47  Aligned_cols=22  Identities=23%  Similarity=0.492  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +++|+||||+||||++..+...
T Consensus         3 pIVi~GPSG~GK~Tl~~~L~~~   24 (186)
T 1ex7_A            3 PIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            5899999999999998776644

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=93.01  E-value=0.068  Score=46.50  Aligned_cols=29  Identities=21%  Similarity=0.221  Sum_probs=23.1

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      ..++|.|.+|+||||++..++..    .|.+++
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~----lg~~~i   36 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLA----LKLEVL   36 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHH----HTCCEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH----hCCCEE
Confidence            47889999999999998877654    366654

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=93.00  E-value=0.058  Score=49.50  Aligned_cols=24  Identities=21%  Similarity=0.357  Sum_probs=20.7

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +-+++|.|+||+||||++..++..
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~   28 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTK   28 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999998887755

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=92.98  E-value=0.052  Score=53.19  Aligned_cols=32  Identities=22%  Similarity=0.184  Sum_probs=25.0

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .+++|+|+||+|||||+..++..+    +  +.++|.+
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l----~--~~iis~D   39 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKF----N--GEIISGD   39 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT----T--EEEEECC
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHc----C--Cceeccc
Confidence            388999999999999988877542    3  5566765

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=92.97  E-value=0.024  Score=55.73  Aligned_cols=28  Identities=32%  Similarity=0.490  Sum_probs=24.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +.+|++++|.|++|+||||++.-++...
T Consensus       168 i~~g~~v~i~G~~GsGKTTll~~l~g~~  195 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTTYIKSIMEFI  195 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHHHHHHGGGGS
T ss_pred             ccCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            7889999999999999999987766543

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=92.95  E-value=0.069  Score=48.99  Aligned_cols=24  Identities=17%  Similarity=0.284  Sum_probs=20.1

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +..+.|.|++|+||||++..++..
T Consensus         5 ~~~i~i~G~~GsGKSTl~~~L~~~   28 (227)
T 1cke_A            5 APVITIDGPSGAGKGTLCKAMAEA   28 (227)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999998877654

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=92.89  E-value=0.043  Score=53.18  Aligned_cols=32  Identities=28%  Similarity=0.560  Sum_probs=25.9

Q ss_pred             hhhhhhccCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          287 ALNELYNVLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       287 ~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      .+++++.+..|+++.|.|++|+||||++..++
T Consensus       159 gv~~lf~~l~geiv~l~G~sG~GKSTll~~l~  190 (301)
T 1u0l_A          159 GIEELKEYLKGKISTMAGLSGVGKSSLLNAIN  190 (301)
T ss_dssp             THHHHHHHHSSSEEEEECSTTSSHHHHHHHHS
T ss_pred             CHHHHHHHhcCCeEEEECCCCCcHHHHHHHhc
Confidence            35566665678999999999999999977665

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=92.88  E-value=0.052  Score=53.69  Aligned_cols=31  Identities=35%  Similarity=0.617  Sum_probs=24.2

Q ss_pred             hhhhhccCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          288 LNELYNVLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       288 LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      ++.+....+|+++.|.|+||+|||||+..++
T Consensus       206 l~~L~~~~~G~~~~lvG~sG~GKSTLln~L~  236 (358)
T 2rcn_A          206 LKPLEEALTGRISIFAGQSGVGKSSLLNALL  236 (358)
T ss_dssp             HHHHHHHHTTSEEEEECCTTSSHHHHHHHHH
T ss_pred             HHHHHHhcCCCEEEEECCCCccHHHHHHHHh
Confidence            3444334479999999999999999987665

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=92.86  E-value=0.072  Score=46.26  Aligned_cols=28  Identities=25%  Similarity=0.170  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      .++|.|.+|+||||++..++...    |.+++
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l----~~~~i   29 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSL----NIPFY   29 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHH----TCCEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh----CCCEE
Confidence            47899999999999988877542    55543

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=92.84  E-value=0.074  Score=47.90  Aligned_cols=23  Identities=26%  Similarity=0.465  Sum_probs=19.8

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .+++|.|++|+||||++..++..
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~   38 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKD   38 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            47999999999999998877644

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=92.83  E-value=0.93  Score=48.00  Aligned_cols=144  Identities=10%  Similarity=0.020  Sum_probs=69.4

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhc------CCeEEEEeCCCC-HHHHHHHHHHHh---hCCC---ccccccCCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHA------GWKFVLCSMENK-VREHARKLLEKH---IKKP---FFEANYGGS  362 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~------g~~vl~~s~E~~-~~~~~~r~~~~~---~~~~---~~~i~~~~~  362 (539)
                      .|.-+++.++||+|||...+-.+...+...      +.++++++.--. ..++..++....   .+..   ...+. +  
T Consensus        59 ~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~-g--  135 (579)
T 3sqw_A           59 EDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLV-G--  135 (579)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEEC-T--
T ss_pred             CCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEE-C--
Confidence            467788999999999974443344433321      247888875422 233443333221   1111   11111 1  


Q ss_pred             CCCCCHHHHHHHHHHhhc-c-ceeEeecCCCCCCHHHHHHHHHHH--HHHcCCcEEEEccccccccCCCCCCCHHHHHHH
Q 009230          363 AERMTVEEFEQGKAWLSN-T-FSLIRCENDSLPSIKWVLDLAKAA--VLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQ  438 (539)
Q Consensus       363 ~~~l~~~~~~~~~~~l~~-~-~~~i~~~~~~~~~~~~i~~~i~~~--~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~  438 (539)
                        ..+   +......+.. . .++|       .|++.+...+...  .....+++||||-...+...     .-...+..
T Consensus       136 --g~~---~~~~~~~l~~~~~~IlV-------~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~-----gf~~~~~~  198 (579)
T 3sqw_A          136 --GTD---FRAAMNKMNKLRPNIVI-------ATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEI-----GFRDDLET  198 (579)
T ss_dssp             --TSC---HHHHHHHHHHHCCSEEE-------ECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTST-----TTHHHHHH
T ss_pred             --Ccc---HHHHHHHHhcCCCCEEE-------ECHHHHHHHHHhccccccccCCEEEEEChHHhhcC-----CCHHHHHH
Confidence              111   1111122211 2 2333       1456666555543  12246899999966665432     12233444


Q ss_pred             HHHHHHHHHHH--hCcEEEEEec
Q 009230          439 MLTMVKRFAQH--HACHVWFVAH  459 (539)
Q Consensus       439 ~~~~Lk~lA~~--~~i~vi~~~q  459 (539)
                      ++..+......  .++.+++++-
T Consensus       199 i~~~l~~~~~~~~~~~~~l~~SA  221 (579)
T 3sqw_A          199 ISGILNEKNSKSADNIKTLLFSA  221 (579)
T ss_dssp             HHHHHHHHCSSCTTCCEEEEEES
T ss_pred             HHHHhhhhhcccccCceEEEEec
Confidence            44444332211  1678888876

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=92.82  E-value=0.061  Score=47.62  Aligned_cols=23  Identities=26%  Similarity=0.556  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .+.|.|++|+|||||+.-++-..
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l   24 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            46899999999999998877554

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=92.78  E-value=0.063  Score=51.85  Aligned_cols=33  Identities=18%  Similarity=0.100  Sum_probs=24.8

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      +.+++|+||||+|||+++..++..      .+..++|.+
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~------~~~~iis~D   35 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKR------LNGEVISGD   35 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHT------TTEEEEECC
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHh------CccceeecC
Confidence            358899999999999998877643      334556654

>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=92.78  E-value=0.09  Score=56.48  Aligned_cols=50  Identities=16%  Similarity=0.375  Sum_probs=39.7

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH-HHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV-REHARKLL  346 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~-~~~~~r~~  346 (539)
                      +.+++|.|+||+|||+++..++..+....+.+|++++.-..+ .++..|+.
T Consensus       195 ~~~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv~a~tn~A~~~l~~~l~  245 (624)
T 2gk6_A          195 RPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIH  245 (624)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEEEESSHHHHHHHHHHHH
T ss_pred             CCCeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEeCcHHHHHHHHHHHH
Confidence            569999999999999999999988776347899998876544 45666654

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=92.76  E-value=0.068  Score=48.90  Aligned_cols=30  Identities=23%  Similarity=0.325  Sum_probs=23.6

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      |-.++|.|+||+||||++..++...    |.+++
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~~l----~~~~i   34 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKKEY----GLAHL   34 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHH----CCEEE
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh----CceEE
Confidence            4578999999999999988887653    55544

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=92.74  E-value=0.073  Score=49.28  Aligned_cols=23  Identities=26%  Similarity=0.252  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      -++.|.|+||+||||++..++..
T Consensus        10 ~~i~i~G~~GsGKsTla~~la~~   32 (233)
T 3r20_A           10 LVVAVDGPAGTGKSSVSRGLARA   32 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            37999999999999998877655

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=92.69  E-value=0.077  Score=48.21  Aligned_cols=22  Identities=23%  Similarity=0.382  Sum_probs=18.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++|.|+||+||||.+..++.+
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~   23 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKE   23 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4678899999999998877754

>3ez2_A Plasmid partition protein A; type IA, DNA binding, winged-HTH, DNA bindin; HET: ADP EPE; 2.05A {Escherichia coli} PDB: 3ez6_A* 3ez7_A

Probab=92.63  E-value=0.09  Score=53.04  Aligned_cols=40  Identities=8%  Similarity=0.066  Sum_probs=33.6

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHH-----hcCCeEEEEeCCCCH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINE-----HAGWKFVLCSMENKV  338 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~-----~~g~~vl~~s~E~~~  338 (539)
                      +.+..+..|+||||++.++|..++.     ..|.+|+++.++...
T Consensus       111 Iav~s~KGGvGKTT~a~nLA~~La~~~~~~~~g~rVlliD~D~q~  155 (398)
T 3ez2_A          111 IFISNLKGGVSKTVSTVSLAHAMRAHPHLLMEDLRILVIDLDPQS  155 (398)
T ss_dssp             EEECCSSSSSSHHHHHHHHHHHHHHCTTTGGGCCCEEEEEECTTC
T ss_pred             EEEEeCCCCccHHHHHHHHHHHHHhcchhhcCCCeEEEEeCCCCC
Confidence            4555588999999999999999985     349999999999643

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=92.63  E-value=0.07  Score=51.42  Aligned_cols=33  Identities=21%  Similarity=0.155  Sum_probs=25.0

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ..+++|+||||+|||+++..++..      .+..++|.+
T Consensus        10 ~~~i~i~GptgsGKt~la~~La~~------~~~~iis~D   42 (316)
T 3foz_A           10 PKAIFLMGPTASGKTALAIELRKI------LPVELISVD   42 (316)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHH------SCEEEEECC
T ss_pred             CcEEEEECCCccCHHHHHHHHHHh------CCCcEEecc
Confidence            358999999999999998887644      234456655

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=92.63  E-value=0.067  Score=48.74  Aligned_cols=22  Identities=18%  Similarity=0.398  Sum_probs=18.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++|.|+||+||||++..++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEK   23 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3678999999999998877643

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=92.62  E-value=0.1  Score=50.19  Aligned_cols=34  Identities=18%  Similarity=0.172  Sum_probs=26.7

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .-++|.|+||+|||+++..++...    +.++++++..
T Consensus        51 ~~vll~G~~GtGKT~la~~la~~l----~~~~~~i~~~   84 (310)
T 1ofh_A           51 KNILMIGPTGVGKTEIARRLAKLA----NAPFIKVEAT   84 (310)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH----TCCEEEEEGG
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh----CCCEEEEcch
Confidence            457799999999999999887653    5677777653

>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=92.58  E-value=0.099  Score=49.59  Aligned_cols=33  Identities=18%  Similarity=0.329  Sum_probs=26.1

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      ..-++|.|+||+|||+++..++..    .+.+++.++
T Consensus        64 ~~~vLl~G~~GtGKT~la~~ia~~----~~~~~~~i~   96 (272)
T 1d2n_A           64 LVSVLLEGPPHSGKTALAAKIAEE----SNFPFIKIC   96 (272)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHH----HTCSEEEEE
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHH----hCCCEEEEe
Confidence            357889999999999999888765    266766664

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=92.48  E-value=0.11  Score=53.84  Aligned_cols=63  Identities=17%  Similarity=0.206  Sum_probs=49.2

Q ss_pred             CccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH
Q 009230          277 DEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA  342 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~  342 (539)
                      ....+.||+..+|-++-+.+|.-..|.|++|+|||+++.+++.+ +  +..-++|...-+..+++.
T Consensus       207 ~~epl~TGirvID~l~PigkGqr~~I~g~~g~GKT~L~~~ia~~-~--~~~~~V~~~iGER~~Ev~  269 (588)
T 3mfy_A          207 PEVPLITGQRVIDTFFPQAKGGTAAIPGPAGSGKTVTQHQLAKW-S--DAQVVIYIGCGERGNEMT  269 (588)
T ss_dssp             SCSEECCSCHHHHHHSCEETTCEEEECSCCSHHHHHHHHHHHHH-S--SCSEEEEEECCSSSSHHH
T ss_pred             CCcccccCcchhhccCCcccCCeEEeecCCCCCHHHHHHHHHhc-c--CCCEEEEEEecccHHHHH
Confidence            34568899999999988999999999999999999999887644 1  234566777666665543

>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=92.45  E-value=0.15  Score=49.74  Aligned_cols=36  Identities=14%  Similarity=0.242  Sum_probs=29.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .+++++|+||+|||+++..++..    .+.++++++....
T Consensus        49 ~~~L~~G~~G~GKT~la~~la~~----l~~~~~~i~~~~~   84 (324)
T 3u61_B           49 HIILHSPSPGTGKTTVAKALCHD----VNADMMFVNGSDC   84 (324)
T ss_dssp             SEEEECSSTTSSHHHHHHHHHHH----TTEEEEEEETTTC
T ss_pred             eEEEeeCcCCCCHHHHHHHHHHH----hCCCEEEEccccc
Confidence            48899999999999998887654    3788999987654

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=92.44  E-value=0.096  Score=48.45  Aligned_cols=25  Identities=28%  Similarity=0.397  Sum_probs=21.4

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++-.++|.|+||+||||++..++..
T Consensus        15 ~~~~I~l~G~~GsGKsT~a~~La~~   39 (233)
T 1ak2_A           15 KGVRAVLLGPPGAGKGTQAPKLAKN   39 (233)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3458999999999999998888765

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=92.43  E-value=0.083  Score=48.55  Aligned_cols=23  Identities=17%  Similarity=0.105  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +++|.|+||+||||++..++...
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999988887653

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=92.42  E-value=0.072  Score=48.14  Aligned_cols=21  Identities=24%  Similarity=0.219  Sum_probs=18.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++.|.|++|+||||++..++.
T Consensus         4 ~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999887754

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=92.40  E-value=0.087  Score=45.07  Aligned_cols=25  Identities=32%  Similarity=0.620  Sum_probs=21.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |.+| +++|.|++|+|||+++-.+..
T Consensus        21 f~~g-~~~I~G~NGsGKStil~Ai~~   45 (149)
T 1f2t_A           21 FKEG-INLIIGQNGSGKSSLLDAILV   45 (149)
T ss_dssp             CCSE-EEEEECCTTSSHHHHHHHHHH
T ss_pred             cCCC-eEEEECCCCCCHHHHHHHHHH
Confidence            5555 999999999999999876654

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=92.38  E-value=0.077  Score=51.60  Aligned_cols=32  Identities=22%  Similarity=0.222  Sum_probs=24.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .+++|+|+||+||||++..++..    .+  ..+++.+
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~----l~--~~iis~D   37 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADA----LP--CELISVD   37 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHH----SC--EEEEEEC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH----cC--CcEEecc
Confidence            48999999999999998877644    23  4556654

>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=92.38  E-value=0.46  Score=42.53  Aligned_cols=54  Identities=15%  Similarity=0.031  Sum_probs=32.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHH-----hcCCeEEEEeCCC-CHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINE-----HAGWKFVLCSMEN-KVREHARKLLE  347 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~-----~~g~~vl~~s~E~-~~~~~~~r~~~  347 (539)
                      +..|.-+++.+++|+|||..+...+.....     ..+.+++|+..-- -..++..++..
T Consensus        35 ~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~   94 (207)
T 2gxq_A           35 ALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTA   94 (207)
T ss_dssp             HHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHHHHHHHHH
T ss_pred             HcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHHHHHHHHH
Confidence            334566889999999999765554444432     1356788886542 23444444433

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=92.28  E-value=0.047  Score=56.98  Aligned_cols=28  Identities=29%  Similarity=0.325  Sum_probs=24.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +..|+.++|+|++|+||||++..++..+
T Consensus       257 v~~g~~i~I~GptGSGKTTlL~aL~~~i  284 (511)
T 2oap_1          257 IEHKFSAIVVGETASGKTTTLNAIMMFI  284 (511)
T ss_dssp             HHTTCCEEEEESTTSSHHHHHHHHGGGS
T ss_pred             HhCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            7889999999999999999988766443

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=92.27  E-value=0.052  Score=50.20  Aligned_cols=35  Identities=14%  Similarity=0.135  Sum_probs=27.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      ..+|+++.|.|++|+||||++..++..     +..|.+..
T Consensus        17 ~~~g~~i~i~G~~GsGKSTl~~~L~~~-----~g~v~~~~   51 (230)
T 2vp4_A           17 GTQPFTVLIEGNIGSGKTTYLNHFEKY-----KNDICLLT   51 (230)
T ss_dssp             TCCCEEEEEECSTTSCHHHHHHTTGGG-----TTTEEEEC
T ss_pred             CCCceEEEEECCCCCCHHHHHHHHHhc-----cCCeEEEe
Confidence            678999999999999999998776543     44565543

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=92.26  E-value=0.073  Score=47.99  Aligned_cols=29  Identities=21%  Similarity=0.033  Sum_probs=22.7

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEE
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLC  332 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~  332 (539)
                      .+.|.|++|+||||++..++.     .|.++++.
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-----~g~~~i~~   31 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-----LGAYVLDA   31 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-----TTCEEEEH
T ss_pred             EEEEECCCCcCHHHHHHHHHH-----CCCEEEEc
Confidence            578999999999999887764     26666654

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=92.18  E-value=0.092  Score=50.04  Aligned_cols=34  Identities=24%  Similarity=0.412  Sum_probs=25.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +++|  ++|.|+||+|||+++..++...    +.+.++++
T Consensus        72 ~~~g--vll~Gp~GtGKTtl~~~i~~~~----~~~~i~~~  105 (278)
T 1iy2_A           72 IPKG--VLLVGPPGVGKTHLARAVAGEA----RVPFITAS  105 (278)
T ss_dssp             CCCE--EEEECCTTSSHHHHHHHHHHHT----TCCEEEEE
T ss_pred             CCCe--EEEECCCcChHHHHHHHHHHHc----CCCEEEec
Confidence            6677  8899999999999988777542    34555554

>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=92.18  E-value=0.18  Score=51.84  Aligned_cols=56  Identities=18%  Similarity=0.207  Sum_probs=40.4

Q ss_pred             cCCCcEEEEEcCCCCChhHH-HHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEW-IDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~-~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      +..|..+++.|+||+|||+. ++.++..+.. .+.+++|++.   -..++..+.....|.+
T Consensus        18 l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~-~~~~~lvl~P---tr~La~Q~~~~l~g~~   74 (459)
T 2z83_A           18 LRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ-QRLRTAVLAP---TRVVAAEMAEALRGLP   74 (459)
T ss_dssp             GSTTCEEEECCCTTSCTTTTHHHHHHHHHHH-TTCCEEEEEC---SHHHHHHHHHHTTTSC
T ss_pred             HhcCCcEEEECCCCCCHHHHHHHHHHHHHHh-CCCcEEEECc---hHHHHHHHHHHhcCce
Confidence            77889999999999999985 6666666555 4888999983   3445555554444544

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=92.16  E-value=1.5  Score=39.57  Aligned_cols=39  Identities=10%  Similarity=0.009  Sum_probs=26.6

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHh--cCCeEEEEeCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEH--AGWKFVLCSME  335 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~--~g~~vl~~s~E  335 (539)
                      |.-+++.+++|+|||..++-.+......  .+.+++|+..-
T Consensus        51 ~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt   91 (220)
T 1t6n_A           51 GMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHT   91 (220)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSC
T ss_pred             CCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCC
Confidence            4458899999999997766555554332  13478888743

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=92.15  E-value=0.047  Score=49.32  Aligned_cols=31  Identities=23%  Similarity=0.280  Sum_probs=25.8

Q ss_pred             hhhhhhccCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          287 ALNELYNVLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       287 ~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      .++. +.+.+|..++|.|++|+|||||+..++
T Consensus        17 ~l~~-~~~~~~~~v~lvG~~g~GKSTLl~~l~   47 (210)
T 1pui_A           17 DIRH-LPSDTGIEVAFAGRSNAGKSSALNTLT   47 (210)
T ss_dssp             SGGG-SSCSCSEEEEEEECTTSSHHHHHTTTC
T ss_pred             CHhH-CCCCCCcEEEEECCCCCCHHHHHHHHh
Confidence            4444 458899999999999999999987765

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=92.09  E-value=0.18  Score=51.61  Aligned_cols=39  Identities=23%  Similarity=0.220  Sum_probs=28.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ..+..-++|.|+||+|||+++..++..+   .+.++++++..
T Consensus       164 ~~~~~~vLL~GppGtGKT~lA~aia~~~---~~~~~~~v~~~  202 (444)
T 2zan_A          164 RTPWRGILLFGPPGTGKSYLAKAVATEA---NNSTFFSISSS  202 (444)
T ss_dssp             GCCCSEEEEECSTTSSHHHHHHHHHHHC---CSSEEEEECCC
T ss_pred             CCCCceEEEECCCCCCHHHHHHHHHHHc---CCCCEEEEeHH
Confidence            3444578899999999999998887653   26677666543

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=92.08  E-value=0.11  Score=55.13  Aligned_cols=37  Identities=24%  Similarity=0.190  Sum_probs=31.2

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +|.+++|.|.||+||||++..++..+... |.+++++.
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L~~~-G~~~v~lD   87 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYLVCH-GIPCYTLD   87 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEES
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHHhc-CCeEEEec
Confidence            56799999999999999999999877654 88877764

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=92.02  E-value=0.1  Score=46.86  Aligned_cols=30  Identities=30%  Similarity=0.216  Sum_probs=23.5

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      ..++.|+|++||||||++..++..    .|.+++
T Consensus        12 ~~iIgltG~~GSGKSTva~~L~~~----lg~~vi   41 (192)
T 2grj_A           12 HMVIGVTGKIGTGKSTVCEILKNK----YGAHVV   41 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHH----HCCEEE
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh----cCCEEE
Confidence            357889999999999998877754    266654

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=92.01  E-value=0.096  Score=52.44  Aligned_cols=24  Identities=21%  Similarity=0.350  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .+++|+||||+|||+++..++...
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~   26 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKF   26 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             cEEEEECcchhhHHHHHHHHHHHC
Confidence            488999999999999999988664

>4a8j_A Elongator complex protein 4; transcription; 2.10A {Saccharomyces cerevisiae} PDB: 4ejs_A

Probab=92.00  E-value=0.1  Score=51.06  Aligned_cols=90  Identities=11%  Similarity=0.081  Sum_probs=56.3

Q ss_pred             CHHHHHHHHHHHHHHcC--CcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHh--CcEEEEEecCCCCCCCCCC
Q 009230          394 SIKWVLDLAKAAVLRHG--VRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHH--ACHVWFVAHPRQLHNWVGE  469 (539)
Q Consensus       394 ~~~~i~~~i~~~~~~~~--~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~--~i~vi~~~q~r~~~~~~~~  469 (539)
                      ....++..+...+....  +-.|+|=|+..-.-... .......+-.++..||.|.+.+  +++++++...--.      
T Consensus       199 ~y~~lL~~I~~~i~~~~~~ilRIvI~SLgSP~wy~~-~~~~~~~ll~FL~~LRaLlR~~~~~~v~~iTlP~~l~------  271 (361)
T 4a8j_A          199 PVSTILSQIEQTIKRNDKKLIRIVIPSLLHPAMYPP-KMFESSEIIGLMHGVRSLVKKYYERVVLFASISIDII------  271 (361)
T ss_dssp             CHHHHHHHHHHHHHHTTTSEEEEEETTTTCTTTSCG-GGGBHHHHHHHHHHHHHHHHHTTTTEEEEEEEECTTS------
T ss_pred             hHHHHHHHHHHHHhcCCCceEEEEecCCCCcccCCC-cccCHHHHHHHHHHHHHHHhhcCCceEEEEEEChHHc------
Confidence            56678888877765533  44677776665432111 1123456788999999999987  4455555442111      


Q ss_pred             CCCcccccccccchhccceEEEEEeC
Q 009230          470 PPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       470 ~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                       +.  .  =...++..+|.||.|..-
T Consensus       272 -~~--~--l~~rle~l~D~vi~L~pF  292 (361)
T 4a8j_A          272 -TP--P--LLVLLRNMFDSVINLEPF  292 (361)
T ss_dssp             -CH--H--HHHHHHHHCSEEEEEEEC
T ss_pred             -Ch--H--HHHHHHHhCcEEEEeeec
Confidence             11  1  124789999999999873

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=91.94  E-value=0.13  Score=46.79  Aligned_cols=37  Identities=22%  Similarity=0.119  Sum_probs=30.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .++|.|.+|+|||||+..++.....  ..++..++.+..
T Consensus        32 ~i~i~G~~g~GKTTl~~~l~~~~~~--~~~~~~i~~d~~   68 (221)
T 2wsm_A           32 AVNIMGAIGSGKTLLIERTIERIGN--EVKIGAMLGDVV   68 (221)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHTT--TSCEEEEECSCC
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhcc--CCeEEEEecCCC
Confidence            6889999999999999999877543  367888887764

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=91.90  E-value=0.14  Score=54.07  Aligned_cols=40  Identities=30%  Similarity=0.330  Sum_probs=33.0

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-CeEEEEeCC
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAG-WKFVLCSME  335 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-~~vl~~s~E  335 (539)
                      +.|-+++|.|.||+||||++..++..+... | .++.+++.+
T Consensus       394 q~~~~I~l~GlsGSGKSTiA~~La~~L~~~-G~~~~~~lD~D  434 (573)
T 1m8p_A          394 TQGFTIFLTGYMNSGKDAIARALQVTLNQQ-GGRSVSLLLGD  434 (573)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHHHH-CSSCEEEEEHH
T ss_pred             ccceEEEeecCCCCCHHHHHHHHHHHhccc-CCceEEEECcH
Confidence            356789999999999999999999887664 6 888887743

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=91.84  E-value=0.096  Score=47.70  Aligned_cols=21  Identities=24%  Similarity=0.404  Sum_probs=18.5

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|+||+||||++..++..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~   23 (214)
T 1e4v_A            3 IILLGAPVAGKGTQAQFIMEK   23 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            689999999999998888764

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=91.78  E-value=0.089  Score=50.70  Aligned_cols=22  Identities=36%  Similarity=0.816  Sum_probs=19.7

Q ss_pred             cEEEEEcCCCCChhHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .+++|.|+||+||||++..++.
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~   24 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIA   24 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999988775

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=91.71  E-value=0.13  Score=47.60  Aligned_cols=27  Identities=19%  Similarity=0.182  Sum_probs=22.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ..+|..+.|.|++|+||||++..++..
T Consensus        13 ~~~~~~i~i~G~~gsGKst~~~~l~~~   39 (236)
T 1q3t_A           13 KMKTIQIAIDGPASSGKSTVAKIIAKD   39 (236)
T ss_dssp             -CCCCEEEEECSSCSSHHHHHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            567889999999999999998877653

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=91.69  E-value=0.15  Score=53.33  Aligned_cols=37  Identities=14%  Similarity=0.235  Sum_probs=29.8

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      +...++|.|+||+|||+++..++..+    |.++++++...
T Consensus        76 ~~~~lLL~GppGtGKTtla~~la~~l----~~~~i~in~s~  112 (516)
T 1sxj_A           76 VFRAAMLYGPPGIGKTTAAHLVAQEL----GYDILEQNASD  112 (516)
T ss_dssp             SCSEEEEECSTTSSHHHHHHHHHHHT----TCEEEEECTTS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc----CCCEEEEeCCC
Confidence            34588999999999999988877653    78888887653

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=91.68  E-value=0.14  Score=53.91  Aligned_cols=49  Identities=24%  Similarity=0.332  Sum_probs=38.0

Q ss_pred             hhhhhhhc--c----CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          286 RALNELYN--V----LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       286 ~~LD~~~~--l----~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      +.+...+.  +    ..+.+++|+|.+|+||||++..++..+..+ |.++.+++.+
T Consensus       355 ~eV~~~lr~~~~~~~~~~~~I~l~G~~GsGKSTia~~La~~L~~~-G~~~~~ld~D  409 (546)
T 2gks_A          355 PEVAEILAETYVPKHKQGFCVWLTGLPCAGKSTIAEILATMLQAR-GRKVTLLDGD  409 (546)
T ss_dssp             HHHHHHHHHHSCCGGGCCEEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEECHH
T ss_pred             hhHHHHHHHhhccccccceEEEccCCCCCCHHHHHHHHHHHhhhc-CCeEEEECch
Confidence            44555554  3    347789999999999999999999877664 8888888743

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=91.66  E-value=0.085  Score=51.10  Aligned_cols=47  Identities=13%  Similarity=0.057  Sum_probs=34.0

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA  342 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~  342 (539)
                      ..+.-++|.|+||+|||+++..++..... .+.+++++++..-+..+.
T Consensus        23 ~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~-~~~~~v~v~~~~~~~~l~   69 (304)
T 1ojl_A           23 PSDATVLIHGDSGTGKELVARALHACSAR-SDRPLVTLNCAALNESLL   69 (304)
T ss_dssp             STTSCEEEESCTTSCHHHHHHHHHHHSSC-SSSCCCEEECSSCCHHHH
T ss_pred             CCCCcEEEECCCCchHHHHHHHHHHhCcc-cCCCeEEEeCCCCChHHH
Confidence            33456889999999999999888765444 367888887665444443

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=91.65  E-value=0.1  Score=50.85  Aligned_cols=23  Identities=22%  Similarity=0.497  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .+++|+|++|+||||++..++..
T Consensus         5 ~v~~i~G~~GaGKTTll~~l~~~   27 (318)
T 1nij_A            5 AVTLLTGFLGAGKTTLLRHILNE   27 (318)
T ss_dssp             EEEEEEESSSSSCHHHHHHHHHS
T ss_pred             cEEEEEecCCCCHHHHHHHHHhh
Confidence            58999999999999998887754

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=91.64  E-value=0.088  Score=53.48  Aligned_cols=24  Identities=29%  Similarity=0.601  Sum_probs=20.8

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      ...+++|+|+||+||||++..++.
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~  280 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLV  280 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999887764

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=91.63  E-value=0.094  Score=47.04  Aligned_cols=22  Identities=32%  Similarity=0.209  Sum_probs=19.1

Q ss_pred             cEEEEEcCCCCChhHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .++.|+|++|+||||++..++.
T Consensus         9 ~~I~i~G~~GsGKST~~~~La~   30 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAALLRS   30 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999877664

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=91.59  E-value=0.11  Score=45.30  Aligned_cols=24  Identities=42%  Similarity=0.328  Sum_probs=20.9

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|.-++|.|+||+||||+++.++.
T Consensus        15 ~G~gvli~G~SGaGKStlal~L~~   38 (181)
T 3tqf_A           15 DKMGVLITGEANIGKSELSLALID   38 (181)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHH
Confidence            466789999999999999888775

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=91.49  E-value=0.13  Score=46.35  Aligned_cols=22  Identities=23%  Similarity=0.327  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++.|+|++|+||||++..++..
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~   25 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAA   25 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            7899999999999998877654

>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=91.42  E-value=0.17  Score=55.85  Aligned_cols=51  Identities=16%  Similarity=0.367  Sum_probs=39.4

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH-HHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV-REHARKLL  346 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~-~~~~~r~~  346 (539)
                      .+.+++|.|+||+|||+++..++..+....+.+|+..+.-..+ .++..|+.
T Consensus       370 ~~~~~lI~GppGTGKT~ti~~~i~~l~~~~~~~ilv~a~tn~A~~~l~~~l~  421 (800)
T 2wjy_A          370 QRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIH  421 (800)
T ss_dssp             TSSEEEEECCTTSCHHHHHHHHHHHHHTTCSSCEEEEESSHHHHHHHHHHHH
T ss_pred             cCCeEEEEcCCCCCHHHHHHHHHHHHHHcCCCcEEEEcCcHHHHHHHHHHHH
Confidence            3569999999999999999999888776447899988766443 45555554

>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=91.41  E-value=0.77  Score=48.76  Aligned_cols=112  Identities=10%  Similarity=-0.034  Sum_probs=59.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHHHHhhCCCccccccCCCCCCCCHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFE  372 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~  372 (539)
                      +..|.-+++.+|||+|||.. .++..  .. .+..+++++.--. ..+...++..  .|++...+.     +..+.++..
T Consensus        56 il~g~d~lv~~pTGsGKTl~-~~lpa--l~-~~g~~lVisP~~~L~~q~~~~l~~--~gi~~~~l~-----~~~~~~~~~  124 (591)
T 2v1x_A           56 TMAGKEVFLVMPTGGGKSLC-YQLPA--LC-SDGFTLVICPLISLMEDQLMVLKQ--LGISATMLN-----ASSSKEHVK  124 (591)
T ss_dssp             HHTTCCEEEECCTTSCTTHH-HHHHH--HT-SSSEEEEECSCHHHHHHHHHHHHH--HTCCEEECC-----SSCCHHHHH
T ss_pred             HHcCCCEEEEECCCChHHHH-HHHHH--HH-cCCcEEEEeCHHHHHHHHHHHHHh--cCCcEEEEe-----CCCCHHHHH
Confidence            33465688999999999953 33322  12 3568888875422 2334444433  255543332     245666655


Q ss_pred             HHHHHhh---c-cceeEeecCCCCCCHHH------HHHHHHHHHHHcCCcEEEEccccccc
Q 009230          373 QGKAWLS---N-TFSLIRCENDSLPSIKW------VLDLAKAAVLRHGVRGLVIDPYNELD  423 (539)
Q Consensus       373 ~~~~~l~---~-~~~~i~~~~~~~~~~~~------i~~~i~~~~~~~~~~~vvID~~~~l~  423 (539)
                      .....+.   . ..+++       .+++.      +.+.+........+.+||||-...+.
T Consensus       125 ~~~~~l~~~~~~~~Ilv-------~Tpe~L~~~~~~~~~l~~~~~~~~i~~iViDEAH~is  178 (591)
T 2v1x_A          125 WVHAEMVNKNSELKLIY-------VTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCS  178 (591)
T ss_dssp             HHHHHHHCTTCCCCEEE-------ECHHHHHSCHHHHHHHHHHHHTTCEEEEEEETGGGGS
T ss_pred             HHHHHhhcccCCCCEEE-------EChhHhhccHHHHHHHHhhhhccCCcEEEEECccccc
Confidence            5544442   1 12322       13333      33334443344578999999666554

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=91.38  E-value=0.12  Score=47.19  Aligned_cols=29  Identities=28%  Similarity=0.284  Sum_probs=22.6

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      +-+++|+|++|+||||++..++.     .|.+++
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~-----lg~~~i   32 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD-----LGINVI   32 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH-----TTCEEE
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH-----cCCEEE
Confidence            45889999999999999887753     266544

>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=91.36  E-value=0.48  Score=43.24  Aligned_cols=40  Identities=15%  Similarity=-0.021  Sum_probs=25.2

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHH--------hcCCeEEEEeCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINE--------HAGWKFVLCSME  335 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~--------~~g~~vl~~s~E  335 (539)
                      .|.-+++.+++|+|||...+-.+.....        ..+..++|+..-
T Consensus        56 ~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt  103 (228)
T 3iuy_A           56 QGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPT  103 (228)
T ss_dssp             TTCCEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSS
T ss_pred             CCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCC
Confidence            4555789999999999654433333221        136678888743

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=91.36  E-value=0.12  Score=50.81  Aligned_cols=24  Identities=17%  Similarity=0.443  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +.++|.|+||+||||++.-++..+
T Consensus        52 ~~~ll~Gp~G~GKTTLa~~ia~~l   75 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAHIIASEL   75 (334)
T ss_dssp             CCEEEESSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Confidence            578999999999999999887654

>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=91.22  E-value=0.13  Score=54.10  Aligned_cols=26  Identities=19%  Similarity=0.445  Sum_probs=23.3

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +|..++|.|+||+|||+++..++...
T Consensus       107 ~g~~vll~Gp~GtGKTtlar~ia~~l  132 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLAKSIAKSL  132 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhc
Confidence            78999999999999999999887654

>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=91.17  E-value=1.1  Score=39.85  Aligned_cols=42  Identities=12%  Similarity=0.027  Sum_probs=26.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh--cCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEH--AGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~--~g~~vl~~s~E  335 (539)
                      +..|.-+++.+++|+|||...+-.+......  .+.+++|+..-
T Consensus        37 ~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt   80 (206)
T 1vec_A           37 ALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPT   80 (206)
T ss_dssp             HHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSC
T ss_pred             HccCCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCc
Confidence            4445668899999999996544333333211  24578888743

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=91.16  E-value=0.16  Score=50.75  Aligned_cols=34  Identities=15%  Similarity=0.209  Sum_probs=26.5

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ..-++|.|+||+|||+++..++..+    +.+++.++.
T Consensus        72 ~~~ill~Gp~GtGKT~la~~la~~l----~~~~~~~~~  105 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQTLAKHL----DIPIAISDA  105 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT----TCCEEEEEG
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHh----CCCEEEecc
Confidence            3457899999999999998887543    667777654

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=91.01  E-value=0.15  Score=50.64  Aligned_cols=34  Identities=18%  Similarity=0.248  Sum_probs=26.1

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +.-++|.|+||+|||+++..++...    +.+++.++.
T Consensus        51 ~~~vll~GppGtGKT~la~~ia~~~----~~~~~~~~~   84 (363)
T 3hws_A           51 KSNILLIGPTGSGKTLLAETLARLL----DVPFTMADA   84 (363)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT----TCCEEEEEH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHc----CCCEEEech
Confidence            4467899999999999988887553    667666653

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=91.01  E-value=0.21  Score=51.86  Aligned_cols=36  Identities=25%  Similarity=0.388  Sum_probs=28.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      +++|  ++|.|+||+|||+++..++..    .+.+.++++..
T Consensus        63 ip~G--vLL~GppGtGKTtLaraIa~~----~~~~~i~i~g~   98 (499)
T 2dhr_A           63 IPKG--VLLVGPPGVGKTHLARAVAGE----ARVPFITASGS   98 (499)
T ss_dssp             CCSE--EEEECSSSSSHHHHHHHHHHH----TTCCEEEEEGG
T ss_pred             CCce--EEEECCCCCCHHHHHHHHHHH----hCCCEEEEehh
Confidence            6667  889999999999998877754    25677777754

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=90.90  E-value=0.089  Score=53.16  Aligned_cols=22  Identities=41%  Similarity=0.439  Sum_probs=19.1

Q ss_pred             cEEEEEcCCCCChhHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      ..+.|.|++|+|||||+..++-
T Consensus        70 ~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           70 LNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCcHHHHHHHHhC
Confidence            3999999999999999877664

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=90.85  E-value=0.14  Score=44.78  Aligned_cols=23  Identities=39%  Similarity=0.687  Sum_probs=19.3

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      +|.-++|.|++|+|||||+..++
T Consensus         3 ~~~ki~ivG~~g~GKStLl~~l~   25 (172)
T 2gj8_A            3 HGMKVVIAGRPNAGKSSLLNALA   25 (172)
T ss_dssp             -CEEEEEEESTTSSHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHh
Confidence            56678999999999999987765

>3ez9_A Para; DNA binding, winged-HTH, partition, biosynthetic protein; 2.80A {Salmonella enterica subsp} PDB: 3ezf_A

Probab=90.81  E-value=0.096  Score=52.95  Aligned_cols=39  Identities=8%  Similarity=0.097  Sum_probs=24.9

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHH-----hcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINE-----HAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~-----~~g~~vl~~s~E~~  337 (539)
                      +.++.|..|+||||++.++|..++.     +.|.+|+++.++..
T Consensus       114 Iav~s~KGGvGKTT~a~nLA~~LA~~g~~~~~g~rVlliD~D~~  157 (403)
T 3ez9_A          114 IFVVNLKGGVSKTVSTVTLAHALRVHQDLLRHDLRILVIDLDPQ  157 (403)
T ss_dssp             EEECCC--------CHHHHHHHHHSCGGGGGGCCCEEEEEESSS
T ss_pred             EEEEcCCCCchHHHHHHHHHHHHHhcchhhcCCCeEEEEeCCCC
Confidence            5555589999999999999999983     24999999999853

>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=90.79  E-value=0.16  Score=49.34  Aligned_cols=34  Identities=21%  Similarity=0.319  Sum_probs=27.1

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ..++|.|+||+|||+++..++...    +.++.+++..
T Consensus        39 ~~vll~G~~GtGKT~la~~i~~~~----~~~~~~~~~~   72 (324)
T 1hqc_A           39 EHLLLFGPPGLGKTTLAHVIAHEL----GVNLRVTSGP   72 (324)
T ss_dssp             CCCEEECCTTCCCHHHHHHHHHHH----TCCEEEECTT
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHh----CCCEEEEecc
Confidence            467899999999999999887653    5677777654

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=90.79  E-value=0.2  Score=49.08  Aligned_cols=32  Identities=9%  Similarity=0.133  Sum_probs=24.7

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      -++|.|+||+|||+++..++..    .+.++..++.
T Consensus        57 ~vll~G~~GtGKT~la~~ia~~----~~~~~~~~~~   88 (338)
T 3pfi_A           57 HILFSGPAGLGKTTLANIISYE----MSANIKTTAA   88 (338)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHH----TTCCEEEEEG
T ss_pred             eEEEECcCCCCHHHHHHHHHHH----hCCCeEEecc
Confidence            4789999999999999888544    3566666654

>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome condensation, condensin, SMC, N subunit, ABC-type ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus ducreyi} PDB: 3euk_A*

Probab=90.78  E-value=0.11  Score=53.59  Aligned_cols=36  Identities=17%  Similarity=0.244  Sum_probs=28.7

Q ss_pred             Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          284 GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       284 g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|..|+.+.- +.+ +++.|.|++|+|||||+.-++--
T Consensus        16 ~~~~l~~vsl~i~~-e~~~liG~nGsGKSTLl~~l~Gl   52 (483)
T 3euj_A           16 NWNGFFARTFDFDE-LVTTLSGGNGAGKSTTMAGFVTA   52 (483)
T ss_dssp             EETTEEEEEEECCS-SEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ccccccceEEEEcc-ceEEEECCCCCcHHHHHHHHhcC
Confidence            3556665544 888 99999999999999998876643

>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=90.77  E-value=0.54  Score=51.57  Aligned_cols=106  Identities=19%  Similarity=0.122  Sum_probs=61.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHHHHhh--CCCccccccCCCCCCCCHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLLEKHI--KKPFFEANYGGSAERMTVEEFEQGK  375 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~~~~~--~~~~~~i~~~~~~~~l~~~~~~~~~  375 (539)
                      -.++.|++|+|||..++..+...... |..++++..... +.++..++.....  ++....+.     +..+..+.....
T Consensus       391 ~~Ll~a~TGSGKTlvall~il~~l~~-g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~-----G~~~~~~r~~~~  464 (780)
T 1gm5_A          391 NRLLQGDVGSGKTVVAQLAILDNYEA-GFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLI-----GATTPSEKEKIK  464 (780)
T ss_dssp             CCEEECCSSSSHHHHHHHHHHHHHHH-TSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECC-----SSSCHHHHHHHH
T ss_pred             cEEEEcCCCCCHHHHHHHHHHHHHHc-CCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEe-----CCCCHHHHHHHH
Confidence            57899999999999888777777665 889999886532 4455555544433  33332222     245555555555


Q ss_pred             HHhhcc--ceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccc
Q 009230          376 AWLSNT--FSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNE  421 (539)
Q Consensus       376 ~~l~~~--~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~  421 (539)
                      +.+...  .++|     +.+  ..+    .....-.++++||||-...
T Consensus       465 ~~l~~g~~~IvV-----gT~--~ll----~~~~~~~~l~lVVIDEaHr  501 (780)
T 1gm5_A          465 SGLRNGQIDVVI-----GTH--ALI----QEDVHFKNLGLVIIDEQHR  501 (780)
T ss_dssp             HHHHSSCCCEEE-----ECT--THH----HHCCCCSCCCEEEEESCCC
T ss_pred             HHHhcCCCCEEE-----ECH--HHH----hhhhhccCCceEEecccch
Confidence            555432  2333     111  111    1111224678999996554

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=90.76  E-value=0.16  Score=46.00  Aligned_cols=27  Identities=30%  Similarity=0.614  Sum_probs=21.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |.+| +++|.|++|+|||+++-.|...+
T Consensus        21 f~~~-~~~I~G~NgsGKStil~ai~~~l   47 (203)
T 3qks_A           21 FKEG-INLIIGQNGSGKSSLLDAILVGL   47 (203)
T ss_dssp             CCSE-EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eCCC-eEEEEcCCCCCHHHHHHHHHHHh
Confidence            5554 99999999999999988765443

>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=90.75  E-value=0.23  Score=50.68  Aligned_cols=38  Identities=21%  Similarity=0.259  Sum_probs=30.9

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      .-++|.|+||+|||+++..++.++... |.+++++....
T Consensus        54 ~h~~i~G~tGsGKs~~~~~li~~~~~~-g~~viv~Dpkg   91 (437)
T 1e9r_A           54 RHLLVNGATGTGKSVLLRELAYTGLLR-GDRMVIVDPNG   91 (437)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHHHHHHT-TCEEEEEEETT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHC-CCcEEEEeCCC
Confidence            467899999999999988888887764 88888887553

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=90.65  E-value=0.28  Score=48.15  Aligned_cols=36  Identities=19%  Similarity=0.211  Sum_probs=27.8

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHh--cCCeEEEEeCC
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEH--AGWKFVLCSME  335 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~--~g~~vl~~s~E  335 (539)
                      ++|.|+||+|||+++..++..+...  ....+..++..
T Consensus        61 ~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~   98 (353)
T 1sxj_D           61 MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNAS   98 (353)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSS
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccc
Confidence            8899999999999999999876531  24566666654

>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=90.65  E-value=0.28  Score=56.02  Aligned_cols=114  Identities=15%  Similarity=0.032  Sum_probs=62.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHHHHhh--CC----CccccccCCCCCCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLLEKHI--KK----PFFEANYGGSAERM  366 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~~~~~--~~----~~~~i~~~~~~~~l  366 (539)
                      +..|.-+++.|++|+|||.+++-++..+... +..+++++.--. ..++..++.....  ++    ....+ .|    ..
T Consensus        68 il~g~dvlv~apTGSGKTl~~lp~l~~~~~~-~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~-~G----g~  141 (1054)
T 1gku_B           68 ILRKESFAATAPTGVGKTSFGLAMSLFLALK-GKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYY-HG----RI  141 (1054)
T ss_dssp             HHTTCCEECCCCBTSCSHHHHHHHHHHHHTT-SCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEEC-CS----SC
T ss_pred             HHhCCCEEEEcCCCCCHHHHHHHHHHHHhhc-CCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEE-eC----CC
Confidence            4567778899999999999777777666554 788888875422 3444444433322  22    11111 12    23


Q ss_pred             CHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccc
Q 009230          367 TVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELD  423 (539)
Q Consensus       367 ~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~  423 (539)
                      +..+..+..+.+....++|       .|+..+.+.+..   -..+++||||-...+.
T Consensus       142 ~~~~~~~~~~~l~~~~IlV-------~TP~~L~~~l~~---L~~l~~lViDEah~~l  188 (1054)
T 1gku_B          142 PKREKENFMQNLRNFKIVI-------TTTQFLSKHYRE---LGHFDFIFVDDVDAIL  188 (1054)
T ss_dssp             CSHHHHHHHHSGGGCSEEE-------EEHHHHHHCSTT---SCCCSEEEESCHHHHH
T ss_pred             ChhhHHHHHhhccCCCEEE-------EcHHHHHHHHHH---hccCCEEEEeChhhhh
Confidence            3333333334444422333       134555444333   2368899999655443

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=90.62  E-value=0.13  Score=49.19  Aligned_cols=28  Identities=32%  Similarity=0.345  Sum_probs=22.7

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      -+++|+|++|+||||++..++ .    .|.+++
T Consensus        76 ~iI~I~G~~GSGKSTva~~La-~----lg~~~i  103 (281)
T 2f6r_A           76 YVLGLTGISGSGKSSVAQRLK-N----LGAYII  103 (281)
T ss_dssp             EEEEEEECTTSCHHHHHHHHH-H----HTCEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHH-H----CCCcEE
Confidence            479999999999999998887 3    276654

>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=90.54  E-value=0.39  Score=47.15  Aligned_cols=48  Identities=10%  Similarity=0.141  Sum_probs=32.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHh-cCCeEEEEeCCCC-HHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEH-AGWKFVLCSMENK-VREHARKL  345 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~-~g~~vl~~s~E~~-~~~~~~r~  345 (539)
                      .-+++.+++|+|||..+...+...... .+.+++++..--. ..++..++
T Consensus        45 ~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~   94 (367)
T 1hv8_A           45 YNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEI   94 (367)
T ss_dssp             SEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCHHHHHHHHHHH
Confidence            578899999999998877666655432 3678888875422 23444444

>3of5_A Dethiobiotin synthetase; structural genomics, center for structural genomics of infec diseases, csgid, ligase; 1.52A {Francisella tularensis subsp}

Probab=90.52  E-value=0.29  Score=45.14  Aligned_cols=34  Identities=18%  Similarity=0.086  Sum_probs=28.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +.+-+-.+|+|||+++..++..+.++ |.+|.||-
T Consensus         7 i~Itgt~t~vGKT~vt~~L~~~l~~~-G~~V~~~K   40 (228)
T 3of5_A            7 FFIIGTDTEVGKTYISTKLIEVCEHQ-NIKSLCLK   40 (228)
T ss_dssp             EEEEESSSSSCHHHHHHHHHHHHHHT-TCCEEEEC
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHHHHC-CCeeEEec
Confidence            44444559999999999999998886 99999984

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=90.51  E-value=0.17  Score=49.79  Aligned_cols=29  Identities=34%  Similarity=0.394  Sum_probs=24.0

Q ss_pred             cCCCcE--EEEEcCCCCChhHHHHHHHHHHH
Q 009230          294 VLPGEL--TIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       294 l~~G~l--~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      +.+|+.  ++|.|++|+||||++..++..+-
T Consensus        19 i~~g~~~~i~l~G~~G~GKTTl~~~la~~l~   49 (359)
T 2ga8_A           19 IEDNYRVCVILVGSPGSGKSTIAEELCQIIN   49 (359)
T ss_dssp             TTTCSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             hccCCeeEEEEECCCCCcHHHHHHHHHHHhC
Confidence            566766  89999999999999988876553

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=90.43  E-value=0.39  Score=55.79  Aligned_cols=40  Identities=13%  Similarity=0.096  Sum_probs=30.6

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHH-h--cCCeEEEEeCCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINE-H--AGWKFVLCSMENK  337 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~-~--~g~~vl~~s~E~~  337 (539)
                      .++.|.|..|+||||+|.+++.+... .  ....++|+++...
T Consensus       148 ~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~  190 (1249)
T 3sfz_A          148 GWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQ  190 (1249)
T ss_dssp             EEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSC
T ss_pred             CEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCc
Confidence            58899999999999999998876432 1  2346888887653

>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=90.29  E-value=1.2  Score=45.29  Aligned_cols=53  Identities=13%  Similarity=0.064  Sum_probs=36.4

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHHHHhhCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLLEKHIKK  352 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~~~~~~~  352 (539)
                      -.+|++++|+|||..+..++.......+.+++++..--. ..+...++ ....+.
T Consensus        25 ~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P~~~L~~q~~~~~-~~~~~~   78 (494)
T 1wp9_A           25 NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESF-RRLFNL   78 (494)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHH-HHHBCS
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHH-HHHhCc
Confidence            567899999999998888877776545789999985422 23343333 334444

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=90.28  E-value=0.12  Score=51.43  Aligned_cols=27  Identities=26%  Similarity=0.354  Sum_probs=23.9

Q ss_pred             cCC--CcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLP--GELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~--G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+  |+.+.|.|++|+|||||+..++..
T Consensus       165 v~~~lg~k~~IvG~nGsGKSTLlk~L~gl  193 (365)
T 1lw7_A          165 ARPFFAKTVAILGGESSGKSVLVNKLAAV  193 (365)
T ss_dssp             TGGGTCEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             HHHhhhCeEEEECCCCCCHHHHHHHHHHH
Confidence            677  999999999999999998887754

>2vf7_A UVRA2, excinuclease ABC, subunit A.; DNA-binding protein, nucleotide-binding, zinc-binding domain, SOS response, metal-binding; HET: ADP; 2.30A {Deinococcus radiodurans} PDB: 2vf8_A*

Probab=90.28  E-value=0.12  Score=57.00  Aligned_cols=29  Identities=31%  Similarity=0.316  Sum_probs=25.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      ++++.|++|+|.+|||||+|+......-.
T Consensus        33 iP~~~l~viTGvSGSGKSSLafdtl~ae~   61 (842)
T 2vf7_A           33 VPRDALVVFTGVSGSGKSSLAFGTLYAEA   61 (842)
T ss_dssp             EESSSEEEEESSTTSSHHHHHTTTHHHHH
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHHHHHH
Confidence            89999999999999999999988665443

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=90.24  E-value=0.098  Score=55.62  Aligned_cols=31  Identities=26%  Similarity=0.427  Sum_probs=25.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      |+++.- +++|+.+.|.|++|+||||++.-++
T Consensus       357 l~~isl~i~~G~~~~ivG~sGsGKSTll~~l~  388 (578)
T 4a82_A          357 LKDINLSIEKGETVAFVGMSGGGKSTLINLIP  388 (578)
T ss_dssp             EEEEEEEECTTCEEEEECSTTSSHHHHHTTTT
T ss_pred             eeeeEEEECCCCEEEEECCCCChHHHHHHHHh
Confidence            444433 8999999999999999999976544

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=90.23  E-value=0.18  Score=50.20  Aligned_cols=26  Identities=31%  Similarity=0.515  Sum_probs=22.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +.+| +++|.|++|+||||++-.++..
T Consensus        21 ~~~g-~~~i~G~NGaGKTTll~ai~~a   46 (365)
T 3qf7_A           21 FQSG-ITVVEGPNGAGKSSLFEAISFA   46 (365)
T ss_dssp             CCSE-EEEEECCTTSSHHHHHHHHHHH
T ss_pred             cCCC-eEEEECCCCCCHHHHHHHHHHH
Confidence            7777 9999999999999998766644

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=90.13  E-value=0.19  Score=46.68  Aligned_cols=26  Identities=19%  Similarity=0.178  Sum_probs=22.0

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +|-+++|.|.+|+||||++..++..+
T Consensus         1 ~~~~i~~~G~~g~GKtt~~~~l~~~l   26 (241)
T 2ocp_A            1 GPRRLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHC
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHc
Confidence            35689999999999999988887653

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=90.07  E-value=0.44  Score=48.71  Aligned_cols=35  Identities=20%  Similarity=0.189  Sum_probs=26.9

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      -++|.|+||+|||+++..++..    .+.+...++....
T Consensus        52 ~vLL~GppGtGKTtlAr~ia~~----~~~~f~~l~a~~~   86 (447)
T 3pvs_A           52 SMILWGPPGTGKTTLAEVIARY----ANADVERISAVTS   86 (447)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH----TTCEEEEEETTTC
T ss_pred             EEEEECCCCCcHHHHHHHHHHH----hCCCeEEEEeccC
Confidence            4899999999999998877755    3566677766543

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=90.04  E-value=0.096  Score=49.46  Aligned_cols=21  Identities=24%  Similarity=0.457  Sum_probs=18.6

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|+||+|||+++..++..
T Consensus        47 vll~G~~GtGKT~la~~la~~   67 (268)
T 2r62_A           47 VLLVGPPGTGKTLLAKAVAGE   67 (268)
T ss_dssp             CCCBCSSCSSHHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHH
Confidence            779999999999999888764

>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=89.94  E-value=0.32  Score=52.00  Aligned_cols=40  Identities=15%  Similarity=0.372  Sum_probs=31.4

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHH---hcCCeEEEEeCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINE---HAGWKFVLCSME  335 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~---~~g~~vl~~s~E  335 (539)
                      .+.+++|.|+||+|||+++..++..+..   ..+.+|+..+.-
T Consensus       163 ~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~APT  205 (608)
T 1w36_D          163 TRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPT  205 (608)
T ss_dssp             TBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSS
T ss_pred             cCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEEEEeCC
Confidence            4679999999999999999988877664   235678777543

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=89.89  E-value=0.22  Score=45.43  Aligned_cols=37  Identities=24%  Similarity=0.260  Sum_probs=27.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .++|.|.+|+|||||+.+++.....  ..++..+..+..
T Consensus        40 ~i~ivG~~gvGKTtl~~~l~~~~~~--~~~~~~i~~d~~   76 (226)
T 2hf9_A           40 AFDFMGAIGSGKTLLIEKLIDNLKD--KYKIACIAGDVI   76 (226)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTT--TCCEEEEEEETT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhcc--CCeEEEEECCCC
Confidence            5778899999999999999977644  355655555543

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=89.67  E-value=0.25  Score=46.46  Aligned_cols=26  Identities=15%  Similarity=0.179  Sum_probs=22.1

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++..-++|.||||+|||.|+..+|..
T Consensus       102 ~~~n~~~l~GppgtGKt~~a~ala~~  127 (267)
T 1u0j_A          102 GKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHhh
Confidence            44567999999999999999988764

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=89.58  E-value=0.26  Score=45.04  Aligned_cols=27  Identities=22%  Similarity=0.422  Sum_probs=23.6

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .+|-+++|.|++|+||||.+..++..+
T Consensus         3 ~~g~~i~~eG~~g~GKst~~~~l~~~l   29 (216)
T 3tmk_A            3 GRGKLILIEGLDRTGKTTQCNILYKKL   29 (216)
T ss_dssp             CCCCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            368899999999999999998887664

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=89.49  E-value=0.28  Score=50.42  Aligned_cols=39  Identities=18%  Similarity=0.290  Sum_probs=27.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ..++.-+++.|+||+|||+++..++..+-.  ..++++++.
T Consensus        60 ~~~~~~iLl~GppGtGKT~la~ala~~l~~--~~~~~~~~~   98 (456)
T 2c9o_A           60 KMAGRAVLLAGPPGTGKTALALAIAQELGS--KVPFCPMVG   98 (456)
T ss_dssp             CCTTCEEEEECCTTSSHHHHHHHHHHHHCT--TSCEEEEEG
T ss_pred             CCCCCeEEEECCCcCCHHHHHHHHHHHhCC--CceEEEEeH
Confidence            334446889999999999999988876421  256666553

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=89.37  E-value=0.2  Score=43.18  Aligned_cols=20  Identities=40%  Similarity=0.516  Sum_probs=17.7

Q ss_pred             EEEEEcCCCCChhHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la  318 (539)
                      .++|.|++|+|||||+..++
T Consensus         5 ~v~lvG~~gvGKStL~~~l~   24 (165)
T 2wji_A            5 EIALIGNPNVGKSTIFNALT   24 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            47899999999999988875

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=89.35  E-value=0.18  Score=52.92  Aligned_cols=26  Identities=19%  Similarity=0.134  Sum_probs=23.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      ..+|+++.|.|++|+|||||+.-++-
T Consensus        22 ~~~Gei~gLiGpNGaGKSTLlkiL~G   47 (538)
T 3ozx_A           22 PKNNTILGVLGKNGVGKTTVLKILAG   47 (538)
T ss_dssp             CCTTEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCCCEEEEECCCCCcHHHHHHHHhc
Confidence            78999999999999999999776653

>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=89.30  E-value=0.5  Score=50.78  Aligned_cols=52  Identities=15%  Similarity=0.157  Sum_probs=38.3

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcC---CeEEEEeCCCC-HHHHHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAG---WKFVLCSMENK-VREHARKLLEK  348 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g---~~vl~~s~E~~-~~~~~~r~~~~  348 (539)
                      ...++|.|+||+|||+.+.+-+.+++.+.+   .+++++++-.. ..++..|+...
T Consensus        22 ~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~   77 (647)
T 3lfu_A           22 RSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQL   77 (647)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHH
Confidence            345678899999999999998888887523   67999887533 45666666543

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=89.21  E-value=0.23  Score=48.43  Aligned_cols=37  Identities=19%  Similarity=0.336  Sum_probs=26.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +..|.-++|.|+||+|||+++..++..+    +.++..+.+
T Consensus        43 l~~~~~vll~G~pGtGKT~la~~la~~~----~~~~~~i~~   79 (331)
T 2r44_A           43 ICTGGHILLEGVPGLAKTLSVNTLAKTM----DLDFHRIQF   79 (331)
T ss_dssp             HHHTCCEEEESCCCHHHHHHHHHHHHHT----TCCEEEEEC
T ss_pred             HHcCCeEEEECCCCCcHHHHHHHHHHHh----CCCeEEEec
Confidence            4445678899999999999998887543    445555443

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=89.18  E-value=0.087  Score=44.64  Aligned_cols=23  Identities=13%  Similarity=-0.055  Sum_probs=18.4

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +.-++|.|+||+|||+++..++.
T Consensus        27 ~~~vll~G~~GtGKt~lA~~i~~   49 (143)
T 3co5_A           27 TSPVFLTGEAGSPFETVARYFHK   49 (143)
T ss_dssp             SSCEEEEEETTCCHHHHHGGGCC
T ss_pred             CCcEEEECCCCccHHHHHHHHHH
Confidence            34578999999999999776653

>1ni3_A YCHF GTPase, YCHF GTP-binding protein; structural genomics, GTP1OBG, PSI, protein structure initiative; 2.80A {Schizosaccharomyces pombe} SCOP: c.37.1.8 d.15.10.2

Probab=89.00  E-value=0.23  Score=49.79  Aligned_cols=29  Identities=28%  Similarity=0.335  Sum_probs=26.1

Q ss_pred             hhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          291 LYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       291 ~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +++ +.+|..+.|.|+||+|||||...++-
T Consensus        13 ~lg~v~~g~~vgiVG~pnaGKSTL~n~Ltg   42 (392)
T 1ni3_A           13 QWGRPGNNLKTGIVGMPNVGKSTFFRAITK   42 (392)
T ss_dssp             CCSSSSSCCEEEEEECSSSSHHHHHHHHHH
T ss_pred             HhccccCCCEEEEECCCCCCHHHHHHHHHC
Confidence            466 88999999999999999999988875

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=88.98  E-value=0.22  Score=42.60  Aligned_cols=20  Identities=30%  Similarity=0.318  Sum_probs=17.5

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||||+..++.
T Consensus         8 i~v~G~~~~GKssl~~~l~~   27 (168)
T 1z2a_A            8 MVVVGNGAVGKSSMIQRYCK   27 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHc
Confidence            57889999999999988764

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=88.91  E-value=0.24  Score=51.13  Aligned_cols=26  Identities=23%  Similarity=0.380  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINE  323 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~  323 (539)
                      .-.+|.|+||+|||+++..++..+..
T Consensus       202 ~~~LL~G~pG~GKT~la~~la~~l~~  227 (468)
T 3pxg_A          202 NNPVLIGEPGVGKTAIAEGLAQQIIN  227 (468)
T ss_dssp             CEEEEESCTTTTTHHHHHHHHHHHHS
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHHHh
Confidence            35689999999999999999888754

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=88.90  E-value=0.51  Score=42.28  Aligned_cols=34  Identities=29%  Similarity=0.400  Sum_probs=28.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +++|-|.-|+||||.+..++..+..+ |.+|++..
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~L~~~-g~~v~~tr   35 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQYLEKR-GKKVILKR   35 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-CCcEEEEE
Confidence            57888999999999999998887764 99987654

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=88.82  E-value=0.35  Score=43.71  Aligned_cols=35  Identities=14%  Similarity=0.327  Sum_probs=28.6

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      |.+++|-|..|+||||.+..++..+. + |.+|++..
T Consensus         2 ~kFI~~EG~dGsGKsTq~~~L~~~L~-~-~~~v~~~~   36 (205)
T 4hlc_A            2 SAFITFEGPEGSGKTTVINEVYHRLV-K-DYDVIMTR   36 (205)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHT-T-TSCEEEEE
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHHH-C-CCCEEEee
Confidence            56899999999999999988887764 3 78877543

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=88.80  E-value=0.3  Score=48.36  Aligned_cols=25  Identities=20%  Similarity=0.290  Sum_probs=21.5

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      ..++|.|++|+|||+++..++..+.
T Consensus        39 ~~~ll~G~~G~GKT~la~~la~~l~   63 (373)
T 1jr3_A           39 HAYLFSGTRGVGKTSIARLLAKGLN   63 (373)
T ss_dssp             SEEEEESCTTSSHHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3789999999999999998886653

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=88.75  E-value=0.22  Score=44.30  Aligned_cols=21  Identities=19%  Similarity=0.316  Sum_probs=18.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .++|.|++|+|||||+..++.
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~   51 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTR   51 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECcCCCCHHHHHHHHhc
Confidence            578999999999999887764

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=88.74  E-value=0.34  Score=49.91  Aligned_cols=38  Identities=21%  Similarity=0.218  Sum_probs=30.5

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ..++++.|.||+||||++..++...-.. +.++..|+.+
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~l~~~-~~~t~~~~~d   76 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRYLNFI-GVPTREFNVG   76 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEEHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHhcc-CCCceEEecc
Confidence            3588999999999999999999887654 6677766644

>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=88.71  E-value=0.21  Score=49.01  Aligned_cols=24  Identities=21%  Similarity=0.296  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      .+++.|++|+|||+++..++..+.
T Consensus        26 a~L~~G~~G~GKt~~a~~la~~l~   49 (334)
T 1a5t_A           26 ALLIQALPGMGDDALIYALSRYLL   49 (334)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             eEEEECCCCchHHHHHHHHHHHHh
Confidence            589999999999999999987764

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=88.65  E-value=0.24  Score=42.06  Aligned_cols=19  Identities=37%  Similarity=0.739  Sum_probs=16.9

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.+|+|||+|+..++
T Consensus         4 i~v~G~~~~GKSsli~~l~   22 (161)
T 2dyk_A            4 VVIVGRPNVGKSSLFNRLL   22 (161)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            5789999999999988776

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=88.64  E-value=0.2  Score=44.13  Aligned_cols=20  Identities=25%  Similarity=0.486  Sum_probs=17.7

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|++|+|||||+..++.
T Consensus         5 v~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            5 LMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEESCTTSSHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            67999999999999988764

>2o5v_A DNA replication and repair protein RECF; ABC ATPase, walker A motif, P-loop, signature motif, replication/recombination complex; HET: DNA; 1.61A {Deinococcus radiodurans}

Probab=88.59  E-value=0.23  Score=49.14  Aligned_cols=35  Identities=23%  Similarity=0.278  Sum_probs=27.5

Q ss_pred             Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          284 GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       284 g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +|..++.+.- +.+| +++|.|++|+|||+++-.+..
T Consensus        13 ~~~~~~~~~~~~~~g-~~~i~G~nG~GKttll~ai~~   48 (359)
T 2o5v_A           13 NYRNLAPGTLNFPEG-VTGIYGENGAGKTNLLEAAYL   48 (359)
T ss_dssp             SBTTCCSEEEECCSE-EEEEECCTTSSHHHHHHHHHH
T ss_pred             CccceeeeEEEEcCC-eEEEECCCCCChhHHHHHHHH
Confidence            4555554433 8888 999999999999999888764

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=88.55  E-value=0.25  Score=42.15  Aligned_cols=20  Identities=25%  Similarity=0.348  Sum_probs=17.3

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|++|+|||+|+..+..
T Consensus         6 i~v~G~~~~GKSsli~~l~~   25 (167)
T 1kao_A            6 VVVLGSGGVGKSALTVQFVT   25 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHc
Confidence            67899999999999877764

>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=88.51  E-value=0.68  Score=42.01  Aligned_cols=42  Identities=7%  Similarity=0.087  Sum_probs=26.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh--cCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEH--AGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~--~g~~vl~~s~E  335 (539)
                      +..|.-+++.+++|+|||....-.+.+....  .+.+++++..-
T Consensus        48 ~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (224)
T 1qde_A           48 IIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPT   91 (224)
T ss_dssp             HHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSS
T ss_pred             HhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECC
Confidence            3345558899999999997633333332211  24578888744

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=88.43  E-value=0.24  Score=42.11  Aligned_cols=20  Identities=35%  Similarity=0.368  Sum_probs=17.4

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      +++.|.+|+|||||+..++.
T Consensus         6 i~v~G~~~~GKssl~~~l~~   25 (166)
T 2ce2_X            6 LVVVGAGGVGKSALTIQLIQ   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            67889999999999888764

>1e69_A Chromosome segregation SMC protein; structural maintenance of chromosomes, coiled coil; 3.1A {Thermotoga maritima} SCOP: c.37.1.12

Probab=88.42  E-value=0.28  Score=47.86  Aligned_cols=25  Identities=36%  Similarity=0.418  Sum_probs=22.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |.+| +++|.|++|+|||+++-.+..
T Consensus        22 ~~~g-~~~i~G~NGsGKS~ll~ai~~   46 (322)
T 1e69_A           22 FSDR-VTAIVGPNGSGKSNIIDAIKW   46 (322)
T ss_dssp             CCSS-EEEEECCTTTCSTHHHHHHHH
T ss_pred             cCCC-cEEEECCCCCcHHHHHHHHHH
Confidence            7788 999999999999999888764

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=88.39  E-value=0.25  Score=44.08  Aligned_cols=22  Identities=23%  Similarity=0.359  Sum_probs=18.4

Q ss_pred             EEEEEcCCCCChhHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      -++|.|++|+|||||+..++..
T Consensus         7 kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            7 KVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            3678999999999998887643

>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=88.28  E-value=0.61  Score=47.56  Aligned_cols=55  Identities=13%  Similarity=0.159  Sum_probs=37.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHH-HHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWI-DALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKK  352 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~-~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~  352 (539)
                      +..|.-+++.|++|+|||..+ +.++..+.. .+..++|++.   -..++..+.....+.
T Consensus         5 l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~-~~~~~lil~P---tr~La~Q~~~~l~~~   60 (440)
T 1yks_A            5 LKKGMTTVLDFHPGAGKTRRFLPQILAECAR-RRLRTLVLAP---TRVVLSEMKEAFHGL   60 (440)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHH-TTCCEEEEES---SHHHHHHHHHHTTTS
T ss_pred             hhCCCCEEEEcCCCCCHHHHHHHHHHHHHHh-cCCeEEEEcc---hHHHHHHHHHHHhcC
Confidence            567889999999999999864 555544544 4778888873   344555554444443

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=88.24  E-value=0.95  Score=50.91  Aligned_cols=52  Identities=17%  Similarity=0.208  Sum_probs=36.4

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHH--HHHhcCCeEEEEeCCCC--HHHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICN--INEHAGWKFVLCSMENK--VREHARKLLE  347 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~--~a~~~g~~vl~~s~E~~--~~~~~~r~~~  347 (539)
                      ...++.|.|+.|+||||+|.+++..  +.......++|+++...  ...+...+..
T Consensus       149 ~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~  204 (1221)
T 1vt4_I          149 PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK  204 (1221)
T ss_dssp             SSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHH
Confidence            3569999999999999999998853  33333456888887643  4445444443

>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome segregation, cell adhesion, kleisin, MIT cell cycle; HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.12

Probab=88.16  E-value=0.31  Score=49.58  Aligned_cols=26  Identities=31%  Similarity=0.385  Sum_probs=23.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +.+|++++|.|++|+|||+++..++.
T Consensus        23 ~~~~~~~~i~G~nG~GKstll~ai~~   48 (430)
T 1w1w_A           23 FGESNFTSIIGPNGSGKSNMMDAISF   48 (430)
T ss_dssp             CTTCSEEEEECSTTSSHHHHHHHHHH
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHHh
Confidence            66789999999999999999888764

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=88.15  E-value=0.24  Score=47.02  Aligned_cols=23  Identities=26%  Similarity=0.355  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .+.|.|++|+|||||+..++-..
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~   26 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQ   26 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            36789999999999988877544

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=88.14  E-value=0.27  Score=42.44  Aligned_cols=19  Identities=21%  Similarity=0.436  Sum_probs=17.0

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.+|+|||+|+..+.
T Consensus         7 i~i~G~~~vGKSsl~~~l~   25 (175)
T 2nzj_A            7 VVLLGDPGVGKTSLASLFA   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECCCCccHHHHHHHHh
Confidence            6789999999999988775

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=88.11  E-value=0.4  Score=52.74  Aligned_cols=36  Identities=25%  Similarity=0.193  Sum_probs=29.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      -++|.|+||+|||+++..++..+.. .+.+++++++.
T Consensus       523 ~~Ll~Gp~GtGKT~lA~ala~~l~~-~~~~~i~i~~s  558 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELARALAESIFG-DEESMIRIDMS  558 (758)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHHHS-CTTCEEEEEGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcC-CCcceEEEech
Confidence            5899999999999999999887754 36788888764

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=88.07  E-value=0.28  Score=41.85  Aligned_cols=20  Identities=25%  Similarity=0.327  Sum_probs=17.3

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+..++.
T Consensus         7 i~v~G~~~~GKssl~~~l~~   26 (168)
T 1u8z_A            7 VIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            67889999999999887763

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=87.97  E-value=0.28  Score=42.07  Aligned_cols=20  Identities=25%  Similarity=0.288  Sum_probs=17.4

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+..++.
T Consensus         6 i~v~G~~~~GKssli~~l~~   25 (172)
T 2erx_A            6 VAVFGAGGVGKSSLVLRFVK   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHc
Confidence            67889999999999887763

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=87.91  E-value=0.29  Score=41.91  Aligned_cols=21  Identities=24%  Similarity=0.381  Sum_probs=17.9

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|++|+|||+|+..+...
T Consensus         6 i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            678899999999998887643

>3fgn_A Dethiobiotin synthetase; biotin biosynthesis, BIOD, ATP-BIND ligase, magnesium, nucleotide-binding; 1.85A {Mycobacterium tuberculosis} PDB: 3fmf_A* 3fmi_A* 3fpa_A*

Probab=87.91  E-value=0.58  Score=43.73  Aligned_cols=130  Identities=14%  Similarity=0.120  Sum_probs=71.4

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe-----CC--CCHHHHHHHHHHHhhCCCcc--ccccCCCCCCCCHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS-----ME--NKVREHARKLLEKHIKKPFF--EANYGGSAERMTVE  369 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s-----~E--~~~~~~~~r~~~~~~~~~~~--~i~~~~~~~~l~~~  369 (539)
                      +.+-+-.+|+|||++++.++..+.++ |.+|.||-     .+  ...-..    +...++.+..  -+...   ..+++.
T Consensus        29 i~Itgt~t~vGKT~vt~gL~~~l~~~-G~~V~~fKPv~~g~~~~~~D~~~----~~~~~g~~~~~~~~~~~---~p~sP~  100 (251)
T 3fgn_A           29 LVVTGTGTGVGKTVVCAALASAARQA-GIDVAVCKPVQTGTARGDDDLAE----VGRLAGVTQLAGLARYP---QPMAPA  100 (251)
T ss_dssp             EEEEESSTTSCHHHHHHHHHHHHHHT-TCCEEEEEEEECCGGGTCCHHHH----HHHHHCCCEEEEEEECS---SSSCHH
T ss_pred             EEEEeCCCCCcHHHHHHHHHHHHHHC-CCeEEEEeeeecCCCCCCHHHHH----HHHHcCCCCCCCCeeEC---CCCChH
Confidence            56666678999999999999998886 99999995     21  111122    2333454311  01100   112221


Q ss_pred             HHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009230          370 EFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQH  449 (539)
Q Consensus       370 ~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~  449 (539)
                      -..    .+.+         .....++.|.+.++++  ..+.|+||||.-..+..+..  ...        .....+|+.
T Consensus       101 ~aa----~~~~---------~~~~~~~~i~~~~~~l--~~~~D~vlIEGagGl~~pl~--~~~--------~~~adla~~  155 (251)
T 3fgn_A          101 AAA----EHAG---------MALPARDQIVRLIADL--DRPGRLTLVEGAGGLLVELA--EPG--------VTLRDVAVD  155 (251)
T ss_dssp             HHH----HHTT---------CCCCCHHHHHHHHHTT--CCTTCEEEEECSSSTTCEEE--TTT--------EEHHHHHHH
T ss_pred             HHH----HHcC---------CCCCCHHHHHHHHHHH--HhcCCEEEEECCCCCcCCcC--ccc--------chHHHHHHH
Confidence            111    1111         1123456666655543  23578999997666553210  000        012346778


Q ss_pred             hCcEEEEEecCC
Q 009230          450 HACHVWFVAHPR  461 (539)
Q Consensus       450 ~~i~vi~~~q~r  461 (539)
                      ++.|||+|+..+
T Consensus       156 l~~pVILV~~~~  167 (251)
T 3fgn_A          156 VAAAALVVVTAD  167 (251)
T ss_dssp             TTCEEEEEECSS
T ss_pred             cCCCEEEEEcCC
Confidence            899999998843

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=87.84  E-value=0.29  Score=41.97  Aligned_cols=19  Identities=21%  Similarity=0.307  Sum_probs=16.9

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.+|+|||+|+..++
T Consensus         5 i~ivG~~~~GKSsli~~l~   23 (169)
T 3q85_A            5 VMLVGESGVGKSTLAGTFG   23 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            5789999999999988875

>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=87.77  E-value=2  Score=51.51  Aligned_cols=143  Identities=13%  Similarity=0.105  Sum_probs=74.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh----------cCCeEEEEeCCCC-HHHHHHHHHHHh--hCCCccccccC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEH----------AGWKFVLCSMENK-VREHARKLLEKH--IKKPFFEANYG  360 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~----------~g~~vl~~s~E~~-~~~~~~r~~~~~--~~~~~~~i~~~  360 (539)
                      +..++=+++++|||+|||..+.-.+.+...+          .+.+++|++.=-. ..+....+-...  .|+....+ .|
T Consensus        92 l~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~~~~~~~gi~V~~~-tG  170 (1724)
T 4f92_B           92 LETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAEL-TG  170 (1724)
T ss_dssp             HTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEC-CS
T ss_pred             HcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHHHHHhhCCCEEEEE-EC
Confidence            6678889999999999998765555544432          2568999985422 223333333322  23332222 22


Q ss_pred             CCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHH---HHHcCCcEEEEccccccccCCCCCCCHHHHHH
Q 009230          361 GSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAA---VLRHGVRGLVIDPYNELDHQRPVSQTETEYVS  437 (539)
Q Consensus       361 ~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~---~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~  437 (539)
                      .  ...+..+       +....++|.       |++.+...++..   ..-..+++||||-.. ++..     ++-..++
T Consensus       171 d--~~~~~~~-------~~~~~IlVt-------TpEkld~llr~~~~~~~l~~v~~vIiDEvH-~l~d-----~RG~~lE  228 (1724)
T 4f92_B          171 D--HQLCKEE-------ISATQIIVC-------TPEKWDIITRKGGERTYTQLVRLIILDEIH-LLHD-----DRGPVLE  228 (1724)
T ss_dssp             S--CSSCCTT-------GGGCSEEEE-------CHHHHHHHTTSSTTHHHHTTEEEEEETTGG-GGGS-----TTHHHHH
T ss_pred             C--CCCCccc-------cCCCCEEEE-------CHHHHHHHHcCCccchhhcCcCEEEEecch-hcCC-----ccHHHHH
Confidence            1  0111111       222223441       344332222211   112468999999664 5432     2334456


Q ss_pred             HHHHHHHHHHHH--hCcEEEEEec
Q 009230          438 QMLTMVKRFAQH--HACHVWFVAH  459 (539)
Q Consensus       438 ~~~~~Lk~lA~~--~~i~vi~~~q  459 (539)
                      .++.++....+.  .++-+|.+|-
T Consensus       229 ~~l~rl~~~~~~~~~~~riI~LSA  252 (1724)
T 4f92_B          229 ALVARAIRNIEMTQEDVRLIGLSA  252 (1724)
T ss_dssp             HHHHHHHHHHHHHTCCCEEEEEEC
T ss_pred             HHHHHHHHHHHhCCCCCcEEEEec
Confidence            666666554443  3577888776

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=87.77  E-value=0.28  Score=42.05  Aligned_cols=20  Identities=20%  Similarity=0.278  Sum_probs=17.4

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+..+..
T Consensus         6 i~v~G~~~~GKssli~~l~~   25 (170)
T 1g16_A            6 ILLIGDSGVGKSCLLVRFVE   25 (170)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHh
Confidence            57889999999999888763

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=87.68  E-value=0.3  Score=41.92  Aligned_cols=21  Identities=19%  Similarity=0.207  Sum_probs=17.7

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+..++..
T Consensus         9 i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            9 VVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            678899999999998887643

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=87.68  E-value=0.3  Score=42.88  Aligned_cols=20  Identities=40%  Similarity=0.516  Sum_probs=17.7

Q ss_pred             EEEEEcCCCCChhHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la  318 (539)
                      -++|.|++|+|||||+..++
T Consensus         9 ~i~lvG~~gvGKStL~~~l~   28 (188)
T 2wjg_A            9 EIALIGNPNVGKSTIFNALT   28 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            47799999999999988876

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=87.65  E-value=0.3  Score=42.27  Aligned_cols=19  Identities=26%  Similarity=0.434  Sum_probs=17.0

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.+|+|||+|+..++
T Consensus        10 i~v~G~~~~GKSsli~~l~   28 (177)
T 1wms_A           10 VILLGDGGVGKSSLMNRYV   28 (177)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            6789999999999988876

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=87.65  E-value=0.31  Score=41.64  Aligned_cols=20  Identities=25%  Similarity=0.295  Sum_probs=17.4

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+..+..
T Consensus         6 i~v~G~~~~GKssli~~l~~   25 (167)
T 1c1y_A            6 LVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHc
Confidence            57889999999999888764

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=87.61  E-value=0.22  Score=53.15  Aligned_cols=28  Identities=21%  Similarity=0.233  Sum_probs=24.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +..|+.++|.|+||+||||++..++...
T Consensus        57 i~~g~~vll~Gp~GtGKTtlar~ia~~l   84 (604)
T 3k1j_A           57 ANQKRHVLLIGEPGTGKSMLGQAMAELL   84 (604)
T ss_dssp             HHTTCCEEEECCTTSSHHHHHHHHHHTS
T ss_pred             ccCCCEEEEEeCCCCCHHHHHHHHhccC
Confidence            7788999999999999999999887644

>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=87.58  E-value=0.55  Score=44.61  Aligned_cols=36  Identities=17%  Similarity=0.014  Sum_probs=28.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      -.+|++++|+|||..+..++.......+.+++++..
T Consensus       130 ~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~~lil~P  165 (282)
T 1rif_A          130 RRILNLPTSAGRSLIQALLARYYLENYEGKILIIVP  165 (282)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECS
T ss_pred             CeEEEcCCCCCcHHHHHHHHHHHHHcCCCeEEEEEC
Confidence            457899999999999888877766653449999974

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=87.57  E-value=0.31  Score=41.77  Aligned_cols=21  Identities=19%  Similarity=0.224  Sum_probs=17.8

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+..++..
T Consensus         9 i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            9 VCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            678899999999998887643

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=87.52  E-value=0.33  Score=46.93  Aligned_cols=36  Identities=19%  Similarity=0.174  Sum_probs=25.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHh-cCCeEEEEeC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEH-AGWKFVLCSM  334 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~-~g~~vl~~s~  334 (539)
                      -++|.|+||+|||+++..++..+... ....++.++.
T Consensus        48 ~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~   84 (327)
T 1iqp_A           48 HLLFAGPPGVGKTTAALALARELFGENWRHNFLELNA   84 (327)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEET
T ss_pred             eEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeec
Confidence            38999999999999999998776432 1133555543

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=87.50  E-value=0.31  Score=43.07  Aligned_cols=21  Identities=33%  Similarity=0.491  Sum_probs=18.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~  319 (539)
                      -++|.|.+|+|||+|+..++.
T Consensus        50 ~i~vvG~~g~GKSsll~~l~~   70 (193)
T 2ged_A           50 SIIIAGPQNSGKTSLLTLLTT   70 (193)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            578999999999999887753

>4a0g_A Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; BIO3-BIO1, biotin synthesis; HET: PLP; 2.50A {Arabidopsis thaliana} PDB: 4a0h_A* 4a0r_A* 4a0f_A*

Probab=87.45  E-value=5.6  Score=43.92  Aligned_cols=35  Identities=11%  Similarity=0.043  Sum_probs=29.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhc-----CCeEEEEe
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHA-----GWKFVLCS  333 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~-----g~~vl~~s  333 (539)
                      .+.+.+-.+|+|||+++.-++..+.+ .     |.+|.||-
T Consensus        36 ~l~I~gt~s~vGKT~vt~gL~r~l~~-~~~~~~G~~V~~fK   75 (831)
T 4a0g_A           36 TYLIWSANTSLGKTLVSTGIAASFLL-QQPSSSATKLLYLK   75 (831)
T ss_dssp             EEEEEESSSSSCHHHHHHHHHHHHHS-CSSCCTTCEEEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHh-cccccCCceEEEEc
Confidence            46666777999999999999987766 5     89999995

---

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	539
d1cr2a_	277	c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase),	5e-25
d1nuia1	192	e.13.1.2 (A:64-255) Primase fragment of primase-he	3e-20
d1nlfa_	274	c.37.1.11 (A:) Hexameric replicative helicase repA	3e-14
d2fcja1	114	c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199	2e-13
d1tf7a1	242	c.37.1.11 (A:14-255) Circadian clock protein KaiC	6e-09
d1tf7a2	242	c.37.1.11 (A:256-497) Circadian clock protein KaiC	3e-08
d2i1qa2	258	c.37.1.11 (A:65-322) DNA repair protein Rad51, cat	1e-07
d1t6t1_	108	c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquif	2e-07
d1n0wa_	242	c.37.1.11 (A:) DNA repair protein Rad51, catalytic	2e-06
d1pzna2	254	c.37.1.11 (A:96-349) DNA repair protein Rad51, cat	2e-05
d1szpa2	251	c.37.1.11 (A:145-395) DNA repair protein Rad51, ca	7e-05

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]} Length = 277

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]

 Score =  102 bits (255), Expect = 5e-25
 Identities = 51/279 (18%), Positives = 98/279 (35%), Gaps = 13/279 (4%)

Query: 265 DEIDAYYHRTSGDEFGISTGWRALNE-LYNVLPGELTIVTGVPNSGKSEWIDALICNINE 323
           + I  +   +      + +G   +N+       GE+ +VT     GKS ++         
Sbjct: 3   ERIREHL-SSEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGT 61

Query: 324 HAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFS 383
             G K  L  +E  V E A  L+  H +    +++     E +   +F+Q    L    +
Sbjct: 62  AMGKKVGLAMLEESVEETAEDLIGLHNRVRLRQSDS-LKREIIENGKFDQWFDELFGNDT 120

Query: 384 LIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMV 443
               ++ +      +L          G   +++D  + +      S       + M T +
Sbjct: 121 FHLYDSFAEAETDRLLAKLAYMRSGLGCDVIILDHISIVVSASGESDERKMIDNLM-TKL 179

Query: 444 KRFAQHHACHVWFVAHPRQLHNWVG----EPPNLYDISGSAHFINKCDNGIVIHRNRDPE 499
           K FA+     +  + H +            P ++ D+ GS       D  I + RN+  +
Sbjct: 180 KGFAKSTGVVLVVICHLKNPDKGKAHEEGRPVSITDLRGSGALRQLSDTIIALERNQQGD 239

Query: 500 AGPIDRVQVCVRKVRNKVVGTIGEAF-LSYNRVTGEYMD 537
                   V VR ++ +  G  G A  + YN+ TG    
Sbjct: 240 ----MPNLVLVRILKCRFTGDTGIAGYMEYNKETGWLEP 274

>d1nuia1 e.13.1.2 (A:64-255) Primase fragment of primase-helicase protein {Bacteriophage T7 [TaxId: 10760]} Length = 192

class: Multi-domain proteins (alpha and beta)
fold: DNA primase core
superfamily: DNA primase core
family: Primase fragment of primase-helicase protein
domain: Primase fragment of primase-helicase protein
species: Bacteriophage T7 [TaxId: 10760]

 Score = 86.5 bits (213), Expect = 3e-20
 Identities = 44/195 (22%), Positives = 68/195 (34%), Gaps = 21/195 (10%)

Query: 54  AYFAERLISAETLRRNRV-MQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEK 112
           +    R IS ET ++    + K  G    +A    +NG +V+ K RD +K F      + 
Sbjct: 16  SALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKS 75

Query: 113 VFYGLDDIEGESD-IIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKY 171
                  +      I++ EGE+D L++ E        V  G                   
Sbjct: 76  DALFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHG------------ASAAK 123

Query: 172 QYLWNCKMYLKQASRIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDAN 231
           +       Y  Q  +IIL  D D  G+   EE A+ +   +      P        KDAN
Sbjct: 124 KTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLP-------CKDAN 176

Query: 232 EVLMYLGPGALKEVV 246
           E  +      + E V
Sbjct: 177 ECHLNGHDREIMEQV 191

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]} Length = 274

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]

 Score = 70.8 bits (172), Expect = 3e-14
 Identities = 39/252 (15%), Positives = 69/252 (27%), Gaps = 21/252 (8%)

Query: 291 LYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHI 350
           L N++ G +  +     +GKS     L   I        V       V     +     I
Sbjct: 23  LPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAI 82

Query: 351 KKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHG 410
                          ++ EE +     L     LI+    SLP+I              G
Sbjct: 83  HHRLH-----ALGAHLSAEERQAVADGL-----LIQPLIGSLPNIMAPEWFDGLKRAAEG 132

Query: 411 VRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEP 470
            R +V+D    L       +  +  ++Q++  ++  A    C + F+ H  +    +G  
Sbjct: 133 RRLMVLD---TLRRFHIEEENASGPMAQVIGRMEAIAADTGCSIVFLHHASKGAAMMGAG 189

Query: 471 PNLYDISGSAHFINKCDNGIVIHRNRDPEAGPI--------DRVQVCVRKVRNKVVGTIG 522
                  GS+  ++       +      EA             V+  V K          
Sbjct: 190 DQQQASRGSSVLVDNIRWQSYLSSMTSAEAEEWGVDDDQRRFFVRFGVSKANYGAPFADR 249

Query: 523 EAFLSYNRVTGE 534
                   V   
Sbjct: 250 WFRRHDGGVLKP 261

>d2fcja1 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 {Bacillus stearothermophilus [TaxId: 1422]} Length = 114

class: Alpha and beta proteins (a/b)
fold: Toprim domain
superfamily: Toprim domain
family: Toprim domain
domain: Hypothetical protein RBSTP2199
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 64.9 bits (158), Expect = 2e-13
 Identities = 21/116 (18%), Positives = 35/116 (30%), Gaps = 16/116 (13%)

Query: 120 IEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKM 179
           +     +IIVEG  DK  +        V V      S           D + + L +   
Sbjct: 1   MRRVEKVIIVEGRSDKQKVAAVLNEPVVIVCTNGTIS-----------DARLEELAD--- 46

Query: 180 YLKQASRIILATDGDPPGQALAEELARRVGRERCWRV-RWPKKNDVDHFKDANEVL 234
              +   + L  D D  G+ L  +  R         + R  ++          +VL
Sbjct: 47  -ELEGYDVYLLADADEAGEKLRRQFRRMFPEAEHLYIDRAYREVAAAPIWHLAQVL 101

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]} Length = 242

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]

 Score = 54.6 bits (130), Expect = 6e-09
 Identities = 27/240 (11%), Positives = 69/240 (28%), Gaps = 36/240 (15%)

Query: 280 GISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK 337
            + T     +++ +  +  G  T+V+G   +GK+ +    + N         V  + E  
Sbjct: 7   KMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEET 66

Query: 338 VREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKW 397
            ++  +                   +    + +            S      + +     
Sbjct: 67  PQDIIKNAR----------------SFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDL 110

Query: 398 --VLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVW 455
             +++    A+ ++  R + ID    +          +    ++  +V R  Q  A  V 
Sbjct: 111 SALIERINYAIQKYRARRVSIDSVTSV---FQQYDASSVVRRELFRLVARLKQIGATTVM 167

Query: 456 FVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRN 515
                 +             I+         DN +++    +   G   R  + + K+R 
Sbjct: 168 TTERIEEYG----------PIARYGVEEFVSDNVVILRNVLE---GERRRRTLEILKLRG 214

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]} Length = 242

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]

 Score = 52.6 bits (125), Expect = 3e-08
 Identities = 32/241 (13%), Positives = 66/241 (27%), Gaps = 41/241 (17%)

Query: 277 DEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM 334
               +S+G   L+E+         + + TG   +GK+  +   + N   +     +    
Sbjct: 4   SNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAYE 63

Query: 335 ENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPS 394
           E++ +                       A    ++  E            I C       
Sbjct: 64  ESRAQLLRN-------------------AYSWGMDFEE----MERQNLLKIVCAYPESAG 100

Query: 395 IKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHV 454
           ++  L + K+ +       + ID  + L      +        Q +  V  +A+      
Sbjct: 101 LEDHLQIIKSEINDFKPARIAIDSLSALARGVSNNA-----FRQFVIGVTGYAKQEEITG 155

Query: 455 WFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVR 514
            F     Q                 +H     D  I++        G + R  + V K+R
Sbjct: 156 LFTNTSDQFMG--------AHSITDSHISTITDTIILLQYVEI--RGEMSRA-INVFKMR 204

Query: 515 N 515
            
Sbjct: 205 G 205

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]} Length = 258

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

 Score = 50.9 bits (120), Expect = 1e-07
 Identities = 20/244 (8%), Positives = 60/244 (24%), Gaps = 23/244 (9%)

Query: 279 FGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN 336
           + +ST    L+ +    +    +T   GV  SGK++ +     N+       +   ++  
Sbjct: 14  WKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSK 73

Query: 337 KVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSI- 395
                 + +        + +       ER+       G    +   +       +     
Sbjct: 74  GEVAQPKAV--------YIDTEGTFRPERIMQMAEHAGIDGQTVLDNTFVARAYNSDMQM 125

Query: 396 ----KWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHA 451
               K    + +   ++  V   +   +      R       + + + +  + + A    
Sbjct: 126 LFAEKIEDLIQEGNNIKLVVIDSLTSTFRNEYTGRGKLAERQQKLGRHMATLNKLADLFN 185

Query: 452 CHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVR 511
           C V          +                          + + +       D+    + 
Sbjct: 186 CVVLVTNQVSAKPDAFFGMAEQAIGGHIVGHA--ATFRFFVRKGKG------DKRVAKLY 237

Query: 512 KVRN 515
              +
Sbjct: 238 DSPH 241

>d1t6t1_ c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquifex aeolicus [TaxId: 63363]} Length = 108

class: Alpha and beta proteins (a/b)
fold: Toprim domain
superfamily: Toprim domain
family: Toprim domain
domain: Hypothetical protein aq 2086
species: Aquifex aeolicus [TaxId: 63363]

 Score = 47.2 bits (112), Expect = 2e-07
 Identities = 17/120 (14%), Positives = 40/120 (33%), Gaps = 30/120 (25%)

Query: 126 IIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQAS 185
           +I+VEG+ DK ++ +    N + +     +                       M   +  
Sbjct: 19  VILVEGKNDKKALSKFSIKNVIDLSGKRYA-------------------DVVDMLEGKWE 59

Query: 186 RIILATDGDPPGQALAEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEV 245
           ++IL  D D  G+ + +++   +  +            VD   +    L       ++E+
Sbjct: 60  KVILLFDLDTHGERINQKMKELLSSQGF---------LVDE--NFRNFLKKWNIIHIEEI 108

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]} Length = 242

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]

 Score = 47.1 bits (110), Expect = 2e-06
 Identities = 24/224 (10%), Positives = 59/224 (26%), Gaps = 17/224 (7%)

Query: 277 DEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM 334
           +   I+TG + L++L    +  G +T + G   +GK+     +   +             
Sbjct: 1   EIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKT----QICHTLAVTCQLPIDRGGG 56

Query: 335 ENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPS 394
           E K      +   +  +       YG S   +            +  ++     +     
Sbjct: 57  EGKAMYIDTEGTFRPERLLAVAERYGLSGSDV----------LDNVAYARAFNTDHQTQL 106

Query: 395 IKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHV 454
           +     +   +     +       Y      R        ++++ L M+ R A      V
Sbjct: 107 LYQASAMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAV 166

Query: 455 WFVAHPRQLHNWVGEPPNLYDISGSAHFI-NKCDNGIVIHRNRD 497
                     +               + I +     + + + R 
Sbjct: 167 VITNQVVAQVDGAAMFAADPKKPIGGNIIAHASTTRLYLRKGRG 210

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 254

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]

 Score = 43.9 bits (102), Expect = 2e-05
 Identities = 30/251 (11%), Positives = 73/251 (29%), Gaps = 27/251 (10%)

Query: 271 YHRTSGDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNI---NEHA 325
           Y +       ISTG ++L++L    +    +T V G   SGK++    L   +    E  
Sbjct: 8   YLKKRATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEG 67

Query: 326 GWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLI 385
           G    +  ++ +      ++ E    +                +E  +         S  
Sbjct: 68  GLNGSVIWIDTENTFRPERIREIAQNRGL------------DPDEVLKHIYVARAFNSNH 115

Query: 386 RCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKR 445
           +         K    L     ++  +   +   +      R       + +++ L  + R
Sbjct: 116 QMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHR 175

Query: 446 FAQHHACHVWFVAHPRQLHN-WVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPID 504
            A  +   V+     +   + + G+P         AH        + + + +        
Sbjct: 176 LANLYDIAVFVTNQVQARPDAFFGDPTRPIGGHILAHS---ATLRVYLRKGKG------G 226

Query: 505 RVQVCVRKVRN 515
           +    +    +
Sbjct: 227 KRIARLIDAPH 237

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 251

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]

 Score = 42.4 bits (98), Expect = 7e-05
 Identities = 28/247 (11%), Positives = 66/247 (26%), Gaps = 23/247 (9%)

Query: 271 YHRTSGDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWK 328
           +H    +   ++TG + L+ L    V  G +T + G   +GKS+    L           
Sbjct: 6   FHMRRSELICLTTGSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIG 65

Query: 329 FVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCE 388
                      E             F        A+R  ++  +      +  ++     
Sbjct: 66  GGEGKCLYIDTEGT-----------FRPVRLVSIAQRFGLDPDDA---LNNVAYARAYNA 111

Query: 389 NDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQ 448
           +  L  +     +   +     V   V+  Y      R        ++++ +  ++R A 
Sbjct: 112 DHQLRLLDAAAQMMSESRFSLIVVDSVMALYRTDFSGRGELSARQMHLAKFMRALQRLAD 171

Query: 449 HHACHVWFVAHPRQLHN-WVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQ 507
                V          +  +   P+    +G     +     +   + +        +  
Sbjct: 172 QFGVAVVVTNQVVAQVDGGMAFNPDPKKPTGGNIMAHSSTTRLGFKKGKG------CQRL 225

Query: 508 VCVRKVR 514
             V    
Sbjct: 226 CKVVDSP 232

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	539
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	100.0
d1nuia1	192	Primase fragment of primase-helicase protein {Bact	99.96
d1dd9a_	314	DNA primase DnaG catalytic core {Escherichia coli	99.93
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	99.9
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	99.89
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	99.88
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	99.85
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	99.81
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	99.81
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	99.78
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	99.76
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	99.72
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	99.72
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	99.69
d2fcja1	114	Hypothetical protein RBSTP2199 {Bacillus stearothe	99.5
d1t6t1_	108	Hypothetical protein aq_2086 {Aquifex aeolicus [Ta	99.43
d1ls1a2	207	GTPase domain of the signal sequence recognition p	98.27
d1g2912	240	Maltose transport protein MalK, N-terminal domain	98.25
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	98.21
d1okkd2	207	GTPase domain of the signal recognition particle r	98.18
d2qy9a2	211	GTPase domain of the signal recognition particle r	98.16
d2awna2	232	Maltose transport protein MalK, N-terminal domain	98.15
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	98.15
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	98.05
d1vmaa2	213	GTPase domain of the signal recognition particle r	98.0
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	97.99
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	97.98
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.97
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	97.94
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	97.93
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	97.88
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	97.85
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	97.83
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	97.81
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	97.8
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	97.65
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	97.63
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	97.62
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	97.43
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.3
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.27
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.16
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.94
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	96.93
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.89
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.87
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.85
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.79
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	96.79
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.78
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.77
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	96.77
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.74
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	96.74
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.73
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	96.47
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.45
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.44
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.4
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	96.4
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	96.32
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.3
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.3
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.28
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	96.21
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.18
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.13
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	96.04
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	96.04
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	96.02
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	95.99
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	95.91
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	95.85
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	95.84
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	95.78
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	95.75
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	95.73
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	95.69
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	95.68
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	95.67
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	95.61
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	95.59
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	95.58
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	95.55
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	95.52
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	95.52
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	95.51
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	95.5
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	95.4
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	95.35
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	95.35
d1xpua3	289	Transcription termination factor Rho, ATPase domai	95.31
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.26
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	95.25
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.18
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.15
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	95.07
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	95.07
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	95.06
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	95.04
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	95.0
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	94.98
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	94.97
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	94.93
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	94.86
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	94.74
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	94.73
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	94.71
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	94.71
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.63
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	94.56
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	94.55
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	94.55
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	94.51
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	94.45
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	94.43
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	94.41
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	94.4
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	94.39
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	94.39
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	94.39
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	94.28
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	94.28
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	94.19
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	94.12
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	94.09
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	94.06
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.02
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	94.0
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	93.99
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	93.94
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	93.93
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	93.91
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	93.9
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	93.9
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	93.69
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	93.53
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	93.42
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	93.23
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	93.2
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	93.17
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	92.98
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	92.96
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	92.7
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	92.65
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	92.59
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	92.54
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	92.52
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	92.48
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	92.31
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	92.14
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.09
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	91.91
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	91.54
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	91.29
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	91.22
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	91.17
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	91.02
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	91.01
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	90.95
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	90.85
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.83
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	90.83
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	90.77
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	90.64
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	90.25
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	90.06
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	90.02
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	90.02
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	89.94
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	89.9
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	89.46
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	89.45
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	89.36
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	89.34
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	89.16
d1nrjb_	209	Signal recognition particle receptor beta-subunit	89.14
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	89.13
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	89.09
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	89.08
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	88.93
d1c9ka_	180	Adenosylcobinamide kinase/adenosylcobinamide phosp	88.86
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	88.74
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	88.69
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	88.67
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	88.64
d1tuea_	205	Replication protein E1 helicase domain {Human papi	88.63
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	88.6
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	88.5
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	88.49
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	88.39
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	88.38
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	88.37
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	88.37
d2fh5b1	207	Signal recognition particle receptor beta-subunit	88.35
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	88.18
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	88.11
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	88.07
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	88.05
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	87.95
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	87.95
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	87.94
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	87.93
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	87.81
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	87.78
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	87.76
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.76
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	87.73
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	87.63
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	87.62
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	87.62
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	87.59
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	87.59
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	87.56
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	87.54
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	87.52
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	87.45
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	87.39
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	87.14
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	87.1
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	86.96
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	86.96
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	86.59
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	86.45
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	86.32
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	86.29
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	86.2
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	86.17
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	85.73
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	85.71
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	85.57
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	85.57
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	85.54
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	85.45
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	85.18
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	84.91
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	84.91
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	84.82
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	84.61
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	84.57
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	84.48
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	83.93
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	83.92
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	83.83
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	83.74
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	83.42
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	83.26
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	82.72
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	82.52
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	81.77
d1vdda_	199	Recombination protein RecR {Deinococcus radioduran	81.18
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	81.07
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	80.97
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	80.92
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	80.2
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	80.18

>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=100.00  E-value=8.1e-40  Score=318.83  Aligned_cols=268  Identities=19%  Similarity=0.191  Sum_probs=188.8

Q ss_pred             HHHHHHHhhccCCCccccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH
Q 009230          264 FDEIDAYYHRTSGDEFGISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA  342 (539)
Q Consensus       264 ~~~i~~~~~~~~~~~~gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~  342 (539)
                      .|++.+.+.. +....+++|||+.||++++ +++|++++|+|+||+|||+|++|++.+++..+|.+|+|||+||+++++.
T Consensus         2 ~e~~~~~~~~-~~~~~~i~TG~~~lD~~~~G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~E~~~~~~~   80 (277)
T d1cr2a_           2 RERIREHLSS-EESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETA   80 (277)
T ss_dssp             HHHHHHHHTS-CCCSCBCCCSCTTHHHHHCSBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEESSSCHHHHH
T ss_pred             hHHHHHHHhC-CCCccccCCCchhHHHHhcCCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeeeccchhhHH
Confidence            3566666554 5666899999999999998 9999999999999999999999999999877799999999999999999


Q ss_pred             HHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEcccccc
Q 009230          343 RKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNEL  422 (539)
Q Consensus       343 ~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l  422 (539)
                      .|+++..+++++....... ...++.+++.++.+.+.....+..++.....+.+++...++..+..+++++||||++ ++
T Consensus        81 ~r~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vvID~l-~~  158 (277)
T d1cr2a_          81 EDLIGLHNRVRLRQSDSLK-REIIENGKFDQWFDELFGNDTFHLYDSFAEAETDRLLAKLAYMRSGLGCDVIILDHI-SI  158 (277)
T ss_dssp             HHHHHHHTTCCGGGCHHHH-HHHHHTSHHHHHHHHHHSSSCEEEECCC-CCCHHHHHHHHHHHHHTTCCSEEEEEEE-EC
T ss_pred             hHHHHHhhcCCchhhcccc-cchhhhHHHHHHHHHhhccceeeeeccccchhHHHHHHHhhhhhhccCcceEEEccc-cc
Confidence            9999999999876543210 000111123344444433222222344567788999999999888999999999955 55


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCC---CCCCCCcccccccccchhccceEEEEEeCCCC
Q 009230          423 DHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNW---VGEPPNLYDISGSAHFINKCDNGIVIHRNRDP  498 (539)
Q Consensus       423 ~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~---~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~  498 (539)
                      +.......+.++.+.+++..|+.||+++||+||+++| +|...++   .+.+|.+++++||+.|+|.||.||.|+|+++.
T Consensus       159 l~~~~~~~~~~~~~~~~~~~l~~lA~~~~i~vi~~~q~~r~~~~~~~~~~~~~~~~~~~gS~~i~~~ad~vl~l~r~~~~  238 (277)
T d1cr2a_         159 VVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHLKNPDKGKAHEEGRPVSITDLRGSGALRQLSDTIIALERNQQG  238 (277)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHCCEEEEEEECC---------------------CHHHHHHCSEEEEEECC---
T ss_pred             ccccccccchhHHHHHHHHHHHHHhhhccccceeecccccccccccccccccchhhhcccccchhhhCcEEEEEEecCcc
Confidence            5433223345567889999999999999999999999 7765433   34578999999999999999999999998765


Q ss_pred             CCCCCCcEEEEEEEeeC-CCcceeeeEEEEEeCCCceeccC
Q 009230          499 EAGPIDRVQVCVRKVRN-KVVGTIGEAFLSYNRVTGEYMDI  538 (539)
Q Consensus       499 ~~~~~~~~~l~i~K~R~-g~~G~~~~~~l~fd~~~~rf~~~  538 (539)
                      +.  ++.+.|.+.|||+ |.+|..  ..+.||++|+||.+.
T Consensus       239 ~~--~~~~~l~v~KnR~~G~~G~~--~~l~~d~~tgr~~~~  275 (277)
T d1cr2a_         239 DM--PNLVLVRILKCRFTGDTGIA--GYMEYNKETGWLEPS  275 (277)
T ss_dssp             -----CEEEEEEEEETTTCCCEEE--EEEEECTTTCCEEEC
T ss_pred             CC--CCeEEEEEEccCCCCCCCCE--EEEEEeCCCCeEcCC
Confidence            42  4678999999995 777664  379999999999875

>d1nuia1 e.13.1.2 (A:64-255) Primase fragment of primase-helicase protein {Bacteriophage T7 [TaxId: 10760]}

class: Multi-domain proteins (alpha and beta)
fold: DNA primase core
superfamily: DNA primase core
family: Primase fragment of primase-helicase protein
domain: Primase fragment of primase-helicase protein
species: Bacteriophage T7 [TaxId: 10760]

Probab=99.96  E-value=3.3e-29  Score=229.24  Aligned_cols=175  Identities=26%  Similarity=0.267  Sum_probs=143.1

Q ss_pred             HHHHHHhcCCCHHHHHHcCcccccCCceeEEEEeEe-eCCEEEEEEeecCCCcccc-cCCCCCccccccccCCCCcEEEE
Q 009230           52 LRAYFAERLISAETLRRNRVMQKRHGHEVVIAFPYW-RNGKLVNCKYRDFNKKFWQ-EKDTEKVFYGLDDIEGESDIIIV  129 (539)
Q Consensus        52 ~~~Yl~~Rgi~~~~~~~~~~~~~~~~~~~~i~fP~~-~~G~~~~~~~R~~~~~~~~-~~~~~~~l~g~~~~~~~~~v~i~  129 (539)
                      ...||++||||.||++.|+++....+...+++||++ .+|+++++++|...+++.. ..+....+|+.+.....++|+||
T Consensus        14 ~~~~L~~RGIs~et~~~~~~~~~~~~~~~~~~~p~~d~~G~~v~~~~R~~~k~~~~~~~~~~~~~~~~~~~~~~~~iiI~   93 (192)
T d1nuia1          14 RYSALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFGKHLWNGGKKIVVT   93 (192)
T ss_dssp             BCCCBGGGTBCHHHHHHHTEEEEEETTEEEEEEEEECTTSCEEEEEEECTTCCCEEEECCCTTCCTTGGGCCCBSCCEEE
T ss_pred             ChhhhhhCcCCHHHHHHCCeEEEeeCCeEEEEEeeECCCCCEEEEEcccccccceeccCCCCCcceeeeccccCcEEEEE
Confidence            346899999999999999987666666778899977 8999999999998766654 34567788998888888899999


Q ss_pred             echhhHHHHHHhCCCceE--EcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCccchHHHHHHHHH
Q 009230          130 EGEMDKLSMEEAGFLNCV--SVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELARR  207 (539)
Q Consensus       130 EG~~Dalsl~~~g~~~~v--~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~~G~~~~~~~~~~  207 (539)
                      |||+||||++|+++.+..  +++.++..              ...++.+.+++|+++++|+||+|||+||+++++++++.
T Consensus        94 EGe~Dals~~q~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~l~~~~~Vvl~~DnD~AG~~aa~~~~~~  159 (192)
T d1nuia1          94 EGEIDMLTVMELQDCKYPVVSLGHGASA--------------AKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQV  159 (192)
T ss_dssp             SSHHHHHHHHHHHTTCSCEECCTTTTTT--------------HHHHHHHTHHHHTTBSCEEEECCSSHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHhcCCCcceeecCcchhh--------------hhhHHhHHHHHhcCCCeEEEEcCCCHHHHHHHHHHHHH
Confidence            999999999999875433  33333322              12345566788889999999999999999999999999


Q ss_pred             hcCCceEEEecCCCCCCCCCCChHHHHHhcCcchHHHHHH
Q 009230          208 VGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVE  247 (539)
Q Consensus       208 l~~~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~~~~~~  247 (539)
                      ++..+|+++.+|       +||+||+|++++.+++.+.++
T Consensus       160 l~~~~~~~~~~~-------~KD~nd~l~~~~~~~~~~~i~  192 (192)
T d1nuia1         160 LPAGKVRVAVLP-------CKDANECHLNGHDREIMEQVW  192 (192)
T ss_dssp             SCTTTEEECCCS-------SSSHHHHHTTTTHHHHHHHHC
T ss_pred             cCCCcEEEecCC-------CcCHHHHHHcCCHHHHHHhhC
Confidence            988888877654       799999999999988888764

>d1dd9a_ e.13.1.1 (A:) DNA primase DnaG catalytic core {Escherichia coli [TaxId: 562]}

class: Multi-domain proteins (alpha and beta)
fold: DNA primase core
superfamily: DNA primase core
family: DNA primase DnaG catalytic core
domain: DNA primase DnaG catalytic core
species: Escherichia coli [TaxId: 562]

Probab=99.93  E-value=2.7e-25  Score=216.02  Aligned_cols=181  Identities=20%  Similarity=0.329  Sum_probs=145.7

Q ss_pred             CCCcHHHHHHHHhcCCCHHHHHHcCcccccCC-----------------------------------ceeEEEEeEe-eC
Q 009230           46 EPLGNELRAYFAERLISAETLRRNRVMQKRHG-----------------------------------HEVVIAFPYW-RN   89 (539)
Q Consensus        46 ~p~~~~~~~Yl~~Rgi~~~~~~~~~~~~~~~~-----------------------------------~~~~i~fP~~-~~   89 (539)
                      .+.++.+++||++|||++++++.|.+++...+                                   ..+||+||+. ..
T Consensus        19 ~~~~~~a~~YL~~Rgl~~~~i~~f~lGyap~~~~~l~~~l~~~~~~~~~l~~~gl~~~~~~g~~~d~F~~ri~fPI~d~~   98 (314)
T d1dd9a_          19 QPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSYDRFRERVMFPIRDKR   98 (314)
T ss_dssp             SGGGHHHHHHHHHTTCCHHHHHHHTCEEECSSSCHHHHHHCSSHHHHHHHHHTTSEEEC---CEEESCCSEEEEEEECTT
T ss_pred             CCchHHHHHHHHHCCCCHHHHHHcccccCcccHHHHHHHHhhCCCchhhhhhhhheeeccccccchhccceeEEEEeccc
Confidence            46667899999999999999999998754211                                   1469999988 88


Q ss_pred             CEEEEEEeecC---CCcccccC-----CCCCcccccccc----CCCCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCC
Q 009230           90 GKLVNCKYRDF---NKKFWQEK-----DTEKVFYGLDDI----EGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSV  157 (539)
Q Consensus        90 G~~~~~~~R~~---~~~~~~~~-----~~~~~l~g~~~~----~~~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~  157 (539)
                      |++++|.+|.+   .++|.+.+     .+...+||++..    ...++|+||||++|+++++|+|+.+||+. +|++.. 
T Consensus        99 g~~i~f~gR~~~~~~~KY~ns~et~~f~k~~~ly~~~~a~~~~~~~~~~iivEG~~Dvi~l~q~Gi~n~Va~-~Gta~t-  176 (314)
T d1dd9a_          99 GRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVAS-LGTSTT-  176 (314)
T ss_dssp             SCEEEEEEEESSSCSCSEEECCCCSSCCTTTCCBTHHHHHHTCSSCSCEEEESSHHHHHHHHHTTCCCEEEC-CC-CCC-
T ss_pred             ceEEEEeeeecccccccccCCCccccccchhhcccHHHHHhhhccccceEEEechHHHHHHHHcccccchhH-Hhhhhh-
Confidence            99999999998   46787755     467889998764    44678999999999999999999999995 566531 


Q ss_pred             CCCCCCChhhhhhhHHHHhHHHHhcc-CCEEEEEecCCccchHHHHHHHHHh-----cCCceEEEecCCCCCCCCCCChH
Q 009230          158 SKKNVPSEEQDTKYQYLWNCKMYLKQ-ASRIILATDGDPPGQALAEELARRV-----GRERCWRVRWPKKNDVDHFKDAN  231 (539)
Q Consensus       158 ~~~~l~~~~~~~~~~~l~~~~~~l~~-~~~ivl~~DnD~~G~~~~~~~~~~l-----~~~~~~~~~~p~~~~~~~~kD~n  231 (539)
                            .           .++..|.+ .++|++|+|+|.||++|+.+..+.+     .+..++++.+|      .++||+
T Consensus       177 ------~-----------~~~~~l~~~~~~i~l~~D~D~AG~~A~~r~~~~~~~~~~~g~~v~v~~lp------~g~DPD  233 (314)
T d1dd9a_         177 ------A-----------DHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLP------DGEDPD  233 (314)
T ss_dssp             ------H-----------HHHHHHHHHCSEEEEEEESSHHHHHHHHHHHHHHGGGCCTTCEEEEEEEC------TTCCHH
T ss_pred             ------h-----------HHHHHHHhcCCceEEEeecCcchhhHHHhHHHHhhHHhcCCCeEEEEecc------CcCCHH
Confidence                  1           12344444 4799999999999999999887764     23467888888      689999


Q ss_pred             HHHHhcCcchHHHHHHhccc
Q 009230          232 EVLMYLGPGALKEVVENAEL  251 (539)
Q Consensus       232 d~l~~~g~~~~~~~~~~A~~  251 (539)
                      |+++++|.+++.+++++|.+
T Consensus       234 e~l~k~G~e~~~~ll~~a~~  253 (314)
T d1dd9a_         234 TLVRKEGKEAFEARMEQAMP  253 (314)
T ss_dssp             HHHHHHHHHHHHHHHTTCEE
T ss_pred             HHHHhcCHHHHHHHHhcCCC
Confidence            99999999999999998875

>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=99.90  E-value=5.5e-23  Score=198.52  Aligned_cols=214  Identities=14%  Similarity=0.103  Sum_probs=139.0

Q ss_pred             Cchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh---------cCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          284 GWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEH---------AGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       284 g~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~---------~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      +-|.+|.+++ +.||++++|+|+||+|||+|++|+|.+++..         .+.+|+|+++|++..++..|+.+...+. 
T Consensus        15 ~~p~~d~li~G~~pg~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~E~~~~~~~~Rl~~~~~~~-   93 (274)
T d1nlfa_          15 APPPLDYVLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGAHL-   93 (274)
T ss_dssp             CCCCCCEEETTEETTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSSCHHHHHHHHHHHHTTS-
T ss_pred             CCCCHHHHhCCccCCcEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEeccchHHHHHHHHHHHhhcc-
Confidence            4467888887 7789999999999999999999999998863         1358999999999999999987654432 


Q ss_pred             ccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCC--HHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCC
Q 009230          354 FFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPS--IKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQT  431 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~--~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~  431 (539)
                                   +.+........+    .+. ........  .......+  .....++++||||++..+...   .++
T Consensus        94 -------------~~~~~~~~~~~~----~~~-~~~~~~~~~~~~~~~~~~--~~~~~~~~lvviD~l~~~~~~---~~~  150 (274)
T d1nlfa_          94 -------------SAEERQAVADGL----LIQ-PLIGSLPNIMAPEWFDGL--KRAAEGRRLMVLDTLRRFHIE---EEN  150 (274)
T ss_dssp             -------------CHHHHHHHHHHE----EEC-CCTTSCCCTTSHHHHHHH--HHHHTTCSEEEEECGGGGCCS---CTT
T ss_pred             -------------Chhhhhcccccc----eec-cccCccchhHHHHHHHHH--HHhccCccEEecCchhhhccc---ccc
Confidence                         333333222221    111 11111111  11222222  223468999999988877643   345


Q ss_pred             HHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCC--------CCCCC
Q 009230          432 ETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDP--------EAGPI  503 (539)
Q Consensus       432 ~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~--------~~~~~  503 (539)
                      +...+.+++..|+.+|++++|+|++++|.++.....+.....++++||++|.+.||+++.|.+.++.        +....
T Consensus       151 ~~~~~~~~~~~l~~la~~~~~~vi~v~H~~K~~~~~~~~~~~~~~~Gssai~~~a~~v~~l~r~~~~~~~~~~~~~~~~~  230 (274)
T d1nlfa_         151 ASGPMAQVIGRMEAIAADTGCSIVFLHHASKGAAMMGAGDQQQASRGSSVLVDNIRWQSYLSSMTSAEAEEWGVDDDQRR  230 (274)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCCEEEEEEEC--------------------CTGGGCSCEEEEEECCHHHHHHTTCCTTSGG
T ss_pred             chhhHHHHHHHHHHHhhcCCCceehhhhccccccccCCcccccccccHHHHHhhccEEEEEEecchhhhhhccCcccccC
Confidence            6677889999999999999999999999444332234456678899999999999999999997532        11122


Q ss_pred             CcEEEEEEEeeCCCccee
Q 009230          504 DRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       504 ~~~~l~i~K~R~g~~G~~  521 (539)
                      ..+.+.+.|+|+|+.|..
T Consensus       231 ~~~~~~v~K~~~~~~~~~  248 (274)
T d1nlfa_         231 FFVRFGVSKANYGAPFAD  248 (274)
T ss_dssp             GEEEEEEEECSSSSCCCC
T ss_pred             cEEEEEEEeeCCCCCCce
Confidence            357889999999998864

>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=99.89  E-value=6.4e-22  Score=187.26  Aligned_cols=204  Identities=16%  Similarity=0.183  Sum_probs=153.4

Q ss_pred             ccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCCcc
Q 009230          278 EFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFF  355 (539)
Q Consensus       278 ~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~~~  355 (539)
                      ...+|||++.||++++  +++|++++|+|+||+|||+|++|++.+++.+ +.+|+|+++|+++..+.+++...  +.   
T Consensus         5 ~~ri~TG~~~LD~~l~GGi~~gsl~li~G~pGsGKT~l~~qia~~~~~~-~~~~~~is~e~~~~~~~~~~~~~--~~---   78 (242)
T d1tf7a2           5 NVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACAN-KERAILFAYEESRAQLLRNAYSW--GM---   78 (242)
T ss_dssp             CCEECCSCHHHHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTT-TCCEEEEESSSCHHHHHHHHHTT--SC---
T ss_pred             CCccCCCcHHHHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHh-ccccceeeccCCHHHHHHHHHHc--CC---
Confidence            3469999999999996  9999999999999999999999999998885 99999999999999887776431  22   


Q ss_pred             ccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCCCCCHHHH
Q 009230          356 EANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPVSQTETEY  435 (539)
Q Consensus       356 ~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~  435 (539)
                                 +.++.      .......+.........+.++...+...+.+.+++++|||++..+...     .....
T Consensus        79 -----------~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~vviDs~~~~~~~-----~~~~~  136 (242)
T d1tf7a2          79 -----------DFEEM------ERQNLLKIVCAYPESAGLEDHLQIIKSEINDFKPARIAIDSLSALARG-----VSNNA  136 (242)
T ss_dssp             -----------CHHHH------HHTTSEEECCCCGGGSCHHHHHHHHHHHHHTTCCSEEEEECHHHHTSS-----SCHHH
T ss_pred             -----------ChHHH------hhcCceEEEEeecchhhHHHHHHHHHHHHHhcCCceeeeecchhhhcC-----CCHHH
Confidence                       11221      111122221112334567788888888888899999999988877643     23455


Q ss_pred             HHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEEEEEEEeeC
Q 009230          436 VSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRN  515 (539)
Q Consensus       436 ~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~l~i~K~R~  515 (539)
                      +..++..|..+++++++++++++|......        ....|+..+.+.||.++.++.......   ..+.+.|.|+|.
T Consensus       137 ~~~~~~~l~~~~~~~~~~~i~~~~~~~~~~--------~~~~~~~~~~~~ad~vi~l~~~~~~~~---~~R~i~v~K~R~  205 (242)
T d1tf7a2         137 FRQFVIGVTGYAKQEEITGLFTNTSDQFMG--------AHSITDSHISTITDTIILLQYVEIRGE---MSRAINVFKMRG  205 (242)
T ss_dssp             HHHHHHHHHHHHHHTTCEEEEEEECSSSSC--------CCSSCSSCCTTTCSEEEEEEEEEETTE---EEEEEEEEEESS
T ss_pred             HHHHHHHHHHHHHHcCCeEEEEEeeEeecc--------ccccCCcceeeecceEEEEEEeecCCc---eEEEEEEEecCC
Confidence            678889999999999999999999433321        234567789999999999987654221   146789999999


Q ss_pred             CCcce
Q 009230          516 KVVGT  520 (539)
Q Consensus       516 g~~G~  520 (539)
                      ++...
T Consensus       206 ~~~~~  210 (242)
T d1tf7a2         206 SWHDK  210 (242)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            86543

>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=99.88  E-value=6.9e-22  Score=186.32  Aligned_cols=209  Identities=12%  Similarity=0.036  Sum_probs=151.9

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCCC
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKP  353 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~~  353 (539)
                      ....+||||+++||++++  +++|++++|+|+||+|||+|++|++.+.+.+.+.+++|+++|++++.+..++.+  .+..
T Consensus         3 ~~~~~i~TGi~~LD~~l~GGi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~e~~~~~~~~~~~~--~~~~   80 (242)
T d1tf7a1           3 QAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARS--FGWD   80 (242)
T ss_dssp             SSCCEECCCCTTHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESSSCHHHHHHHHGG--GTCC
T ss_pred             CCCCcccCCcHHHHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCcccccccCCHHHHHHHHHH--cCCC
Confidence            355789999999999995  999999999999999999999999999888768899999999999987655532  1211


Q ss_pred             ccccccCCCCCCCCHHHHHHHHHHhhccceeEe-----ecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCC
Q 009230          354 FFEANYGGSAERMTVEEFEQGKAWLSNTFSLIR-----CENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPV  428 (539)
Q Consensus       354 ~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~-----~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~  428 (539)
                      .              +...   ...........     .......+...+.+.+..++.+++++++|||++..+....  
T Consensus        81 ~--------------~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~i~~~~~~~viiD~~~~l~~~~--  141 (242)
T d1tf7a1          81 L--------------AKLV---DEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQY--  141 (242)
T ss_dssp             H--------------HHHH---HTTSEEEEECCCCSSCCSCCSSHHHHHHHHHHHHHHHHHTCSEEEEECSTTTSTTT--
T ss_pred             h--------------HHHH---HhcchhhhhhccchhhhhhhccccHHHHHHHHHHHHHhhccchhhhhHHHHHHHhc--
Confidence            1              1111   10000000000     0001222345677888888889999999999887776432  


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCcEE
Q 009230          429 SQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQ  507 (539)
Q Consensus       429 ~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~~~  507 (539)
                        .....+...+..+..+++++++++++++| +....          +..+++.+++.+|.++.++...+.+.   ....
T Consensus       142 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~d~i~~~~~~~~~~~---~~r~  206 (242)
T d1tf7a1         142 --DASSVVRRELFRLVARLKQIGATTVMTTERIEEYG----------PIARYGVEEFVSDNVVILRNVLEGER---RRRT  206 (242)
T ss_dssp             --CCHHHHHHHHHHHHHHHHHHTCEEEEEEECSSSSS----------CSSTTSCHHHHCSEEEEEEEECSTTC---CEEE
T ss_pred             --cChhHHHHHHHHHHHHHHhcCCceEEeeccccccc----------ccccCcceeeeccEEEEEEEeeeCCe---eEEE
Confidence              23455667888999999999999999999 54432          34567788899999999987665432   3678


Q ss_pred             EEEEEeeCCCcce
Q 009230          508 VCVRKVRNKVVGT  520 (539)
Q Consensus       508 l~i~K~R~g~~G~  520 (539)
                      +.|.|+|+++.+.
T Consensus       207 l~v~K~R~~~~~~  219 (242)
T d1tf7a1         207 LEILKLRGTSHMK  219 (242)
T ss_dssp             EEEEEETTSCCCC
T ss_pred             EEEEEcCCCCCCC
Confidence            9999999876543

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=99.85  E-value=1.3e-20  Score=178.13  Aligned_cols=217  Identities=16%  Similarity=0.089  Sum_probs=152.9

Q ss_pred             CCccccccCchhhhhhh--c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhCC
Q 009230          276 GDEFGISTGWRALNELY--N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKK  352 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~--~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~~  352 (539)
                      .....||||.+.||.++  | +++|.++.|+|+||+|||+|+++++.++..+ |..|+|++.|.+...-  |  +...|+
T Consensus        30 ~~~~~isTG~~~lD~~Lg~GGi~~g~itei~G~~gsGKTtl~l~~~~~~q~~-g~~~vyidtE~~~~~~--~--a~~~Gv  104 (263)
T d1u94a1          30 MDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE-GKTCAFIDAEHALDPI--Y--ARKLGV  104 (263)
T ss_dssp             CCCCEECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEESSCCCCHH--H--HHHTTC
T ss_pred             CCCCeEccCCHHHHHHhcCCCccCceEEEEecCCCcHHHHHHHHHHHHHHcC-CCEEEEEccccccCHH--H--HHHhCC
Confidence            45568999999999988  3 9999999999999999999999999999885 9999999999875432  1  122354


Q ss_pred             CccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccC---CCC-
Q 009230          353 PFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQ---RPV-  428 (539)
Q Consensus       353 ~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~---~~~-  428 (539)
                      +..                         +++++     ...+.+++.+.++.+.+...+++|||||+..+...   ... 
T Consensus       105 d~d-------------------------~v~~~-----~~~~~E~~~~~i~~l~~~~~~~liViDSi~al~~~~e~~~~~  154 (263)
T d1u94a1         105 DID-------------------------NLLCS-----QPDTGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEI  154 (263)
T ss_dssp             CGG-------------------------GCEEE-----CCSSHHHHHHHHHHHHHHTCCSEEEEECGGGCCCHHHHTTC-
T ss_pred             CHH-------------------------HEEEe-----cCCCHHHHHHHHHHHHhcCCCCEEEEECccccccchhccccc
Confidence            432                         23343     23467788888888888888999999999988531   110 


Q ss_pred             C----CCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCC---CCCC
Q 009230          429 S----QTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRD---PEAG  501 (539)
Q Consensus       429 ~----~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~---~~~~  501 (539)
                      .    ......+...++.|..++.+++++||++.|.+...+.....|  ....|+..+.+.++++|.|.+...   .+..
T Consensus       155 ~~~~~~~~a~~l~~~~~~l~~~~~~~~~~vi~~NQv~~~~~~~~g~~--~~~~GG~al~~~~~~rl~l~k~~~~k~g~~~  232 (263)
T d1u94a1         155 GDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKIGVMFGNP--ETTTGGNALKFYASVRLDIRRIGAVKEGENV  232 (263)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHHHHTCEEEEEEC----------------CTTCSHHHHHCSEEEEEEEEEEEESSSSE
T ss_pred             ccchHHHHHHHHHHHHHHHHHhhhccCceEEEEEEEEeccccccCCC--ccccccchhheeeEEEEEEEeccccccCCce
Confidence            1    111235678899999999999999999999553322111112  123688899999999999977431   1111


Q ss_pred             CCCcEEEEEEEeeCCCcceeeeEEEEEe
Q 009230          502 PIDRVQVCVRKVRNKVVGTIGEAFLSYN  529 (539)
Q Consensus       502 ~~~~~~l~i~K~R~g~~G~~~~~~l~fd  529 (539)
                      ....+++.+.|||.++.+....+.+.||
T Consensus       233 iG~~~r~~v~Knr~~~p~~~~~f~i~~~  260 (263)
T d1u94a1         233 VGSETRVKVVKNKIAAPFKQAEFQILYG  260 (263)
T ss_dssp             EEEEEEEEEEEESSBCSCCEEEEEEETT
T ss_pred             eeeEEEEEEEeCCCCCCCCEEEEEEEcC
Confidence            1124568899999999988765666655

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.81  E-value=7.3e-19  Score=165.92  Aligned_cols=216  Identities=16%  Similarity=0.103  Sum_probs=153.2

Q ss_pred             CCccccccCchhhhhhh--c-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH-HHHHHHHHHhhC
Q 009230          276 GDEFGISTGWRALNELY--N-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR-EHARKLLEKHIK  351 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~--~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~-~~~~r~~~~~~~  351 (539)
                      .....||||.+.||.++  | ++.|.++.|+|++|+|||+||++++.++... |..|+|+..|.+.. +.+++     .|
T Consensus        36 ~~~~~i~TG~~~lD~~lg~gG~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~-g~~~vyIDtE~~~~~e~a~~-----~G  109 (269)
T d1mo6a1          36 QPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAA-GGVAAFIDAEHALDPDYAKK-----LG  109 (269)
T ss_dssp             CCSCCBCCSCHHHHHHTSSSSBCSSSEEEEECSSSSSHHHHHHHHHHHHHHT-TCEEEEEESSCCCCHHHHHH-----HT
T ss_pred             CccceEccCCHHHHHhhccCCcccceeEEEecCCCcHHHHHHHHHHHHHhcC-CCEEEEEECCccCCHHHHHH-----hC
Confidence            44567999999999998  3 9999999999999999999999999887775 99999999997642 22222     25


Q ss_pred             CCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccC---CCC
Q 009230          352 KPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQ---RPV  428 (539)
Q Consensus       352 ~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~---~~~  428 (539)
                      ++..                         +++++     ...+.+++.+.++.+..+..+++|||||+..+...   ...
T Consensus       110 vD~d-------------------------~il~~-----~~~~~E~~~~~~~~l~~~~~~~liIiDSi~al~~~~E~e~~  159 (269)
T d1mo6a1         110 VDTD-------------------------SLLVS-----QPDTGEQALEIADMLIRSGALDIVVIDSVAALVPRAELEGE  159 (269)
T ss_dssp             CCGG-------------------------GCEEE-----CCSSHHHHHHHHHHHHHTTCEEEEEEECSTTCCCHHHHC--
T ss_pred             CCHH-------------------------HeEEe-----cCCCHHHHHHHHHHHHhcCCCCEEEEecccccccHHHhccc
Confidence            5432                         23443     23467888888888888888999999999988731   110


Q ss_pred             ----CC-CHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCC---CC
Q 009230          429 ----SQ-TETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDP---EA  500 (539)
Q Consensus       429 ----~~-~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~---~~  500 (539)
                          .. .....+...++.|..++.++++++++++|.+..-+.....|.  -..|...+.+.|+++|.|.+.+..   +.
T Consensus       160 ~~~~~~~~~a~~l~~~l~~l~~~~~~~~~~vi~~NQv~~~~~~~~g~~~--~~~GG~al~~~ss~rl~l~k~~~~kdg~~  237 (269)
T d1mo6a1         160 MGDSHVGLQARLMSQALRKMTGALNNSGTTAIFINQLRDKIGVMFGSPE--TTTGGKALKFYASVRMDVRRVETLKDGTN  237 (269)
T ss_dssp             -----CCHHHHHHHHHHHHHHHHHHHHTCEEEEEECC---------------CTTHHHHHHHCSEEEEEEEEECCBCSSS
T ss_pred             cccchHHHHHHHHHHHHHHHHHHHhhcCchhhhhheeeccCccccCCce--ecccccceeeeeeEEEEEEecceeccCCc
Confidence                01 122457788999999999999999999995543221111222  235889999999999999774421   11


Q ss_pred             CCCCcEEEEEEEeeCCCcceeeeEEEEEe
Q 009230          501 GPIDRVQVCVRKVRNKVVGTIGEAFLSYN  529 (539)
Q Consensus       501 ~~~~~~~l~i~K~R~g~~G~~~~~~l~fd  529 (539)
                      .....+.+.+.|||.++.|....+.+.|+
T Consensus       238 ~iG~~~~~kv~Knr~~~p~~~a~f~I~~~  266 (269)
T d1mo6a1         238 AVGNRTRVKVVKNKCLAPFKQAEFDILYG  266 (269)
T ss_dssp             BCEEEEEEEEEEESSSCSCEEEEEEEETT
T ss_pred             eEEEEEEEEEEECCCCCCCCEEEEEEEeC
Confidence            11224578999999999988765666654

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=99.81  E-value=5.6e-19  Score=166.97  Aligned_cols=216  Identities=15%  Similarity=0.130  Sum_probs=151.5

Q ss_pred             CCccccccCchhhhhhhc---cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHH-HHHHHHHHhhC
Q 009230          276 GDEFGISTGWRALNELYN---VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVRE-HARKLLEKHIK  351 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~---l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~-~~~r~~~~~~~  351 (539)
                      .....||||.+.||.+++   ++.|.++.|+|++|+|||+|+++++.++... |..|+|+..|.+... .+++     .|
T Consensus        33 ~~~~~i~TGs~~lD~~Lg~GGip~g~itei~G~~~sGKT~l~l~~~~~aqk~-g~~v~yiDtE~~~~~~~a~~-----~G  106 (268)
T d1xp8a1          33 LDVQVVSTGSLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKA-GGTCAFIDAEHALDPVYARA-----LG  106 (268)
T ss_dssp             CCCCEECCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT-TCCEEEEESSCCCCHHHHHH-----TT
T ss_pred             CCCCeEcCCCHHHHHHhcCCCccCceEEEEecCCccchHHHHHHHHHHHHhC-CCEEEEEECCccCCHHHHHH-----hC
Confidence            455689999999999993   9999999999999999999999999998775 999999999965432 2222     36


Q ss_pred             CCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCC--CC
Q 009230          352 KPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRP--VS  429 (539)
Q Consensus       352 ~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~--~~  429 (539)
                      ++..                         +++++     ...+.++..+.++.+..+..+++|||||+..+.....  ..
T Consensus       107 vd~d-------------------------~i~~~-----~~~~~E~~~~~~~~l~~~~~~~liIiDSi~al~~r~e~~~~  156 (268)
T d1xp8a1         107 VNTD-------------------------ELLVS-----QPDNGEQALEIMELLVRSGAIDVVVVDSVAALTPRAEIEGD  156 (268)
T ss_dssp             CCGG-------------------------GCEEE-----CCSSHHHHHHHHHHHHTTTCCSEEEEECTTTCCCSTTC---
T ss_pred             CCch-------------------------hEEEE-----cCCCHHHHHHHHHHHHhcCCCcEEEEecccccccHHHHccc
Confidence            5432                         22343     2346777778888887777899999999999874211  10


Q ss_pred             -C-----CHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCC---
Q 009230          430 -Q-----TETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEA---  500 (539)
Q Consensus       430 -~-----~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~---  500 (539)
                       .     .....+...++.|..++.+++++++++.|.+..-+.....|  ..-.|...+.+.+++.|.|.+..+..+   
T Consensus       157 ~~~~~~~~~a~~l~~~lr~l~~~~~~~~~~vi~tNQv~~~~g~~~g~~--~~~~GG~al~~~ss~rl~l~k~~~~~k~~~  234 (268)
T d1xp8a1         157 MGDSLPGLQARLMSQALRKLTAILSKTGTAAIFINQVREKIGVMYGNP--ETTTGGRALKFYASVRLDVRKIGQPTKVGN  234 (268)
T ss_dssp             -----CCHHHHHHHHHHHHHHHHHTTTCCEEEEEEEC-----------------CHHHHHHHCSEEEEEEEESCCC----
T ss_pred             ccchhHHHHHHHHHHHHHHHHhhhhhcCCeEEEEeEEeeccccccCcc--eeecccchhhhceeEEEEEEecCcccccCC
Confidence             1     12345678889999999999999999999553322111112  123478899999999999987543211   


Q ss_pred             C-CCCcEEEEEEEeeCCCcceeeeEEEEEe
Q 009230          501 G-PIDRVQVCVRKVRNKVVGTIGEAFLSYN  529 (539)
Q Consensus       501 ~-~~~~~~l~i~K~R~g~~G~~~~~~l~fd  529 (539)
                      . ....+.+.+.|||.++.+....+.+.|+
T Consensus       235 ~~iG~~v~~kv~Knr~~~p~~~~~~~i~~~  264 (268)
T d1xp8a1         235 DAVANTVKIKTVKNKVAAPFKEVELALVYG  264 (268)
T ss_dssp             --CEEEEEEEEEEESSSCCCCEEEEEEETT
T ss_pred             ceEEEEEEEEEEECCcCCCCCEEEEEEecC
Confidence            1 1234678999999999887655555554

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=99.78  E-value=6.9e-19  Score=166.71  Aligned_cols=215  Identities=11%  Similarity=0.078  Sum_probs=141.1

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc---------------CCeEEEEeCCCCH
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHA---------------GWKFVLCSMENKV  338 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~---------------g~~vl~~s~E~~~  338 (539)
                      ....++||||+.||++++  +++|++++|+|+||+|||+|++|+|.+++...               +.+++|+++|.+.
T Consensus        11 ~~~~~i~TG~~~LD~ll~GGl~~G~l~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~e~~~   90 (258)
T d2i1qa2          11 STVWKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTF   90 (258)
T ss_dssp             TTCCEECCSCHHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCC
T ss_pred             CCCceecCCCHHHHHhcCCCccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEeecccchhcCceEEEEEecCCc
Confidence            556789999999999995  99999999999999999999999999998641               3468888888664


Q ss_pred             HHHHHHHHHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCH-HHHHHHHHHHHHHcCCcEEEEc
Q 009230          339 REHARKLLEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSI-KWVLDLAKAAVLRHGVRGLVID  417 (539)
Q Consensus       339 ~~~~~r~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~-~~i~~~i~~~~~~~~~~~vvID  417 (539)
                      .....+..........              .       .......++..  .....+ +.+......+.....+.++++|
T Consensus        91 ~~~~~~~~~~~~~~~~--------------~-------~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~vid  147 (258)
T d2i1qa2          91 RPERIMQMAEHAGIDG--------------Q-------TVLDNTFVARA--YNSDMQMLFAEKIEDLIQEGNNIKLVVID  147 (258)
T ss_dssp             CHHHHHHHHHHHTCCH--------------H-------HHHHTEEEEEC--SSHHHHHHHHHTHHHHHHTTCEEEEEEEE
T ss_pred             CHHHHHHHHhhcchhh--------------h-------hhhhcceeecc--CchhhHHHHHHHHHHHHHHhcccceeeee
Confidence            4443343332222111              0       11112223211  111111 2233333344444567899999


Q ss_pred             cccccccCCCCC-C---CHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEE
Q 009230          418 PYNELDHQRPVS-Q---TETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIH  493 (539)
Q Consensus       418 ~~~~l~~~~~~~-~---~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~  493 (539)
                      ++..+....... .   ........++..++.++..++++++++.|.+....  ...+......|+..+++.+|.+|.++
T Consensus       148 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~i~l~  225 (258)
T d2i1qa2         148 SLTSTFRNEYTGRGKLAERQQKLGRHMATLNKLADLFNCVVLVTNQVSAKPD--AFFGMAEQAIGGHIVGHAATFRFFVR  225 (258)
T ss_dssp             CSSHHHHHHCCCTTSHHHHHHHHHHHHHHHHHHHHHTTCEEEEEECEECC---------CCEESSHHHHHHHCSEEEEEE
T ss_pred             EEEEeechhccccccchhhHHHHHHHHHHHHHhhhhcceEEEeecceEeccc--cccCCcccccCcchhhhhceEEEEEE
Confidence            887765422111 1   12334567888999999999999999998333222  12334445678889999999999999


Q ss_pred             eCCCCCCCCCCcEEEEEEEeeCCCccee
Q 009230          494 RNRDPEAGPIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       494 r~~~~~~~~~~~~~l~i~K~R~g~~G~~  521 (539)
                      +.+.      +.+.+.|.|+|+++.|++
T Consensus       226 ~~~~------~~r~l~v~K~R~~~~~~~  247 (258)
T d2i1qa2         226 KGKG------DKRVAKLYDSPHLPDAEA  247 (258)
T ss_dssp             ECST------TEEEEEEEECSSSCCEEE
T ss_pred             EcCC------CEEEEEEEECCCCCCceE
Confidence            8653      367899999999988764

>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=99.76  E-value=1.1e-17  Score=158.57  Aligned_cols=212  Identities=13%  Similarity=0.099  Sum_probs=135.9

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-----cCCeEEEEeCCCCHHHHHHHHHHH
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEH-----AGWKFVLCSMENKVREHARKLLEK  348 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-----~g~~vl~~s~E~~~~~~~~r~~~~  348 (539)
                      ....++|||++.||.+++  +++|++++|+|+||+|||+|++|++.+.+.+     .+..++|+..|........+....
T Consensus        13 ~~i~ri~TGi~~LD~ll~GGlp~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (254)
T d1pzna2          13 ATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREIAQ   92 (254)
T ss_dssp             HTCCEECCSCHHHHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHHHHHHH
T ss_pred             cCCCeECCCCHHHHHhhcCCccCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHHHHHHH
Confidence            456789999999999996  9999999999999999999999999998753     267899999987655444444333


Q ss_pred             hhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHH---HHH-HHHHH----HHHcCCcEEEEcccc
Q 009230          349 HIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKW---VLD-LAKAA----VLRHGVRGLVIDPYN  420 (539)
Q Consensus       349 ~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~---i~~-~i~~~----~~~~~~~~vvID~~~  420 (539)
                      ..+.+              .+..       .....++.     ......   ... .....    .....++++++|++.
T Consensus        93 ~~~~~--------------~~~~-------~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viDs~~  146 (254)
T d1pzna2          93 NRGLD--------------PDEV-------LKHIYVAR-----AFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLT  146 (254)
T ss_dssp             TTTCC--------------HHHH-------GGGEEEEE-----CCSHHHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSS
T ss_pred             hcCCC--------------hHHh-------hhhhhhhh-----hccchhHHHHHHhhhhhhHHHHhhccCceeEeecchh
Confidence            32322              1111       11112221     111111   111 11111    112457899999888


Q ss_pred             ccccCCC-CCC---CHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeCC
Q 009230          421 ELDHQRP-VSQ---TETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNR  496 (539)
Q Consensus       421 ~l~~~~~-~~~---~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~  496 (539)
                      .+..... ...   .....+...+..++.++...++++++++|.+....  ...+......|+..+++.+|.++.|.+.+
T Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~l~~~~  224 (254)
T d1pzna2         147 SHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQVQARPD--AFFGDPTRPIGGHILAHSATLRVYLRKGK  224 (254)
T ss_dssp             TTHHHHCCSTTTHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECC-----------------CCCCCTTCSEEEEEEECT
T ss_pred             heeehhhcccchhhhhHHHHHHHHHHHHHHhhccceEEEecceEeeccC--cccCCceeecCceeehhhceEEEEEEecC
Confidence            7653221 111   22345667888889999999999999999443321  22344455668888999999999999865


Q ss_pred             CCCCCCCCcEEEEEEEeeCCCccee
Q 009230          497 DPEAGPIDRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       497 ~~~~~~~~~~~l~i~K~R~g~~G~~  521 (539)
                      .      ....+.|.|+|+++.|..
T Consensus       225 ~------~~R~~~v~K~R~~~~~~~  243 (254)
T d1pzna2         225 G------GKRIARLIDAPHLPEGEA  243 (254)
T ss_dssp             T------SEEEEEESCSSSSCCSEE
T ss_pred             C------CeEEEEEEECCCCCCeEE
Confidence            3      257899999999988763

>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=99.72  E-value=1.1e-17  Score=157.95  Aligned_cols=217  Identities=14%  Similarity=0.116  Sum_probs=143.4

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-----cCCeEEEEeCCCCHHHHHHHHHHH
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEH-----AGWKFVLCSMENKVREHARKLLEK  348 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-----~g~~vl~~s~E~~~~~~~~r~~~~  348 (539)
                      .....||||++.||.+++  |++|++++|+|+||+|||+|++|++.+++..     .+.+++|++.|.+......+....
T Consensus        11 ~~~~~i~TGi~~LD~ll~GGi~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   90 (251)
T d1szpa2          11 SELICLTTGSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLVSIAQ   90 (251)
T ss_dssp             HSSCEECCSCHHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGGGGHHHHH
T ss_pred             cCCCeecCCCHHHHhhhCCCCcCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHHHHHHHHH
Confidence            456789999999999996  9999999999999999999999999876542     267999999998754333332222


Q ss_pred             hhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCC-
Q 009230          349 HIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRP-  427 (539)
Q Consensus       349 ~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~-  427 (539)
                      ..+.+.              +.       ......++..  .....................+.++++|++..+..... 
T Consensus        91 ~~~~~~--------------~~-------~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~  147 (251)
T d1szpa2          91 RFGLDP--------------DD-------ALNNVAYARA--YNADHQLRLLDAAAQMMSESRFSLIVVDSVMALYRTDFS  147 (251)
T ss_dssp             HTCCCH--------------HH-------HGGGEEEEEC--CSTTTHHHHHHHTHHHHHHSCEEEEEEETGGGGGSCC--
T ss_pred             hcCCch--------------hh-------hhcceEEEec--cchhHHHHHHHHHHHHhhccccceeeehhhhhhhhhhhc
Confidence            223221              11       1122233321  22233444455555566667889999998888765321 


Q ss_pred             ---CCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCC
Q 009230          428 ---VSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPI  503 (539)
Q Consensus       428 ---~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~  503 (539)
                         ...........++..|..++...++++++++| ..+........+......|+..+.+.+|.+|.+.+.+.      
T Consensus       148 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~~i~l~~~~~------  221 (251)
T d1szpa2         148 GRGELSARQMHLAKFMRALQRLADQFGVAVVVTNQVVAQVDGGMAFNPDPKKPTGGNIMAHSSTTRLGFKKGKG------  221 (251)
T ss_dssp             ---CTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECC----------------CHHHHHHHHCSEEEEEEECST------
T ss_pred             cccchhhHHHHHHHHHHHHHhhhhhcceEEEEEEEEEeccCccccccCcceeccCccchhhheeEEEEEEecCC------
Confidence               11122335567889999999999999999999 44443222222344456788899999999999997653      


Q ss_pred             CcEEEEEEEeeCCCccee
Q 009230          504 DRVQVCVRKVRNKVVGTI  521 (539)
Q Consensus       504 ~~~~l~i~K~R~g~~G~~  521 (539)
                      ....+.|.|+|.++.+..
T Consensus       222 ~~r~l~i~K~r~~~~~~~  239 (251)
T d1szpa2         222 CQRLCKVVDSPCLPEAEC  239 (251)
T ss_dssp             TEEEEECCSCSSSCCCCC
T ss_pred             cEEEEEEEECCCCCCeeE
Confidence            367899999999987753

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=6.8e-17  Score=153.22  Aligned_cols=216  Identities=14%  Similarity=0.132  Sum_probs=136.2

Q ss_pred             CCccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHh-----cCCeEEEEeCCCCHHHHHHHHHHH
Q 009230          276 GDEFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEH-----AGWKFVLCSMENKVREHARKLLEK  348 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~-----~g~~vl~~s~E~~~~~~~~r~~~~  348 (539)
                      .....||||++.||++++  +++|++++|+|+||+|||+|++|++.+++..     .+..++|++.|........+.+..
T Consensus        14 ~~~~ri~TGi~~LD~~lgGGip~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (258)
T d1v5wa_          14 KMVFHITTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIAD   93 (258)
T ss_dssp             GGCCCBCCSCHHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHHHHH
T ss_pred             cCCceecCCCHHHHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHHHHHHHh
Confidence            344679999999999996  9999999999999999999999999987653     246899999997654333333322


Q ss_pred             hhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHH--cCCcEEEEccccccccCC
Q 009230          349 HIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLR--HGVRGLVIDPYNELDHQR  426 (539)
Q Consensus       349 ~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~--~~~~~vvID~~~~l~~~~  426 (539)
                      ..+.              ..+.      .+ .+..+++.  .....+.++...+......  ..++++++|++..+....
T Consensus        94 ~~~~--------------~~~~------~~-~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~vid~~~~~~~~~  150 (258)
T d1v5wa_          94 RFNV--------------DHDA------VL-DNVLYARA--YTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFRVD  150 (258)
T ss_dssp             HTTC--------------CHHH------HH-HTEEEEEC--CSTTHHHHHHHHHHHHHHHSCSSEEEEEEETSGGGHHHH
T ss_pred             hhcc--------------cchh------hh-hccccccc--CcHHHHHHHHHHHHHHhhhhccCceEEEeeehhhhhhcc
Confidence            2111              1111      11 22333322  2333333444434333322  346899999888775422


Q ss_pred             CCC----CCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCC
Q 009230          427 PVS----QTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAG  501 (539)
Q Consensus       427 ~~~----~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~  501 (539)
                      ...    ......+..++..|+.++.++++++++++| ..................++..+.+.+|.++.+.+.+.    
T Consensus       151 ~~~~~~~~~~~~~l~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~l~~~~~----  226 (258)
T d1v5wa_         151 FSGRGELAERQQKLAQMLSRLQKISEEYNVAVFVTNQMTADPGATMTFQADPKKPIGGHILAHASTTRISLRKGRG----  226 (258)
T ss_dssp             CCGGGCHHHHHHHHHHHHHHHHHHHHHHTCEEEEEECC-------------------CCTTTTSSSEEEEEEESST----
T ss_pred             ccCCcchhHHHHHHHHHHHHHHHHHHhcCCEEEEeeeEeecccccccccCCceeecccceehheeEEEEEEEEcCC----
Confidence            111    123345678999999999999999999999 44433222222333456678889999999999987643    


Q ss_pred             CCCcEEEEEEEeeCCCcce
Q 009230          502 PIDRVQVCVRKVRNKVVGT  520 (539)
Q Consensus       502 ~~~~~~l~i~K~R~g~~G~  520 (539)
                        ....+.|.|+|+++.+.
T Consensus       227 --~~R~l~i~K~r~~~~~~  243 (258)
T d1v5wa_         227 --ELRIAKIYDSPEMPENE  243 (258)
T ss_dssp             --TEEEEEEEECTTCCSSC
T ss_pred             --CEEEEEEEeCCCCCCcE
Confidence              25778999999987654

>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=99.69  E-value=2.6e-16  Score=145.82  Aligned_cols=215  Identities=13%  Similarity=0.118  Sum_probs=124.1

Q ss_pred             ccccccCchhhhhhhc--cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc-----CCeEEEEeCCCCHHHHHHHHHHHhh
Q 009230          278 EFGISTGWRALNELYN--VLPGELTIVTGVPNSGKSEWIDALICNINEHA-----GWKFVLCSMENKVREHARKLLEKHI  350 (539)
Q Consensus       278 ~~gi~tg~~~LD~~~~--l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~-----g~~vl~~s~E~~~~~~~~r~~~~~~  350 (539)
                      ..+||||++.||.+++  +++|++++|+|+||+|||+|++|++.+++...     +..+.++..+........+......
T Consensus         2 ~~ri~TG~~~LD~ll~GGi~~G~v~~i~G~~GsGKT~l~l~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (242)
T d1n0wa_           2 IIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERY   81 (242)
T ss_dssp             CCEECCSCHHHHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHHHHHHHT
T ss_pred             CCEEcCCCHHHHHhhcCCCcCCEEEEEEeCCCCCHHHHHHHHHHHHHHhhccccccceehhhhhhhhhHHHHHHHHHhhc
Confidence            4679999999999996  99999999999999999999999999987641     2456666666443322222211111


Q ss_pred             CCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccCCCC-C
Q 009230          351 KKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPV-S  429 (539)
Q Consensus       351 ~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~~~~-~  429 (539)
                                    ....+..       ......+..  .......................++.+|+...+...... .
T Consensus        82 --------------~~~~~~~-------~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  138 (242)
T d1n0wa_          82 --------------GLSGSDV-------LDNVAYARA--FNTDHQTQLLYQASAMMVESRYALLIVDSATALYRTDYSGR  138 (242)
T ss_dssp             --------------TCCHHHH-------HHTEEEEEC--CSHHHHHHHHHHHHHHHHHSCEEEEEEETSSGGGC------
T ss_pred             --------------ccchhhh-------hhhhhhhhh--hchhhhhhhhhhhhhhhhhhhheeecccceeeeehhhhhcc
Confidence                          1111111       111122211  111122233333334445566788888877766543211 1


Q ss_pred             ---CCHHHHHHHHHHHHHHHHHHhCcEEEEEec-CCCCCCCCCCCCCcccccccccchhccceEEEEEeCCCCCCCCCCc
Q 009230          430 ---QTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDR  505 (539)
Q Consensus       430 ---~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q-~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~~~~~~~~~~~  505 (539)
                         .........++..|+.++...+++++++.| +..........+......++..+++.+|.+|.|++.+.      ..
T Consensus       139 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~l~~~~~------~~  212 (242)
T d1n0wa_         139 GELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQVDGAAMFAADPKKPIGGNIIAHASTTRLYLRKGRG------ET  212 (242)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHCCEEEEEC-------------------------CCTTCEEEEEEECST------TE
T ss_pred             cchhhhHHHHHHHHHHHHHhhhhcceeEEEEEEEeccccccceeecccccccchhhHHHhCcEEEEEEEcCC------cE
Confidence               112345567888999999999999999999 44433323334555566778889999999999998653      25


Q ss_pred             EEEEEEEeeCCCccee
Q 009230          506 VQVCVRKVRNKVVGTI  521 (539)
Q Consensus       506 ~~l~i~K~R~g~~G~~  521 (539)
                      ..+.|.|+|+++.+.+
T Consensus       213 r~~~i~K~r~~~~~~~  228 (242)
T d1n0wa_         213 RICKIYDSPCLPEAEA  228 (242)
T ss_dssp             EEEEECCBTTBSCEEE
T ss_pred             EEEEEEeCCCCCCeEE
Confidence            6789999999987653

>d2fcja1 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: Toprim domain
superfamily: Toprim domain
family: Toprim domain
domain: Hypothetical protein RBSTP2199
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.50  E-value=4.6e-15  Score=121.00  Aligned_cols=104  Identities=19%  Similarity=0.173  Sum_probs=73.0

Q ss_pred             CCCCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCccchHH
Q 009230          121 EGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQAL  200 (539)
Q Consensus       121 ~~~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~~G~~~  200 (539)
                      ++.++|+||||++|+++++|+|..+++++++|+....              .++.+ +....+.++||||+|||.+|+++
T Consensus         2 k~~~~viIvEG~~D~~~l~~~g~~~vv~~~~gg~~~~--------------~~~~~-l~~~~~~~~Iii~~D~D~aG~~~   66 (114)
T d2fcja1           2 RRVEKVIIVEGRSDKQKVAAVLNEPVVIVCTNGTISD--------------ARLEE-LADELEGYDVYLLADADEAGEKL   66 (114)
T ss_dssp             CCCCEEEEESSHHHHHHHHHHBSSCCEEEECCSCCCH--------------HHHHH-HHHHTTTSEEEEECCSSHHHHHH
T ss_pred             CcCCEEEEEcCHHHHHHHHHcCCCCeEEeCCCccccH--------------HHHHH-HHHHhCCCcEEEEeCCChHHHHH
Confidence            4568999999999999999999999999986665321              11211 12223467999999999999999


Q ss_pred             HHHHHHHhcCCceEEEecCCCCCCCCCCChHHHHHhcCcchHHHHHHhcc
Q 009230          201 AEELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALKEVVENAE  250 (539)
Q Consensus       201 ~~~~~~~l~~~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~~~~~~~A~  250 (539)
                      +++++++|+..+  .+.++     ...+|++++..    +...+.++.|.
T Consensus        67 a~~l~~~l~~~~--~~~i~-----~~~~~v~~~p~----~~~~~~l~~~~  105 (114)
T d2fcja1          67 RRQFRRMFPEAE--HLYID-----RAYREVAAAPI----WHLAQVLLRAR  105 (114)
T ss_dssp             HHHHHHHCTTSE--EECCC-----TTTCSTTTSCH----HHHHHHHHHTT
T ss_pred             HHHHHHHCCCCc--EEEec-----ccccchhhCcH----HHHHHHHHhcc
Confidence            999999997643  34345     35677666533    33445555443

>d1t6t1_ c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Toprim domain
superfamily: Toprim domain
family: Toprim domain
domain: Hypothetical protein aq 2086
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.43  E-value=3.9e-14  Score=113.64  Aligned_cols=90  Identities=17%  Similarity=0.227  Sum_probs=69.6

Q ss_pred             CCcEEEEechhhHHHHHHhCCCceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHH-HHhccCCEEEEEecCCccchHHH
Q 009230          123 ESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCK-MYLKQASRIILATDGDPPGQALA  201 (539)
Q Consensus       123 ~~~v~i~EG~~Dalsl~~~g~~~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~-~~l~~~~~ivl~~DnD~~G~~~~  201 (539)
                      .+.|+||||++|++|++++|+.++|++. |+..                   .++. ..+..+++|||++|+|.||++++
T Consensus        16 ~~~viiVEG~~Dv~al~~~Gi~n~va~~-Gt~~-------------------~~~~~~l~~~~~~vii~~D~D~aG~~aa   75 (108)
T d1t6t1_          16 REAVILVEGKNDKKALSKFSIKNVIDLS-GKRY-------------------ADVVDMLEGKWEKVILLFDLDTHGERIN   75 (108)
T ss_dssp             TTSEEEESSHHHHHHHHTTTCCCEEECT-TSCH-------------------HHHHHHHTTTCSEEEECCCSSHHHHHHH
T ss_pred             CCcEEEEechHHHHHHHHhCCceEEeCC-CCcc-------------------HHHHHHHHhcCCeEEEEeCCCHHHHHHH
Confidence            4679999999999999999999988864 5432                   1112 23445789999999999999999


Q ss_pred             HHHHHHhcCCceEEEecCCCCCCCCCCChHHHHHhcCcchHH
Q 009230          202 EELARRVGRERCWRVRWPKKNDVDHFKDANEVLMYLGPGALK  243 (539)
Q Consensus       202 ~~~~~~l~~~~~~~~~~p~~~~~~~~kD~nd~l~~~g~~~~~  243 (539)
                      .++...|....+.+           ..|+.+++++.+.+.+.
T Consensus        76 ~kl~~~L~~~g~~v-----------d~~~~~~l~~~~~~~ie  106 (108)
T d1t6t1_          76 QKMKELLSSQGFLV-----------DENFRNFLKKWNIIHIE  106 (108)
T ss_dssp             HHHHHHHHHTTCEE-----------ECHHHHHHHHTTCCCGG
T ss_pred             HHHHHHHHHcCCCC-----------CcCHHHHHHHHhHHHHh
Confidence            99999996544322           36889999887766554

>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=98.27  E-value=1.3e-05  Score=71.08  Aligned_cols=64  Identities=19%  Similarity=0.267  Sum_probs=47.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH--HHHHHHhhCCCccccc
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA--RKLLEKHIKKPFFEAN  358 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~--~r~~~~~~~~~~~~i~  358 (539)
                      +....++++.|++|+||||.+..+|..+..+ |.+|++++++--.---.  -+..+..+++++....
T Consensus         7 ~~~~~vi~lvGp~GvGKTTTiaKLA~~~~~~-g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~   72 (207)
T d1ls1a2           7 LKDRNLWFLVGLQGSGKTTTAAKLALYYKGK-GRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVM   72 (207)
T ss_dssp             CCSSEEEEEECCTTTTHHHHHHHHHHHHHHT-TCCEEEEECCSSCHHHHHHHHHHHHHHTCCEEECC
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHHHC-CCcEEEEecccccchHHHHHHHHHHhcCCcccccc
Confidence            3445789999999999999999999998875 99999999985422111  2334566677766543

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=98.25  E-value=4.6e-06  Score=75.69  Aligned_cols=61  Identities=13%  Similarity=0.165  Sum_probs=45.4

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+|+++++|.=+       ++.+ .....++.+.|+++.+++|++||+++|.-.                  .+...||
T Consensus       155 ~~~P~iLllDEPt-------~~LD-~~~~~~i~~~l~~l~~~~g~tvi~vTHd~~------------------~~~~~~d  208 (240)
T d1g2912         155 VRKPQVFLMDEPL-------SNLD-AKLRVRMRAELKKLQRQLGVTTIYVTHDQV------------------EAMTMGD  208 (240)
T ss_dssp             HTCCSEEEEECTT-------TTSC-HHHHHHHHHHHHHHHHHHTCEEEEEESCHH------------------HHHHHCS
T ss_pred             hcCCCEEEecCCC-------cccC-HHHHHHHHHHHHHHHhccCCEEEEEcCCHH------------------HHHHhCC
Confidence            3689999999222       2233 345567899999999999999999999311                  2456899


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .|++|+.
T Consensus       209 rv~vm~~  215 (240)
T d1g2912         209 RIAVMNR  215 (240)
T ss_dssp             EEEEEET
T ss_pred             EEEEEEC
Confidence            9999985

>d1l2ta_ c.37.1.12 (A:) MJ0796 {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: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=98.21  E-value=6.2e-06  Score=74.37  Aligned_cols=178  Identities=15%  Similarity=0.108  Sum_probs=91.2

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC---CCHHHHHHHHHHHhhCCCccc-----
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME---NKVREHARKLLEKHIKKPFFE-----  356 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E---~~~~~~~~r~~~~~~~~~~~~-----  356 (539)
                      ..|+.+-- +.+||++.|.|++|+||||++.-++ .+.......|.|..-+   +++.++.. +.....|+=++.     
T Consensus        19 ~al~~isl~i~~Ge~~~iiG~sGsGKSTLl~~i~-gl~~p~sG~I~~~g~~i~~~~~~~~~~-~r~~~ig~v~Q~~~l~~   96 (230)
T d1l2ta_          19 YALKNVNLNIKEGEFVSIMGPSGSGKSTMLNIIG-CLDKPTEGEVYIDNIKTNDLDDDELTK-IRRDKIGFVFQQFNLIP   96 (230)
T ss_dssp             EEEEEEEEEECTTCEEEEECSTTSSHHHHHHHHT-TSSCCSEEEEEETTEECTTCCHHHHHH-HHHHHEEEECTTCCCCT
T ss_pred             EEEeceEEEEcCCCEEEEECCCCCCcchhhHhcc-CCCCCCcceeEECCEEcCcCChhhcch-hhcceEEEEecchhhCc
Confidence            34565544 9999999999999999999966333 3222222345444333   44554432 111111110000     


Q ss_pred             ---ccc-------CCCCCCCCHHHHH-HHHHHhhcccee--EeecCCCCCCHH--HHHHHHHHHHHHcCCcEEEEccccc
Q 009230          357 ---ANY-------GGSAERMTVEEFE-QGKAWLSNTFSL--IRCENDSLPSIK--WVLDLAKAAVLRHGVRGLVIDPYNE  421 (539)
Q Consensus       357 ---i~~-------~~~~~~l~~~~~~-~~~~~l~~~~~~--i~~~~~~~~~~~--~i~~~i~~~~~~~~~~~vvID~~~~  421 (539)
                         +..       ......++.++.. ++.+.+..--+.  +........+=.  +-...++.  -..+|+++++|-=+ 
T Consensus        97 ~~tv~eni~~~~~~~~~~~~~~~~~~~~~~~~l~~~~L~~~~~~~~p~~LSGGqkQRvaIAra--L~~~P~lLllDEPT-  173 (230)
T d1l2ta_          97 LLTALENVELPLIFKYRGAMSGEERRKRALECLKMAELEERFANHKPNQLSGGQQQRVAIARA--LANNPPIILADQPT-  173 (230)
T ss_dssp             TSCHHHHHHHHHHTCCSSCCCHHHHHHHHHHHHHHTTCCGGGTTCCGGGSCHHHHHHHHHHHH--HTTCCSEEEEESTT-
T ss_pred             CccHHHHHhHHHHHhccCCCCHHHHHHHHHHHHHhhchhhhhhcCChhhCCHHHHHHHHHHhh--hhcCCCEEEecCCc-
Confidence               000       0001123433332 233333211000  000001112212  22233333  23689999999222 


Q ss_pred             cccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          422 LDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       422 l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                            ++.+ .....++++.|+++.+++|++||+++|.-.                   ..+.||.++.|+.
T Consensus       174 ------s~LD-~~~~~~i~~~l~~l~~~~g~tii~vTHd~~-------------------~a~~~drv~~m~~  220 (230)
T d1l2ta_         174 ------GALD-SKTGEKIMQLLKKLNEEDGKTVVVVTHDIN-------------------VARFGERIIYLKD  220 (230)
T ss_dssp             ------TTSC-HHHHHHHHHHHHHHHHTTCCEEEEECSCHH-------------------HHTTSSEEEEEET
T ss_pred             ------cccC-HHHHHHHHHHHHHHHHhhCCEEEEECCCHH-------------------HHHhCCEEEEEEC
Confidence                  2233 345578999999999999999999999311                   2257899999974

>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=98.18  E-value=1.5e-05  Score=70.73  Aligned_cols=59  Identities=22%  Similarity=0.312  Sum_probs=44.2

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC---HHHHHHHHHHHhhCCCccc
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK---VREHARKLLEKHIKKPFFE  356 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~---~~~~~~r~~~~~~~~~~~~  356 (539)
                      .+.++++.|++|+||||.+..+|..+.. .|.+|++++++--   +.+.+ +.++...++++..
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~~~~~-~g~kV~lit~Dt~R~gA~eQL-~~~a~~l~i~~~~   66 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGRYYQN-LGKKVMFCAGDTFRAAGGTQL-SEWGKRLSIPVIQ   66 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHT-TTCCEEEECCCCSSTTHHHHH-HHHHHHHTCCEEC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHH-CCCcEEEEEeccccccchhhH-hhcccccCceEEe
Confidence            3568999999999999999999987765 5999999999942   32222 3445566776543

>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=98.16  E-value=1.7e-05  Score=70.29  Aligned_cols=39  Identities=21%  Similarity=0.289  Sum_probs=34.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .++++.|++|+||||.+..+|..+.. .|.+|+.++++--
T Consensus        10 ~vi~lvGptGvGKTTTiAKLA~~~~~-~g~kV~lit~Dt~   48 (211)
T d2qy9a2          10 FVILMVGVNGVGKTTTIGKLARQFEQ-QGKSVMLAAGDTF   48 (211)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHT-TTCCEEEECCCTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHH-CCCcEEEEecccc
Confidence            47889999999999999999988765 4999999999853

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, 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: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=98.15  E-value=2.8e-07  Score=83.46  Aligned_cols=61  Identities=13%  Similarity=0.139  Sum_probs=45.2

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+|+++++|-=+       ++.+ .....+++..|+++.++.|++||+++|.-.                  ...+.||
T Consensus       146 ~~~P~illlDEPt-------s~LD-~~~~~~i~~~l~~l~~~~g~tii~vTHd~~------------------~a~~~~d  199 (232)
T d2awna2         146 VAEPSVFLLDEPL-------SNLD-AALRVQMRIEISRLHKRLGRTMIYVTHDQV------------------EAMTLAD  199 (232)
T ss_dssp             HTCCSEEEEESTT-------TTSC-HHHHHHHHHHHHHHHHHSCCEEEEEESCHH------------------HHHHHCS
T ss_pred             hcCCCEEEEcCCC-------CCCC-HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH------------------HHHHhCC
Confidence            3689999999222       2233 344567889999999999999999999321                  2456899


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .+++|+.
T Consensus       200 ri~vm~~  206 (232)
T d2awna2         200 KIVVLDA  206 (232)
T ss_dssp             EEEEEET
T ss_pred             EEEEEEC
Confidence            9999974

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=98.15  E-value=2.3e-06  Score=77.56  Aligned_cols=60  Identities=17%  Similarity=0.164  Sum_probs=45.0

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+|+++++|-=+       ++.+ .....++.+.|+++.++.|++|++++|.-.                  ...+.||.
T Consensus       153 ~~P~iLllDEPt-------s~LD-~~~~~~i~~ll~~l~~~~g~tii~vTHd~~------------------~a~~~~dr  206 (239)
T d1v43a3         153 VEPDVLLMDEPL-------SNLD-AKLRVAMRAEIKKLQQKLKVTTIYVTHDQV------------------EAMTMGDR  206 (239)
T ss_dssp             TCCSEEEEESTT-------TTSC-HHHHHHHHHHHHHHHHHHTCEEEEEESCHH------------------HHHHHCSE
T ss_pred             cCCCceeecCCc-------ccCC-HHHHHHHHHHHHHHHHhcCCeEEEEeCCHH------------------HHHHhCCE
Confidence            689999999222       2233 344567889999999999999999999321                  24578999


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      +++|..
T Consensus       207 i~vm~~  212 (239)
T d1v43a3         207 IAVMNR  212 (239)
T ss_dssp             EEEEET
T ss_pred             EEEEEC
Confidence            999984

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=98.05  E-value=1.3e-06  Score=78.74  Aligned_cols=61  Identities=11%  Similarity=0.075  Sum_probs=45.5

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+|+++++|-=+       ++.+ .....++.+.|+.+.++.+++||+++|.-.                  ...+.||.
T Consensus       144 ~~P~iLllDEPt-------s~LD-~~~~~~i~~~l~~l~~~~g~tii~vtHd~~------------------~~~~~~dr  197 (229)
T d3d31a2         144 TNPKILLLDEPL-------SALD-PRTQENAREMLSVLHKKNKLTVLHITHDQT------------------EARIMADR  197 (229)
T ss_dssp             SCCSEEEEESSS-------TTSC-HHHHHHHHHHHHHHHHHTTCEEEEEESCHH------------------HHHHHCSE
T ss_pred             ccCCceeecCCC-------cCCC-HHHHHHHHHHHHHHHhcCCcEEEEEcCCHH------------------HHHHhCCE
Confidence            689999999222       2233 344567889999999999999999999322                  24568999


Q ss_pred             EEEEEeC
Q 009230          489 GIVIHRN  495 (539)
Q Consensus       489 vl~l~r~  495 (539)
                      +++|+.-
T Consensus       198 v~vm~~G  204 (229)
T d3d31a2         198 IAVVMDG  204 (229)
T ss_dssp             EEEESSS
T ss_pred             EEEEECC
Confidence            9999754

>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=98.00  E-value=5.8e-05  Score=67.01  Aligned_cols=39  Identities=23%  Similarity=0.278  Sum_probs=34.6

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      .++++.|++|+||||.+..+|.++..+ |.+|.+++++--
T Consensus        12 ~vi~lvGptGvGKTTTiAKLAa~~~~~-~~kV~lit~Dt~   50 (213)
T d1vmaa2          12 FVIMVVGVNGTGKTTSCGKLAKMFVDE-GKSVVLAAADTF   50 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEEECTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHC-CCceEEEeeccc
Confidence            578889999999999999999988664 999999999953

>d1g6ha_ c.37.1.12 (A:) MJ1267 {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: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.99  E-value=7.1e-06  Score=75.56  Aligned_cols=35  Identities=31%  Similarity=0.516  Sum_probs=28.5

Q ss_pred             chhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          285 WRALNELYN-VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       285 ~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      ...|+.+.- +++||++.|.|++|+||||++.-++-
T Consensus        17 ~~aL~~vs~~v~~Gei~~liG~nGaGKSTLl~~i~G   52 (254)
T d1g6ha_          17 FKALDGVSISVNKGDVTLIIGPNGSGKSTLINVITG   52 (254)
T ss_dssp             EEEEEEECCEEETTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             eEEEcceEEEECCCCEEEEECCCCCcHHHHHHHHHC
Confidence            445666655 99999999999999999999776553

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=97.98  E-value=7.5e-06  Score=74.24  Aligned_cols=178  Identities=18%  Similarity=0.152  Sum_probs=91.6

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHhhCCCccccc-cC
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---ENKVREHARKLLEKHIKKPFFEAN-YG  360 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---E~~~~~~~~r~~~~~~~~~~~~i~-~~  360 (539)
                      ..|+++-- +.+|+++.|.|++|+||||++.-++- +..-....+.|..-   +++..++.. +- ...|.=++... ..
T Consensus        19 ~al~~vsl~i~~Ge~~~iiG~sGsGKSTLl~~i~G-l~~p~sG~I~~~g~~i~~~~~~~~~~-~r-r~ig~VfQ~~~l~~   95 (240)
T d3dhwc1          19 QALNNVSLHVPAGQIYGVIGASGAGKSTLIRCVNL-LERPTEGSVLVDGQELTTLSESELTK-AR-RQIGMIFQHFNLLS   95 (240)
T ss_dssp             EEEEEEEEEECSSCEEEEEESTTSSHHHHHHHHTT-SSCCSEEEEEETTEEECTTCHHHHHH-HH-HHEEECCSSCCCCT
T ss_pred             EEeeceeEEEcCCCEEEEECCCCCCHHHHHHHHcC-CccccCCceEEcCeEeeeCChhhhhh-hh-ccccccccccccCC
Confidence            34565544 99999999999999999999765542 21111223333322   234544321 11 11221111100 00


Q ss_pred             -----------CCCCCCCHHHHH-HHHHHhhcc--ceeEeecCCCCCCHHH--HHHHHHHHHHHcCCcEEEEcccccccc
Q 009230          361 -----------GSAERMTVEEFE-QGKAWLSNT--FSLIRCENDSLPSIKW--VLDLAKAAVLRHGVRGLVIDPYNELDH  424 (539)
Q Consensus       361 -----------~~~~~l~~~~~~-~~~~~l~~~--~~~i~~~~~~~~~~~~--i~~~i~~~~~~~~~~~vvID~~~~l~~  424 (539)
                                 .....++.++.. ++.+.+..-  ..+. .......+-.+  -...++.  -..+|++++.|-=+.   
T Consensus        96 ~~tv~eni~~~l~~~~~~~~~~~~~v~~~L~~vgL~~~~-~~~~~~LSGG~~QRvaiAra--L~~~P~lLllDEPt~---  169 (240)
T d3dhwc1          96 SRTVFGNVALPLELDNTPKDEVKRRVTELLSLVGLGDKH-DSYPSNLSGGQKQRVAIARA--LASNPKVLLCDEATS---  169 (240)
T ss_dssp             TSBHHHHHHHHHHTTTCCTTHHHHHHHHHHHHHSTTTTT-SSCBSCCCHHHHHHHHHHHH--HHTCCSEEEEESGGG---
T ss_pred             CccHHHHHHHHHHHcCCCHHHHHHHHHHHHHHcCCchhh-hCChhhCCHHHHHHHHHhhh--hccCCCeEEeccccc---
Confidence                       000012222222 222222210  0000 00012222222  2233333  336899999993222   


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEeC
Q 009230          425 QRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRN  495 (539)
Q Consensus       425 ~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r~  495 (539)
                          +.+ .....++++.|+++.+++|++||+++|.-.                  .+.+.||.+++|+.-
T Consensus       170 ----~LD-~~~~~~i~~~l~~l~~~~g~tvi~vTHdl~------------------~~~~~~dri~vl~~G  217 (240)
T d3dhwc1         170 ----ALD-PATTRSILELLKDINRRLGLTILLITHEMD------------------VVKRICDCVAVISNG  217 (240)
T ss_dssp             ----SSC-HHHHHHHHHHHHHHHHHHCCEEEEEBSCHH------------------HHHHHCSEEEEEETT
T ss_pred             ----cCC-HHHhhHHHHHHHHHHhccCCEEEEEcCCHH------------------HHHHhCCEEEEEECC
Confidence                222 344568999999999999999999999321                  245689999999853

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=97.97  E-value=7.9e-05  Score=65.99  Aligned_cols=57  Identities=19%  Similarity=0.278  Sum_probs=37.9

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH--HHHHHHhhCCCcc
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA--RKLLEKHIKKPFF  355 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~--~r~~~~~~~~~~~  355 (539)
                      .++++.|++|+||||.+..+|..+..+ |.+|.+++++--.---.  .+..+...|+++.
T Consensus        13 ~vi~lvGptGvGKTTTiAKLA~~~~~~-g~kV~lit~Dt~R~ga~eQL~~~a~~l~v~~~   71 (211)
T d1j8yf2          13 YVIMLVGVQGTGKATTAGKLAYFYKKK-GFKVGLVGADVYRPAALEQLQQLGQQIGVPVY   71 (211)
T ss_dssp             EEEEEECSCCC----HHHHHHHHHHHT-TCCEEEEECCCSSHHHHHHHHHHHHHHTCCEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHC-CCceEEEEeeccccchhHHHHHhccccCccee
Confidence            578889999999999999999887764 99999999985421111  1334555666554

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.94  E-value=8.4e-06  Score=75.03  Aligned_cols=61  Identities=16%  Similarity=0.211  Sum_probs=43.2

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+|+++++|-=+       ++.+ .....++++.|++++++ |++|++++|.-.                  .+...||
T Consensus       165 ~~~P~llilDEPT-------~gLD-~~~~~~i~~ll~~l~~~-g~til~vtHdl~------------------~~~~~ad  217 (258)
T d1b0ua_         165 AMEPDVLLFDEPT-------SALD-PELVGEVLRIMQQLAEE-GKTMVVVTHEMG------------------FARHVSS  217 (258)
T ss_dssp             HTCCSEEEEESTT-------TTSC-HHHHHHHHHHHHHHHHT-TCCEEEECSCHH------------------HHHHHCS
T ss_pred             hcCCCEEEecccc-------ccCC-HHHHHHHHHhhhhhccc-CCceEEEeCCHH------------------HHHHhCC
Confidence            3689999999222       2333 34456788888888765 899999999311                  2457899


Q ss_pred             eEEEEEeC
Q 009230          488 NGIVIHRN  495 (539)
Q Consensus       488 ~vl~l~r~  495 (539)
                      .+++|+.-
T Consensus       218 ri~vm~~G  225 (258)
T d1b0ua_         218 HVIFLHQG  225 (258)
T ss_dssp             EEEEEETT
T ss_pred             EEEEEECC
Confidence            99999853

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon 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: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=97.93  E-value=4.3e-06  Score=75.80  Aligned_cols=60  Identities=13%  Similarity=0.083  Sum_probs=43.9

Q ss_pred             cCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccce
Q 009230          409 HGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDN  488 (539)
Q Consensus       409 ~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~  488 (539)
                      .+|++++.|.=+.-+       + .....+++..|+++.++.|++||+++|.-.                  .+...||.
T Consensus       157 ~~P~llllDEPt~~L-------D-~~~~~~i~~~i~~l~~~~g~tvi~vTHd~~------------------~~~~~~dr  210 (242)
T d1oxxk2         157 KDPSLLLLDEPFSNL-------D-ARMRDSARALVKEVQSRLGVTLLVVSHDPA------------------DIFAIADR  210 (242)
T ss_dssp             TCCSEEEEESTTTTS-------C-GGGHHHHHHHHHHHHHHHCCEEEEEESCHH------------------HHHHHCSE
T ss_pred             hcccceeecCCccCC-------C-HHHHHHHHHHHHHHHhccCCEEEEEECCHH------------------HHHHhCCE
Confidence            589999999333222       2 123467888899999999999999999321                  13468999


Q ss_pred             EEEEEe
Q 009230          489 GIVIHR  494 (539)
Q Consensus       489 vl~l~r  494 (539)
                      +++|..
T Consensus       211 i~vm~~  216 (242)
T d1oxxk2         211 VGVLVK  216 (242)
T ss_dssp             EEEEET
T ss_pred             EEEEEC
Confidence            999974

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=97.88  E-value=7.1e-06  Score=74.78  Aligned_cols=61  Identities=13%  Similarity=0.239  Sum_probs=43.8

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      ..+|+++++|-       +..+.+ .....++.+.|++++++ |++|++++|.-.                  .+.+.||
T Consensus       155 ~~~P~lLllDE-------Pt~gLD-~~~~~~i~~~i~~l~~~-g~til~~tH~l~------------------~~~~~~d  207 (240)
T d1ji0a_         155 MSRPKLLMMDE-------PSLGLA-PILVSEVFEVIQKINQE-GTTILLVEQNAL------------------GALKVAH  207 (240)
T ss_dssp             TTCCSEEEEEC-------TTTTCC-HHHHHHHHHHHHHHHHT-TCCEEEEESCHH------------------HHHHHCS
T ss_pred             HhCCCEeeecC-------CCcCCC-HHHHHHHHHHHHHHHhC-CCEEEEEeCCHH------------------HHHHhCC
Confidence            46899999992       222333 34456788888888766 999999999311                  2457899


Q ss_pred             eEEEEEeC
Q 009230          488 NGIVIHRN  495 (539)
Q Consensus       488 ~vl~l~r~  495 (539)
                      .+++|+.-
T Consensus       208 rv~vl~~G  215 (240)
T d1ji0a_         208 YGYVLETG  215 (240)
T ss_dssp             EEEEEETT
T ss_pred             EEEEEECC
Confidence            99999853

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.85  E-value=5e-05  Score=69.59  Aligned_cols=173  Identities=16%  Similarity=0.197  Sum_probs=88.4

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHhhCCC---ccc---
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---ENKVREHARKLLEKHIKKP---FFE---  356 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---E~~~~~~~~r~~~~~~~~~---~~~---  356 (539)
                      .|+.+.- +++|+.+.|.|++|+|||||+.-++-- .......|.+-..   +.+...+..++ +....-+   ...   
T Consensus        30 ~L~~isl~i~~Ge~iaivG~sGsGKSTLl~ll~gl-~~p~~G~I~i~g~~i~~~~~~~~r~~i-~~v~Q~~~l~~~ti~~  107 (253)
T d3b60a1          30 ALRNINLKIPAGKTVALVGRSGSGKSTIASLITRF-YDIDEGHILMDGHDLREYTLASLRNQV-ALVSQNVHLFNDTVAN  107 (253)
T ss_dssp             SEEEEEEEECTTCEEEEEECTTSSHHHHHHHHTTT-TCCSEEEEEETTEETTTBCHHHHHHTE-EEECSSCCCCSSBHHH
T ss_pred             eeeceEEEEcCCCEEEEECCCCChHHHHHHHHhcc-cCCCccEEEECCcccchhhhhhhhheE-EEEeeccccCCcchhh
Confidence            4555544 999999999999999999997655422 2111223333221   23444443332 1111111   000   


Q ss_pred             -cccCCCCCCCCHHHHHHHH------HHhhcc---c-eeEeecCCCCCCH--HHHHHHHHHHHHHcCCcEEEEccccccc
Q 009230          357 -ANYGGSAERMTVEEFEQGK------AWLSNT---F-SLIRCENDSLPSI--KWVLDLAKAAVLRHGVRGLVIDPYNELD  423 (539)
Q Consensus       357 -i~~~~~~~~l~~~~~~~~~------~~l~~~---~-~~i~~~~~~~~~~--~~i~~~i~~~~~~~~~~~vvID~~~~l~  423 (539)
                       +..+ .....+.+++.++.      +.+...   . ..+ -+.....+-  .+-+..++.+.  .+++++++|.-+.- 
T Consensus       108 n~~~~-~~~~~~~~~i~~a~~~~~l~~~i~~l~~gl~t~~-~~~~~~LSGGqkQRvaiARal~--~~p~ililDEpts~-  182 (253)
T d3b60a1         108 NIAYA-RTEEYSREQIEEAARMAYAMDFINKMDNGLDTII-GENGVLLSGGQRQRIAIARALL--RDSPILILDEATSA-  182 (253)
T ss_dssp             HHHTT-TTSCCCHHHHHHHHHTTTCHHHHHHSTTGGGSBC-CTTSCSSCHHHHHHHHHHHHHH--HCCSEEEEETTTSS-
T ss_pred             hhhhc-CcccCCHHHHHHHHHHHhHHHHHHhccccchhhh-cCCCCCcCHHHHHHHHHHHHHh--cCCCEEEecccccc-
Confidence             1111 11235666655442      222211   1 111 011112232  23344444444  47899999944322 


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          424 HQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                            .+ ......+++.|+.+.+  +.+||+++|.-..                  + ..||.|++|..
T Consensus       183 ------LD-~~~~~~i~~~l~~l~~--~~Tvi~itH~l~~------------------~-~~~D~v~vl~~  225 (253)
T d3b60a1         183 ------LD-TESERAIQAALDELQK--NRTSLVIAHRLST------------------I-EQADEIVVVED  225 (253)
T ss_dssp             ------CC-HHHHHHHHHHHHHHHT--TSEEEEECSCGGG------------------T-TTCSEEEEEET
T ss_pred             ------CC-HHHHHHHHHHHHHhcc--CCEEEEEECCHHH------------------H-HhCCEEEEEEC
Confidence                  22 2334567777777754  7899999993211                  2 36999999974

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=97.83  E-value=4.8e-05  Score=69.08  Aligned_cols=172  Identities=15%  Similarity=0.142  Sum_probs=89.4

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHhhCCCc---cc---
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---ENKVREHARKLLEKHIKKPF---FE---  356 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---E~~~~~~~~r~~~~~~~~~~---~~---  356 (539)
                      .|+.+.- +.+|+.+.|.|++|+|||||+.-++--..- ....+.+-..   +.+...+.+++ +....-+.   ..   
T Consensus        18 vL~~isl~i~~Ge~vaIvG~sGsGKSTLl~ll~gl~~p-~~G~I~i~g~~i~~~~~~~lr~~i-~~v~Q~~~lf~~Ti~e   95 (241)
T d2pmka1          18 ILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIP-ENGQVLIDGHDLALADPNWLRRQV-GVVLQDNVLLNRSIID   95 (241)
T ss_dssp             EEEEEEEEEETTCEEEEECSTTSSHHHHHHHHTTSSCC-SEEEEEETTEETTTSCHHHHHHHE-EEECSSCCCTTSBHHH
T ss_pred             eEeeeEEEEcCCCEEEEECCCCCCHHHHHHHHHhcCCC-CCCEEEECCEEecccchhhhhceE-EEEecccccCCccccc
Confidence            3555544 999999999999999999997765533211 1223333222   24555554332 22221110   00   


Q ss_pred             -cccCCCCCCCCHHHHHHHH------HHhhccce----eEeecCCCCCCHH--HHHHHHHHHHHHcCCcEEEEccccccc
Q 009230          357 -ANYGGSAERMTVEEFEQGK------AWLSNTFS----LIRCENDSLPSIK--WVLDLAKAAVLRHGVRGLVIDPYNELD  423 (539)
Q Consensus       357 -i~~~~~~~~l~~~~~~~~~------~~l~~~~~----~i~~~~~~~~~~~--~i~~~i~~~~~~~~~~~vvID~~~~l~  423 (539)
                       +..+  ....+.+++..+.      +.+...+.    .+. ......+-.  +-+..++.+  -.+++++++|.-+.- 
T Consensus        96 Ni~~~--~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~i~-~~g~~LSGGq~QRvalARal--~~~p~ililDEpts~-  169 (241)
T d2pmka1          96 NISLA--NPGMSVEKVIYAAKLAGAHDFISELREGYNTIVG-EQGAGLSGGQRQRIAIARAL--VNNPKILIFDEATSA-  169 (241)
T ss_dssp             HHCTT--STTCCHHHHHHHHHHHTCHHHHTTSTTGGGSBCS-TTTTCCCHHHHHHHHHHHHH--TTCCSEEEECCCCSC-
T ss_pred             ccccc--CccccHHHHHHHHHHHhhHHHHHhhhcchhhhcC-CCCCccCHHHHHHHhhhhhh--hcccchhhhhCCccc-
Confidence             1111  1234555544432      22222111    110 111122322  233334433  357899999944332 


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          424 HQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                            .+ ......+++.|+.+++  +.+||+++|.-..                  + ..||.|++|..
T Consensus       170 ------LD-~~~~~~i~~~l~~l~~--~~Tvi~itH~l~~------------------~-~~~D~i~vl~~  212 (241)
T d2pmka1         170 ------LD-YESEHVIMRNMHKICK--GRTVIIIAHRLST------------------V-KNADRIIVMEK  212 (241)
T ss_dssp             ------CC-HHHHHHHHHHHHHHHT--TSEEEEECSSGGG------------------G-TTSSEEEEEET
T ss_pred             ------cC-HHHHHHHHHHHHHHhC--CCEEEEEECCHHH------------------H-HhCCEEEEEEC
Confidence                  22 2334567778887765  7899999993221                  2 36899999974

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC 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: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.81  E-value=2.5e-05  Score=71.50  Aligned_cols=175  Identities=19%  Similarity=0.194  Sum_probs=89.8

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHhhCCCc---cc---
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---ENKVREHARKLLEKHIKKPF---FE---  356 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---E~~~~~~~~r~~~~~~~~~~---~~---  356 (539)
                      .|+.+.- +.+|+++.|.|++|+|||||+.-++--. ......|.+-..   +.+...+.++ ++....-+.   ..   
T Consensus        29 vL~~isl~i~~Ge~vaivG~sGsGKSTLl~li~gl~-~p~~G~I~i~g~~i~~~~~~~~r~~-i~~v~Q~~~lf~~tv~e  106 (251)
T d1jj7a_          29 VLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLY-QPTGGQLLLDGKPLPQYEHRYLHRQ-VAAVGQEPQVFGRSLQE  106 (251)
T ss_dssp             SEEEEEEEECTTCEEEEECSTTSSHHHHHHHHTTSS-CCSEEEEEETTEEGGGBCHHHHHHH-EEEECSSCCCCSSBHHH
T ss_pred             eEeceEEEEcCCCEEEEECCCCCcHHHHHHHHhccc-CCCcCEEEECCEecchhhhHHHHHH-hhhccccccccCcchhh
Confidence            3555544 9999999999999999999976544221 111223433222   2344444333 222221111   00   


Q ss_pred             -cccCCCCCCCCHHHHHHHH------HHhhccc----eeEeecCCCCCCHH--HHHHHHHHHHHHcCCcEEEEccccccc
Q 009230          357 -ANYGGSAERMTVEEFEQGK------AWLSNTF----SLIRCENDSLPSIK--WVLDLAKAAVLRHGVRGLVIDPYNELD  423 (539)
Q Consensus       357 -i~~~~~~~~l~~~~~~~~~------~~l~~~~----~~i~~~~~~~~~~~--~i~~~i~~~~~~~~~~~vvID~~~~l~  423 (539)
                       +..+ .....+..+...+.      +.+...+    ..+. ......+-.  +-+..++.+  -.+++++++|.-+.  
T Consensus       107 ni~~g-~~~~~~~~~~~~~~~~~~~~~~i~~l~~g~~~~i~-~~~~~LSGGqkQRvaiARal--~~~p~ililDEpTs--  180 (251)
T d1jj7a_         107 NIAYG-LTQKPTMEEITAAAVKSGAHSFISGLPQGYDTEVD-EAGSQLSGGQRQAVALARAL--IRKPCVLILDDATS--  180 (251)
T ss_dssp             HHHCS-CSSCCCHHHHHHHHHHHTCHHHHHTSTTGGGCBCC-SSCSSSCHHHHHHHHHHHHH--TTCCSEEEEESTTT--
T ss_pred             hhhhh-hcccchHHHHHHHHHHHHHHHHHHhccccchhhHh-ccCccCChhHceEEEEeecc--ccCCcEEEecCcCc--
Confidence             1111 01122333322221      2222211    1110 111222322  233333433  35799999993332  


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          424 HQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                           +.+. ....++++.|+.+.++.+.+||+++|.-.                  .+ +.||.|++|..
T Consensus       181 -----~LD~-~~~~~i~~~l~~l~~~~~~Tvi~itH~l~------------------~~-~~aDrI~vl~~  226 (251)
T d1jj7a_         181 -----ALDA-NSQLQVEQLLYESPERYSRSVLLITQHLS------------------LV-EQADHILFLEG  226 (251)
T ss_dssp             -----TCCH-HHHHHHHHHHHTCGGGGGCEEEEECSCHH------------------HH-HTCSEEEEEET
T ss_pred             -----ccCh-hhHHHHHHHHHHHhhhcCCEEEEEeCCHH------------------HH-HhCCEEEEEEC
Confidence                 2232 33456888888888899999999999311                  13 45999999974

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {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: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=97.80  E-value=7e-05  Score=67.84  Aligned_cols=61  Identities=16%  Similarity=0.156  Sum_probs=42.6

Q ss_pred             HHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhcc
Q 009230          407 LRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKC  486 (539)
Q Consensus       407 ~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~a  486 (539)
                      -..+++++++|--+       .+.+. ....++.+.|+.++++ |.+|++++|.-.                  .+...|
T Consensus       148 l~~~p~illLDEPt-------~gLD~-~~~~~i~~~i~~~~~~-g~tii~~tH~l~------------------~~~~~~  200 (238)
T d1vpla_         148 LMVNPRLAILDEPT-------SGLDV-LNAREVRKILKQASQE-GLTILVSSHNML------------------EVEFLC  200 (238)
T ss_dssp             HTTCCSEEEEESTT-------TTCCH-HHHHHHHHHHHHHHHT-TCEEEEEECCHH------------------HHTTTC
T ss_pred             HhcCCCEEEecCCC-------CCCCH-HHHHHHHHHHHHHHhc-CCEEEEEeCCHH------------------HHHHhC
Confidence            34689999999222       23343 3455677788887755 999999999311                  245689


Q ss_pred             ceEEEEEe
Q 009230          487 DNGIVIHR  494 (539)
Q Consensus       487 D~vl~l~r  494 (539)
                      |.|++|+.
T Consensus       201 drv~vl~~  208 (238)
T d1vpla_         201 DRIALIHN  208 (238)
T ss_dssp             SEEEEEET
T ss_pred             CEEEEEEC
Confidence            99999985

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {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: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.65  E-value=0.00012  Score=64.50  Aligned_cols=150  Identities=10%  Similarity=0.049  Sum_probs=76.5

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhc-------------CCeEEEEeC------CCCHHHHHHHH
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHA-------------GWKFVLCSM------ENKVREHARKL  345 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~-------------g~~vl~~s~------E~~~~~~~~r~  345 (539)
                      +-|+.+.- +.+|+++.|.|++|+|||||+.-++--.--..             ..++.|+.-      +++.++.+.-.
T Consensus        15 ~vl~~is~~i~~Gei~~l~G~NGsGKSTLl~~i~gl~~p~~G~I~~~g~~i~~~~~~i~~~~~~~~~~~~~t~~~~l~~~   94 (200)
T d1sgwa_          15 PVLERITMTIEKGNVVNFHGPNGIGKTTLLKTISTYLKPLKGEIIYNGVPITKVKGKIFFLPEEIIVPRKISVEDYLKAV   94 (200)
T ss_dssp             EEEEEEEEEEETTCCEEEECCTTSSHHHHHHHHTTSSCCSEEEEEETTEEGGGGGGGEEEECSSCCCCTTSBHHHHHHHH
T ss_pred             eEEeceEEEEcCCCEEEEECCCCChHHHHHHHHhcccccCCCEEEECCEehhHhcCcEEEEeecccCCCCcCHHHHHHHH
Confidence            34555544 99999999999999999999876653221111             123444432      23344333222


Q ss_pred             HHHhhCCCccccccCCCCCCCCHHHHHHHHHHhhccceeEeecCCCCCCHHHHHHHHHHHHHHcCCcEEEEccccccccC
Q 009230          346 LEKHIKKPFFEANYGGSAERMTVEEFEQGKAWLSNTFSLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQ  425 (539)
Q Consensus       346 ~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~i~~~i~~~~~~~~~~~vvID~~~~l~~~  425 (539)
                       ....+.            ..+.+++.++.+.+.-.  -+. ...+..+-.+.....-..+...+++++++|--+.-+. 
T Consensus        95 -~~~~~~------------~~~~~~~~~~l~~~~~~--~~~-~~~~~LSgG~~qrv~ia~al~~~~~llllDEPt~gLD-  157 (200)
T d1sgwa_          95 -ASLYGV------------KVNKNEIMDALESVEVL--DLK-KKLGELSQGTIRRVQLASTLLVNAEIYVLDDPVVAID-  157 (200)
T ss_dssp             -HHHTTC------------CCCHHHHHHHHHHTTCC--CTT-SBGGGSCHHHHHHHHHHHHTTSCCSEEEEESTTTTSC-
T ss_pred             -HHhcCC------------ccCHHHHHHHHHHcCCc--ccc-cccCcCCCcHHHHHHHHHHHhcCCCEEEEcCcccccC-
Confidence             222221            23344444433332210  000 0011223333222222223346899999994333221 


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEec
Q 009230          426 RPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH  459 (539)
Q Consensus       426 ~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q  459 (539)
                            . .....+++.|++++++.++.|+..+|
T Consensus       158 ------~-~~~~~i~~~l~~~~~~~~~~ii~~~~  184 (200)
T d1sgwa_         158 ------E-DSKHKVLKSILEILKEKGIVIISSRE  184 (200)
T ss_dssp             ------T-TTHHHHHHHHHHHHHHHSEEEEEESS
T ss_pred             ------H-HHHHHHHHHHHHHHhCCCEEEEEEec
Confidence                  1 12346788888999988876665444

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {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: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.63  E-value=8.4e-06  Score=73.68  Aligned_cols=61  Identities=11%  Similarity=0.034  Sum_probs=45.5

Q ss_pred             HcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccc
Q 009230          408 RHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCD  487 (539)
Q Consensus       408 ~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD  487 (539)
                      -.+|+++++|-=+       ++.+ ......+.+.|+.++++++++||+++|.-.                  .+.+.||
T Consensus       142 ~~~P~illlDEPt-------s~LD-~~~~~~i~~~i~~l~~~~g~tvi~vtHd~~------------------~~~~~ad  195 (240)
T d2onka1         142 VIQPRLLLLDEPL-------SAVD-LKTKGVLMEELRFVQREFDVPILHVTHDLI------------------EAAMLAD  195 (240)
T ss_dssp             TTCCSSBEEESTT-------SSCC-HHHHHHHHHHHHHHHHHHTCCEEEEESCHH------------------HHHHHCS
T ss_pred             hccCCceEecCcc-------ccCC-HHHHHHHHHHHHHHHHhcCCeEEEEeCCHH------------------HHHHhCC
Confidence            3689999999222       2233 345567899999999999999999999421                  2457899


Q ss_pred             eEEEEEe
Q 009230          488 NGIVIHR  494 (539)
Q Consensus       488 ~vl~l~r  494 (539)
                      .+++|+.
T Consensus       196 ri~vm~~  202 (240)
T d2onka1         196 EVAVMLN  202 (240)
T ss_dssp             EEEEEET
T ss_pred             EEEEEEC
Confidence            9999974

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.62  E-value=6.7e-05  Score=68.64  Aligned_cols=172  Identities=16%  Similarity=0.128  Sum_probs=87.2

Q ss_pred             hhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHhhCCCc---cc---
Q 009230          287 ALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---ENKVREHARKLLEKHIKKPF---FE---  356 (539)
Q Consensus       287 ~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---E~~~~~~~~r~~~~~~~~~~---~~---  356 (539)
                      .|+.+.- +.+|+.+.|.|++|+|||||+.-++- +..-....|.+-..   +.+...+..++ +....-+.   ..   
T Consensus        33 vL~~isl~i~~Ge~vaivG~sGsGKSTLl~ll~g-l~~p~~G~I~i~g~~i~~~~~~~lr~~i-~~v~Q~~~lf~~Ti~e  110 (255)
T d2hyda1          33 ILKDINLSIEKGETVAFVGMSGGGKSTLINLIPR-FYDVTSGQILIDGHNIKDFLTGSLRNQI-GLVQQDNILFSDTVKE  110 (255)
T ss_dssp             SEEEEEEEECTTCEEEEECSTTSSHHHHHTTTTT-SSCCSEEEEEETTEEGGGSCHHHHHHTE-EEECSSCCCCSSBHHH
T ss_pred             ceeceEEEEcCCCEEEEECCCCCcHHHHHHHHHh-cCCccccccccCCEEcccCCHHHhhhee-eeeeccccCCCCCHHH
Confidence            3555544 99999999999999999999664432 11111223333221   24455443332 22111110   01   


Q ss_pred             -cccCCCCCCCCHHHHHHHH------HHhhccc---e-eEeecCCCCCCHH--HHHHHHHHHHHHcCCcEEEEccccccc
Q 009230          357 -ANYGGSAERMTVEEFEQGK------AWLSNTF---S-LIRCENDSLPSIK--WVLDLAKAAVLRHGVRGLVIDPYNELD  423 (539)
Q Consensus       357 -i~~~~~~~~l~~~~~~~~~------~~l~~~~---~-~i~~~~~~~~~~~--~i~~~i~~~~~~~~~~~vvID~~~~l~  423 (539)
                       +..+  ....+++++.++.      +++...+   . .+. +.....+-.  +-+..++.+.  .+++++++|.-+.- 
T Consensus       111 Ni~~g--~~~~~~~~~~~al~~~~l~~~i~~lp~gl~t~i~-~~g~~LSgGq~QRi~iARal~--~~p~ililDEpts~-  184 (255)
T d2hyda1         111 NILLG--RPTATDEEVVEAAKMANAHDFIMNLPQGYDTEVG-ERGVKLSGGQKQRLSIARIFL--NNPPILILDEATSA-  184 (255)
T ss_dssp             HHGGG--CSSCCHHHHHHHHHHTTCHHHHHTSTTGGGCBCC-GGGTTSCHHHHHHHHHHHHHH--HCCSEEEEESTTTT-
T ss_pred             HHhcc--CcCCCHHHHHHHHHHhCCHHHHHhccccccchhc-CCCCCcCHHHHHHHHHHHHHh--cCCCEEEEeCcccc-
Confidence             1111  1234556655443      2222211   0 110 001122322  2333444433  47899999944332 


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceEEEEEe
Q 009230          424 HQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR  494 (539)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~vl~l~r  494 (539)
                            .+. ..-..+++.|+.+.+  +.+||+++|.-..                  + ..||.|++|..
T Consensus       185 ------LD~-~t~~~i~~~l~~l~~--~~TvI~itH~~~~------------------~-~~~D~ii~l~~  227 (255)
T d2hyda1         185 ------LDL-ESESIIQEALDVLSK--DRTTLIVAHRLST------------------I-THADKIVVIEN  227 (255)
T ss_dssp             ------CCH-HHHHHHHHHHHHHTT--TSEEEEECSSGGG------------------T-TTCSEEEEEET
T ss_pred             ------CCH-HHHHHHHHHHHHHhc--CCEEEEEeCCHHH------------------H-HhCCEEEEEEC
Confidence                  222 233567777777664  7799999993221                  2 36899999974

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=97.43  E-value=0.00013  Score=65.72  Aligned_cols=59  Identities=12%  Similarity=0.145  Sum_probs=40.5

Q ss_pred             CCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecCCCCCCCCCCCCCcccccccccchhccceE
Q 009230          410 GVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHPRQLHNWVGEPPNLYDISGSAHFINKCDNG  489 (539)
Q Consensus       410 ~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~r~~~~~~~~~~~~~~l~gs~~i~~~aD~v  489 (539)
                      +++++++|-       +..+.+ ......+.+.|+.+++ .|++||+++|.=                  ..+...||.+
T Consensus       150 ~p~llllDE-------Pt~gLD-~~~~~~i~~~i~~l~~-~g~tii~vtHdl------------------~~~~~~~dri  202 (231)
T d1l7vc_         150 AGQLLLLDE-------PMNSLD-VAQQSALDKILSALCQ-QGLAIVMSSHDL------------------NHTLRHAHRA  202 (231)
T ss_dssp             TCCEEEESS-------CSTTCC-HHHHHHHHHHHHHHHH-TTCEEEECCCCH------------------HHHHHHCSBC
T ss_pred             CCCEEEEcC-------CCCCCC-HHHHHHHHHHHHHHHh-CCCEEEEEeCCH------------------HHHHHHCCEE
Confidence            568999992       222334 3455677888888866 599999999931                  1245688888


Q ss_pred             EEEEeC
Q 009230          490 IVIHRN  495 (539)
Q Consensus       490 l~l~r~  495 (539)
                      ++|+.-
T Consensus       203 ~vl~~G  208 (231)
T d1l7vc_         203 WLLKGG  208 (231)
T ss_dssp             CBEETT
T ss_pred             EEEECC
Confidence            888753

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.30  E-value=0.00075  Score=59.91  Aligned_cols=36  Identities=17%  Similarity=0.397  Sum_probs=31.5

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      +.|.|++|+|||.|+..++..+..+ +..++|++...
T Consensus        39 l~l~G~~G~GKTHLl~A~~~~~~~~-~~~~~~~~~~~   74 (213)
T d1l8qa2          39 IFIYGSVGTGKTHLLQAAGNEAKKR-GYRVIYSSADD   74 (213)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHHHT-TCCEEEEEHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHHhccC-ccceEEechHH
Confidence            5799999999999999999888775 89999998653

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.27  E-value=0.0025  Score=55.91  Aligned_cols=36  Identities=22%  Similarity=0.245  Sum_probs=31.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ++++.|.||+||||++..|+...... +.++..++.+
T Consensus         4 li~l~GlpgsGKSTla~~L~~~l~~~-~~~~~~~~~D   39 (213)
T d1bifa1           4 LIVMVGLPARGKTYISKKLTRYLNFI-GVPTREFNVG   39 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc-CCCCeEEccc
Confidence            78999999999999999999887764 8888877754

>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=97.16  E-value=0.00018  Score=61.19  Aligned_cols=39  Identities=18%  Similarity=0.201  Sum_probs=33.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV  338 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~  338 (539)
                      ++.|+|++|+|||||+..++..+..+ |.+|.++-.+...
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l~~~-g~~v~v~~~d~~~   42 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPALCAR-GIRPGLIKHTHHD   42 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHT-TCCEEEEEECCC-
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHC-CCeEEEecccccc
Confidence            68999999999999999999998876 9999888766543

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.94  E-value=0.00063  Score=58.20  Aligned_cols=46  Identities=9%  Similarity=0.144  Sum_probs=30.4

Q ss_pred             HHHHcCCcEEEEccccccccCCCCCCCHHHHHHHHHHHHHHHHHHhCcEEEEEecC
Q 009230          405 AVLRHGVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAHP  460 (539)
Q Consensus       405 ~~~~~~~~~vvID~~~~l~~~~~~~~~~~~~~~~~~~~Lk~lA~~~~i~vi~~~q~  460 (539)
                      .+...+++++++|.......     .     ...+...|..+.++.+.++++++|.
T Consensus        94 ~~~~~~~~vlllDE~~~~~~-----~-----~~~~~~~l~~~l~~~~~~il~~~h~  139 (178)
T d1ye8a1          94 EAKKDRRKVIIIDEIGKMEL-----F-----SKKFRDLVRQIMHDPNVNVVATIPI  139 (178)
T ss_dssp             HHHHCTTCEEEECCCSTTGG-----G-----CHHHHHHHHHHHTCTTSEEEEECCS
T ss_pred             HHHhcCCCceeecCCCccch-----h-----hHHHHHHHHHHhccCCCEEEEEEcc
Confidence            34557899999995422221     1     1245566666677788999999994

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.93  E-value=0.00076  Score=61.75  Aligned_cols=67  Identities=22%  Similarity=0.211  Sum_probs=56.3

Q ss_pred             CCccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHH
Q 009230          276 GDEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHA  342 (539)
Q Consensus       276 ~~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~  342 (539)
                      .....+.||+..+|-++-+-+|+=..|.|++|+|||+|+.+++.+..+.+..-++|...-+..+++.
T Consensus        47 ~i~~~l~TGIraID~l~pigkGQr~~If~~~g~GKt~l~~~i~~~~~~~~~~v~V~~~iGer~~ev~  113 (276)
T d2jdid3          47 VEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGN  113 (276)
T ss_dssp             CCCCEECCSCHHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHHTTTCSSEEEEEEESCCHHHHH
T ss_pred             CCCcccccCceeeeeeccccCCCEEEeeCCCCCCHHHHHHHHHHHHHhhCCCeEEEEEeccChHHHH
Confidence            3445689999999999889999999999999999999999999987765455677888888877654

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.89  E-value=0.0038  Score=56.95  Aligned_cols=31  Identities=26%  Similarity=0.338  Sum_probs=24.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      =+++.||||+|||+++..++..    .+.++++++
T Consensus        40 giLL~GppGtGKT~l~~ala~~----~~~~~~~i~   70 (258)
T d1e32a2          40 GILLYGPPGTGKTLIARAVANE----TGAFFFLIN   70 (258)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH----TTCEEEEEC
T ss_pred             eeEEecCCCCCchHHHHHHHHH----hCCeEEEEE
Confidence            3789999999999997766654    478888765

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.87  E-value=0.0029  Score=57.94  Aligned_cols=37  Identities=19%  Similarity=0.309  Sum_probs=28.6

Q ss_pred             ccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          293 NVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       293 ~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      |+.+..-++|.|+||+|||+++..+|..    .|.++++++
T Consensus        37 g~~~~~giLL~Gp~GtGKT~l~~ala~~----~~~~~~~~~   73 (265)
T d1r7ra3          37 GMTPSKGVLFYGPPGCGKTLLAKAIANE----CQANFISIK   73 (265)
T ss_dssp             CCCCCCEEEEBCCTTSSHHHHHHHHHHH----TTCEEEEEC
T ss_pred             CCCCCCeEEEECCCCCcchhHHHHHHHH----hCCcEEEEE
Confidence            3444456889999999999998887655    478877775

>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=96.85  E-value=0.00042  Score=59.45  Aligned_cols=36  Identities=22%  Similarity=0.202  Sum_probs=30.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .++|+|+||+||||++.+++..+... |..|.++...
T Consensus         3 ~v~ItG~~GtGKTtl~~~i~~~l~~~-~~~v~~~~~~   38 (189)
T d2i3ba1           3 HVFLTGPPGVGKTTLIHKASEVLKSS-GVPVDGFYTE   38 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHHHT-TCCCEEEECC
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHC-CCEEEEEEec
Confidence            47899999999999999999888775 7777766544

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=96.79  E-value=0.0025  Score=58.02  Aligned_cols=34  Identities=24%  Similarity=0.259  Sum_probs=26.9

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ..-+++.||||+|||+++..+|..    .+.++++++.
T Consensus        45 ~~~iLL~GppGtGKT~la~~iA~~----~~~~~~~i~~   78 (256)
T d1lv7a_          45 PKGVLMVGPPGTGKTLLAKAIAGE----AKVPFFTISG   78 (256)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH----HTCCEEEECS
T ss_pred             CCeEEeeCCCCCCccHHHHHHHHH----cCCCEEEEEh
Confidence            345789999999999998888754    3778877654

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=96.79  E-value=0.002  Score=60.36  Aligned_cols=43  Identities=26%  Similarity=0.254  Sum_probs=31.0

Q ss_pred             ccccCchhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHHHHHH
Q 009230          280 GISTGWRALNELYN-VLPGELTIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       280 gi~tg~~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      +.+-..+.+.+.++ -.+....++.|+||+|||.++..+|..+.
T Consensus       105 ~~~~~~~~~~~~~~~~~~~g~~l~~G~pG~GKT~la~ala~~~~  148 (321)
T d1w44a_         105 ELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALG  148 (321)
T ss_dssp             TCCSBCCEEEEETTEEEESEEEEEECSSSSCHHHHHHHHHHHHH
T ss_pred             cccccchHHHHHhhcccCCceEEEECCCCccHHHHHHHHHHHhc
Confidence            34434566666777 44445777899999999999998887653

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=96.78  E-value=0.0018  Score=58.67  Aligned_cols=32  Identities=25%  Similarity=0.318  Sum_probs=26.4

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      -+++.||||+|||+++..++..    .+.++++++.
T Consensus        44 giLl~GppGtGKT~la~aia~~----~~~~~~~i~~   75 (247)
T d1ixza_          44 GVLLVGPPGVGKTHLARAVAGE----ARVPFITASG   75 (247)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH----TTCCEEEEEH
T ss_pred             eEEEecCCCCChhHHHHHHHHH----cCCCEEEEEh
Confidence            4789999999999998888753    4888888763

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.77  E-value=0.00075  Score=57.18  Aligned_cols=38  Identities=18%  Similarity=0.379  Sum_probs=33.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      ++.|+|.+|+|||||+..++..+..+ |.+|..+-.+..
T Consensus         3 ii~I~G~~gSGKTTli~~l~~~L~~~-g~~v~vik~d~~   40 (165)
T d1xjca_           3 VWQVVGYKHSGKTTLMEKWVAAAVRE-GWRVGTVKHHGH   40 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEECCC-
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhC-CCeEEEEEeccC
Confidence            67899999999999999999998886 999999876654

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=96.77  E-value=0.00068  Score=62.79  Aligned_cols=52  Identities=17%  Similarity=0.291  Sum_probs=42.5

Q ss_pred             chhhhhhhc--cCCC-cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          285 WRALNELYN--VLPG-ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       285 ~~~LD~~~~--l~~G-~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +|.|..+..  -++| .+++++|.-|+||||++.++|..++.. |++|+++.++..
T Consensus         5 ~~~~~~~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~lA~~-G~rVllvD~Dp~   59 (279)
T d1ihua2           5 IPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADM-GFDVHLTTSDPA   59 (279)
T ss_dssp             CCCHHHHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEESCCC
T ss_pred             CccHHHHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CCcEEEEeCCCC
Confidence            345555554  3333 688999999999999999999999996 999999999965

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.74  E-value=0.0019  Score=55.01  Aligned_cols=21  Identities=33%  Similarity=0.726  Sum_probs=19.0

Q ss_pred             cEEEEEcCCCCChhHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la  318 (539)
                      .|++++|.||+|||||+.+++
T Consensus        15 ~liil~G~pGsGKST~a~~l~   35 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTFIQEHL   35 (172)
T ss_dssp             CEEEEECCTTSSHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            699999999999999987764

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=96.74  E-value=0.00048  Score=56.57  Aligned_cols=42  Identities=17%  Similarity=0.217  Sum_probs=37.2

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR  339 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~  339 (539)
                      |.|.+|.||-.+||||-+++.+.+.... |.+|+++...++.+
T Consensus         2 G~L~~i~GpMfsGKTteLi~~~~~~~~~-~~kv~~ikp~~D~R   43 (139)
T d2b8ta1           2 GWIEFITGPMFAGKTAELIRRLHRLEYA-DVKYLVFKPKIDTR   43 (139)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHT-TCCEEEEEECCCGG
T ss_pred             cEEEEEEccccCHHHHHHHHHHHHHHHC-CCcEEEEEEccccc
Confidence            7899999999999999999998887764 99999999888754

>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=96.73  E-value=0.00045  Score=58.93  Aligned_cols=36  Identities=31%  Similarity=0.437  Sum_probs=28.8

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .|.+++|.|+||+||||++..++    ...|.++++++.+
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~La----~~lg~~~~~~~~d   38 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEALA----NLPGVPKVHFHSD   38 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHH----TCSSSCEEEECTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHH----HHhCCCEEEecHH
Confidence            47899999999999999976554    4457888877764

>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=96.47  E-value=0.0084  Score=55.64  Aligned_cols=51  Identities=22%  Similarity=0.331  Sum_probs=37.4

Q ss_pred             cCCCcEEEEEcCCCCChhH-HHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSE-WIDALICNINEHAGWKFVLCSMENKVREHARKLLEK  348 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~-~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~  348 (539)
                      |++|..++|.|+||+|||+ ++..++...... |.+++|++.   -..++..+...
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~-~~~~lvi~P---tr~La~q~~~~   57 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR-GLRTLILAP---TRVVAAEMEEA   57 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH-TCCEEEEES---SHHHHHHHHHH
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc-CCEEEEEcc---HHHHHHHHHHH
Confidence            7899999999999999995 655666555554 889999964   34455444443

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.45  E-value=0.0017  Score=55.12  Aligned_cols=35  Identities=34%  Similarity=0.396  Sum_probs=28.7

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      .+|-++.|+|.||+||||++..++..+... +....
T Consensus         4 ~~g~~I~l~G~~GsGKTTia~~La~~L~~~-~~~~~   38 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIARALQVTLNQQ-GGRSV   38 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHHHH-CSSCE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhhc-CCCch
Confidence            468889999999999999999999888765 44333

>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=96.44  E-value=0.00081  Score=55.81  Aligned_cols=33  Identities=27%  Similarity=0.531  Sum_probs=24.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .+++|+|+||+||||++..++.    . .....+++.+
T Consensus         3 klIii~G~pGsGKTTla~~L~~----~-~~~~~~~~~d   35 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIA----K-NPGFYNINRD   35 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH----H-STTEEEECHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH----h-CCCCEEechH
Confidence            5889999999999999876643    2 4456666644

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {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: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=96.40  E-value=0.012  Score=55.40  Aligned_cols=43  Identities=23%  Similarity=0.298  Sum_probs=35.3

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVRE  340 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~  340 (539)
                      .-.+.|+|+||+|||||+..++.+.... |.+|.+++.+-+...
T Consensus        54 ~~~IgitG~pGaGKSTLi~~l~~~~~~~-g~~vavlavDpss~~   96 (327)
T d2p67a1          54 TLRLGVTGTPGAGKSTFLEAFGMLLIRE-GLKVAVIAVDPSSPV   96 (327)
T ss_dssp             SEEEEEEECTTSCHHHHHHHHHHHHHHT-TCCEEEEEECCC---
T ss_pred             ceEEEeeCCCCCCHHHHHHHHHHHHHhc-CCceeeecCCCceee
Confidence            4578899999999999999999888775 999999998866553

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.40  E-value=0.0059  Score=56.09  Aligned_cols=38  Identities=18%  Similarity=0.157  Sum_probs=31.7

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhc--CCeEEEEeCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHA--GWKFVLCSMEN  336 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~--g~~vl~~s~E~  336 (539)
                      ++.|+|++||||||++..+...+...+  ...|..+|++.
T Consensus        29 iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~Dd   68 (286)
T d1odfa_          29 FIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDD   68 (286)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGG
T ss_pred             EEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCC
Confidence            777999999999999999988876643  35789999883

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=96.32  E-value=0.0015  Score=57.85  Aligned_cols=34  Identities=24%  Similarity=0.219  Sum_probs=30.3

Q ss_pred             EEEEcC-CCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          300 TIVTGV-PNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       300 ~~i~G~-~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +.|+|. ||+||||++.++|..++++ |++|++|..
T Consensus         4 ~~i~gt~~GVGKTtvs~~La~aLa~~-G~rVl~id~   38 (224)
T d1byia_           4 YFVTGTDTEVGKTVASCALLQAAKAA-GYRTAGYKP   38 (224)
T ss_dssp             EEEEESSTTSCHHHHHHHHHHHHHHT-TCCEEEECS
T ss_pred             EEEEECCCCccHHHHHHHHHHHHHHC-CCeEEEECc
Confidence            567777 6999999999999999997 999999964

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.30  E-value=0.0018  Score=56.00  Aligned_cols=36  Identities=22%  Similarity=0.400  Sum_probs=30.0

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ++.|+|++|+|||||+..++..+... +..+..++..
T Consensus        24 iIgI~G~~GSGKSTla~~L~~~l~~~-~~~~~~~~~~   59 (198)
T d1rz3a_          24 VLGIDGLSRSGKTTLANQLSQTLREQ-GISVCVFHMD   59 (198)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHT-TCCEEEEEGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhccc-cccceecccc
Confidence            45699999999999999999887764 8888777644

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=96.30  E-value=0.0011  Score=56.10  Aligned_cols=23  Identities=35%  Similarity=0.422  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .+++|+|+||+||||++..++..
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~   25 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQ   25 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            48999999999999998877654

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.28  E-value=0.0015  Score=55.96  Aligned_cols=36  Identities=25%  Similarity=0.493  Sum_probs=30.6

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      .+++|.|+||+||||++..++..+-.. +.++..++.
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~-~~~~~~~~~   37 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKE-GVNYKMVSF   37 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTT-TCCCEEEEH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHc-CCCeEEEec
Confidence            489999999999999999999887664 778777764

>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=96.21  E-value=0.0019  Score=52.35  Aligned_cols=55  Identities=15%  Similarity=0.098  Sum_probs=38.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHHHHHhhC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIK  351 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r~~~~~~~  351 (539)
                      +++|+.++|.++||+|||..+...+.+.+...+..++++..-   ..+.........+
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~p~---~~l~~q~~~~~~~   58 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPT---RVVLSEMKEAFHG   58 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESS---HHHHHHHHHHTTT
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeeecc---hhHHHHHHHHhhh
Confidence            788999999999999999877666555555557788887744   3344444443333

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.18  E-value=0.0016  Score=55.00  Aligned_cols=31  Identities=23%  Similarity=0.348  Sum_probs=24.9

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      .+.+++|.|+||+||||++..++.++    |.+.+
T Consensus         5 ~~~iivl~G~~GsGKsT~a~~La~~l----~~~~~   35 (171)
T d1knqa_           5 DHHIYVLMGVSGSGKSAVASEVAHQL----HAAFL   35 (171)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHHH----TCEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh----CCCee
Confidence            46799999999999999999887653    55544

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.13  E-value=0.0022  Score=56.47  Aligned_cols=42  Identities=19%  Similarity=0.074  Sum_probs=34.7

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      =..|-++.|+|.||+||||++..++..+....+.++.++..+
T Consensus        21 ~~kg~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldgD   62 (208)
T d1m7ga_          21 NQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGD   62 (208)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcch
Confidence            356779999999999999999999988866557888877654

>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=96.04  E-value=0.012  Score=50.95  Aligned_cols=47  Identities=15%  Similarity=0.071  Sum_probs=34.0

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLL  346 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~  346 (539)
                      ++|++|+|+|||..+.-++...+.+.+.+++|+..... .++...++.
T Consensus        26 ~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~~~L~~q~~~~~~   73 (200)
T d1wp9a1          26 CLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFR   73 (200)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHH
T ss_pred             eEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCchHHHHHHHHHHH
Confidence            56889999999987777777666666889999986533 344444443

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=96.04  E-value=0.0031  Score=58.58  Aligned_cols=37  Identities=24%  Similarity=0.286  Sum_probs=34.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      +++++|.-|+||||++.++|..+|++ |.+|+.++++-
T Consensus        10 ~i~~sGKGGVGKTTvaa~lA~~lA~~-G~rVLlvD~Dp   46 (296)
T d1ihua1          10 YLFFTGKGGVGKTSISCATAIRLAEQ-GKRVLLVSTDP   46 (296)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEECCT
T ss_pred             EEEEECCCcChHHHHHHHHHHHHHHC-CCCEEEEeCCC
Confidence            78899999999999999999999996 99999999994

>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=96.02  E-value=0.0052  Score=55.11  Aligned_cols=52  Identities=17%  Similarity=0.089  Sum_probs=38.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC-CHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN-KVREHARKLL  346 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~-~~~~~~~r~~  346 (539)
                      +..|+=+++.+|||+|||.+++-.+...+.. |.+++|+..-- =..++..++-
T Consensus        55 ~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~-~~rvliv~Pt~~La~Q~~~~l~  107 (237)
T d1gkub1          55 ILRKESFAATAPTGVGKTSFGLAMSLFLALK-GKRCYVIFPTSLLVIQAAETIR  107 (237)
T ss_dssp             HHTTCCEECCCCBTSCSHHHHHHHHHHHHTT-SCCEEEEESCHHHHHHHHHHHH
T ss_pred             HHCCCCEEEEecCCChHHHHHHHHHHHHHHh-cCeEEEEeccHHHHHHHHHHHH
Confidence            5578778899999999998887777777664 88999998642 2345555543

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=95.99  E-value=0.0027  Score=54.53  Aligned_cols=36  Identities=25%  Similarity=0.419  Sum_probs=30.7

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      .+++|.|.||+||||++..++..+..+ |..+..++.
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L~~~-~~~~~~~~~   37 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEILDNQ-GINNKIINY   37 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHTT-TCCEEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc-CCCEEEEEC
Confidence            368899999999999999999887664 888888873

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=95.91  E-value=0.0021  Score=54.21  Aligned_cols=27  Identities=30%  Similarity=0.607  Sum_probs=22.0

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      ++|+|+||+||||++..++..    .|.+++
T Consensus         7 I~i~G~pGsGKTTia~~La~~----l~~~~i   33 (173)
T d1rkba_           7 ILLTGTPGVGKTTLGKELASK----SGLKYI   33 (173)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH----HCCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHH----HCCcEE
Confidence            679999999999998877754    377765

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.85  E-value=0.0018  Score=56.04  Aligned_cols=37  Identities=24%  Similarity=0.190  Sum_probs=29.6

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +|-++.|+|.||+||||++..++..+-.. ...+.++.
T Consensus        18 ~g~vI~L~G~pGSGKTTiAk~La~~l~~~-~~~~~~~~   54 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVSMALEEYLVCH-GIPCYTLD   54 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHHHHHHHHHHHT-TCCEEEEC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc-CCCccchh
Confidence            56788899999999999999999887664 55555543

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.84  E-value=0.008  Score=55.14  Aligned_cols=65  Identities=17%  Similarity=0.199  Sum_probs=51.3

Q ss_pred             CccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcC-------CeEEEEeCCCCHHHH
Q 009230          277 DEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAG-------WKFVLCSMENKVREH  341 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g-------~~vl~~s~E~~~~~~  341 (539)
                      ....+.||++.+|-++-+.+|+=..|.|++|+|||+++++++.+....+.       .-++|.-.-+..+++
T Consensus        48 i~e~l~TGIraID~l~pig~GQr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~  119 (285)
T d2jdia3          48 VREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTV  119 (285)
T ss_dssp             CCSBCCCSCHHHHHHSCCBTTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHH
T ss_pred             CCcccccCceEEecccCccCCCEEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHH
Confidence            44568899999999988999999999999999999999999988765422       235555555665554

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=95.78  E-value=0.0029  Score=53.45  Aligned_cols=34  Identities=18%  Similarity=0.236  Sum_probs=25.9

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ..+++|+|+||+||||++..++..    .+.+++.++.
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~----l~~~~~~~~~   36 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSV----LPEPWLAFGV   36 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH----SSSCEEEEEH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH----cCCCeEEeec
Confidence            358999999999999998877654    4666655543

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.75  E-value=0.009  Score=52.42  Aligned_cols=38  Identities=26%  Similarity=0.350  Sum_probs=33.7

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      ++|-+++|.|+.|+||||.+..++..+... |.+|.++.
T Consensus         1 ~rG~lI~ieG~dGsGKsT~~~~L~~~L~~~-g~~v~~~~   38 (209)
T d1nn5a_           1 RRGALIVLEGVDRAGKSTQSRKLVEALCAA-GHRAELLR   38 (209)
T ss_dssp             CCCCEEEEEESTTSSHHHHHHHHHHHHHHT-TCCEEEEE
T ss_pred             CCeeEEEEECCCCCCHHHHHHHHHHHHHHC-CCcEEEEe
Confidence            478999999999999999999998887775 99998775

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=95.73  E-value=0.0033  Score=53.09  Aligned_cols=26  Identities=23%  Similarity=0.475  Sum_probs=21.6

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|-.++|+|+||+||||++..++..
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~   28 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAE   28 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHH
Confidence            35567899999999999998877755

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {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: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.69  E-value=0.006  Score=54.24  Aligned_cols=39  Identities=15%  Similarity=0.305  Sum_probs=34.2

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV  338 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~  338 (539)
                      +.+.++..|+||||++.++|..++.. |.+|+++.++...
T Consensus         4 Iav~s~KGGvGKTtia~nlA~~la~~-g~~VlliD~D~~~   42 (232)
T d1hyqa_           4 ITVASGKGGTGKTTITANLGVALAQL-GHDVTIVDADITM   42 (232)
T ss_dssp             EEEEESSSCSCHHHHHHHHHHHHHHT-TCCEEEEECCCSS
T ss_pred             EEEECCCCCChHHHHHHHHHHHHHhC-CCCEEEEeCCCCC
Confidence            45667999999999999999999985 9999999988643

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.68  E-value=0.0072  Score=53.01  Aligned_cols=41  Identities=12%  Similarity=0.294  Sum_probs=34.4

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +|.+++|-|..|+||||++..++..+... |.+++.+..|-.
T Consensus         1 rgkfIviEG~dGsGKsT~~~~L~~~L~~~-g~~~~~~~~ep~   41 (210)
T d4tmka_           1 RSKYIVIEGLEGAGKTTARNVVVETLEQL-GIRDMVFTREPG   41 (210)
T ss_dssp             CCCEEEEEECTTSCHHHHHHHHHHHHHHT-TCCCEEEEESSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHhC-CCCeEEEecCCC
Confidence            58899999999999999999998887764 888777776643

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {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: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.67  E-value=0.0065  Score=54.13  Aligned_cols=40  Identities=23%  Similarity=0.375  Sum_probs=33.7

Q ss_pred             CcEE-EEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          297 GELT-IVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       297 G~l~-~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      |.++ +.++..|+||||++.++|..++.. |.+|+++.++..
T Consensus         2 ~~vIav~~~kGGvGKTtia~nLA~~la~~-g~~VlliD~D~~   42 (237)
T d1g3qa_           2 GRIISIVSGKGGTGKTTVTANLSVALGDR-GRKVLAVDGDLT   42 (237)
T ss_dssp             CEEEEEECSSTTSSHHHHHHHHHHHHHHT-TCCEEEEECCTT
T ss_pred             CeEEEEECCCCCCcHHHHHHHHHHHHHhC-CCCEEEEeCCCC
Confidence            4444 445889999999999999999985 999999998854

>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=95.61  E-value=0.0048  Score=55.26  Aligned_cols=32  Identities=16%  Similarity=0.214  Sum_probs=24.6

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      -++++||||+|||+++..++.+    .+.+...++.
T Consensus        37 ~~L~~GPpGtGKT~lA~~la~~----~~~~~~~~~~   68 (238)
T d1in4a2          37 HVLLAGPPGLGKTTLAHIIASE----LQTNIHVTSG   68 (238)
T ss_dssp             CEEEESSTTSSHHHHHHHHHHH----HTCCEEEEET
T ss_pred             eEEEECCCCCcHHHHHHHHHhc----cCCCcccccC
Confidence            3689999999999998877655    3666666654

>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=95.59  E-value=0.012  Score=53.62  Aligned_cols=27  Identities=19%  Similarity=0.293  Sum_probs=24.2

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHh
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEH  324 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~  324 (539)
                      .-.+|.|+||+|||+++..+|..+...
T Consensus        40 ~n~lLVG~~GvGKTalv~~la~ri~~~   66 (268)
T d1r6bx2          40 NNPLLVGESGVGKTAIAEGLAWRIVQG   66 (268)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCcEEECCCCCcHHHHHHHHHHHHHhC
Confidence            567899999999999999999988874

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=95.58  E-value=0.0051  Score=56.24  Aligned_cols=67  Identities=19%  Similarity=0.191  Sum_probs=52.0

Q ss_pred             CccccccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHH
Q 009230          277 DEFGISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARK  344 (539)
Q Consensus       277 ~~~gi~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~~~~r  344 (539)
                      ....+.||++.+|-++-+.+|+=..|.|++|+|||+++.+++.+...+ ..-++|...-+...+...-
T Consensus        47 ~~~~l~TGi~~ID~l~pig~GQr~~Ifg~~g~GKt~l~~~~~~~~~~~-~~v~V~~~iGer~~Ev~e~  113 (276)
T d1fx0a3          47 VYEPLQTGLIAIDAMIPVGRGQRELIIGDRQTGKTAVATDTILNQQGQ-NVICVYVAIGQKASSVAQV  113 (276)
T ss_dssp             CCSBCCCSCTTTTTTSCCBTTCBCBEEESSSSSHHHHHHHHHHTCCTT-TCEEEEEEESCCHHHHHHH
T ss_pred             CCccccccceEEeccccccCCceEeeccCCCCChHHHHHHHHhhhccc-CceeeeeeecchhHHHHHH
Confidence            345688999999999889999999999999999999999977665442 4566666666666655443

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

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: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=95.55  E-value=0.0077  Score=56.59  Aligned_cols=41  Identities=32%  Similarity=0.365  Sum_probs=34.7

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR  339 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~  339 (539)
                      -.+.|+|+||+|||||+..++.++... |.+|..+..+-+..
T Consensus        52 ~~igitG~pGaGKSTli~~l~~~~~~~-g~~vaViavDpss~   92 (323)
T d2qm8a1          52 IRVGITGVPGVGKSTTIDALGSLLTAA-GHKVAVLAVDPSST   92 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHHT-TCCEEEEEECGGGG
T ss_pred             eEEeeeCCCCCCHHHHHHHHHHHHhhc-CCceeeeecccccH
Confidence            468899999999999999999887764 99999998885443

>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=95.52  E-value=0.027  Score=50.88  Aligned_cols=76  Identities=22%  Similarity=0.135  Sum_probs=54.6

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHHHHhhCCC--ccccccCCCCCCCCHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLLEKHIKKP--FFEANYGGSAERMTVEEFEQGK  375 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~~~~~~~~--~~~i~~~~~~~~l~~~~~~~~~  375 (539)
                      ..+|.|..|+|||..++..+..+... |+.|++...+.. +.+...++.......+  ..-+.     +.++..+..++.
T Consensus       106 ~rLL~GdvGSGKT~Va~~a~~~~~~~-g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~-----~~~~~~~r~~~~  179 (264)
T d1gm5a3         106 NRLLQGDVGSGKTVVAQLAILDNYEA-GFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLI-----GATTPSEKEKIK  179 (264)
T ss_dssp             CCEEECCSSSSHHHHHHHHHHHHHHH-TSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECC-----SSSCHHHHHHHH
T ss_pred             eeeeeccccccccHHHHHHHHHHHhc-ccceeEEeehHhhhHHHHHHHHHhhhhccccceeec-----cccchHHHHHHH
Confidence            56899999999999999999888885 999999998865 4566667666554333  22221     256777766666


Q ss_pred             HHhhc
Q 009230          376 AWLSN  380 (539)
Q Consensus       376 ~~l~~  380 (539)
                      ..+.+
T Consensus       180 ~~~~~  184 (264)
T d1gm5a3         180 SGLRN  184 (264)
T ss_dssp             HHHHS
T ss_pred             HHHHC
Confidence            66654

>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=95.52  E-value=0.061  Score=45.99  Aligned_cols=28  Identities=21%  Similarity=0.364  Sum_probs=24.6

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHh
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEH  324 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~  324 (539)
                      ..-.+|.|+||+|||+++..+|..++..
T Consensus        43 k~n~lLvG~pGVGKTalv~~LA~ri~~~   70 (195)
T d1jbka_          43 KNNPVLIGEPGVGKTAIVEGLAQRIING   70 (195)
T ss_dssp             SCEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCCeEEEecCCcccHHHHHHHHHHHHhC
Confidence            3567899999999999999999998864

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=95.51  E-value=0.0027  Score=54.16  Aligned_cols=23  Identities=26%  Similarity=0.329  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ..++|.|+||+||||++..++..
T Consensus         8 K~I~i~G~~GsGKTTla~~La~~   30 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVNKLAAV   30 (192)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999998887765

>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=95.50  E-value=0.0031  Score=52.46  Aligned_cols=28  Identities=21%  Similarity=0.181  Sum_probs=22.0

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      .++|.|+||+||||++..+|.+    .|.+++
T Consensus         4 ~I~l~G~~GsGKSTvak~La~~----L~~~~i   31 (169)
T d1kaga_           4 NIFLVGPMGAGKSTIGRQLAQQ----LNMEFY   31 (169)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH----TTCEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHH----hCCCeE
Confidence            4678899999999998887765    366653

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

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: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=95.40  E-value=0.0056  Score=56.00  Aligned_cols=37  Identities=16%  Similarity=0.224  Sum_probs=33.6

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      .+.|+|.-|+||||++.++|..+|+. |++|+.+.++.
T Consensus         3 ~Iai~gKGGvGKTT~a~nLA~~LA~~-G~rVllID~D~   39 (269)
T d1cp2a_           3 QVAIYGKGGIGKSTTTQNLTSGLHAM-GKTIMVVGCDP   39 (269)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTT-TCCEEEEEECT
T ss_pred             EEEEECCCcCCHHHHHHHHHHHHHhC-CCcEEEEecCC
Confidence            45678999999999999999999986 99999999984

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-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: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.35  E-value=0.0021  Score=57.72  Aligned_cols=28  Identities=21%  Similarity=0.211  Sum_probs=24.9

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHh
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEH  324 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~  324 (539)
                      +.+.+|+||..+|||+++.+++......
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l~~~la   68 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTALIALMA   68 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHHHH
T ss_pred             ceEEEEeccCchhhHHHHHHHHHHHHHH
Confidence            3689999999999999999999887764

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=95.35  E-value=0.021  Score=51.91  Aligned_cols=25  Identities=16%  Similarity=0.149  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINE  323 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~  323 (539)
                      +++|.|+||+|||+++..++..+..
T Consensus        48 ~l~l~GppGtGKT~l~~~l~~~l~~   72 (287)
T d1w5sa2          48 IYGSIGRVGIGKTTLAKFTVKRVSE   72 (287)
T ss_dssp             EEECTTCCSSSHHHHHHHHHHHHHH
T ss_pred             EEEeECCCCCCHHHHHHHHHHHHHh
Confidence            3566899999999999999887654

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=95.31  E-value=0.0076  Score=55.21  Aligned_cols=61  Identities=13%  Similarity=0.145  Sum_probs=47.3

Q ss_pred             cccCchhhhhhhccCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeE-EEEeCCCCHHHH
Q 009230          281 ISTGWRALNELYNVLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKF-VLCSMENKVREH  341 (539)
Q Consensus       281 i~tg~~~LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~v-l~~s~E~~~~~~  341 (539)
                      .+++...+|-++-+.+|+=..|.|++|+|||+++.+++.+...++..-| ++...++..+++
T Consensus        27 ~~~~~r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~~~~~~~~~~v~~~~~iger~~ev   88 (289)
T d1xpua3          27 EDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEV   88 (289)
T ss_dssp             THHHHHHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHHHHHHHCTTSEEEEEEEEECHHHH
T ss_pred             ccccceeeeecccccCCCeeeEeCCCCCCHHHHHHHHHHHHhhcCCCeEEEEEeeceeHHHH
Confidence            3466678888888999999999999999999999999999877644434 444445666554

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.26  E-value=0.0055  Score=52.45  Aligned_cols=24  Identities=25%  Similarity=0.426  Sum_probs=20.8

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |.+++|.||||+||||++..++..
T Consensus         2 G~iivl~GpsG~GK~tl~~~L~~~   25 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVVRCLRER   25 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhh
Confidence            889999999999999997766544

>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=95.25  E-value=0.011  Score=47.70  Aligned_cols=42  Identities=17%  Similarity=0.238  Sum_probs=36.7

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV  338 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~  338 (539)
                      +|.|.+|+||-.+|||+-+++.+.+.-.. |.+|+.|..+.+.
T Consensus         1 ~G~L~li~GpMfsGKTt~Li~~~~~~~~~-g~~v~~ikp~~D~   42 (133)
T d1xbta1           1 RGQIQVILGPMFSGKSTELMRRVRRFQIA-QYKCLVIKYAKDT   42 (133)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHTT-TCCEEEEEETTCC
T ss_pred             CcEEEEEEecccCHHHHHHHHHHHHHHHc-CCcEEEEeccccc
Confidence            69999999999999999999998876654 8999999877654

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=95.18  E-value=0.0065  Score=55.76  Aligned_cols=36  Identities=22%  Similarity=0.173  Sum_probs=28.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      ++.|+|++|+||||++..+...+-.. +.+++.++.+
T Consensus         6 IIgIaG~SGSGKTTva~~l~~i~~~~-~v~~~iI~~D   41 (288)
T d1a7ja_           6 IISVTGSSGAGTSTVKHTFDQIFRRE-GVKAVSIEGD   41 (288)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHHHH-TCCEEEEEGG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHhhc-CCCeEEEeCC
Confidence            78999999999999999988776654 8899888877

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=95.15  E-value=0.0084  Score=53.57  Aligned_cols=35  Identities=14%  Similarity=0.355  Sum_probs=28.6

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      +++|+|++|+|||||+..+..+..  .+..+..++.+
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~~--~~~~~~ivn~d   36 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYLE--DNYKVAYVNLD   36 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHT--TTSCEEEEECC
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh--hCCeEEEEecC
Confidence            578999999999999999986643  37788888754

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=95.07  E-value=0.0062  Score=52.60  Aligned_cols=23  Identities=26%  Similarity=0.449  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .+++|.|+||+||||++..++.+
T Consensus         7 ~iI~i~G~pGSGKsT~a~~La~~   29 (194)
T d1qf9a_           7 NVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            48899999999999998877754

>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=95.07  E-value=0.0096  Score=54.00  Aligned_cols=49  Identities=14%  Similarity=0.143  Sum_probs=34.9

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC--CCHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME--NKVREHARKLL  346 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E--~~~~~~~~r~~  346 (539)
                      ..++|.|+||+|||+++..++.++....+.+++++..-  .........+.
T Consensus        44 ~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   94 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIA   94 (276)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHH
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchhhhhhhhhhhhhH
Confidence            36889999999999999998888755446677776543  33454544443

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.06  E-value=0.0043  Score=57.18  Aligned_cols=33  Identities=24%  Similarity=0.433  Sum_probs=26.8

Q ss_pred             hhhhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          286 RALNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       286 ~~LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      |-|+++.- +.+|+++.|.|++|+|||||+.-++
T Consensus        50 pvL~~isl~i~~Ge~vaivG~nGsGKSTLl~~i~   83 (281)
T d1r0wa_          50 PVLKNINLNIEKGEMLAITGSTGSGKTSLLMLIL   83 (281)
T ss_dssp             EEEEEEEEEECTTCEEEEEESTTSSHHHHHHHHH
T ss_pred             eEEeCeEEEEcCCCEEEEECCCCChHHHHHHHHh
Confidence            34555544 9999999999999999999976654

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=95.04  E-value=0.0052  Score=55.27  Aligned_cols=31  Identities=23%  Similarity=0.338  Sum_probs=25.0

Q ss_pred             hhhhhc-cCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          288 LNELYN-VLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       288 LD~~~~-l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      |+++.- +++|+.+.|.|++|+|||||+.-++
T Consensus        18 L~~isl~i~~Ge~vaivG~sGsGKSTLl~ll~   49 (242)
T d1mv5a_          18 LRDISFEAQPNSIIAFAGPSGGGKSTIFSLLE   49 (242)
T ss_dssp             EEEEEEEECTTEEEEEECCTTSSHHHHHHHHT
T ss_pred             eeeeEEEEcCCCEEEEECCCCCCHHHHHHHHH
Confidence            444433 9999999999999999999876544

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {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: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=95.00  E-value=0.0078  Score=55.97  Aligned_cols=37  Identities=16%  Similarity=0.194  Sum_probs=31.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHh-cCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEH-AGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~-~g~~vl~~s~E  335 (539)
                      ++.|+|++|+|||||+..+...+... .+.+|..+|++
T Consensus        82 iIGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D  119 (308)
T d1sq5a_          82 IISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTD  119 (308)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGG
T ss_pred             EEEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeee
Confidence            88899999999999999988776532 26789999988

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=94.98  E-value=0.01  Score=53.49  Aligned_cols=32  Identities=19%  Similarity=0.385  Sum_probs=25.0

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      .-+++.||||+|||+++..+|..    .+.+++.++
T Consensus        41 ~~vLL~GppGtGKT~la~alA~~----~~~~~~~i~   72 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALAAKIAEE----SNFPFIKIC   72 (246)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH----HTCSEEEEE
T ss_pred             eEEEEECcCCCCHHHHHHHHhhc----ccccccccc
Confidence            35789999999999998887654    377777654

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=94.97  E-value=0.0088  Score=57.13  Aligned_cols=38  Identities=21%  Similarity=0.214  Sum_probs=31.1

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      .+.+..+++.||||+|||+|+..+|..    .|.+++.+++-
T Consensus       151 ~~~~~~~~~~g~~~~gk~~~~~~~~~~----~~~~~i~in~s  188 (362)
T d1svma_         151 IPKKRYWLFKGPIDSGKTTLAAALLEL----CGGKALNVNLP  188 (362)
T ss_dssp             CTTCCEEEEECSTTSSHHHHHHHHHHH----HCCEEECCSSC
T ss_pred             CCCcCeEEEECCCCCCHHHHHHHHHHH----cCCCEEEEECc
Confidence            777789999999999999998887755    37888777543

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

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: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=94.93  E-value=0.011  Score=54.60  Aligned_cols=37  Identities=22%  Similarity=0.297  Sum_probs=33.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      .++|.|.-|+||||++.++|..+++. |++|+.+.++.
T Consensus         4 ~IaisgKGGVGKTT~a~NLA~~LA~~-G~rVLlID~Dp   40 (289)
T d2afhe1           4 QCAIYGKGGIGKSTTTQNLVAALAEM-GKKVMIVGCDP   40 (289)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHT-TCCEEEEEECS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-CCCEEEEecCC
Confidence            35678999999999999999999986 99999999984

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=94.86  E-value=0.0062  Score=55.48  Aligned_cols=33  Identities=18%  Similarity=0.273  Sum_probs=25.3

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ..++|+||||+|||+++..+|..    .+.+++.++.
T Consensus        33 ~~ilL~GpPGtGKT~la~~la~~----~~~~~~~i~~   65 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLRSAIFEE----TQGNVIVIDN   65 (273)
T ss_dssp             EEEEEECCTTSCTHHHHHHHHHH----TTTCCEEECT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH----hhcceEEEec
Confidence            46899999999999998776654    3566666654

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=94.74  E-value=0.0086  Score=50.93  Aligned_cols=21  Identities=19%  Similarity=0.564  Sum_probs=18.2

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|+||+||||.+..++.+
T Consensus         3 I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAA   23 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            679999999999998877655

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=94.73  E-value=0.0055  Score=59.66  Aligned_cols=43  Identities=26%  Similarity=0.339  Sum_probs=33.6

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVRE  340 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~~  340 (539)
                      .++.+++|+|++|+||||.+..++..+... +.+  +++.|.|++.
T Consensus       156 ~~~GliLvtGpTGSGKSTTl~~~l~~~~~~-~~~--i~tiEdPiE~  198 (401)
T d1p9ra_         156 RPHGIILVTGPTGSGKSTTLYAGLQELNSS-ERN--ILTVEDPIEF  198 (401)
T ss_dssp             SSSEEEEEECSTTSCHHHHHHHHHHHHCCT-TSC--EEEEESSCCS
T ss_pred             hhhceEEEEcCCCCCccHHHHHHhhhhcCC-Cce--EEEeccCccc
Confidence            344599999999999999999988776443 455  4699998873

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.71  E-value=0.017  Score=51.89  Aligned_cols=35  Identities=14%  Similarity=0.277  Sum_probs=28.1

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      ...+|.||||+|||+++..+|.+    .+..+.+++..+
T Consensus        53 ~~lll~GPpG~GKTt~a~~la~~----~~~~~~~~~~~~   87 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAHLVAQE----LGYDILEQNASD   87 (253)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHH----TTCEEEEECTTS
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH----HHhhhhcccccc
Confidence            47899999999999998877654    477888887653

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, 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: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.71  E-value=0.01  Score=52.61  Aligned_cols=36  Identities=22%  Similarity=0.443  Sum_probs=30.6

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK  337 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~  337 (539)
                      +++|+|.-|+|||||+.+++.+   ..|.++..+..|+.
T Consensus         5 v~iitGFLGaGKTTll~~lL~~---~~~~riaVI~Ne~g   40 (222)
T d1nija1           5 VTLLTGFLGAGKTTLLRHILNE---QHGYKIAVIENEFG   40 (222)
T ss_dssp             EEEEEESSSSSCHHHHHHHHHS---CCCCCEEEECSSCC
T ss_pred             EEEEeeCCCCCHHHHHHHHHhc---CCCCcEEEEEeccc
Confidence            7899999999999999888764   24889999988864

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=94.63  E-value=0.012  Score=50.58  Aligned_cols=26  Identities=27%  Similarity=0.353  Sum_probs=20.6

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|--++|.|+|||||||.+..+|.+
T Consensus         1 p~~~riil~G~pGSGKsT~a~~La~~   26 (190)
T d1ak2a1           1 PKGVRAVLLGPPGAGKGTQAPKLAKN   26 (190)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCccEEEEECCCCCCHHHHHHHHHHH
Confidence            35555678899999999998877754

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=94.56  E-value=0.0093  Score=53.33  Aligned_cols=32  Identities=19%  Similarity=0.280  Sum_probs=24.3

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      +++.||||+|||+++.-++..    .+.+...++..
T Consensus        38 ~Ll~GPpG~GKTtla~~la~~----~~~~~~~~~~~   69 (239)
T d1ixsb2          38 LLLFGPPGLGKTTLAHVIAHE----LGVNLRVTSGP   69 (239)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH----HTCCEEEEETT
T ss_pred             EEEECCCCCCHHHHHHHHHHH----hCCCeEeccCC
Confidence            579999999999998877654    36666666644

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.55  E-value=0.0089  Score=52.43  Aligned_cols=37  Identities=24%  Similarity=0.259  Sum_probs=28.0

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHh----cCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEH----AGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~----~g~~vl~~s~E  335 (539)
                      ++.|+|++|||||||+..++..+...    .+..+..++++
T Consensus         4 iIgI~G~~gSGKSTla~~L~~~l~~~~~~~~~~~~~vi~~D   44 (213)
T d1uj2a_           4 LIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQD   44 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTTGGGSCGGGCSEEEEEGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhchhccccCCCceEEEecc
Confidence            57799999999999999888775432    13457777765

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=94.55  E-value=0.0088  Score=51.64  Aligned_cols=26  Identities=23%  Similarity=0.423  Sum_probs=21.5

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      +..+.+++|.|+||+||||.+..++.
T Consensus         5 ~~~~~iI~l~G~pGSGKsT~a~~La~   30 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGTQCEKIVQ   30 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHHHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHH
Confidence            44567899999999999999877654

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {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: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=94.51  E-value=0.0092  Score=52.85  Aligned_cols=27  Identities=26%  Similarity=0.283  Sum_probs=24.3

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHh
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEH  324 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~  324 (539)
                      ++++|+||..+|||+++.+++......
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilA   62 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLA   62 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHH
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHH
Confidence            589999999999999999999887664

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=94.45  E-value=0.01  Score=50.94  Aligned_cols=21  Identities=24%  Similarity=0.510  Sum_probs=17.7

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|+||+||||++..++.+
T Consensus         6 I~i~GppGsGKsT~a~~La~~   26 (189)
T d1zaka1           6 VMISGAPASGKGTQCELIKTK   26 (189)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            679999999999998776644

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.43  E-value=0.012  Score=50.68  Aligned_cols=22  Identities=23%  Similarity=0.401  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++|.|+||+||||.+..++.+
T Consensus         3 iI~i~GppGSGKsT~a~~La~~   24 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCARIVEK   24 (194)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999998887755

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=94.41  E-value=0.011  Score=50.29  Aligned_cols=22  Identities=23%  Similarity=0.530  Sum_probs=18.6

Q ss_pred             EEEEcCCCCChhHHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      ++|.|+|||||||.+..++.+.
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            5789999999999988777653

>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=94.40  E-value=0.03  Score=51.68  Aligned_cols=48  Identities=23%  Similarity=0.313  Sum_probs=35.2

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHhcC---CeEEEEeCCCC-HHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEHAG---WKFVLCSMENK-VREHARKLLE  347 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~~g---~~vl~~s~E~~-~~~~~~r~~~  347 (539)
                      .+|.|+||+|||+.+++-+..++.+.+   .+|+++++--. +.++..|+..
T Consensus        17 ~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~   68 (306)
T d1uaaa1          17 CLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQ   68 (306)
T ss_dssp             EEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHH
T ss_pred             EEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHH
Confidence            467799999999999988877776533   47999998644 3455555543

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=94.39  E-value=0.012  Score=49.65  Aligned_cols=28  Identities=21%  Similarity=0.370  Sum_probs=22.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      .++|.|+||+||||++..+|..+    |++.+
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~L----g~~~i   31 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARAL----GYEFV   31 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHH----TCEEE
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh----CCCEE
Confidence            46788999999999988887553    77743

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.39  E-value=0.011  Score=50.20  Aligned_cols=22  Identities=23%  Similarity=0.369  Sum_probs=18.7

Q ss_pred             EEEEcCCCCChhHHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      ++|.|+||+||||.+..++.+.
T Consensus         3 I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            5788999999999988877553

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.39  E-value=0.012  Score=51.32  Aligned_cols=24  Identities=42%  Similarity=0.576  Sum_probs=21.3

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      |.+++|+||||+||||+...++..
T Consensus         2 G~livi~GPSG~GK~tl~~~L~~~   25 (205)
T d1s96a_           2 GTLYIVSAPSGAGKSSLIQALLKT   25 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhh
Confidence            789999999999999998877655

>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=94.28  E-value=0.069  Score=47.14  Aligned_cols=77  Identities=13%  Similarity=0.013  Sum_probs=53.9

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHHHHHhhCCCc--cccccCCCCCCCCHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKLLEKHIKKPF--FEANYGGSAERMTVEEFEQG  374 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~~~~~~~~~~--~~i~~~~~~~~l~~~~~~~~  374 (539)
                      ...+|.|.+|+|||.+++..+..++.+ |..|++...|.. ..++..++-......+.  .-+.     ...+..+..++
T Consensus        77 ~~~LL~GdvGsGKT~V~~~a~~~~~~~-g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~-----~~~~~~~~~~~  150 (233)
T d2eyqa3          77 MDRLVCGDVGFGKTEVAMRAAFLAVDN-HKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMIS-----RFRSAKEQTQI  150 (233)
T ss_dssp             CEEEEECCCCTTTHHHHHHHHHHHHTT-TCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEES-----TTSCHHHHHHH
T ss_pred             cCeEEEcCCCCCcHHHHHHHHHHHHHc-CCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEecc-----CcccchhHHHH
Confidence            478899999999999999999888875 999999998865 45566666555444332  2221     24666666665


Q ss_pred             HHHhhc
Q 009230          375 KAWLSN  380 (539)
Q Consensus       375 ~~~l~~  380 (539)
                      ...+.+
T Consensus       151 ~~~~~~  156 (233)
T d2eyqa3         151 LAEVAE  156 (233)
T ss_dssp             HHHHHT
T ss_pred             HHHHhC
Confidence            555544

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.28  E-value=0.013  Score=49.08  Aligned_cols=27  Identities=30%  Similarity=0.475  Sum_probs=20.8

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      ++|.|.||+||||++..++..+    |++++
T Consensus         4 IvliG~~G~GKSTig~~La~~l----~~~fi   30 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKAL----GVGLL   30 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH----TCCEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHh----CCCeE
Confidence            4566999999999988887553    66643

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.19  E-value=0.014  Score=50.42  Aligned_cols=31  Identities=29%  Similarity=0.482  Sum_probs=23.7

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      .+++|.|+||+||||++..++.+      +...|+|.
T Consensus         9 ~iI~i~GppGSGKsT~a~~La~~------~g~~~is~   39 (196)
T d1ukza_           9 SVIFVLGGPGAGKGTQCEKLVKD------YSFVHLSA   39 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH------SSCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH------hCCeEEeh
Confidence            47888999999999998877643      34456674

>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=94.12  E-value=0.035  Score=45.01  Aligned_cols=44  Identities=25%  Similarity=0.122  Sum_probs=36.2

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR  339 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~  339 (539)
                      ..|.|.+|.||-.+||||-+++.+.+.... |.+|++|....+.+
T Consensus         5 ~~G~l~lI~GpMfSGKTteLi~~~~~~~~~-g~~vl~i~~~~D~R   48 (141)
T d1xx6a1           5 DHGWVEVIVGPMYSGKSEELIRRIRRAKIA-KQKIQVFKPEIDNR   48 (141)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEEEC----
T ss_pred             cceeEEEEEeccccHHHHHHHHHHHHhhhc-CCcEEEEEeccccc
Confidence            368999999999999999999999888775 99999999887643

>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=94.09  E-value=0.014  Score=54.58  Aligned_cols=35  Identities=23%  Similarity=0.245  Sum_probs=24.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      .+++ -+++.||||+|||.+|..+|..+    +.+...++
T Consensus        47 ~~~~-~iLl~GPpG~GKT~lAkalA~~~----~~~~~~i~   81 (309)
T d1ofha_          47 VTPK-NILMIGPTGVGKTEIARRLAKLA----NAPFIKVE   81 (309)
T ss_dssp             CCCC-CEEEECCTTSSHHHHHHHHHHHH----TCCEEEEE
T ss_pred             CCCc-eEEEECCCCCCHHHHHHHHhhcc----ccchhccc
Confidence            3444 44678999999999999888653    44544444

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=94.06  E-value=0.024  Score=51.26  Aligned_cols=34  Identities=24%  Similarity=0.395  Sum_probs=26.3

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +..++|.|++|+|||+++.+++..    .+....|+.+
T Consensus        29 ~~~i~i~G~~G~GKTsLl~~~~~~----~~~~~~~i~~   62 (283)
T d2fnaa2          29 APITLVLGLRRTGKSSIIKIGINE----LNLPYIYLDL   62 (283)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHH----HTCCEEEEEG
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHHH----CCCCeEEEEe
Confidence            468999999999999999887654    3566666654

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=94.02  E-value=0.014  Score=50.15  Aligned_cols=29  Identities=24%  Similarity=0.257  Sum_probs=21.3

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ++|.|+||+||||++..++.+    .|.+  ++|.
T Consensus         9 IiliG~PGSGKtT~a~~La~~----~g~~--~is~   37 (189)
T d2ak3a1           9 AAIMGAPGSGKGTVSSRITKH----FELK--HLSS   37 (189)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH----BCCE--EEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHH----HCCe--EEcH
Confidence            567799999999998877754    3544  5564

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.00  E-value=0.015  Score=49.39  Aligned_cols=21  Identities=24%  Similarity=0.404  Sum_probs=18.0

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|+|||||||.+..++.+
T Consensus         3 I~i~G~pGSGKsT~~~~La~~   23 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEK   23 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            568899999999998887754

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.99  E-value=0.016  Score=49.35  Aligned_cols=21  Identities=24%  Similarity=0.360  Sum_probs=17.7

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|+|||||||++..++..
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~   25 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQER   25 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            567799999999998887754

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal 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: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=93.94  E-value=0.014  Score=51.48  Aligned_cols=31  Identities=29%  Similarity=0.573  Sum_probs=23.7

Q ss_pred             hhhhhccCCCcEEEEEcCCCCChhHHHHHHH
Q 009230          288 LNELYNVLPGELTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       288 LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la  318 (539)
                      +|.+..+-+|..+++.|+||+|||||+..+.
T Consensus        86 ~~~L~~~l~~kt~~~~G~SGVGKSTLiN~L~  116 (225)
T d1u0la2          86 IEELKEYLKGKISTMAGLSGVGKSSLLNAIN  116 (225)
T ss_dssp             HHHHHHHHSSSEEEEECSTTSSHHHHHHHHS
T ss_pred             HhhHHHHhcCCeEEEECCCCCCHHHHHHhhc
Confidence            4444443368899999999999999987664

>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=93.93  E-value=0.015  Score=51.51  Aligned_cols=37  Identities=19%  Similarity=0.171  Sum_probs=26.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHh-cCCeEEEEeCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEH-AGWKFVLCSME  335 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~-~g~~vl~~s~E  335 (539)
                      ..+|.||||+|||+++..+|..+... ....++.++..
T Consensus        47 ~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~s   84 (231)
T d1iqpa2          47 HLLFAGPPGVGKTTAALALARELFGENWRHNFLELNAS   84 (231)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETT
T ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEecC
Confidence            36899999999999999988776431 13456666543

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=93.91  E-value=0.017  Score=50.66  Aligned_cols=23  Identities=17%  Similarity=0.336  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +++|.||||+||||.+..++.++
T Consensus         5 iI~I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            78899999999999988777653

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=93.90  E-value=0.032  Score=48.29  Aligned_cols=35  Identities=20%  Similarity=0.346  Sum_probs=30.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      +++|.|..|+||||++..++..+... |.+|.++..
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l~~~-g~~v~~~~~   36 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAFRAA-GRSVATLAF   36 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEES
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-CCCEEEEec
Confidence            68899999999999999999887664 999988754

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=93.90  E-value=0.017  Score=48.17  Aligned_cols=27  Identities=30%  Similarity=0.412  Sum_probs=21.1

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          300 TIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      ++|.|+||+||||++..+|..+    |.+++
T Consensus         3 I~liG~~GsGKsTi~k~La~~l----~~~~~   29 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKDL----DLVFL   29 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH----TCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHh----CCCEE
Confidence            5677999999999988877664    66644

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=93.69  E-value=0.02  Score=50.30  Aligned_cols=30  Identities=20%  Similarity=0.308  Sum_probs=22.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      ++.|.||||+||||.|..||.++    |.+  |+|.
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~l----g~~--~ist   34 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDF----GFT--YLDT   34 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHH----CCE--EEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh----CCc--EECH
Confidence            45688999999999988877664    555  5553

>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=93.53  E-value=0.049  Score=43.57  Aligned_cols=45  Identities=16%  Similarity=0.147  Sum_probs=30.5

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENK-VREHARKL  345 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~-~~~~~~r~  345 (539)
                      -...+|.+++|+|||+++..++    ...|.+++++..-.. .++...++
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~----~~~~~~vli~~P~~~l~~q~~~~~   53 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAY----AAQGYKVLVLNPSVAATLGFGAYM   53 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHH----HTTTCCEEEEESCHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHHHHH----HHcCCcEEEEcChHHHHHHHHHHH
Confidence            3678999999999998765443    335889998886533 33343333

>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=93.42  E-value=0.018  Score=51.67  Aligned_cols=23  Identities=26%  Similarity=0.281  Sum_probs=20.4

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      .+|.|+||+|||+++..++.++.
T Consensus        36 lll~Gp~G~GKTt~~~~la~~l~   58 (252)
T d1sxje2          36 LLLYGPNGTGKKTRCMALLESIF   58 (252)
T ss_dssp             EEEECSTTSSHHHHHHTHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHhhc
Confidence            67999999999999999887753

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.23  E-value=0.024  Score=50.24  Aligned_cols=24  Identities=29%  Similarity=0.379  Sum_probs=21.1

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICNINE  323 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~  323 (539)
                      .+|.||||+|||+++..++..+..
T Consensus        36 lll~Gp~G~GKTtl~~~i~~~l~~   59 (237)
T d1sxjd2          36 MLFYGPPGTGKTSTILALTKELYG   59 (237)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCChHHHHHHHHHHHcC
Confidence            689999999999999999987643

>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=93.20  E-value=0.12  Score=49.21  Aligned_cols=27  Identities=22%  Similarity=0.402  Sum_probs=22.8

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHh
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEH  324 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~  324 (539)
                      .-.+|.|+||+|||+++-.+|..+...
T Consensus        44 ~n~llvG~~GvGKtaiv~~la~~i~~~   70 (387)
T d1qvra2          44 NNPVLIGEPGVGKTAIVEGLAQRIVKG   70 (387)
T ss_dssp             CCCEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CCCeEECCCCCCHHHHHHHHHHHHHhC
Confidence            345777999999999999999888774

>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=93.17  E-value=0.035  Score=51.59  Aligned_cols=47  Identities=19%  Similarity=0.355  Sum_probs=33.0

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcC---CeEEEEeCCCCH-HHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAG---WKFVLCSMENKV-REHARKL  345 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g---~~vl~~s~E~~~-~~~~~r~  345 (539)
                      -++|.|+||+|||+.+++-+..+..+.+   .+++++++--.. .++..|+
T Consensus        26 ~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~   76 (318)
T d1pjra1          26 PLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERV   76 (318)
T ss_dssp             CEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHH
T ss_pred             CEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHH
Confidence            3567789999999999887777766422   478999877543 3444444

>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=92.98  E-value=0.028  Score=49.51  Aligned_cols=24  Identities=25%  Similarity=0.502  Sum_probs=20.8

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICNINE  323 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a~  323 (539)
                      +++.||||+|||+++.-++..+..
T Consensus        39 ~ll~Gp~G~GKTt~a~~la~~l~~   62 (224)
T d1sxjb2          39 MIISGMPGIGKTTSVHCLAHELLG   62 (224)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHG
T ss_pred             EEEECCCCCCchhhHHHHHHHHhc
Confidence            679999999999999988877653

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=92.96  E-value=0.028  Score=46.06  Aligned_cols=20  Identities=20%  Similarity=0.363  Sum_probs=17.5

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|+||+|||||+..++.
T Consensus         3 ivlvG~~~vGKSsLi~~l~~   22 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKL   22 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            57999999999999988754

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {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: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=92.70  E-value=0.037  Score=45.66  Aligned_cols=28  Identities=14%  Similarity=0.233  Sum_probs=25.0

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .++|.++.+.|.=|+|||||+..++..+
T Consensus        30 ~~~g~ii~L~G~LGaGKTtfvr~~~~~l   57 (158)
T d1htwa_          30 TEKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             CSSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCCeEEEEecCCCccHHHHHHHHHhhc
Confidence            4789999999999999999998888664

>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=92.65  E-value=0.032  Score=49.11  Aligned_cols=23  Identities=35%  Similarity=0.436  Sum_probs=20.2

Q ss_pred             EEEEcCCCCChhHHHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      +++.|+||+|||+++..++..+.
T Consensus        38 lLl~Gp~G~GKttl~~~la~~l~   60 (227)
T d1sxjc2          38 LLFYGPPGTGKTSTIVALAREIY   60 (227)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCChhHHHHHHHHHhh
Confidence            67999999999999999887753

>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=92.59  E-value=0.062  Score=50.97  Aligned_cols=42  Identities=17%  Similarity=0.384  Sum_probs=32.0

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHh---cCCeEEEEeCCCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEH---AGWKFVLCSMENK  337 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~---~g~~vl~~s~E~~  337 (539)
                      .+.+++|.|+||+|||+.+..++..+...   .+.+|+..+.-..
T Consensus       162 ~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgk  206 (359)
T d1w36d1         162 TRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGK  206 (359)
T ss_dssp             TBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHH
T ss_pred             cCCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHH
Confidence            35699999999999999998877666542   3667888775543

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.54  E-value=0.034  Score=47.47  Aligned_cols=23  Identities=22%  Similarity=0.460  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .++|.||||+||||++..++...
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~~~   25 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHC
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            47899999999999988876554

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.52  E-value=0.036  Score=47.48  Aligned_cols=23  Identities=22%  Similarity=0.381  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      .++|.||||+||||++..++...
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            37899999999999988777664

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.48  E-value=0.045  Score=46.36  Aligned_cols=24  Identities=17%  Similarity=0.320  Sum_probs=19.9

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ..+++|.||+|+||||++..++..
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~~L~~~   26 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKNTLITK   26 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHh
Confidence            358999999999999998766643

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {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: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=92.31  E-value=0.016  Score=51.18  Aligned_cols=33  Identities=21%  Similarity=0.368  Sum_probs=24.1

Q ss_pred             hhhhhccCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          288 LNELYNVLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       288 LD~~~~l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +|.+..+-.|..+++.|+||+|||||+..+.-.
T Consensus        88 l~~L~~~l~~~~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          88 LADIIPHFQDKTTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             CTTTGGGGTTSEEEEEESHHHHHHHHHHHHCC-
T ss_pred             HHHHHHhhccceEEEECCCCccHHHHHHhhccH
Confidence            344444335778999999999999998877643

>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=92.14  E-value=0.063  Score=52.23  Aligned_cols=37  Identities=22%  Similarity=0.262  Sum_probs=30.8

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMEN  336 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~  336 (539)
                      -++|.|.||+|||+++..++.++... |.+++++....
T Consensus        52 H~~I~G~tGsGKT~~l~~li~~~~~~-g~~~iiiD~kg   88 (433)
T d1e9ra_          52 HLLVNGATGTGKSVLLRELAYTGLLR-GDRMVIVDPNG   88 (433)
T ss_dssp             CEEEEECTTSSHHHHHHHHHHHHHHT-TCEEEEEEETT
T ss_pred             eEEEEeCCCCcHHHHHHHHHHHHHhC-CCCEEEEeCCh
Confidence            36899999999999998888888775 88888887653

>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=91.91  E-value=0.038  Score=48.09  Aligned_cols=24  Identities=21%  Similarity=0.296  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      -+++.|++|+|||+++..+|..+.
T Consensus        26 ~lLl~Gp~G~GKtt~a~~~a~~l~   49 (207)
T d1a5ta2          26 ALLIQALPGMGDDALIYALSRYLL   49 (207)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHHHhcc
Confidence            488999999999999999987764

>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=91.54  E-value=0.045  Score=47.23  Aligned_cols=41  Identities=15%  Similarity=0.118  Sum_probs=28.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      +..|.-+++.+|+|+|||+.+.-.+...... +.+++|+..-
T Consensus        37 l~~~~~~il~apTGsGKT~~a~l~i~~~~~~-~~~vl~l~P~   77 (202)
T d2p6ra3          37 VFSGKNLLLAMPTAAGKTLLAEMAMVREAIK-GGKSLYVVPL   77 (202)
T ss_dssp             HTTCSCEEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEEESS
T ss_pred             HHcCCCEEEEcCCCCchhHHHHHHHHHHhhc-cCcceeeccc
Confidence            3345557899999999998765444444443 6788888654

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=91.29  E-value=0.11  Score=48.12  Aligned_cols=34  Identities=21%  Similarity=0.245  Sum_probs=25.6

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      |....+++||||+|||.++..+|..+    +.+.+.++
T Consensus        51 p~~~~lf~Gp~GvGKT~lak~la~~l----~~~~i~~d   84 (315)
T d1r6bx3          51 PVGSFLFAGPTGVGKTEVTVQLSKAL----GIELLRFD   84 (315)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHHHH----TCEEEEEE
T ss_pred             CceEEEEECCCcchhHHHHHHHHhhc----cCCeeEec
Confidence            33467899999999999999988653    55655444

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=91.22  E-value=0.35  Score=39.45  Aligned_cols=38  Identities=13%  Similarity=0.052  Sum_probs=30.4

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSME  335 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E  335 (539)
                      +|-+.+.+ .+|=||||-|+-+|..++- +|.+|+++-+=
T Consensus         2 kG~i~vyt-G~GKGKTTAAlG~alRA~G-~G~rV~ivQFl   39 (157)
T d1g5ta_           2 RGIIIVFT-GNGKGKTTAAFGTAARAVG-HGKNVGVVQFI   39 (157)
T ss_dssp             CCCEEEEE-SSSSCHHHHHHHHHHHHHH-TTCCEEEEESS
T ss_pred             CcEEEEEe-CCCCCcHHHHHHHHHHHhc-CCCEEEEEEEe
Confidence            45444444 5799999999999999887 59999999764

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=91.17  E-value=0.054  Score=44.60  Aligned_cols=20  Identities=20%  Similarity=0.403  Sum_probs=17.5

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.||+|||||+..+..
T Consensus         8 I~ivG~~~vGKSSLi~~~~~   27 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQV   27 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            67999999999999987753

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=91.02  E-value=0.061  Score=45.19  Aligned_cols=24  Identities=33%  Similarity=0.282  Sum_probs=20.0

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|.=++|.|+||+|||++++.++.
T Consensus        13 ~g~gvl~~G~sG~GKStlal~l~~   36 (176)
T d1kkma_          13 YGLGVLITGDSGVGKSETALELVQ   36 (176)
T ss_dssp             TTEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHH
Confidence            456789999999999999887654

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {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: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=91.01  E-value=0.054  Score=46.30  Aligned_cols=19  Identities=42%  Similarity=0.700  Sum_probs=17.6

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|+||+|||||+..+.
T Consensus        26 I~lvG~~n~GKSTLin~L~   44 (195)
T d1svia_          26 IALAGRSNVGKSSFINSLI   44 (195)
T ss_dssp             EEEEEBTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHhc
Confidence            8899999999999998886

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {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: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=90.95  E-value=0.054  Score=46.17  Aligned_cols=27  Identities=30%  Similarity=0.338  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      ++.|+|++||||||++-.+     ...|.+++
T Consensus         5 IIgitG~~gSGKstva~~l-----~~~g~~~~   31 (191)
T d1uf9a_           5 IIGITGNIGSGKSTVAALL-----RSWGYPVL   31 (191)
T ss_dssp             EEEEEECTTSCHHHHHHHH-----HHTTCCEE
T ss_pred             EEEEECCCCCCHHHHHHHH-----HHCCCeEE
Confidence            5669999999999997644     23487765

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=90.85  E-value=0.08  Score=45.87  Aligned_cols=27  Identities=30%  Similarity=0.401  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      ++.|+|.+||||||++..+    . ..|.+|+
T Consensus         5 iIgitG~igSGKStv~~~l----~-~~G~~vi   31 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAF----A-DLGINVI   31 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHH----H-HTTCEEE
T ss_pred             EEEEECCCcCCHHHHHHHH----H-HCCCcEE
Confidence            6779999999999987543    2 2487755

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=90.83  E-value=0.057  Score=45.14  Aligned_cols=19  Identities=26%  Similarity=0.511  Sum_probs=16.7

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.||+|||||+.++.
T Consensus        18 I~vvG~~~~GKSsLi~rl~   36 (177)
T d1zj6a1          18 VIIVGLDNAGKTTILYQFS   36 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            6788999999999988764

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {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: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.83  E-value=0.061  Score=43.93  Aligned_cols=19  Identities=26%  Similarity=0.489  Sum_probs=16.4

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|+||+|||+|+..+.
T Consensus         3 I~liG~~nvGKSSLln~l~   21 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLK   21 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            5689999999999988755

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=90.77  E-value=0.066  Score=44.97  Aligned_cols=24  Identities=38%  Similarity=0.320  Sum_probs=20.3

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .|.=++|.|++|+|||++++.++.
T Consensus        14 ~g~gvli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          14 FGVGVLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHH
Confidence            456689999999999999888764

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {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: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=90.64  E-value=0.064  Score=44.71  Aligned_cols=20  Identities=35%  Similarity=0.679  Sum_probs=17.6

Q ss_pred             EEEEEcCCCCChhHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la  318 (539)
                      .++|.|.||+|||||+.+++
T Consensus         2 ~V~liG~~n~GKSsLi~~L~   21 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLV   21 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            46899999999999988875

>d1qvra3 c.37.1.20 (A:536-850) 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=90.25  E-value=0.091  Score=48.78  Aligned_cols=38  Identities=16%  Similarity=0.176  Sum_probs=28.0

Q ss_pred             CCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEe
Q 009230          295 LPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCS  333 (539)
Q Consensus       295 ~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s  333 (539)
                      +|....+++||||+|||.++..+|..+.- .+.+++.+.
T Consensus        51 kp~~~~lf~Gp~G~GKt~lak~la~~l~~-~~~~~~~~~   88 (315)
T d1qvra3          51 RPIGSFLFLGPTGVGKTELAKTLAATLFD-TEEAMIRID   88 (315)
T ss_dssp             SCSEEEEEBSCSSSSHHHHHHHHHHHHHS-SGGGEEEEC
T ss_pred             CCceEEEEECCCcchHHHHHHHHHHHhcC-CCcceEEEe
Confidence            34447789999999999999999987743 244555453

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=90.06  E-value=0.1  Score=45.00  Aligned_cols=27  Identities=26%  Similarity=0.315  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEE
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFV  330 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl  330 (539)
                      ++.|+|++||||||++.-+     ...|.+|+
T Consensus         4 iIgITG~igSGKStv~~~l-----~~~G~~vi   30 (205)
T d1jjva_           4 IVGLTGGIGSGKTTIANLF-----TDLGVPLV   30 (205)
T ss_dssp             EEEEECSTTSCHHHHHHHH-----HTTTCCEE
T ss_pred             EEEEECCCCCCHHHHHHHH-----HHCCCeEE
Confidence            5679999999999986533     33577765

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.02  E-value=0.079  Score=43.79  Aligned_cols=20  Identities=30%  Similarity=0.318  Sum_probs=17.5

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.++..
T Consensus         5 v~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            57899999999999988764

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=90.02  E-value=0.081  Score=44.12  Aligned_cols=25  Identities=36%  Similarity=0.283  Sum_probs=20.3

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .|.=++|.|++|+|||++++.++..
T Consensus        14 ~g~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          14 YGVGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHc
Confidence            4566899999999999998776644

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G 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: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=89.94  E-value=0.076  Score=43.57  Aligned_cols=19  Identities=42%  Similarity=0.807  Sum_probs=16.6

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|+||+|||||+.++.
T Consensus         4 I~lvG~~nvGKSsLin~l~   22 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALA   22 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            6799999999999987665

>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=89.90  E-value=0.091  Score=46.58  Aligned_cols=24  Identities=21%  Similarity=0.296  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNIN  322 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a  322 (539)
                      .++|.|+||+|||+++..++..+-
T Consensus        36 ~~Ll~Gp~G~GKtt~a~~~~~~l~   59 (239)
T d1njfa_          36 AYLFSGTRGVGKTSIARLLAKGLN   59 (239)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHHHhc
Confidence            578999999999999998777654

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=89.46  E-value=0.07  Score=44.66  Aligned_cols=20  Identities=25%  Similarity=0.434  Sum_probs=17.0

Q ss_pred             EEEEEcCCCCChhHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la  318 (539)
                      =++|.|++|+|||||+..+.
T Consensus        15 kI~lvG~~~vGKTsLl~~l~   34 (186)
T d1f6ba_          15 KLVFLGLDNAGKTTLLHMLK   34 (186)
T ss_dssp             EEEEEEETTSSHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            36789999999999987764

>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=89.36  E-value=0.05  Score=50.81  Aligned_cols=42  Identities=24%  Similarity=0.340  Sum_probs=29.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVR  339 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~~  339 (539)
                      ++.+.-++|+|++|+|||||+..++..+-  ...+++.+  |.+.+
T Consensus       163 v~~~~nili~G~tgSGKTT~l~al~~~i~--~~~rivti--Ed~~E  204 (323)
T d1g6oa_         163 IAIGKNVIVCGGTGSGKTTYIKSIMEFIP--KEERIISI--EDTEE  204 (323)
T ss_dssp             HHHTCCEEEEESTTSSHHHHHHHHGGGSC--TTCCEEEE--ESSCC
T ss_pred             HHhCCCEEEEeeccccchHHHHHHhhhcc--cccceeec--cchhh
Confidence            44455689999999999999887765543  25676644  76655

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=89.34  E-value=0.096  Score=43.23  Aligned_cols=19  Identities=21%  Similarity=0.546  Sum_probs=16.4

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|++|+|||+|+.++.
T Consensus         5 i~i~G~~~~GKTsLl~~l~   23 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIA   23 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            4678999999999988875

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=89.16  E-value=0.095  Score=43.23  Aligned_cols=19  Identities=21%  Similarity=0.455  Sum_probs=16.5

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.+|+|||+|+..+.
T Consensus         5 i~ivG~~~~GKTsLi~~l~   23 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFN   23 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHc
Confidence            5789999999999988763

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {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: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.14  E-value=0.097  Score=44.96  Aligned_cols=21  Identities=33%  Similarity=0.491  Sum_probs=18.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~  319 (539)
                      .++|.|+||+|||||+..+..
T Consensus         5 ~V~lvG~~n~GKTSLln~l~~   25 (209)
T d1nrjb_           5 SIIIAGPQNSGKTSLLTLLTT   25 (209)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            578999999999999888763

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {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: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.13  E-value=0.1  Score=43.57  Aligned_cols=20  Identities=25%  Similarity=0.217  Sum_probs=17.2

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+..++.
T Consensus         6 ivvvG~~~vGKTsli~r~~~   25 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTD   25 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            57889999999999887764

>d1wmsa_ c.37.1.8 (A:) Rab9a {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: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.09  E-value=0.1  Score=43.59  Aligned_cols=20  Identities=25%  Similarity=0.405  Sum_probs=17.9

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.+++.
T Consensus         9 I~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            67999999999999988874

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {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: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.08  E-value=0.1  Score=43.15  Aligned_cols=21  Identities=24%  Similarity=0.252  Sum_probs=17.9

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.+++.+
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578899999999999887643

>d1kaoa_ c.37.1.8 (A:) Rap2a {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: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.93  E-value=0.11  Score=43.08  Aligned_cols=20  Identities=25%  Similarity=0.348  Sum_probs=17.4

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.+++.
T Consensus         6 i~lvG~~~vGKTsLi~r~~~   25 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVT   25 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            57889999999999988764

>d1c9ka_ c.37.1.11 (A:) Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU
species: Salmonella typhimurium [TaxId: 90371]

Probab=88.86  E-value=0.18  Score=42.43  Aligned_cols=43  Identities=28%  Similarity=0.361  Sum_probs=28.3

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeCCCCH-HHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKV-REHARKLL  346 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~E~~~-~~~~~r~~  346 (539)
                      +++|.|++.+|||.||-+++    . .+.+++|+.+=.+. .++..|+.
T Consensus         1 iiLVtGGarSGKS~~AE~l~----~-~~~~~~YiAT~~~~D~em~~RI~   44 (180)
T d1c9ka_           1 MILVTGGARSGKSRHAEALI----G-DAPQVLYIATSQILDDEMAARIQ   44 (180)
T ss_dssp             CEEEEECTTSSHHHHHHHHH----C-SCSSEEEEECCCC------CHHH
T ss_pred             CEEEECCCCccHHHHHHHHH----h-cCCCcEEEEccCCCCHHHHHHHH
Confidence            57999999999999988764    3 36788888764332 33444443

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=88.74  E-value=0.11  Score=43.81  Aligned_cols=20  Identities=20%  Similarity=0.433  Sum_probs=17.3

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.+++.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            57999999999999888753

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {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: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.69  E-value=0.11  Score=43.25  Aligned_cols=20  Identities=20%  Similarity=0.396  Sum_probs=17.4

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.++..
T Consensus         5 i~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            57889999999999988764

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {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: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.67  E-value=0.11  Score=43.03  Aligned_cols=20  Identities=35%  Similarity=0.368  Sum_probs=17.5

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.++..
T Consensus         6 i~viG~~~vGKTsli~~l~~   25 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQ   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57889999999999998864

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=88.64  E-value=0.1  Score=43.80  Aligned_cols=20  Identities=40%  Similarity=0.431  Sum_probs=17.0

Q ss_pred             EEEEEcCCCCChhHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la  318 (539)
                      -++|.|+||+|||||...+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~   21 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLT   21 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            36899999999999987764

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

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 protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=88.63  E-value=0.13  Score=43.94  Aligned_cols=27  Identities=22%  Similarity=0.191  Sum_probs=23.4

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .++...++|.|||++|||.|++.++..
T Consensus        50 ~PKkn~i~~~GP~~TGKS~f~~sl~~~   76 (205)
T d1tuea_          50 TPKKNCLVFCGPANTGKSYFGMSFIHF   76 (205)
T ss_dssp             CTTCSEEEEESCGGGCHHHHHHHHHHH
T ss_pred             CCCceEEEEECCCCccHHHHHHHHHHH
Confidence            666789999999999999999887654

>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=88.60  E-value=0.15  Score=49.56  Aligned_cols=49  Identities=24%  Similarity=0.274  Sum_probs=33.8

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC---------CCCHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM---------ENKVREHARKLLE  347 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~---------E~~~~~~~~r~~~  347 (539)
                      +.|. =+++.||||+|||.++..+|..    .+.|.+.+..         -...+.++.+++.
T Consensus        47 i~ks-NILliGPTGvGKTlLAr~LAk~----l~VPFv~~daT~fTeaGYvG~DVesii~~L~~  104 (443)
T d1g41a_          47 VTPK-NILMIGPTGVGKTEIARRLAKL----ANAPFIKVEATKFTEVGYVGKEVDSIIRDLTD  104 (443)
T ss_dssp             CCCC-CEEEECCTTSSHHHHHHHHHHH----TTCCEEEEEGGGGC----CCCCTHHHHHHHHH
T ss_pred             cccc-cEEEECCCCCCHHHHHHHHHHH----hCCCEEEeecceeeecceeecchhHHHHHHHH
Confidence            4444 5778999999999998888753    2667555532         1346777888764

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {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: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.50  E-value=0.12  Score=43.70  Aligned_cols=19  Identities=16%  Similarity=0.307  Sum_probs=16.6

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.+|+|||+|+.+++
T Consensus         8 i~ivG~~~vGKTsLi~~l~   26 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYT   26 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHh
Confidence            5688999999999988775

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {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: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.49  E-value=0.12  Score=42.94  Aligned_cols=20  Identities=25%  Similarity=0.288  Sum_probs=17.1

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.+++.
T Consensus         5 i~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            46889999999999888764

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.39  E-value=0.12  Score=45.07  Aligned_cols=26  Identities=23%  Similarity=0.495  Sum_probs=22.9

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      +|.+++|-|.-|+||||.+..++..+
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~~~L   27 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILYKKL   27 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CeEEEEEECCCCCcHHHHHHHHHHHH
Confidence            68999999999999999988877554

>d1mh1a_ c.37.1.8 (A:) Rac {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: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.38  E-value=0.12  Score=43.52  Aligned_cols=21  Identities=24%  Similarity=0.275  Sum_probs=18.1

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.+++..
T Consensus         8 ivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           8 CVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678899999999999988743

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

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: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=88.37  E-value=0.078  Score=45.26  Aligned_cols=23  Identities=17%  Similarity=0.286  Sum_probs=19.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      -+++|.|..|+||||++..++.+
T Consensus        10 ~~I~ieG~~GsGKTTl~~~L~~~   32 (197)
T d2vp4a1          10 FTVLIEGNIGSGKTTYLNHFEKY   32 (197)
T ss_dssp             EEEEEECSTTSCHHHHHHTTGGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            38999999999999998876643

>d1r2qa_ c.37.1.8 (A:) Rab5a {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: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.37  E-value=0.12  Score=42.84  Aligned_cols=21  Identities=19%  Similarity=0.300  Sum_probs=18.0

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.+++..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578899999999999988743

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.35  E-value=0.12  Score=44.50  Aligned_cols=21  Identities=24%  Similarity=0.366  Sum_probs=18.0

Q ss_pred             EEEEEcCCCCChhHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~  319 (539)
                      -++|.|+||+|||+|+..+..
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~   22 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLT   22 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            378999999999999887764

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {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: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.18  E-value=0.12  Score=42.97  Aligned_cols=20  Identities=30%  Similarity=0.278  Sum_probs=17.7

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.+++.
T Consensus         8 i~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            67889999999999998864

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {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: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.07  E-value=0.12  Score=43.00  Aligned_cols=21  Identities=29%  Similarity=0.400  Sum_probs=18.0

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.++..+
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999887643

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=88.05  E-value=0.13  Score=42.61  Aligned_cols=21  Identities=14%  Similarity=0.325  Sum_probs=18.1

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      +++.|.+|+|||+|+..++.+
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            678999999999999887654

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {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: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.95  E-value=0.13  Score=42.46  Aligned_cols=20  Identities=15%  Similarity=0.154  Sum_probs=17.5

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+..++.
T Consensus         6 ivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            57899999999999988764

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, 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: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.95  E-value=0.14  Score=42.62  Aligned_cols=20  Identities=35%  Similarity=0.689  Sum_probs=17.7

Q ss_pred             EEEEEcCCCCChhHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la  318 (539)
                      .++|.|.||+|||||...+.
T Consensus         7 ~I~iiG~~nvGKSSLin~L~   26 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLL   26 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            47899999999999988775

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {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: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.94  E-value=0.13  Score=42.56  Aligned_cols=20  Identities=20%  Similarity=0.233  Sum_probs=17.3

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.+++.
T Consensus         7 v~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           7 IAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            56789999999999988764

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {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: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.93  E-value=0.13  Score=42.53  Aligned_cols=20  Identities=20%  Similarity=0.307  Sum_probs=17.6

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.+++.
T Consensus         5 i~lvG~~~vGKTsli~r~~~   24 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLT   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57889999999999988775

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {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: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.81  E-value=0.13  Score=42.71  Aligned_cols=20  Identities=15%  Similarity=0.278  Sum_probs=17.7

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.+++.
T Consensus         8 i~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            57899999999999988874

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {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: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.78  E-value=0.13  Score=42.40  Aligned_cols=20  Identities=20%  Similarity=0.278  Sum_probs=17.3

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      +++.|.+|+|||+|+.+++.
T Consensus         5 i~vvG~~~vGKTSli~~l~~   24 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVE   24 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            56889999999999988764

>d1w1wa_ c.37.1.12 (A:) Smc head 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: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.76  E-value=0.13  Score=49.32  Aligned_cols=26  Identities=31%  Similarity=0.385  Sum_probs=21.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |..+.+++|.|++|+|||+++-.|..
T Consensus        22 f~~~~l~~i~G~NGsGKS~ileAi~~   47 (427)
T d1w1wa_          22 FGESNFTSIIGPNGSGKSNMMDAISF   47 (427)
T ss_dssp             CTTCSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHH
Confidence            55456999999999999999888754

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=87.73  E-value=0.12  Score=42.94  Aligned_cols=19  Identities=26%  Similarity=0.564  Sum_probs=16.5

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.+|+|||+|+.++.
T Consensus        19 I~vvG~~~vGKSsLi~~l~   37 (176)
T d1fzqa_          19 ILLLGLDNAGKTTLLKQLA   37 (176)
T ss_dssp             EEEEESTTSSHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            6789999999999987663

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

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: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=87.63  E-value=0.18  Score=45.69  Aligned_cols=49  Identities=12%  Similarity=-0.012  Sum_probs=31.4

Q ss_pred             CcEEEEEcCCCCChhHHHHHHHHHHHH--h-cCCeEEEEeC--CCCHHHHHHHH
Q 009230          297 GELTIVTGVPNSGKSEWIDALICNINE--H-AGWKFVLCSM--ENKVREHARKL  345 (539)
Q Consensus       297 G~l~~i~G~~G~GKT~~~~~la~~~a~--~-~g~~vl~~s~--E~~~~~~~~r~  345 (539)
                      ..++.|.|..|+||||+|.++..+...  . +-..++|++.  ..+...+...+
T Consensus        44 ~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~   97 (277)
T d2a5yb3          44 SFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFT   97 (277)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHH
Confidence            358889999999999999988755321  1 1235677754  34444444333

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {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: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.62  E-value=0.13  Score=42.77  Aligned_cols=20  Identities=30%  Similarity=0.278  Sum_probs=17.3

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.++..
T Consensus         9 v~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           9 LVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            67889999999999988764

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {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: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.62  E-value=0.14  Score=42.63  Aligned_cols=20  Identities=20%  Similarity=0.366  Sum_probs=17.4

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+..+..
T Consensus         7 i~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            67899999999999988764

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.59  E-value=0.14  Score=42.01  Aligned_cols=21  Identities=29%  Similarity=0.295  Sum_probs=18.2

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.+++..
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578999999999999988743

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {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: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=87.59  E-value=0.16  Score=42.49  Aligned_cols=20  Identities=35%  Similarity=0.705  Sum_probs=17.7

Q ss_pred             EEEEEcCCCCChhHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la  318 (539)
                      .++|.|.+|+|||||+..++
T Consensus         7 ~I~lvG~~~~GKSSLin~l~   26 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLL   26 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            68899999999999987764

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {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: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.56  E-value=0.15  Score=42.32  Aligned_cols=20  Identities=15%  Similarity=0.192  Sum_probs=17.6

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.++..
T Consensus         9 i~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            67999999999999888764

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=87.54  E-value=0.15  Score=42.29  Aligned_cols=20  Identities=25%  Similarity=0.327  Sum_probs=17.3

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.+++.
T Consensus         7 ivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            57889999999999888763

>d1c1ya_ c.37.1.8 (A:) Rap1A {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: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.52  E-value=0.15  Score=42.14  Aligned_cols=20  Identities=25%  Similarity=0.295  Sum_probs=17.3

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.++..
T Consensus         6 ivvvG~~~vGKTsli~r~~~   25 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHc
Confidence            57889999999999888764

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.45  E-value=0.15  Score=42.13  Aligned_cols=20  Identities=20%  Similarity=0.199  Sum_probs=17.3

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.++..
T Consensus         7 i~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            56789999999999998764

>d2gjsa1 c.37.1.8 (A:91-258) Rad {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: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.39  E-value=0.15  Score=42.19  Aligned_cols=19  Identities=26%  Similarity=0.420  Sum_probs=16.6

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.+|+|||+|+.++.
T Consensus         4 i~lvG~~~vGKTsLi~~~~   22 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFG   22 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHh
Confidence            5788999999999988765

>d1kmqa_ c.37.1.8 (A:) RhoA {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: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.14  E-value=0.15  Score=42.59  Aligned_cols=21  Identities=14%  Similarity=0.131  Sum_probs=17.2

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.+++.+
T Consensus         5 ivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           5 LVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            467799999999998887643

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {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: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.10  E-value=0.15  Score=43.42  Aligned_cols=20  Identities=20%  Similarity=0.175  Sum_probs=17.8

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.++..
T Consensus         9 ivvvG~~~vGKTsli~~l~~   28 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSD   28 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHhh
Confidence            67889999999999998874

>d1ek0a_ c.37.1.8 (A:) Ypt51 {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: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.96  E-value=0.17  Score=41.93  Aligned_cols=21  Identities=24%  Similarity=0.381  Sum_probs=17.6

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.++...
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            467899999999998887643

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {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: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=86.96  E-value=0.12  Score=43.48  Aligned_cols=19  Identities=26%  Similarity=0.459  Sum_probs=16.1

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      +.|.|+||+|||||+..+.
T Consensus         4 VaiiG~~nvGKSSLin~L~   22 (185)
T d1lnza2           4 VGLVGFPSVGKSTLLSVVS   22 (185)
T ss_dssp             EEEESSTTSSHHHHHHHSE
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            5689999999999987653

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {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: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.59  E-value=0.17  Score=41.56  Aligned_cols=20  Identities=20%  Similarity=0.388  Sum_probs=17.4

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.++..
T Consensus         3 v~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            57889999999999998764

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.45  E-value=0.18  Score=41.72  Aligned_cols=20  Identities=25%  Similarity=0.235  Sum_probs=17.3

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      +++.|.+|+|||+|+..++.
T Consensus         7 i~lvG~~~vGKTsll~~~~~   26 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQ   26 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            56789999999999988865

>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=86.32  E-value=0.5  Score=40.51  Aligned_cols=38  Identities=13%  Similarity=0.164  Sum_probs=23.5

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHH-HhcCCeEEEEeCC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNIN-EHAGWKFVLCSME  335 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a-~~~g~~vl~~s~E  335 (539)
                      .-+++.+++|+|||....-.+.... ...+-.++++..-
T Consensus        43 ~d~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~lil~pt   81 (208)
T d1hv8a1          43 YNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPT   81 (208)
T ss_dssp             SEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSC
T ss_pred             CCeeeechhcccccceeecccccccccccCcceEEEeec
Confidence            3677889999999975544443322 2234566666543

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=86.29  E-value=0.11  Score=43.34  Aligned_cols=19  Identities=21%  Similarity=0.385  Sum_probs=16.5

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.+|+|||+|+.+++
T Consensus        15 IvlvG~~~vGKTSli~rl~   33 (173)
T d1e0sa_          15 ILMLGLDAAGKTTILYKLK   33 (173)
T ss_dssp             EEEEEETTSSHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            5688999999999988764

>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=86.20  E-value=0.59  Score=39.75  Aligned_cols=35  Identities=20%  Similarity=0.027  Sum_probs=23.2

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      .|+=+++.+|||+|||.... +.  ... ...+++|+..
T Consensus        39 ~g~~vlv~apTGsGKT~~~~-~~--~~~-~~~~~~~v~P   73 (206)
T d1oywa2          39 SGRDCLVVMPTGGGKSLCYQ-IP--ALL-LNGLTVVVSP   73 (206)
T ss_dssp             TTCCEEEECSCHHHHHHHHH-HH--HHH-SSSEEEEECS
T ss_pred             cCCCEEEEcCCCCCCcchhh-hh--hhh-ccCceEEecc
Confidence            35556889999999986542 22  223 4677777764

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {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: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.17  E-value=0.19  Score=41.89  Aligned_cols=20  Identities=20%  Similarity=0.287  Sum_probs=17.6

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+..+..
T Consensus        10 i~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            67899999999999988764

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {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: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=85.73  E-value=0.11  Score=43.59  Aligned_cols=20  Identities=30%  Similarity=0.411  Sum_probs=17.0

Q ss_pred             EEEEEcCCCCChhHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la  318 (539)
                      -++|.|.||+|||||+..+.
T Consensus        18 ~I~lvG~~NvGKSSL~n~L~   37 (188)
T d1puia_          18 EVAFAGRSNAGKSSALNTLT   37 (188)
T ss_dssp             EEEEEECTTSSHHHHHTTTC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            37899999999999987663

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=85.71  E-value=0.13  Score=43.08  Aligned_cols=19  Identities=21%  Similarity=0.419  Sum_probs=16.5

Q ss_pred             EEEEEcCCCCChhHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDAL  317 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~l  317 (539)
                      =++|.|.+|+|||||+.++
T Consensus        19 KI~lvG~~~vGKTsLi~~l   37 (182)
T d1moza_          19 RILILGLDGAGKTTILYRL   37 (182)
T ss_dssp             EEEEEEETTSSHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3678999999999998776

>d1e69a_ c.37.1.12 (A:) Smc head 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: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.57  E-value=0.2  Score=45.89  Aligned_cols=25  Identities=36%  Similarity=0.418  Sum_probs=20.2

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~  319 (539)
                      |.++ +++|.|+.|+|||+++-.+..
T Consensus        22 f~~~-lnvlvG~NgsGKS~iL~Ai~~   46 (308)
T d1e69a_          22 FSDR-VTAIVGPNGSGKSNIIDAIKW   46 (308)
T ss_dssp             CCSS-EEEEECCTTTCSTHHHHHHHH
T ss_pred             CCCC-eEEEECCCCCcHHHHHHHHHH
Confidence            5444 999999999999999766643

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {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: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=85.57  E-value=0.21  Score=41.82  Aligned_cols=19  Identities=37%  Similarity=0.697  Sum_probs=16.3

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.+|+|||||+..++
T Consensus        11 V~iiG~~~~GKSTLin~l~   29 (186)
T d1mkya2          11 VAIVGRPNVGKSTLFNAIL   29 (186)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            5788999999999987664

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {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: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.54  E-value=0.22  Score=41.39  Aligned_cols=19  Identities=21%  Similarity=0.373  Sum_probs=16.6

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.+|+|||+|+..+.
T Consensus         6 v~lvG~~~vGKTsLi~~~~   24 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFA   24 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHH
Confidence            5789999999999988765

>d2ngra_ c.37.1.8 (A:) CDC42 {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: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.45  E-value=0.2  Score=42.34  Aligned_cols=21  Identities=24%  Similarity=0.275  Sum_probs=17.7

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.++...
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568899999999999887643

>d1i2ma_ c.37.1.8 (A:) Ran {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: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.18  E-value=0.11  Score=43.10  Aligned_cols=21  Identities=14%  Similarity=0.417  Sum_probs=16.6

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.+++..
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            567899999999998887654

>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=84.91  E-value=0.22  Score=47.08  Aligned_cols=26  Identities=19%  Similarity=0.272  Sum_probs=20.9

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~  320 (539)
                      .+++. +++.||||+|||-++..+|..
T Consensus        66 ~p~~n-iLfiGPTGvGKTElAk~LA~~   91 (364)
T d1um8a_          66 LSKSN-ILLIGPTGSGKTLMAQTLAKH   91 (364)
T ss_dssp             CCCCC-EEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCcc-eeeeCCCCccHHHHHHHHHhh
Confidence            56665 567799999999999888754

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {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: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=84.91  E-value=0.16  Score=42.45  Aligned_cols=19  Identities=37%  Similarity=0.595  Sum_probs=16.2

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      +.|.|.||+|||||+..+.
T Consensus         4 VaivG~~nvGKSTLin~L~   22 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMT   22 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            5688999999999987764

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {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: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.82  E-value=0.23  Score=41.82  Aligned_cols=21  Identities=19%  Similarity=0.238  Sum_probs=18.0

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.+++.+
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            688999999999998887643

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.61  E-value=0.24  Score=41.47  Aligned_cols=21  Identities=19%  Similarity=0.403  Sum_probs=17.8

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.+++.+
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578899999999998887653

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.57  E-value=0.15  Score=42.35  Aligned_cols=21  Identities=14%  Similarity=0.145  Sum_probs=7.9

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.+++.+
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578899999999999888754

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=84.48  E-value=0.16  Score=47.31  Aligned_cols=21  Identities=33%  Similarity=0.343  Sum_probs=18.4

Q ss_pred             EEEEEcCCCCChhHHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~  319 (539)
                      =++|.|+||+|||+++..++.
T Consensus        30 ~vLl~G~pG~GKT~lar~~~~   50 (333)
T d1g8pa_          30 GVLVFGDRGTGKSTAVRALAA   50 (333)
T ss_dssp             CEEEECCGGGCTTHHHHHHHH
T ss_pred             eEEEECCCCccHHHHHHHHHH
Confidence            468999999999999888774

>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=83.93  E-value=0.53  Score=40.26  Aligned_cols=33  Identities=15%  Similarity=-0.001  Sum_probs=24.4

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      .-.+|.+++|+|||..++.++.    ..+.+++++..
T Consensus        86 ~~~ll~~~tG~GKT~~a~~~~~----~~~~~~Liv~p  118 (206)
T d2fz4a1          86 KRGCIVLPTGSGKTHVAMAAIN----ELSTPTLIVVP  118 (206)
T ss_dssp             SEEEEEESSSTTHHHHHHHHHH----HSCSCEEEEES
T ss_pred             CCcEEEeCCCCCceehHHhHHH----HhcCceeEEEc
Confidence            3457888999999987665443    34788998875

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G 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: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.92  E-value=0.28  Score=40.88  Aligned_cols=20  Identities=35%  Similarity=0.375  Sum_probs=17.0

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      +++.|.+|+|||+|+.+++.
T Consensus         8 i~vlG~~~vGKTsLi~~~~~   27 (175)
T d2bmja1           8 LGVLGDARSGKSSLIHRFLT   27 (175)
T ss_dssp             EEEECCTTTTHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            56889999999999987753

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {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: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=83.83  E-value=0.33  Score=42.63  Aligned_cols=20  Identities=35%  Similarity=0.554  Sum_probs=17.0

Q ss_pred             EEEEEcCCCCChhHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la  318 (539)
                      ++.|+|+.||||||++..++
T Consensus         3 iIgiTG~igSGKsTva~~l~   22 (241)
T d1deka_           3 LIFLSGVKRSGKDTTADFIM   22 (241)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            68899999999999876554

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase 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: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=83.74  E-value=0.1  Score=42.73  Aligned_cols=19  Identities=37%  Similarity=0.760  Sum_probs=16.9

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      ++|.|.||+|||||+..+.
T Consensus         3 I~liG~~n~GKSSLin~l~   21 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLL   21 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            5789999999999988875

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=83.42  E-value=0.053  Score=46.28  Aligned_cols=27  Identities=22%  Similarity=0.297  Sum_probs=21.6

Q ss_pred             cCCCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          294 VLPGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       294 l~~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      |.+| +++|.|+.|+||||++-.|..-+
T Consensus        22 f~~~-~tvi~G~NGsGKStil~Ai~~~L   48 (222)
T d1qhla_          22 LDEL-VTTLSGGNGAGKSTTMAAFVTAL   48 (222)
T ss_dssp             HHHH-HHHHHSCCSHHHHHHHHHHHHHH
T ss_pred             cCCC-eEEEECCCCCCHHHHHHHHHHHh
Confidence            4444 89999999999999988776443

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.26  E-value=0.18  Score=44.22  Aligned_cols=26  Identities=19%  Similarity=0.160  Sum_probs=22.0

Q ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHH
Q 009230          296 PGELTIVTGVPNSGKSEWIDALICNI  321 (539)
Q Consensus       296 ~G~l~~i~G~~G~GKT~~~~~la~~~  321 (539)
                      ++.+++|-|+.|+||||++..++.++
T Consensus         1 ~~k~I~ieG~dGsGKST~~~~L~~~l   26 (241)
T d1p5zb_           1 RIKKISIEGNIAAGKSTFVNILKQLC   26 (241)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGGC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            35789999999999999988877653

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.72  E-value=0.31  Score=41.16  Aligned_cols=18  Identities=28%  Similarity=0.599  Sum_probs=16.6

Q ss_pred             EEEEcCCCCChhHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDAL  317 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~l  317 (539)
                      ++|.|.+|+|||+|+.++
T Consensus         5 ivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            578899999999999998

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=82.52  E-value=0.31  Score=43.52  Aligned_cols=20  Identities=30%  Similarity=0.473  Sum_probs=17.0

Q ss_pred             EEEEEcCCCCChhHHHHHHH
Q 009230          299 LTIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la  318 (539)
                      -++|.|.||+||||++..+.
T Consensus        34 ~I~LvG~tg~GKSSliN~il   53 (257)
T d1h65a_          34 TILVMGKGGVGKSSTVNSII   53 (257)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHh
Confidence            36688999999999987775

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=81.77  E-value=0.36  Score=40.28  Aligned_cols=19  Identities=21%  Similarity=0.209  Sum_probs=16.8

Q ss_pred             EEEEcCCCCChhHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALI  318 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la  318 (539)
                      +.|.|+|++|||||+..+.
T Consensus         8 IaiiG~~naGKSTL~n~L~   26 (179)
T d1wb1a4           8 LGIFGHIDHGKTTLSKVLT   26 (179)
T ss_dssp             EEEEECTTSSHHHHHHHHH
T ss_pred             EEEEeCCCCcHHHHHHHHH
Confidence            6789999999999988775

>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]}

class: Multi-domain proteins (alpha and beta)
fold: Recombination protein RecR
superfamily: Recombination protein RecR
family: Recombination protein RecR
domain: Recombination protein RecR
species: Deinococcus radiodurans [TaxId: 1299]

Probab=81.18  E-value=2.7  Score=35.21  Aligned_cols=89  Identities=24%  Similarity=0.185  Sum_probs=57.4

Q ss_pred             CCcEEEEechhhHHHHHHhCCC-ceEEcCCCCCCCCCCCCCCChhhhhhhHHHHhHHHHhccCCEEEEEecCCccchHHH
Q 009230          123 ESDIIIVEGEMDKLSMEEAGFL-NCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALA  201 (539)
Q Consensus       123 ~~~v~i~EG~~Dalsl~~~g~~-~~v~l~~g~~~~~~~~~l~~~~~~~~~~~l~~~~~~l~~~~~ivl~~DnD~~G~~~~  201 (539)
                      ...+.|||-..|.+++-..|.. ...-|-+|.-+....- -|..   ..   +...+..+.+.++|||+++..--|+.-+
T Consensus        79 ~~~iCVVE~~~Dl~~iE~t~~y~G~YhVL~G~ispl~gi-~p~~---l~---i~~L~~r~~~~~EiIlA~~~t~EGe~Ta  151 (199)
T d1vdda_          79 QRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGV-GPDK---LH---IKPLLPRVGQGMEVILATGTTVEGDATA  151 (199)
T ss_dssp             TTEEEEESSHHHHHHTTTTSSCCSEEEECSSCCBGGGTB-CTTT---ST---TGGGGGGCCTTCEEEECCCSSHHHHHHH
T ss_pred             cceEEEEecHHHHHHHHhcccchhhhhhhcCccCcccCC-Cccc---hh---hhHHHHhccCCcEEEEEecCCcchHHHH
Confidence            4579999999999999988742 2222223443211110 1110   00   1122344556789999999999999999


Q ss_pred             HHHHHHhcCCceEEEec
Q 009230          202 EELARRVGRERCWRVRW  218 (539)
Q Consensus       202 ~~~~~~l~~~~~~~~~~  218 (539)
                      .-+.+.|....+.+-++
T Consensus       152 ~yi~~~l~~~~ikitrl  168 (199)
T d1vdda_         152 LYLQRLLEPLGAAISRI  168 (199)
T ss_dssp             HHHHHHHTTSSCEEEEC
T ss_pred             HHHHHHhhhcCceEEee
Confidence            99999997766766664

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.07  E-value=0.44  Score=40.04  Aligned_cols=21  Identities=29%  Similarity=0.420  Sum_probs=17.9

Q ss_pred             EEEEcCCCCChhHHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALICN  320 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~~  320 (539)
                      ++|.|.+|+|||+|+.++...
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            578899999999999988544

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=80.97  E-value=0.46  Score=41.15  Aligned_cols=20  Identities=25%  Similarity=0.385  Sum_probs=17.5

Q ss_pred             EEEEcCCCCChhHHHHHHHH
Q 009230          300 TIVTGVPNSGKSEWIDALIC  319 (539)
Q Consensus       300 ~~i~G~~G~GKT~~~~~la~  319 (539)
                      ++|.|.+|+|||+|+.++..
T Consensus         9 illlG~~~vGKTsll~~~~~   28 (221)
T d1azta2           9 LLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            57899999999999998853

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=80.92  E-value=0.24  Score=26.80  Aligned_cols=10  Identities=40%  Similarity=1.212  Sum_probs=9.0

Q ss_pred             CcccccCCCCCC
Q 009230            1 MCFRAKCGWKGS   12 (539)
Q Consensus         1 ~C~~~~cg~~~~   12 (539)
                      +||  |||..|.
T Consensus         8 kCf--NCGkeGH   17 (29)
T d1nc8a_           8 RCW--NCGKEGH   17 (29)
T ss_dssp             BCT--TTSCBSS
T ss_pred             Eee--cCCccch
Confidence            699  9999995

>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=80.20  E-value=0.85  Score=41.10  Aligned_cols=36  Identities=17%  Similarity=0.014  Sum_probs=28.4

Q ss_pred             EEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC
Q 009230          299 LTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM  334 (539)
Q Consensus       299 l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~  334 (539)
                      -.++..++|+|||..+..++.......+.+++++..
T Consensus       130 ~~il~~pTGsGKT~i~~~i~~~~~~~~~~k~Liivp  165 (282)
T d1rifa_         130 RRILNLPTSAGRSLIQALLARYYLENYEGKILIIVP  165 (282)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECS
T ss_pred             CceeEEEcccCccHHHHHHHHHhhhcccceEEEEEc
Confidence            467888999999998887776665554678999874

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=80.18  E-value=0.98  Score=39.77  Aligned_cols=48  Identities=15%  Similarity=0.072  Sum_probs=31.1

Q ss_pred             cEEEEEcCCCCChhHHHHHHHHHHHHhcCCeEEEEeC-CCCHHHHHHHHH
Q 009230          298 ELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSM-ENKVREHARKLL  346 (539)
Q Consensus       298 ~l~~i~G~~G~GKT~~~~~la~~~a~~~g~~vl~~s~-E~~~~~~~~r~~  346 (539)
                      .=++|.|++|+|||.+|..+...... ...+...+.+ .++.......+.
T Consensus        24 ~pvlI~Ge~GtGK~~~A~~ih~~s~~-~~~~~~~~~~~~~~~~~~~~~lf   72 (247)
T d1ny5a2          24 CPVLITGESGVGKEVVARLIHKLSDR-SKEPFVALNVASIPRDIFEAELF   72 (247)
T ss_dssp             SCEEEECSTTSSHHHHHHHHHHHSTT-TTSCEEEEETTTSCHHHHHHHHH
T ss_pred             CCEEEECCCCcCHHHHHHHHHHhcCC-cccccccchhhhhhhcccHHHhc
Confidence            45789999999999998877643322 2445555555 466665555554